Outlines

These AP Biology outlines correspond to Campbell's Biology, 7th Edition. These outlines, along with the AP Biology Slides, will help you prepare for the AP Biology Exam.

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Chapter 01 - Exploring Life

Chapter 1 Exploring Life
Lecture Outline

Overview: Biology’s Most Exciting Era

  • Biology is the scientific study of life.
  • You are starting your study of biology during its most exciting era.
  • The largest and best-equipped community of scientists in history is beginning to solve problems that once seemed unsolvable.
    • Biology is an ongoing inquiry about the nature of life.
  • Biologists are moving closer to understanding:
    • How a single cell develops into an adult animal or plant.
    • How plants convert solar energy into the chemical energy of food.
    • How the human mind works.
    • How living things interact in biological communities.
    • How the diversity of life evolved from the first microbes.
  • Research breakthroughs in genetics and cell biology are transforming medicine and agriculture.
    • Neuroscience and evolutionary biology are reshaping psychology and sociology.
    • Molecular biology is providing new tools for anthropology and criminology.
    • New models in ecology are helping society to evaluate environmental issues, such as the causes and biological consequences of global warming.
  • Unifying themes pervade all of biology.

Concept 1.1 Biologists explore life from the microscopic to the global scale

  • Life’s basic characteristic is a high degree of order.
  • Each level of biological organization has emergent properties.
  • Biological organization is based on a hierarchy of structural levels, each building on the levels below.
    • At the lowest level are atoms that are ordered into complex biological molecules.
    • Biological molecules are organized into structures called organelles, the components of cells.
    • Cells are the fundamental unit of structure and function of living things.
  • Some organisms consist of a single cell; others are multicellular aggregates of specialized cells.
  • Whether multicellular or unicellular, all organisms must accomplish the same functions: uptake and processing of nutrients, excretion of wastes, response to environmental stimuli, and reproduction.
    • Multicellular organisms exhibit three major structural levels above the cell: similar cells are grouped into tissues, several tissues coordinate to form organs, and several organs form an organ system.
  • For example, to coordinate locomotory movements, sensory information travels from sense organs to the brain, where nervous tissues composed of billions of interconnected neurons—supported by connective tissue—coordinate signals that travel via other neurons to the individual muscle cells.
    • Organisms belong to populations, localized groups of organisms belonging to the same species.
    • Populations of several species in the same area comprise a biological community.
    • Populations interact with their physical environment to form an ecosystem.
    • The biosphere consists of all the environments on Earth that are inhabited by life.

    Organisms interact continuously with their environment.

  • Each organism interacts with its environment, which includes other organisms as well as nonliving factors.
  • Both organism and environment are affected by the interactions between them.
  • The dynamics of any ecosystem include two major processes: the cycling of nutrients and the flow of energy from sunlight to producers to consumers.
    • In most ecosystems, producers are plants and other photosynthetic organisms that convert light energy to chemical energy.
    • Consumers are organisms that feed on producers and other consumers.
  • All the activities of life require organisms to perform work, and work requires a source of energy.
    • The exchange of energy between an organism and its environment often involves the transformation of energy from one form to another.
    • In all energy transformations, some energy is lost to the surroundings as heat.
    • In contrast to chemical nutrients, which recycle within an ecosystem, energy flows through an ecosystem, usually entering as light and exiting as heat.

    Cells are an organism’s basic unit of structure and function.

  • The cell is the lowest level of structure that is capable of performing all the activities of life.
    • For example, the ability of cells to divide is the basis of all reproduction and the basis of growth and repair of multicellular organisms.
  • Understanding how cells work is a major research focus of modern biology.
  • At some point, all cells contain deoxyribonucleic acid, or DNA, the heritable material that directs the cell’s activities.
    • DNA is the substance of genes, the units of inheritance that transmit information from parents to offspring.
  • Each of us began life as a single cell stocked with DNA inherited from our parents.
    • DNA in human cells is organized into chromosomes.
    • Each chromosome has one very long DNA molecule, with hundreds or thousands of genes arranged along its length.
    • The DNA of chromosomes replicates as a cell prepares to divide.
    • Each of the two cellular offspring inherits a complete set of genes.
  • In each cell, the genes along the length of DNA molecules encode the information for building the cell’s other molecules.
    • DNA thus directs the development and maintenance of the entire organism.
  • Most genes program the cell’s production of proteins.
  • Each DNA molecule is made up of two long chains arranged in a double helix.
    • Each link of a chain is one of four nucleotides, encoding the cell’s information in chemical letters.
  • The sequence of nucleotides along each gene codes for a specific protein with a unique shape and function.
    • Almost all cellular activities involve the action of one or more proteins.
    • DNA provides the heritable blueprints, but proteins are the tools that actually build and maintain the cell.
  • All forms of life employ essentially the same genetic code.
    • Because the genetic code is universal, it is possible to engineer cells to produce proteins normally found only in some other organism.
  • The library of genetic instructions that an organism inherits is called its genome.
    • The chromosomes of each human cell contain about 3 billion nucleotides, including genes coding for more than 70,000 kinds of proteins, each with a specific function.
  • Every cell is enclosed by a membrane that regulates the passage of material between a cell and its surroundings.
    • Every cell uses DNA as its genetic material.
  • There are two basic types of cells: prokaryotic cells and eukaryotic cells.
  • The cells of the microorganisms called bacteria and archaea are prokaryotic.
  • All other forms of life have more complex eukaryotic cells.
  • Eukaryotic cells are subdivided by internal membranes into various organelles.
    • In most eukaryotic cells, the largest organelle is the nucleus, which contains the cell’s DNA as chromosomes.
    • The other organelles are located in the cytoplasm, the entire region between the nucleus and outer membrane of the cell.
  • Prokaryotic cells are much simpler and smaller than eukaryotic cells.
    • In a prokaryotic cell, DNA is not separated from the cytoplasm in a nucleus.
    • There are no membrane-enclosed organelles in the cytoplasm.
  • All cells, regardless of size, shape, or structural complexity, are highly ordered structures that carry out complicated processes necessary for life.

Concept 1.2 Biological systems are much more than the sum of their parts

  • “The whole is greater than the sum of its parts.”
  • The combination of components can form a more complex organization called a system.
    • Examples of biological systems are cells, organisms, and ecosystems.
  • Consider the levels of life.
    • With each step upward in the hierarchy of biological order, novel properties emerge that are not present at lower levels.
  • These emergent properties result from the arrangements and interactions between components as complexity increases.
    • A cell is much more than a bag of molecules.
    • Our thoughts and memories are emergent properties of a complex network of neurons.
  • This theme of emergent properties accents the importance of structural arrangement.
  • The emergent properties of life are not supernatural or unique to life but simply reflect a hierarchy of structural organization.
    • The emergent properties of life are particularly challenging because of the unparalleled complexity of living systems.
  • The complex organization of life presents a dilemma to scientists seeking to understand biological processes.
    • We cannot fully explain a higher level of organization by breaking it down into its component parts.
    • At the same time, it is futile to try to analyze something as complex as an organism or cell without taking it apart.
  • Reductionism, reducing complex systems to simpler components, is a powerful strategy in biology.
    • The Human Genome Project—the sequencing of the genome of humans and many other species—is heralded as one of the greatest scientific achievements ever.
    • Research is now moving on to investigate the function of genes and the coordination of the activity of gene products.
  • Biologists are beginning to complement reductionism with new strategies for understanding the emergent properties of life—how all of the parts of biological systems are functionally integrated.
  • The ultimate goal of systems biology is to model the dynamic behavior of whole biological systems.
    • Accurate models allow biologists to predict how a change in one or more variables will impact other components and the whole system.
  • Scientists investigating ecosystems pioneered this approach in the 1960s with elaborate models diagramming the interactions of species and nonliving components in ecosystems.
  • Systems biology is now becoming increasingly important in cellular and molecular biology, driven in part by the deluge of data from the sequencing of genomes and our increased understanding of protein functions.
    • In 2003, a large research team published a network of protein interactions within a cell of a fruit fly.
  • Three key research developments have led to the increased importance of systems biology.
    1. High-throughput technology. Systems biology depends on methods that can analyze biological materials very quickly and produce enormous amounts of data. An example is the automatic DNA-sequencing machines used by the Human Genome Project.
    2. Bioinformatics. The huge databases from high-throughput methods require computing power, software, and mathematical models to process and integrate information.
    3. Interdisciplinary research teams. Systems biology teams may include engineers, medical scientists, physicists, chemists, mathematicians, and computer scientists as well as biologists.

    Regulatory mechanisms ensure a dynamic balance in living systems.

  • Chemical processes within cells are accelerated, or catalyzed, by specialized protein molecules, called enzymes.
  • Each type of enzyme catalyzes a specific chemical reaction.
    • In many cases, reactions are linked into chemical pathways, each step with its own enzyme.
  • How does a cell coordinate its various chemical pathways?
    • Many biological processes are self-regulating: the output or product of a process regulates that very process.
    • In negative feedback, or feedback inhibition, accumulation of an end product of a process slows or stops that process.
  • Though less common, some biological processes are regulated by positive feedback, in which an end product speeds up its own production.
    • Feedback is common to life at all levels, from the molecular level to the biosphere.
  • Such regulation is an example of the integration that makes living systems much greater than the sum of their parts.

Concept 1.3 Biologists explore life across its great diversity of species

  • Biology can be viewed as having two dimensions: a “vertical” dimension covering the size scale from atoms to the biosphere and a “horizontal” dimension that stretches across the diversity of life.
    • The latter includes not only present-day organisms, but also those that have existed throughout life’s history.

    Living things show diversity and unity.

  • Life is enormously diverse.
    • Biologists have identified and named about 1.8 million species.
  • This diversity includes 5,200 known species of prokaryotes, 100,000 fungi, 290,000 plants, 50,000 vertebrates, and 1,000,000 insects.
  • Thousands of newly identified species are added each year.
    • Estimates of the total species count range from 10 million to more than 200 million.
  • In the face of this complexity, humans are inclined to categorize diverse items into a smaller number of groups.
    • Taxonomy is the branch of biology that names and classifies species into a hierarchical order.
  • Until the past decade, biologists divided the diversity of life into five kingdoms.
  • New methods, including comparisons of DNA among organisms, have led to a reassessment of the number and boundaries of the kingdoms.
  • Various classification schemes now include six, eight, or even dozens of kingdoms.
  • Coming from this debate has been the recognition that there are three even higher levels of classifications, the domains.
    • The three domains are Bacteria, Archaea, and Eukarya.
    • The first two domains, domain Bacteria and domain Archaea, consist of prokaryotes.
  • All the eukaryotes are now grouped into various kingdoms of the domain Eukarya.
    • The recent taxonomic trend has been to split the single-celled eukaryotes and their close relatives into several kingdoms.
    • Domain Eukarya also includes the three kingdoms of multicellular eukaryotes: the kingdoms Plantae, Fungi, and Animalia.
  • These kingdoms are distinguished partly by their modes of nutrition.
    • Most plants produce their own sugars and food by photosynthesis.
    • Most fungi are decomposers that absorb nutrients by breaking down dead organisms and organic wastes.
    • Animals obtain food by ingesting other organisms.
  • Underlying the diversity of life is a striking unity, especially at the lower levels of organization.
    • The universal genetic language of DNA unites prokaryotes and eukaryotes.
    • Among eukaryotes, unity is evident in many details of cell structure.
    • Above the cellular level, organisms are variously adapted to their ways of life.
  • How do we account for life’s dual nature of unity and diversity?
    • The process of evolution explains both the similarities and differences among living things.

Concept 1.4 Evolution accounts for life’s unity and diversity

  • The history of life is a saga of a changing Earth billions of years old, inhabited by a changing cast of living forms.
  • Charles Darwin brought evolution into focus in 1859 when he presented two main concepts in one of the most important and controversial books ever written, On the Origin of Species by Natural Selection.
  • Darwin’s first point was that contemporary species arose from a succession of ancestors through “descent with modification.”
    • This term captured the duality of life’s unity and diversity: unity in the kinship among species that descended from common ancestors and diversity in the modifications that evolved as species branched from their common ancestors.
  • Darwin’s second point was his mechanism for descent with modification: natural selection.
  • Darwin inferred natural selection by connecting two observations:
    • Observation 1: Individual variation. Individuals in a population of any species vary in many heritable traits.
    • Observation 2: Overpopulation and competition. Any population can potentially produce far more offspring than the environment can support. This creates a struggle for existence among variant members of a population.
    • Inference: Unequal reproductive success. Darwin inferred that those individuals with traits best suited to the local environment would leave more healthy, fertile offspring.
    • Inference: Evolutionary adaptation. Unequal reproductive success can lead to adaptation of a population to its environment. Over generations, heritable traits that enhance survival and reproductive success will tend to increase in frequency among a population’s individuals. The population evolves.
  • Natural selection, by its cumulative effects over vast spans of time, can produce new species from ancestral species.
    • For example, a population fragmented into several isolated populations in different environments may gradually diversify into many species as each population adapts over many generations to different environmental problems.
  • Fourteen species of finches found on the Galápagos Islands diversified after an ancestral finch species reached the archipelago from the South American mainland.
    • Each species is adapted to exploit different food sources on different islands.
  • Biologists’ diagrams of evolutionary relationships generally take a treelike form.
  • Just as individuals have a family tree, each species is one twig of a branching tree of life.
    • Similar species like the Galápagos finches share a recent common ancestor.
    • Finches share a more distant ancestor with all other birds.
    • The common ancestor of all vertebrates is even more ancient.
    • Trace life back far enough, and there is a shared ancestor of all living things.
  • All of life is connected through its long evolutionary history.

Concept 1.5 Biologists use various forms of inquiry to explore life

  • The word science is derived from a Latin verb meaning “to know.”
  • At the heart of science is inquiry, people asking questions about nature and focusing on specific questions that can be answered.
  • The process of science blends two types of exploration: discovery science and hypothesis-based science.
    • Discovery science is mostly about discovering nature.
    • Hypothesis-based science is mostly about explaining nature.
    • Most scientific inquiry combines the two approaches.
  • Discovery science describes natural structures and processes as accurately as possible through careful observation and analysis of data.
    • Discovery science built our understanding of cell structure and is expanding our databases of genomes of diverse species.
  • Observation is the use of the senses to gather information, which is recorded as data.
  • Data can be qualitative or quantitative.
    • Quantitative data are numerical measurements.
    • Qualitative data may be in the form of recorded descriptions.
    • Jane Goodall has spent decades recording her observations of chimpanzee behavior during field research in Gambia.
  • She has also collected volumes of quantitative data over that time.
  • Discovery science can lead to important conclusions based on inductive reasoning.
    • Through induction, we derive generalizations based on a large number of specific observations.
  • In science, inquiry frequently involves the proposing and testing of hypotheses.
    • A hypothesis is a tentative answer to a well-framed question.
  • It is usually an educated postulate, based on past experience and the available data of discovery science.
  • A scientific hypothesis makes predictions that can be tested by recording additional observations or by designing experiments.
  • A type of logic called deduction is built into hypothesis-based science.
    • In deductive reasoning, reasoning flows from the general to the specific.
    • From general premises, we extrapolate to a specific result that we should expect if the premises are true.
  • In hypothesis-based science, deduction usually takes the form of predictions about what we should expect if a particular hypothesis is correct.
    • We test the hypothesis by performing the experiment to see whether or not the results are as predicted.
    • Deductive logic takes the form of “If . . . then” logic.
  • Scientific hypotheses must be testable.
    • There must be some way to check the validity of the idea.
  • Scientific hypotheses must be falsifiable.
    • There must be some observation or experiment that could reveal if a hypothesis is actually not true.
  • The ideal in hypothesis-based science is to frame two or more alternative hypotheses and design experiments to falsify them.
  • No amount of experimental testing can prove a hypothesis.
  • A hypothesis gains support by surviving various tests that could falsify it, while testing falsifies alternative hypotheses.
  • Facts, in the form of verifiable observations and repeatable experimental results, are the prerequisites of science.

    We can explore the scientific method.

  • There is an idealized process of inquiry called the scientific method.
    • Very few scientific inquiries adhere rigidly to the sequence of steps prescribed by the textbook scientific method.
    • Discovery science has contributed a great deal to our understanding of nature without most of the steps of the so-called scientific method.
  • We will consider a case study of scientific research.
  • This case begins with a set of observations and generalizations from discovery science.
  • Many poisonous animals have warning coloration that signals danger to potential predators.
    • Imposter species mimic poisonous species, although they are harmless.
    • An example is the bee fly, a nonstinging insect that mimics a honeybee.
    • What is the function of such mimicry? What advantage does it give the mimic?
  • In 1862, Henry Bates proposed that mimics benefit when predators mistake them for harmful species.
    • This deception may lower the mimic’s risk of predation.
  • In 2001, David and Karin Pfennig and William Harcombe of the University of North Carolina designed a set of field experiments to test Bates’s mimicry hypothesis.
  • In North and South Carolina, a poisonous snake called the eastern coral snake has warning red, yellow, and black coloration.
  • Predators avoid these snakes. It is unlikely that predators learn to avoid coral snakes, as a strike is usually lethal.
  • Natural selection may have favored an instinctive recognition and avoidance of the warning coloration of the coral snake.
  • The nonpoisonous scarlet king snake mimics the ringed coloration of the coral snake.
  • Both king snakes and coral snake live in the Carolinas, but the king snake’s range also extends into areas without coral snakes.
  • The distribution of these two species allowed the Pfennigs and Harcombe to test a key prediction of the mimicry hypothesis.
    • Mimicry should protect the king snake from predators, but only in regions where coral snakes live.
    • Predators in non–coral snake areas should attack king snakes more frequently than predators that live in areas where coral snakes are present.
  • To test the mimicry hypothesis, Harcombe made hundreds of artificial snakes.
    • The experimental group had the red, black, and yellow ring pattern of king snakes.
    • The control group had plain, brown coloring.
  • Equal numbers of both types were placed at field sites, including areas where coral snakes are absent.
  • After four weeks, the scientists retrieved the fake snakes and counted bite or claw marks.
    • Foxes, coyotes, raccoons, and black bears attacked snake models.
  • The data fit the predictions of the mimicry hypothesis.
    • The ringed snakes were attacked by predators less frequently than the brown snakes only within the geographic range of the coral snakes.
  • The snake mimicry experiment provides an example of how scientists design experiments to test the effect of one variable by canceling out the effects of unwanted variables.
    • The design is called a controlled experiment.
    • An experimental group (artificial king snakes) is compared with a control group (artificial brown snakes).
    • The experimental and control groups differ only in the one factor the experiment is designed to test—the effect of the snake’s coloration on the behavior of predators.
    • The brown artificial snakes allowed the scientists to rule out such variables as predator density and temperature as possible determinants of number of predator attacks.
  • Scientists do not control the experimental environment by keeping all variables constant.
    • Researchers usually “control” unwanted variables, not by eliminating them but by canceling their effects using control groups.

    Let’s look at the nature of science.

  • There are limitations to the kinds of questions that science can address.
  • These limits are set by science’s requirements that hypotheses are testable and falsifiable and that observations and experimental results be repeatable.
  • The limitations of science are set by its naturalism.
    • Science seeks natural causes for natural phenomena.
    • Science cannot support or falsify supernatural explanations, which are outside the bounds of science.
  • Everyday use of the term theory implies an untested speculation.
  • The term theory has a very different meaning in science.
  • A scientific theory is much broader in scope than a hypothesis.
    • This is a hypothesis: “Mimicking poisonous snakes is an adaptation that protects nonpoisonous snakes from predators.”
    • This is a theory: “Evolutionary adaptations evolve by natural selection.”
  • A theory is general enough to generate many new, specific hypotheses that can be tested.
  • Compared to any one hypothesis, a theory is generally supported by a much more massive body of evidence.
  • The theories that become widely adopted in science (such as the theory of adaptation by natural selection) explain many observations and are supported by a great deal of evidence.
  • In spite of the body of evidence supporting a widely accepted theory, scientists may have to modify or reject theories when new evidence is found.
    • As an example, the five-kingdom theory of biological diversity eroded as new molecular methods made it possible to test some of the hypotheses about the relationships between living organisms.
  • Scientists may construct models in the form of diagrams, graphs, computer programs, or mathematical equations.
    • Models may range from lifelike representations to symbolic schematics.
  • Science is an intensely social activity.
    • Most scientists work in teams, which often include graduate and undergraduate students.
  • Both cooperation and competition characterize scientific culture.
    • Scientists attempt to confirm each other’s observations and may repeat experiments.
    • They share information through publications, seminars, meetings, and personal communication.
    • Scientists may be very competitive when converging on the same research question.
  • Science as a whole is embedded in the culture of its times.
    • For example, recent increases in the proportion of women in biology have had an impact on the research being performed.
  • For instance, there has been a switch in focus in studies of the mating behavior of animals from competition among males for access to females to the role that females play in choosing mates.
    • Recent research has revealed that females prefer bright coloration that “advertises” a male’s vigorous health, a behavior that enhances a female’s probability of having healthy offspring.
  • Some philosophers of science argue that scientists are so influenced by cultural and political values that science is no more objective than other ways of “knowing nature.”
    • At the other extreme are those who view scientific theories as though they were natural laws.
  • The reality of science is somewhere in between.
  • The cultural milieu affects scientific fashion, but need for repeatability in observation and hypothesis testing distinguishes science from other fields.
  • If there is “truth” in science, it is based on a preponderance of the available evidence.

    Science and technology are functions of society.

  • Although science and technology may employ similar inquiry patterns, their basic goals differ.
    • The goal of science is to understand natural phenomena.
    • Technology applies scientific knowledge for some specific purpose.
  • Technology results from scientific discoveries applied to the development of goods and services.
  • Scientists put new technology to work in their research.
  • Science and technology are interdependent.
  • The discovery of the structure of DNA by Watson and Crick sparked an explosion of scientific activity.
    • These discoveries made it possible to manipulate DNA, enabling genetic technologists to transplant foreign genes into microorganisms and mass-produce valuable products.
    • DNA technology and biotechnology have revolutionized the pharmaceutical industry.
    • They have had an important impact on agriculture and the legal profession.
  • The direction that technology takes depends less on science than it does on the needs of humans and the values of society.
    • Debates about technology center more on “should we do it” than “can we do it.”
  • With advances in technology come difficult choices, informed as much by politics, economics, and cultural values as by science.
  • Scientists should educate politicians, bureaucrats, corporate leaders, and voters about how science works and about the potential benefits and hazards of specific technologies.

Concept 1.6 A set of themes connects the concepts of biology

  • In some ways, biology is the most demanding of all sciences, partly because living systems are so complex and partly because biology is a multidisciplinary science that requires knowledge of chemistry, physics, and mathematics.
  • Biology is also the science most connected to the humanities and social sciences.

Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-1

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Chapter 1 Exploring Life76 KB
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Chapter 02 - The Chemical Context of Life

Chapter 2 The Chemical Context of Life
Lecture Outline

Overview: Chemical Foundations of Biology

  • Living organisms and the world they live in are subject to the basic laws of physics and chemistry.
  • Biology is a multidisciplinary science, drawing on insights from other sciences.
  • Life can be organized into a hierarchy of structural levels.
  • At each successive level, additional emergent properties appear.

Concept 2.1 Matter consists of chemical elements in pure form and in combinations called compounds

  • Organisms are composed of matter.
    • Matter is anything that takes up space and has mass.
    • Matter is made up of elements.
  • An element is a substance that cannot be broken down into other substances by chemical reactions.
    • There are 92 naturally occurring elements.
    • Each element has a unique symbol, usually the first one or two letters of the name. Some of the symbols are derived from Latin or German names.
  • A compound is a substance consisting of two or more elements in a fixed ratio.
  • Table salt (sodium chloride or NaCl) is a compound with equal numbers of atoms of the elements chlorine and sodium.
  • While pure sodium is a metal and chlorine is a gas, they combine to form an edible compound. This change in characteristics when elements combine to form a compound is an example of an emergent property.

    25 chemical elements are essential to life.

  • About 25 of the 92 natural elements are known to be essential for life.
    • Four elements—carbon (C), oxygen (O), hydrogen (H), and nitrogen (N)—make up 96% of living matter.
    • Most of the remaining 4% of an organism’s weight consists of phosphorus (P), sulfur (S), calcium (Ca), and potassium (K).
  • Trace elements are required by an organism but only in minute quantities.
    • Some trace elements, like iron (Fe), are required by all organisms.
    • Other trace elements are required by only some species.
      • For example, a daily intake of 0.15 milligrams of iodine is required for normal activity of the human thyroid gland.

Concept 2.2 An element’s properties depend on the structure of its atoms

  • Each element consists of unique atoms.
  • An atom is the smallest unit of matter that still retains the properties of an element.
    • Atoms are composed of even smaller parts, called subatomic particles.
    • Two of these, neutrons and protons, are packed together to form a dense core, the atomic nucleus, at the center of an atom.
    • Electrons can be visualized as forming a cloud of negative charge around the nucleus.
  • Each electron has one unit of negative charge.
  • Each proton has one unit of positive charge.
  • Neutrons are electrically neutral.
  • The attractions between the positive charges in the nucleus and the negative charges of the electrons keep the electrons in the vicinity of the nucleus.
  • A neutron and a proton are almost identical in mass, about 1.7 × 10?24 gram per particle.
  • For convenience, a smaller unit of measure, the dalton, is used to measure the mass of subatomic particles, atoms, or molecules.
  • The mass of a neutron or a proton is close to 1 dalton.
  • The mass of an electron is about 1/2000 that of a neutron or proton.
  • Therefore, we typically ignore the contribution of electrons when determining the total mass of an atom.
  • All atoms of a particular element have the same number of protons in their nuclei.
    • This number of protons is the element’s unique atomic number.
    • The atomic number is written as a subscript before the symbol for the element. For example, 2He means that an atom of helium has 2 protons in its nucleus.
  • Unless otherwise indicated, atoms have equal numbers of protons and electrons and, therefore, no net charge.
    • Therefore, the atomic number tells us the number of protons and the number of electrons that are found in a neutral atom of a specific element.
  • The mass number is the sum of the number of protons and neutrons in the nucleus of an atom.
    • Therefore, we can determine the number of neutrons in an atom by subtracting the number of protons (the atomic number) from the mass number.
    • The mass number is written as a superscript before an element’s symbol (for example, 4He).
  • The atomic weight of an atom, a measure of its mass, can be approximated by the mass number.
    • For example, 4He has a mass number of 4 and an estimated atomic weight of 4 daltons. More precisely, its atomic weight is 4.003 daltons.
  • While all atoms of a given element have the same number of protons, they may differ in the number of neutrons.
  • Two atoms of the same element that differ in the number of neutrons are called isotopes.
  • In nature, an element occurs as a mixture of isotopes.
    • For example, 99% of carbon atoms have 6 neutrons (12C).
    • Most of the remaining 1% of carbon atoms have 7 neutrons (13C) while the rarest carbon isotope, with 8 neutrons, is 14C.
  • Most isotopes are stable; they do not tend to lose particles.
    • Both 12C and 13C are stable isotopes.
  • The nuclei of some isotopes are unstable and decay spontaneously, emitting particles and energy.
    • 14C is one of these unstable isotopes, or radioactive isotopes.
    • When 14C decays, one of its neutrons is converted to a proton and an electron.
    • This converts 14C to 14N, transforming the atom to a different element.
  • Radioactive isotopes have many applications in biological research.
    • Radioactive decay rates can be used to date fossils.
    • Radioactive isotopes can be used to trace atoms through metabolic processes.
  • Radioactive isotopes are also used to diagnose medical disorders.
    • For example, a known quantity of a substance labeled with a radioactive isotope can be injected into the blood, and its rate of excretion in the urine can be measured.
    • Also, radioactive tracers can be used with imaging instruments to monitor chemical processes in the body.
  • While useful in research and medicine, the energy emitted in radioactive decay is hazardous to life.
    • This energy can destroy molecules within living cells.
    • The severity of damage depends on the type and amount of radiation that the organism absorbs.

    Electron configuration influences the chemical behavior of an atom.

  • Simplified models of the atom greatly distort the atom’s relative dimensions.
  • To gain an accurate perspective of the relative proportions of an atom, if the nucleus was the size of a golf ball, the electrons would be moving about 1 kilometer from the nucleus.
    • Atoms are mostly empty space.
  • When two elements interact during a chemical reaction, it is actually their electrons that are involved.
  • The nuclei do not come close enough to interact.
  • The electrons of an atom vary in the amount of energy they possess.
  • Energy is the ability to do work.
  • Potential energy is the energy that matter stores because of its position or location.
    • Water stored behind a dam has potential energy that can be used to do work turning electric generators.
    • Because potential energy has been expended, the water stores less energy at the bottom of the dam than it did in the reservoir.
  • Electrons have potential energy because of their position relative to the nucleus.
    • The negatively charged electrons are attracted to the positively charged nucleus.
    • The farther electrons are from the nucleus, the more potential energy they have.
  • Changes in an electron’s potential energy can only occur in steps of a fixed amount, moving the electron to a fixed location relative to the nucleus.
    • An electron cannot exist between these fixed locations.
  • The different states of potential energy that the electrons of an atom can have are called energy levels or electron shells.
    • The first shell, closest to the nucleus, has the lowest potential energy.
    • Electrons in outer shells have more potential energy.
    • Electrons can change their position only if they absorb or release a quantity of energy that matches the difference in potential energy between the two levels.
  • The chemical behavior of an atom is determined by its electron configuration—the distribution of electrons in its electron shells.
    • The first 18 elements, including those most important in biological processes, can be arranged in 8 columns and 3 rows.
      • Elements in the same row fill the same shells with electrons.
      • Moving from left to right, each element adds one electron (and proton) from the element before.
  • The first electron shell can hold only 2 electrons.
    • The two electrons of helium fill the first shell.
  • Atoms with more than two electrons must place the extra electrons in higher shells.
    • For example, lithium, with three electrons, has two in the first shell and one in the second shell.
  • The second shell can hold up to 8 electrons.
    • Neon, with 10 total electrons, has two in the first shell and eight in the second, filling both shells.
  • The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, the valence shell.
    • Electrons in the valence shell are known as valence electrons.
    • Lithium has one valence electron; neon has eight.
  • Atoms with the same number of valence electrons have similar chemical behaviors.
  • An atom with a completed valence shell, like neon, is nonreactive.
  • All other atoms are chemically reactive because they have incomplete valence shells.
  • The paths of electrons are often portrayed as concentric paths, like planets orbiting the sun.
  • In reality, an electron occupies a more complex three-dimensional space, an orbital.
  • The orbital represents the space in which the electron is found 90% of the time.
    • Each orbital can hold a maximum of two electrons.
    • The first shell has room for a single spherical 1s orbital for its pair of electrons.
    • The second shell can pack pairs of electrons into a spherical 2s orbital and three dumbbell-shaped 2p orbitals.
  • The reactivity of atoms arises from the presence of unpaired electrons in one or more orbitals of their valence shells.
    • Electrons occupy separate orbitals within the valence shell until forced to share orbitals.
      • The four valence electrons of carbon each occupy separate orbitals, but the five valence electrons of nitrogen are distributed into three unshared orbitals and one shared orbital.
  • When atoms interact to complete their valence shells, it is the unpaired electrons that are involved.

Concept 2.3 The formation and function of molecules depend on chemical bonding between atoms

  • Atoms with incomplete valence shells can interact with each other by sharing or transferring valence electrons.
  • These interactions typically result in the atoms remaining close together, held by attractions called chemical bonds.
    • The strongest chemical bonds are covalent bonds and ionic bonds.
  • A covalent bond is formed by the sharing of a pair of valence electrons by two atoms.
    • If two atoms come close enough that their unshared orbitals overlap, they will share their newly paired electrons. Each atom can count both electrons toward its goal of filling the valence shell.
    • For example, if two hydrogen atoms come close enough that their 1s orbitals overlap, then they can share a pair of electrons, with each atom contributing one.
  • Two or more atoms held together by covalent bonds constitute a molecule.
  • We can abbreviate the structure of the molecule by substituting a line for each pair of shared electrons, drawing the structural formula.
    • H—H is the structural formula for the covalent bond between two hydrogen atoms.
  • The molecular formula indicates the number and types of atoms present in a single molecule.
    • H2 is the molecular formula for hydrogen gas.
  • Oxygen needs to add 2 electrons to the 6 already present to complete its valence shell.
    • Two oxygen atoms can form a molecule by sharing two pairs of valence electrons.
    • These atoms have formed a double covalent bond.
  • Every atom has a characteristic total number of covalent bonds that it can form, equal to the number of unpaired electrons in the outermost shell. This bonding capacity is called the atom’s valence.
    • The valence of hydrogen is 1.
    • Oxygen is 2.
    • Nitrogen is 3.
    • Carbon is 4.
    • Phosphorus should have a valence of 3, based on its three unpaired electrons, but in biological molecules it generally has a valence of 5, forming three single covalent bonds and one double bond.
  • Covalent bonds can form between atoms of the same element or atoms of different elements.
    • While both types are molecules, the latter are also compounds.
    • Water, H2O, is a compound in which two hydrogen atoms form single covalent bonds with an oxygen atom.
      • This satisfies the valences of both elements.
      • Methane, CH4, satisfies the valences of both C and H.
  • The attraction of an atom for the shared electrons of a covalent bond is called its electronegativity.
    • Strongly electronegative atoms attempt to pull the shared electrons toward themselves.
  • If electrons in a covalent bond are shared equally, then this is a nonpolar covalent bond.
    • A covalent bond between two atoms of the same element is always nonpolar.
    • A covalent bond between atoms that have similar electronegativities is also nonpolar.
      • Because carbon and hydrogen do not differ greatly in electronegativities, the bonds of CH4 are nonpolar.
  • When two atoms that differ in electronegativity bond, they do not share the electron pair equally and form a polar covalent bond.
    • The bonds between oxygen and hydrogen in water are polar covalent because oxygen has a much higher electronegativity than does hydrogen.
    • Compounds with a polar covalent bond have regions of partial negative charge near the strongly electronegative atom and regions of partial positive charge near the weakly electronegative atom.
  • An ionic bond can form if two atoms are so unequal in their attraction for valence electrons that one atom strips an electron completely from the other.
    • For example, sodium, with one valence electron in its third shell, transfers this electron to chlorine, with 7 valence electrons in its third shell.
    • Now, sodium has a full valence shell (the second) and chlorine has a full valence shell (the third).
  • After the transfer, both atoms are no longer neutral, but have charges and are called ions.
  • Sodium has one more proton than electrons and has a net positive charge.
    • Atoms with positive charges are cations.
  • Chlorine has one more electron than protons and has a net negative charge.
    • Atoms with negative charges are anions.
  • Because of differences in charge, cations and anions are attracted to each other to form an ionic bond.
    • Atoms in an ionic bond need not have acquired their charges by transferring electrons with each other.
  • Compounds formed by ionic bonds are ionic compounds, or salts. An example is NaCl, or table salt.
    • The formula for an ionic compound indicates the ratio of elements in a crystal of that salt. NaCl is not a molecule, but a salt crystal with equal numbers of Na+ and Cl? ions.
  • Ionic compounds can have ratios of elements different from 1:1.
    • For example, the ionic compound magnesium chloride (MgCl2) has 2 chloride atoms per magnesium atom.
      • Magnesium needs to lose 2 electrons to drop to a full outer shell; each chlorine atom needs to gain 1.
  • Entire molecules that have full electrical charges are also called ions.
    • In the salt ammonium chloride (NH4Cl), the anion is Cl? and the cation is NH4+.
  • The strength of ionic bonds depends on environmental conditions, such as moisture.
  • Water can dissolve salts by reducing the attraction between the salt’s anions and cations.

    Weak chemical bonds play important roles in the chemistry of life.

  • Within a cell, weak, brief bonds between molecules are important to a variety of processes.
    • For example, signal molecules from one neuron use weak bonds to bind briefly to receptor molecules on the surface of a receiving neuron.
    • This triggers a response by the recipient.
  • Weak interactions include ionic bonds (weak in water), hydrogen bonds, and van der Waals interactions.
  • Hydrogen bonds form when a hydrogen atom already covalently bonded to a strongly electronegative atom is attracted to another strongly electronegative atom.
    • These strongly electronegative atoms are typically nitrogen or oxygen.
    • These bonds form because a polar covalent bond leaves the hydrogen atom with a partial positive charge and the other atom with a partial negative charge.
    • The partially positive–charged hydrogen atom is attracted to regions of full or partial negative charge on molecules, atoms, or even regions of the same large molecule.
  • For example, ammonia molecules and water molecules interact with weak hydrogen bonds.
    • In the ammonia molecule, the hydrogen atoms have partial positive charges, and the more electronegative nitrogen atom has a partial negative charge.
    • In the water molecule, the hydrogen atoms also have partial positive charges, and the oxygen atom has a partial negative charge.
    • Areas with opposite charges are attracted.
  • Even molecules with nonpolar covalent bonds can have temporary regions of partial negative and positive charge.
    • Because electrons are constantly in motion, there can be periods when they accumulate by chance in one area of a molecule.
    • This creates ever-changing regions of partial negative and positive charge within a molecule.
  • Molecules or atoms in close proximity can be attracted by these fleeting charge differences, creating van der Waals interactions.
  • While individual bonds (ionic, hydrogen, van der Waals) are weak and temporary, collectively they are strong and play important biological roles.

    A molecule’s biological function is related to its shape.

  • The three-dimensional shape of a molecule is an important determinant of its function in a cell.
  • A molecule with two atoms is always linear.
  • However, a molecule with more than two atoms has a more complex shape.
  • The shape of a molecule is determined by the positions of the electron orbitals that are shared by the atoms involved in the bond.
    • When covalent bonds form, the orbitals in the valence shell of each atom rearrange.
  • For atoms with electrons in both s and p orbitals, the formation of a covalent bonds leads to hybridization of the orbitals to four new orbitals in a tetrahedral shape.
  • In a water molecule, two of oxygen’s four hybrid orbitals are shared with hydrogen atoms. The water molecule is shaped like a V, with its two covalent bonds spread apart at an angle of 104.5°.
  • In a methane molecule (CH4), the carbon atom shares all four of its hybrid orbitals with H atoms. The carbon nucleus is at the center of the tetrahedron, with hydrogen nuclei at the four corners.
  • Large organic molecules contain many carbon atoms. In these molecules, the tetrahedral shape of carbon bonded to four other atoms is often a repeating motif.
  • Biological molecules recognize and interact with one another with a specificity based on molecular shape.
  • For example, signal molecules from a transmitting cell have specific shapes that bind to complementary receptor molecules on the surface of the receiving cell.
    • The temporary attachment of the receptor and signal molecule stimulates activity in the receptor cell.
  • Molecules with similar shapes can have similar biological effects.
    • For example, morphine, heroin, and other opiate drugs are similar enough in shape that they can bind to the same receptors as natural signal molecules called endorphins.
    • Binding of endorphins to receptors on brain cells produces euphoria and relieves pain. Opiates mimic these natural endorphin effects.

Concept 2.4 Chemical reactions make and break chemical bonds

  • In chemical reactions, chemical bonds are broken and reformed, leading to new arrangements of atoms.
  • The starting molecules in the process are called reactants, and the final molecules are called products.
  • In a chemical reaction, all of the atoms in the reactants must be present in the products.
    • The reactions must be “balanced”.
    • Matter is conserved in a chemical reaction.
    • Chemical reactions rearrange matter; they do not create or destroy matter.
  • For example, we can recombine the covalent bonds of H2 and O2 to form the new bonds of H2O.
  • In this reaction, two molecules of H2 combine with one molecule of O2 to form two molecules of H2O.
  • Photosynthesis is an important chemical reaction.
    • Humans and other animals ultimately depend on photosynthesis for food and oxygen.
    • Green plants combine carbon dioxide (CO2) from the air and water (H2O) from the soil to create sugar molecules and release molecular oxygen (O2) as a by-product.
    • This chemical reaction is powered by sunlight.
    • The overall process of photosynthesis is 6CO2 + 6H2O --> C6H12O6 + 6O2.
    • This process occurs in a sequence of individual chemical reactions that rearrange the atoms of the reactants to form the products.
  • Some chemical reactions go to completion; that is, all the reactants are converted to products.
  • Most chemical reactions are reversible, with the products in the forward reaction becoming the reactants for the reverse reaction.
  • For example in this reaction: 3H2 + N2 <=> 2NH3 hydrogen and nitrogen molecules combine to form ammonia, but ammonia can decompose to hydrogen and nitrogen molecules.
    • Initially, when reactant concentrations are high, they frequently collide to create products.
    • As products accumulate, they collide to reform reactants.
  • Eventually, the rate of formation of products is the same as the rate of breakdown of products (formation of reactants), and the system is at chemical equilibrium.
    • At equilibrium, products and reactants are continually being formed, but there is no net change in the concentrations of reactants and products.
    • At equilibrium, the concentrations of reactants and products are typically not equal, but their concentrations have stabilized at a particular ratio.

Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 2-1

Subject: 
Subject X2: 

Chapter 03 - Water and the Fitness of the Environment

Chapter 3 Water and the Fitness of the Environment
Lecture Outline

Overview: The Molecule That Supports All of Life

  • Because water is the substance that makes life possible on Earth, astronomers hope to find evidence of water on newly discovered planets orbiting distant stars.
  • Life on Earth began in water and evolved there for 3 billion years before colonizing the land.
  • Even terrestrial organisms are tied to water.
    • Most cells are surrounded by water.
    • Cells are about 70–95% water.
    • Water is a reactant in many of the chemical reactions of life.
  • Water is the only common substance that exists in the natural world in all three physical states of matter: solid ice, liquid water, and water vapor.

Concept 3.1 The polarity of water molecules results in hydrogen bonding

  • In a water molecule, two hydrogen atoms form single polar covalent bonds with an oxygen atom.
    • Because oxygen is more electronegative than hydrogen, the region around the oxygen atom has a partial negative charge.
    • The regions near the two hydrogen atoms have a partial positive charge.
  • A water molecule is a polar molecule in which opposite ends of the molecule have opposite charges.
  • Water has a variety of unusual properties because of the attraction between polar water molecules.
    • The slightly negative regions of one water molecule are attracted to the slightly positive regions of nearby water molecules, forming hydrogen bonds.
    • Each water molecule can form hydrogen bonds with up to four neighbors.

Concept 3.2 Four emergent properties of water contribute to Earth’s fitness for life

    Organisms depend on the cohesion of water molecules.

  • The hydrogen bonds joining water molecules are weak, about 1/20 as strong as covalent bonds.
  • They form, break, and reform with great frequency. Each hydrogen bond lasts only a few trillionths of a second.
  • At any instant, a substantial percentage of all water molecules are bonded to their neighbors, creating a high level of structure.
  • Collectively, hydrogen bonds hold water together, a phenomenon called cohesion.
  • Cohesion among water molecules plays a key role in the transport of water and dissolved nutrients against gravity in plants.
    • Water molecules move from the roots to the leaves of a plant through water-conducting vessels.
    • As water molecules evaporate from a leaf, other water molecules from vessels in the leaf replace them.
    • Hydrogen bonds cause water molecules leaving the vessels to tug on molecules farther down.
    • This upward pull is transmitted down to the roots.
    • Adhesion, clinging of one substance to another, contributes too, as water adheres to the wall of the vessels.
  • Surface tension, a measure of the force necessary to stretch or break the surface of a liquid, is related to cohesion.
  • Water has a greater surface tension than most other liquids because hydrogen bonds among surface water molecules resist stretching or breaking the surface.
  • Water behaves as if covered by an invisible film.
  • Some animals can stand, walk, or run on water without breaking the surface.

    Water moderates temperatures on Earth.

  • Water stabilizes air temperatures by absorbing heat from warmer air and releasing heat to cooler air.
  • Water can absorb or release relatively large amounts of heat with only a slight change in its own temperature.
  • Atoms and molecules have kinetic energy, the energy of motion, because they are always moving.
    • The faster a molecule moves, the more kinetic energy it has.
  • Heat is a measure of the total quantity of kinetic energy due to molecular motion in a body of matter.
  • Temperature measures the intensity of heat in a body of matter due to the average kinetic energy of molecules.
    • As the average speed of molecules increases, a thermometer will record an increase in temperature.
  • Heat and temperature are related, but not identical.
  • When two objects of different temperatures come together, heat passes from the warmer object to the cooler object until the two are the same temperature.
    • Molecules in the cooler object speed up at the expense of kinetic energy of the warmer object.
    • Ice cubes cool a glass of pop by absorbing heat from the pop as the ice melts.
  • In most biological settings, temperature is measured on the Celsius scale (°C).
    • At sea level, water freezes at 0°C and boils at 100°C.
    • Human body temperature is typically 37°C.
  • While there are several ways to measure heat energy, one convenient unit is the calorie (cal).
    • One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1°C.
    • A calorie is released when 1 g of water cools by 1°C.
  • In many biological processes, the kilocalorie (kcal) is more convenient.
    • A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000 g of water by 1°C.
  • Another common energy unit, the joule (J), is equivalent to 0.239 cal.
  • Water stabilizes temperature because it has a high specific heat.
  • The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C.
    • By definition, the specific heat of water is 1 cal per gram per degree Celsius or 1 cal/g/°C.
  • Water has a high specific heat compared to other substances.
    • For example, ethyl alcohol has a specific heat of 0.6 cal/g/°C.
    • The specific heat of iron is 1/10 that of water.
  • Water resists changes in temperature because of its high specific heat.
    • In other words, water absorbs or releases a relatively large quantity of heat for each degree of temperature change.
  • Water’s high specific heat is due to hydrogen bonding.
    • Heat must be absorbed to break hydrogen bonds, and heat is released when hydrogen bonds form.
    • Investment of one calorie of heat causes relatively little change to the temperature of water because much of the energy is used to disrupt hydrogen bonds, not speed up the movement of water molecules.
  • Water’s high specific heat has effects that range from the level of the whole Earth to the level of individual organisms.
    • A large body of water can absorb a large amount of heat from the sun in daytime during the summer and yet warm only a few degrees.
    • At night and during the winter, the warm water will warm cooler air.
    • Therefore, ocean temperatures and coastal land areas have more stable temperatures than inland areas.
    • Living things are made primarily of water. Consequently, they resist changes in temperature better than they would if composed of a liquid with a lower specific heat.
  • The transformation of a molecule from a liquid to a gas is called vaporization or evaporation.
    • This occurs when the molecule moves fast enough to overcome the attraction of other molecules in the liquid.
    • Even in a low-temperature liquid (with low average kinetic energy), some molecules are moving fast enough to evaporate.
    • Heating a liquid increases the average kinetic energy and increases the rate of evaporation.
  • Heat of vaporization is the quantity of heat that a liquid must absorb for 1 g of it to be converted from liquid to gas.
    • Water has a relatively high heat of vaporization, requiring about 580 cal of heat to evaporate 1 g of water at room temperature.
    • This is double the heat required to vaporize the same quantity of alcohol or ammonia.
    • This is because hydrogen bonds must be broken before a water molecule can evaporate from the liquid.
    • Water’s high heat of vaporization moderates climate.
    • Much of the sun’s heat absorbed by tropical oceans is used for evaporation of surface water.
    • As moist tropical air moves to the poles, water vapor condenses to form rain, releasing heat.
  • As a liquid evaporates, the surface of the liquid that remains behind cools, a phenomenon called evaporative cooling.
    • This occurs because the most energetic molecules are the most likely to evaporate, leaving the lower–kinetic energy molecules behind.
  • Evaporative cooling moderates temperature in lakes and ponds.
  • Evaporation of sweat in mammals or evaporation of water from the leaves of plants prevents terrestrial organisms from overheating.
    • Evaporation of water from the leaves of plants or the skin of humans removes excess heat.

    Oceans and lakes don’t freeze solid because ice floats.

  • Water is unusual because it is less dense as a solid than as a cold liquid.
    • Most materials contract as they solidify, but water expands.
    • At temperatures above 4°C, water behaves like other liquids, expanding as it warms and contracting as it cools.
    • Water begins to freeze when its molecules are no longer moving vigorously enough to break their hydrogen bonds.
  • When water reaches 0°C, water becomes locked into a crystalline lattice, with each water molecule bonded to a maximum of four partners.
  • As ice starts to melt, some of the hydrogen bonds break, and water molecules can slip closer together than they can while in the ice state.
  • Ice is about 10% less dense than water at 4°C.
  • Therefore, ice floats on the cool water below.
  • This oddity has important consequences for life.
    • If ice sank, eventually all ponds, lakes, and even the ocean would freeze solid.
    • During the summer, only the upper few centimeters of the ocean would thaw.
    • Instead, the surface layer of ice insulates liquid water below, preventing it from freezing and allowing life to exist under the frozen surface.

    Water is the solvent of life.

  • A liquid that is a completely homogeneous mixture of two or more substances is called a solution.
    • A sugar cube in a glass of water will eventually dissolve to form a uniform solution of sugar and water.
    • The dissolving agent is the solvent, and the substance that is dissolved is the solute.
    • In our example, water is the solvent and sugar is the solute.
  • In an aqueous solution, water is the solvent.
  • Water is not a universal solvent, but it is very versatile because of the polarity of water molecules.
    • Water is an effective solvent because it readily forms hydrogen bonds with charged and polar covalent molecules.
    • For example, when a crystal of salt (NaCl) is placed in water, the Na+ cations interact with the partial negative charges of the oxygen regions of water molecules.
    • The Cl? anions interact with the partial positive charges of the hydrogen regions of water molecules.
  • Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell.
  • Eventually, water dissolves all the ions, resulting in a solution with two solutes: sodium and chloride ions.
  • Polar molecules are also soluble in water because they form hydrogen bonds with water.
  • Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions.
  • Any substance that has an affinity for water is hydrophilic (water-loving).
    • These substances are dominated by ionic or polar bonds.
  • Some hydrophilic substances do not dissolve because their molecules are too large.
    • For example, cotton is hydrophilic because cellulose, its major constituent, has numerous polar covalent bonds. However, its giant cellulose molecules are too large to dissolve in water.
    • Water molecules form hydrogen bonds with the cellulose fibers of cotton, allowing you to dry yourself with your cotton towel as the water is pulled into the towel.
  • Substances that have no affinity for water are hydrophobic (water-fearing).
    • These substances are nonionic and have nonpolar covalent bonds.
    • Because there are no consistent regions with partial or full charges, water molecules cannot form hydrogen bonds with hydrophobic molecules.
    • Oils such as vegetable oil are hydrophobic because the dominant bonds, carbon-carbon and carbon-hydrogen, share electrons equally.
    • Hydrophobic molecules are major ingredients of cell membranes.
  • Biological chemistry is “wet” chemistry with most reactions involving solutes dissolved in water.
  • Chemical reactions depend on collisions of molecules and therefore on the concentrations of solutes in aqueous solution.
  • We measure the number of molecules in units called moles.
  • The actual number of molecules in a mole is called Avogadro’s number, 6.02 × 1023.
  • A mole is equal to the molecular weight of a substance but scaled up from daltons to grams.
  • To illustrate, how could we measure out a mole of table sugar—sucrose (C12H22O11)?
    • A carbon atom weighs 12 daltons, hydrogen 1 dalton, and oxygen 16 daltons.
    • One molecule of sucrose would weigh 342 daltons, the sum of weights of all the atoms in sucrose, or the molecular weight of sucrose.
    • To get one mole of sucrose, we would weigh out 342 g.
  • The advantage of using moles as a measurement is that a mole of one substance has the same number of molecules as a mole of any other substance.
    • If substance A has a molecular weight of 10 daltons and substance B has a molecular weight of 100 daltons, then we know that 10 g of substance A has the same number of molecules as 100 g of substance B.
    • A mole of sucrose contains 6.02 × 1023 molecules and weighs 342 g, while a mole of ethyl alcohol (C2H6O) also contains 6.02 × 1023 molecules but weighs only 46 g because the molecules are smaller.
    • Measuring in moles allows scientists to combine substances in fixed ratios of molecules.
  • In “wet” chemistry, we are typically combining solutions or measuring the quantities of materials in aqueous solutions.
    • The concentration of a material in solution is called its molarity.
    • A one molar solution has one mole of a substance dissolved in one liter of solvent, typically water.
    • To make a 1 molar (1M) solution of sucrose, we would slowly add water to 342 g of sucrose until the total volume was 1 liter and all the sugar was dissolved.

Concept 3.3 Dissociation of water molecules leads to acidic and basic conditions that affect living organisms

  • Occasionally, a hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other.
    • The hydrogen atom leaves its electron behind and is transferred as a single proton—a hydrogen ion (H+).
    • The water molecule that lost the proton is now a hydroxide ion (OH?).
    • The water molecule with the extra proton is now a hydronium ion (H3O+).
  • A simplified way to view this process is to say that a water molecule dissociates into a hydrogen ion and a hydroxide ion:
    • H2O <=> H+ + OH?
  • This reaction is reversible.
  • At equilibrium, the concentration of water molecules greatly exceeds that of H+ and OH?.
  • In pure water, only one water molecule in every 554 million is dissociated.
    • At equilibrium, the concentration of H+ or OH? is 10?7M (at 25°C).
  • Although the dissociation of water is reversible and statistically rare, it is very important in the chemistry of life.
  • Because hydrogen and hydroxide ions are very reactive, changes in their concentrations can drastically affect the chemistry of a cell.
  • Adding certain solutes, called acids and bases, disrupts the equilibrium and modifies the concentrations of hydrogen and hydroxide ions.
  • The pH scale is used to describe how acidic or basic a solution is.

    Organisms are sensitive to changes in pH.

  • An acid is a substance that increases the hydrogen ion concentration in a solution.
    • When hydrochloric acid is added to water, hydrogen ions dissociate from chloride ions: HCl -> H+ + Cl?
    • Addition of an acid makes a solution more acidic.
  • Any substance that reduces the hydrogen ion concentration in a solution is a base.
  • Some bases reduce the H+ concentration directly by accepting hydrogen ions.
    • Ammonia (NH3) acts as a base when the nitrogen’s unshared electron pair attracts a hydrogen ion from the solution, creating an ammonium ion (NH4+).
    • NH3 + H+ <=> NH4+
  • Other bases reduce H+ indirectly by dissociating to OH?, which then combines with H+ to form water.
    • NaOH -> Na+ + OH? OH? + H+ -> H2O
  • Solutions with more OH? than H+ are basic solutions.
  • Solutions with more H+ than OH? are acidic solutions.
  • Solutions in which concentrations of OH? and H+ are equal are neutral solutions.
  • Some acids and bases (HCl and NaOH) are strong acids or bases.
    • These molecules dissociate completely in water.
  • Other acids and bases (NH3) are weak acids or bases.
    • For these molecules, the binding and release of hydrogen ions are reversible.
    • At equilibrium, there will be a fixed ratio of products to reactants.
    • Carbonic acid (H2CO3) is a weak acid:
      • H2CO3 <=> HCO3? + H+
      • At equilibrium, 1% of the H2CO3 molecules will be dissociated.
  • In any solution, the product of the H+ and OH? concentrations is constant at 10?14.
  • Brackets ([H+] and [OH?]) indicate the molar concentration of the enclosed substance.
    • [H+] [OH?] = 10?14
    • In a neutral solution, [H+] = 10?7 M and [OH?] = 10?7 M
  • Adding acid to a solution shifts the balance between H+ and OH? toward H+ and leads to a decline in OH?.
    • If [H+] = 10?5 M, then [OH?] = 10?9 M
    • Hydroxide concentrations decline because some of the additional acid combines with hydroxide to form water.
  • Adding a base does the opposite, increasing OH? concentration and lowering H+ concentration.
  • The H+ and OH? concentrations of solutions can vary by a factor of 100 trillion or more.
  • To express this variation more conveniently, the H+ and OH? concentrations are typically expressed via the pH scale.
    • The pH scale, ranging from 1 to 14, compresses the range of concentrations by employing logarithms.
    • pH = ? log [H+] or [H+] = 10?pH
    • In a neutral solution, [H+] = 10?7 M, and the pH = 7.
  • Values for pH decline as [H+] increase.
  • While the pH scale is based on [H+], values for [OH?] can be easily calculated from the product relationship.
  • The pH of a neutral solution is 7.
  • Acidic solutions have pH values less than 7, and basic solutions have pH values greater than 7.
  • Most biological fluids have pH values in the range of 6 to 8.
    • However, the human stomach has strongly acidic digestive juice with a pH of about 2.
  • Each pH unit represents a tenfold difference in H+ and OH? concentrations.
    • A small change in pH actually indicates a substantial change in H+ and OH? concentrations.
  • The chemical processes in the cell can be disrupted by changes to the H+ and OH? concentrations away from their normal values, usually near pH 7.
  • To maintain cellular pH values at a constant level, biological fluids have buffers.
  • Buffers resist changes to the pH of a solution when H+ or OH? is added to the solution.
    • Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.
    • Buffers typically consist of a weak acid and its corresponding base.
    • One important buffer in human blood and other biological solutions is carbonic acid, which dissociates to yield a bicarbonate ion and a hydrogen ion.
    • The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator. The equilibrium shifts left or right as other metabolic processes add or remove H+ from the solution.

    Acid precipitation threatens the fitness of the environment.

  • Acid precipitation is a serious assault on water quality in some industrialized areas.
    • Uncontaminated rain has a slightly acidic pH of 5.6.
    • The acid is a product of the formation of carbonic acid from carbon dioxide and water.
  • Acid precipitation occurs when rain, snow, or fog has a pH that is more acidic than 5.6.
  • Acid precipitation is caused primarily by sulfur oxides and nitrogen oxides in the atmosphere.
    • These molecules react with water to form strong acids that fall to the surface with rain or snow.
  • The major source of these oxides is the burning of fossil fuels (coal, oil, and gas) in factories and automobiles.
  • The presence of tall smokestacks allows this pollution to spread from its site of origin to contaminate relatively pristine areas thousands of kilometers away.
    • In 2001, rain in the Adirondack Mountains of upstate New York had an average pH of 4.3.
  • The effects of acids in lakes and streams are more pronounced in the spring during snowmelt.
    • As the surface snows melt and drain down through the snowfield, the meltwater accumulates acid and brings it into lakes and streams all at once.
    • The pH of early meltwater may be as low as 3.
  • Acid precipitation has a great impact on the eggs and the early developmental stages of aquatic organisms that are abundant in the spring.
  • Thus, strong acidity can alter the structure of molecules and impact ecological communities.
  • Direct impacts of acid precipitation on forests and terrestrial life are more controversial.
  • However, acid precipitation can impact soils by affecting the solubility of soil minerals.
    • Acid precipitation can wash away key soil buffers and plant nutrients such as calcium and magnesium ions.
    • It can also increase the concentrations of compounds such as aluminum to toxic levels.
    • This has done major damage to forests in Europe and substantial damage of forests in North America.
    • Progress has been made in reducing acid precipitation.

Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 3-1

Subject: 
Subject X2: 

Chapter 04 - Carbon and the Molecular Diversity of Life

Chapter 4    Carbon and the Molecular Diversity of Life
    Lecture Outline

Overview: Carbon – The Backbone of Biological Molecules

  • Although cells are 70–95% water, the rest consists mostly of carbon-based compounds.
  • Carbon is unparalleled in its ability to form large, complex, and diverse molecules.
  • Carbon accounts for the diversity of biological molecules and has made possible the great diversity of living things.
  • Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements.
  • These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P).

Concept 4.1 Organic chemistry is the study of carbon compounds

  • The study of carbon compounds, organic chemistry, deals with any compound with carbon (organic compounds).
  • Organic compounds can range from simple molecules, such as CO2 or CH4, to complex molecules such as proteins, which may weigh more than 100,000 daltons.
  • The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one organism to another.
  • However, because of carbon’s versatility, these few elements can be combined to build an inexhaustible variety of organic molecules.
  • Variations in organic molecules can distinguish even between individuals of a single species.
  • The science of organic chemistry began in attempts to purify and improve the yield of products obtained from other organisms.
  • Initially, chemists learned to synthesize simple compounds in the laboratory, but had no success with more complex compounds.
  • The Swedish chemist Jons Jacob Berzelius was the first to make a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds that were found in the nonliving world.
  • This led early organic chemists to propose vitalism, the belief that physical and chemical laws did not apply to living things.
  • Support for vitalism began to wane as organic chemists learned to synthesize complex organic compounds in the laboratory.
  • In the early 1800s, the German chemist Friedrich Wöhler and his students were able to synthesize urea from totally inorganic materials.
  • In 1953, Stanley Miller at the University of Chicago set up a laboratory simulation of chemical conditions on the primitive Earth and demonstrated the spontaneous synthesis of organic compounds.
  • Such spontaneous synthesis of organic compounds may have been an early stage in the origin of life.
  • Organic chemists finally rejected vitalism and embraced mechanism, accepting that the same physical and chemical laws govern all natural phenomena including the processes of life.
  • Organic chemistry was redefined as the study of carbon compounds regardless of their origin.
  • Organisms do produce the majority of organic compounds.
  • The laws of chemistry apply to inorganic and organic compounds alike.

Concept 4.2 Carbon atoms can form diverse molecules by bonding to four other atoms

  • With a total of 6 electrons, a carbon atom has 2 in the first electron shell and 4 in the second shell.
  • Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons to complete its valence shell.
  • Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds.
  • This tetravalence by carbon makes large, complex molecules possible.
  • When carbon forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles of 109.5°.
  • In molecules with multiple carbons, every carbon bonded to four other atoms has a tetrahedral shape.
  • However, when two carbon atoms are joined by a double bond, all bonds around those carbons are in the same plane and have a flat, three-dimensional structure.
  • The three-dimensional shape of an organic molecule determines its function.
  • The electron configuration of carbon makes it capable of forming covalent bonds with many different elements.
  • The valences of carbon and its partners can be viewed as the building code that governs the architecture of organic molecules.
  • In carbon dioxide, one carbon atom forms two double bonds with two different oxygen atoms.
  • In the structural formula, O=C=O, each line represents a pair of shared electrons. This arrangement completes the valence shells of all atoms in the molecule.
  • While CO2 can be classified as either organic or inorganic, its importance to the living world is clear.
  • CO2 is the source of carbon for all organic molecules found in organisms. It is usually fixed into organic molecules by the process of photosynthesis.
  • Urea, CO(NH2)2, is another simple organic molecule in which each atom forms covalent bonds to complete its valence shell.

    Variation in carbon skeletons contributes to the diversity of organic molecules.

  • Carbon chains form the skeletons of most organic molecules.
  • The skeletons vary in length and may be straight, branched, or arranged in closed rings.
  • The carbon skeletons may include double bonds.
  • Atoms of other elements can be bonded to the atoms of the carbon skeleton.
  • Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms.
  • Hydrocarbons are the major component of petroleum, a fossil fuel that consists of the partially decomposed remains of organisms that lived millions of years ago.
  • Fats are biological molecules that have long hydrocarbon tails attached to a nonhydrocarbon component.
  • Petroleum and fat are hydrophobic compounds that cannot dissolve in water because of their many nonpolar carbon-to-hydrogen bonds.
  • Isomers are compounds that have the same molecular formula but different structures and, therefore, different chemical properties.
  • For example, butane and isobutane have the same molecular formula, C4H10, but butane has a straight skeleton and isobutane has a branched skeleton.
  • The two butanes are structural isomers, molecules that have the same molecular formula but differ in the covalent arrangement of atoms.
  • Geometric isomers are compounds with the same covalent partnerships that differ in the spatial arrangement of atoms around a carbon–carbon double bond.
  • The double bond does not allow atoms to rotate freely around the bond axis.
  • The biochemistry of vision involves a light-induced change in the structure of rhodopsin in the retina from one geometric isomer to another.
  • Enantiomers are molecules that are mirror images of each other.
  • Enantiomers are possible when four different atoms or groups of atoms are bonded to a carbon.
  • In this case, the four groups can be arranged in space in two different ways that are mirror images.
  • They are like left-handed and right-handed versions of the molecule.
  • Usually one is biologically active, while the other is inactive.
  • Even subtle structural differences in two enantiomers have important functional significance because of emergent properties from specific arrangements of atoms.
  • One enantiomer of the drug thalidomide reduced morning sickness, the desired effect, but the other isomer caused severe birth defects.
  • The L-dopa isomer is an effective treatment of Parkinson’s disease, but the D-dopa isomer is inactive.

Concept 4.3 Functional groups are the parts of molecules involved in chemical reactions

  • The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups.
  • If we consider hydrocarbons to be the simplest organic molecules, we can view functional groups as attachments that replace one or more of the hydrogen atoms bonded to the carbon skeleton of the hydrocarbon.
  • Each functional group behaves consistently from one organic molecule to another.
  • The number and arrangement of functional groups help give each molecule its unique properties.
  • As an example, the basic structure of testosterone (a male sex hormone) and estradiol (a female sex hormone) is the same.
  • Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings.
  • These functional groups interact with different targets in the body.
  • There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups.
  • All are hydrophilic and increase the solubility of organic compounds in water.
  • In a hydroxyl group (—OH), a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton.
  • Because of these polar covalent bonds, hydroxyl groups increase the solubility of organic molecules.
  • Organic compounds with hydroxyl groups are alcohols, and their names typically end in -ol.
  • A carbonyl group (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond.
  • If the carbonyl group is on the end of the skeleton, the compound is an aldehyde.
  • If the carbonyl group is within the carbon skeleton, then the compound is a ketone.
  • Isomers with aldehydes versus ketones have different properties.
  • A carboxyl group (—COOH) consists of a carbon atom with a double bond to an oxygen atom and a single bond to the oxygen of a hydroxyl group.
  • Compounds with carboxyl groups are carboxylic acids.
  • A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+).
  • An amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton.
  • Organic compounds with amino groups are amines.
  • The amino group acts as a base because the amino group can pick up a hydrogen ion (H+) from the solution.
  • Amino acids, the building blocks of proteins, have amino and carboxyl groups.
  • A sulfhydryl group (—SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone.
  • This group resembles a hydroxyl group in shape.
  • Organic molecules with sulfhydryl groups are thiols.
  • Two sulfhydryl groups can interact to help stabilize the structure of proteins.
  • A phosphate group (—OPO32?) consists of a phosphorus atom bound to four oxygen atoms (three with single bonds and one with a double bond).
  • A phosphate group connects to the carbon backbone via one of its oxygen atoms.
  • Phosphate groups are anions with two negative charges, as two protons have dissociated from the oxygen atoms.
  • One function of phosphate groups is to transfer energy between organic molecules.
  • Adenosine triphosphate, or ATP, is the primary energy-transferring molecule in living cells.

    These are the chemical elements of life.

  • Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus.
  • These elements are linked by strong covalent bonds.
  • Carbon, with its four covalent bonds, is the basic building block in molecular architecture.
  • The great diversity of organic molecules with their special properties emerges from the unique arrangement of the carbon skeleton and the functional groups attached to the skeleton.
Subject: 
Subject X2: 

Chapter 05 - The Structure and Function of Macromolecules

Chapter 5 The Structure and Function of Macromolecules
Lecture Outline

Overview: The Molecules of Life

  • Within cells, small organic molecules are joined together to form larger molecules.
  • These large macromolecules may consist of thousands of covalently bonded atoms and weigh more than 100,000 daltons.
  • The four major classes of macromolecules are carbohydrates, lipids, proteins, and nucleic acids.

Concept 5.1 Most macromolecules are polymers, built from monomers

  • Three of the four classes of macromolecules—carbohydrates, proteins, and nucleic acids—form chainlike molecules called polymers.
    • A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds.
    • The repeated units are small molecules called monomers.
    • Some of the molecules that serve as monomers have other functions of their own.
  • The chemical mechanisms that cells use to make and break polymers are similar for all classes of macromolecules.
  • Monomers are connected by covalent bonds that form through the loss of a water molecule. This reaction is called a condensation reaction or dehydration reaction.
    • When a bond forms between two monomers, each monomer contributes part of the water molecule that is lost. One monomer provides a hydroxyl group (—OH), while the other provides a hydrogen (—H).
    • Cells invest energy to carry out dehydration reactions.
    • The process is aided by enzymes.
  • The covalent bonds connecting monomers in a polymer are disassembled by hydrolysis, a reaction that is effectively the reverse of dehydration.
    • In hydrolysis, bonds are broken by the addition of water molecules. A hydrogen atom attaches to one monomer, and a hydroxyl group attaches to the adjacent monomer.
    • Our food is taken in as organic polymers that are too large for our cells to absorb. Within the digestive tract, various enzymes direct hydrolysis of specific polymers. The resulting monomers are absorbed by the cells lining the gut and transported to the bloodstream for distribution to body cells.
    • The body cells then use dehydration reaction to assemble the monomers into new polymers that carry out functions specific to the particular cell type.

    An immense variety of polymers can be built from a small set of monomers.

  • Each cell has thousands of different kinds of macromolecules.
    • These molecules vary among cells of the same individual. They vary more among unrelated individuals of a species, and even more between species.
  • This diversity comes from various combinations of the 40–50 common monomers and some others that occur rarely.
    • These monomers can be connected in a great many combinations, just as the 26 letters in the alphabet can be used to create a great diversity of words.

Concept 5.2 Carbohydrates serve as fuel and building material

  • Carbohydrates include sugars and their polymers.
  • The simplest carbohydrates are monosaccharides, or simple sugars.
  • Disaccharides, or double sugars, consist of two monosaccharides joined by a condensation reaction.
  • Polysaccharides are polymers of many monosaccharides.

    Sugars, the smallest carbohydrates, serve as fuel and a source of carbon.

  • Monosaccharides generally have molecular formulas that are some multiple of the unit CH2O.
    • For example, glucose has the formula C6H12O6.
  • Monosaccharides have a carbonyl group (>C=O) and multiple hydroxyl groups (—OH).
    • Depending on the location of the carbonyl group, the sugar is an aldose or a ketose.
    • Most names for sugars end in -ose.
    • Glucose, an aldose, and fructose, a ketose, are structural isomers.
  • Monosaccharides are also classified by the number of carbons in the carbon skeleton.
    • Glucose and other six-carbon sugars are hexoses.
    • Five-carbon backbones are pentoses; three-carbon sugars are trioses.
  • Monosaccharides may also exist as enantiomers.
    • For example, glucose and galactose, both six-carbon aldoses, differ in the spatial arrangement of their parts around asymmetrical carbons.
  • Monosaccharides, particularly glucose, are a major fuel for cellular work.
  • They also function as the raw material for the synthesis of other monomers, such as amino acids and fatty acids.
  • While often drawn as a linear skeleton, monosaccharides in aqueous solutions form rings.
  • Two monosaccharides can join with a glycosidic linkage to form a disaccharide via dehydration.
    • Maltose, malt sugar, is formed by joining two glucose molecules.
    • Sucrose, table sugar, is formed by joining glucose and fructose. Sucrose is the major transport form of sugars in plants.
    • Lactose, milk sugar, is formed by joining glucose and galactose.

    Polysaccharides, the polymers of sugars, have storage and structural roles.

  • Polysaccharides are polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages.
  • Some polysaccharides serve for storage and are hydrolyzed as sugars are needed.
  • Other polysaccharides serve as building materials for the cell or the whole organism.
  • Starch is a storage polysaccharide composed entirely of glucose monomers.
    • Most of these monomers are joined by 1–4 linkages (number 1 carbon to number 4 carbon) between the glucose molecules.
    • The simplest form of starch, amylose, is unbranched and forms a helix.
    • Branched forms such as amylopectin are more complex.
  • Plants store surplus glucose as starch granules within plastids, including chloroplasts, and withdraw it as needed for energy or carbon.
    • Animals that feed on plants, especially parts rich in starch, have digestive enzymes that can hydrolyze starch to glucose.
  • Animals store glucose in a polysaccharide called glycogen.
    • Glycogen is highly branched like amylopectin.
    • Humans and other vertebrates store a day’s supply of glycogen in the liver and muscles.
  • Cellulose is a major component of the tough wall of plant cells.
    • Plants produce almost one hundred billion tons of cellulose per year. It is the most abundant organic compound on Earth.
  • Like starch, cellulose is a polymer of glucose. However, the glycosidic linkages in these two polymers differ.
    • The difference is based on the fact that there are actually two slightly different ring structures for glucose.
    • These two ring forms differ in whether the hydroxyl group attached to the number 1 carbon is fixed above (beta glucose) or below (alpha glucose) the plane of the ring.
  • Starch is a polysaccharide of alpha glucose monomers.
  • Cellulose is a polysaccharide of beta glucose monomers, making every other glucose monomer upside down with respect to its neighbors.
  • The differing glycosidic links in starch and cellulose give the two molecules distinct three-dimensional shapes.
    • While polymers built with alpha glucose form helical structures, polymers built with beta glucose form straight structures.
    • The straight structures built with beta glucose allow H atoms on one strand to form hydrogen bonds with OH groups on other strands.
    • In plant cell walls, parallel cellulose molecules held together in this way are grouped into units called microfibrils, which form strong building materials for plants (and for humans, as lumber).
  • The enzymes that digest starch by hydrolyzing its alpha linkages cannot hydrolyze the beta linkages in cellulose.
    • Cellulose in human food passes through the digestive tract and is eliminated in feces as “insoluble fiber.”
    • As it travels through the digestive tract, cellulose abrades the intestinal walls and stimulates the secretion of mucus, aiding in the passage of food.
  • Some microbes can digest cellulose to its glucose monomers through the use of cellulase enzymes.
  • Many eukaryotic herbivores, from cows to termites, have symbiotic relationships with cellulolytic microbes, providing the microbe and the host animal access to a rich source of energy.
    • Some fungi can also digest cellulose.
  • Another important structural polysaccharide is chitin, used in the exoskeletons of arthropods (including insects, spiders, and crustaceans).
    • Chitin is similar to cellulose, except that it contains a nitrogen-containing appendage on each glucose monomer.
    • Pure chitin is leathery but can be hardened by the addition of calcium carbonate.
  • Chitin also provides structural support for the cell walls of many fungi.

Concept 5.3 Lipids are a diverse group of hydrophobic molecules

  • Unlike other macromolecules, lipids do not form polymers.
  • The unifying feature of lipids is that they all have little or no affinity for water.
  • This is because they consist mostly of hydrocarbons, which form nonpolar covalent bonds.
  • Lipids are highly diverse in form and function.

    Fats store large amounts of energy.

  • Although fats are not strictly polymers, they are large molecules assembled from smaller molecules by dehydration reactions.
  • A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids.
    • Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon.
    • A fatty acid consists of a carboxyl group attached to a long carbon skeleton, often 16 to 18 carbons long.
    • The many nonpolar C—H bonds in the long hydrocarbon skeleton make fats hydrophobic.
    • Fats separate from water because the water molecules hydrogen bond to one another and exclude the fats.
  • In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride.
  • The three fatty acids in a fat can be the same or different.
  • Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds.
    • If the fatty acid has no carbon-carbon double bonds, then the molecule is a saturated fatty acid, saturated with hydrogens at every possible position.
    • If the fatty acid has one or more carbon-carbon double bonds formed by the removal of hydrogen atoms from the carbon skeleton, then the molecule is an unsaturated fatty acid.
  • A saturated fatty acid is a straight chain, but an unsaturated fatty acid has a kink wherever there is a double bond.
  • Fats made from saturated fatty acids are saturated fats.
    • Most animal fats are saturated.
    • Saturated fats are solid at room temperature.
  • Fats made from unsaturated fatty acids are unsaturated fats.
    • Plant and fish fats are liquid at room temperature and are known as oils.
    • The kinks caused by the double bonds prevent the molecules from packing tightly enough to solidify at room temperature.
    • The phrase “hydrogenated vegetable oils” on food labels means that unsaturated fats have been synthetically converted to saturated fats by the addition of hydrogen.
      • Peanut butter and margarine are hydrogenated to prevent lipids from separating out as oil.
    • A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits.
    • The process of hydrogenating vegetable oils produces saturated fats and also unsaturated fats with trans double bonds. These trans fat molecules contribute more than saturated fats to atherosclerosis.
  • The major function of fats is energy storage.
    • A gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch.
    • Because plants are immobile, they can function with bulky energy storage in the form of starch. Plants use oils when dispersal and compact storage is important, as in seeds.
    • Animals must carry their energy stores with them and benefit from having a more compact fuel reservoir of fat.
    • Humans and other mammals store fats as long-term energy reserves in adipose cells that swell and shrink as fat is deposited or withdrawn from storage.
  • Adipose tissue also functions to cushion vital organs, such as the kidneys.
  • A layer of fat can also function as insulation.
    • This subcutaneous layer is especially thick in whales, seals, and most other marine mammals.

    Phospholipids are major components of cell membranes.

  • Phospholipids have two fatty acids attached to glycerol and a phosphate group at the third position.
    • The phosphate group carries a negative charge.
    • Additional smaller groups may be attached to the phosphate group to form a variety of phospholipids.
  • The interaction of phospholipids with water is complex.
    • The fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head.
  • When phospholipids are added to water, they self-assemble into assemblages with the hydrophobic tails pointing toward the interior.
    • This type of structure is called a micelle.
  • Phospholipids are arranged as a bilayer at the surface of a cell.
    • Again, the hydrophilic heads are on the outside of the bilayer, in contact with the aqueous solution, and the hydrophobic tails point toward the interior of the bilayer.
      • The phospholipid bilayer forms a barrier between the cell and the external environment.
    • Phospholipids are the major component of all cell membranes.

    Steroids include cholesterol and certain hormones.

  • Steroids are lipids with a carbon skeleton consisting of four fused rings.
  • Different steroids are created by varying functional groups attached to the rings.
  • Cholesterol, an important steroid, is a component in animal cell membranes.
  • Cholesterol is also the precursor from which all other steroids are synthesized.
    • Many of these other steroids are hormones, including the vertebrate sex hormones.
  • While cholesterol is an essential molecule in animals, high levels of cholesterol in the blood may contribute to cardiovascular disease.
  • Both saturated fats and trans fats exert their negative impact on health by affecting cholesterol levels.

Concept 5.4 Proteins have many structures, resulting in a wide range of functions

  • Proteins account for more than 50% of the dry mass of most cells. They are instrumental in almost everything that an organism does.
    • Protein functions include structural support, storage, transport, cellular signaling, movement, and defense against foreign substances.
    • Most important, protein enzymes function as catalysts in cells, regulating metabolism by selectively accelerating chemical reactions without being consumed.
  • Humans have tens of thousands of different proteins, each with a specific structure and function.
  • Proteins are the most structurally complex molecules known.
    • Each type of protein has a complex three-dimensional shape or conformation.
  • All protein polymers are constructed from the same set of 20 amino acid monomers.
  • Polymers of proteins are called polypeptides.
  • A protein consists of one or more polypeptides folded and coiled into a specific conformation.

    Amino acids are the monomers from which proteins are constructed.

  • Amino acids are organic molecules with both carboxyl and amino groups.
  • At the center of an amino acid is an asymmetric carbon atom called the alpha carbon.
  • Four components are attached to the alpha carbon: a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain).
    • Different R groups characterize the 20 different amino acids.
  • R groups may be as simple as a hydrogen atom (as in the amino acid glycine), or it may be a carbon skeleton with various functional groups attached (as in glutamine).
  • The physical and chemical properties of the R group determine the unique characteristics of a particular amino acid.
    • One group of amino acids has hydrophobic R groups.
    • Another group of amino acids has polar R groups that are hydrophilic.
    • A third group of amino acids includes those with functional groups that are charged (ionized) at cellular pH.
      • Some acidic R groups are negative in charge due to the presence of a carboxyl group.
      • Basic R groups have amino groups that are positive in charge.
      • Note that all amino acids have carboxyl and amino groups. The terms acidic and basic in this context refer only to these groups in the R groups.
    • Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another.
      • The resulting covalent bond is called a peptide bond.
    • Repeating the process over and over creates a polypeptide chain.
      • At one end is an amino acid with a free amino group (the N-terminus) and at the other is an amino acid with a free carboxyl group (the C-terminus).
    • Polypeptides range in size from a few monomers to thousands.
    • Each polypeptide has a unique linear sequence of amino acids.

    The amino acid sequence of a polypeptide can be determined.

  • Frederick Sanger and his colleagues at Cambridge University determined the amino acid sequence of insulin in the 1950s.
    • Sanger used protein-digesting enzymes and other catalysts to hydrolyze the insulin at specific places.
    • The fragments were then separated by a technique called chromatography.
    • Hydrolysis by another agent broke the polypeptide at different sites, yielding a second group of fragments.
    • Sanger used chemical methods to determine the sequence of amino acids in the small fragments.
    • He then searched for overlapping regions among the pieces obtained by hydrolyzing with the different agents.
    • After years of effort, Sanger was able to reconstruct the complete primary structure of insulin.
    • Most of the steps in sequencing a polypeptide have since been automated.

    Protein conformation determines protein function.

  • A functional protein consists of one or more polypeptides that have been twisted, folded, and coiled into a unique shape.
  • It is the order of amino acids that determines what the three-dimensional conformation of the protein will be.
  • A protein’s specific conformation determines its function.
  • When a cell synthesizes a polypeptide, the chain generally folds spontaneously to assume the functional conformation for that protein.
  • The folding is reinforced by a variety of bonds between parts of the chain, which in turn depend on the sequence of amino acids.
    • Many proteins are globular, while others are fibrous in shape.
  • In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule.
    • For example, an antibody binds to a particular foreign substance.
    • An enzyme recognizes and binds to a specific substrate, facilitating a chemical reaction.
    • Natural signal molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans, producing euphoria and relieving pain.
      • Morphine, heroin, and other opiate drugs mimic endorphins because they are similar in shape and can bind to the brain’s endorphin receptors.
  • The function of a protein is an emergent property resulting from its specific molecular order.
  • Three levels of structure—primary, secondary, and tertiary structures—organize the folding within a single polypeptide.
  • Quaternary structure arises when two or more polypeptides join to form a protein.
  • The primary structure of a protein is its unique sequence of amino acids.
    • Lysozyme, an enzyme that attacks bacteria, consists of 129 amino acids.
    • The precise primary structure of a protein is determined by inherited genetic information.
  • Even a slight change in primary structure can affect a protein’s conformation and ability to function.
    • The substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin, the protein that carries oxygen in red blood cells, can cause sickle-cell disease, an inherited blood disorder.
    • The abnormal hemoglobins crystallize, deforming the red blood cells into a sickle shape and clogging capillaries.
  • Most proteins have segments of their polypeptide chains repeatedly coiled or folded.
  • These coils and folds are referred to as secondary structure and result from hydrogen bonds between the repeating constituents of the polypeptide backbone.
    • The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond.
    • Each hydrogen bond is weak, but the sum of many hydrogen bonds stabilizes the structure of part of the protein.
  • Typical secondary structures are coils (an alpha helix) or folds (beta pleated sheets).
  • The structural properties of silk are due to beta pleated sheets.
    • The presence of so many hydrogen bonds makes each silk fiber stronger than a steel strand of the same weight.
  • Tertiary structure is determined by interactions among various R groups.
    • These interactions include hydrogen bonds between polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups.
    • While these three interactions are relatively weak, strong covalent bonds called disulfide bridges that form between the sulfhydryl groups (SH) of two cysteine monomers act to rivet parts of the protein together.
  • Quaternary structure results from the aggregation of two or more polypeptide subunits.
    • Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope.
      • This provides structural strength for collagen’s role in connective tissue.
    • Hemoglobin is a globular protein with quaternary structure.
      • It consists of four polypeptide subunits: two alpha and two beta chains.
      • Both types of subunits consist primarily of alpha-helical secondary structure.
    • Each subunit has a nonpeptide heme component with an iron atom that binds oxygen.
  • What are the key factors determining protein conformation
  • A polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a 3D shape determined and maintained by the interactions responsible for secondary and tertiary structure.
    • The folding occurs as the protein is being synthesized within the cell.
  • However, protein conformation also depends on the physical and chemical conditions of the protein’s environment.
    • Alterations in pH, salt concentration, temperature, or other factors can unravel or denature a protein.
    • These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein’s shape.
  • Most proteins become denatured if the are transferred to an organic solvent. The polypeptide chain refolds so that its hydrophobic regions face outward, toward the solvent.
  • Denaturation can also be caused by heat, which disrupts the weak interactions that stabilize conformation.
    • This explains why extremely high fevers can be fatal. Proteins in the blood become denatured by the high body temperatures.
  • Some proteins can return to their functional shape after denaturation, but others cannot, especially in the crowded environment of the cell.
  • Biochemists now know the amino acid sequences of more than 875,000 proteins and the 3D shapes of about 7,000.
    • Nevertheless, it is still difficult to predict the conformation of a protein from its primary structure alone.
  • Most proteins appear to undergo several intermediate stages before reaching their “mature” configuration.
  • The folding of many proteins is assisted by chaperonins or chaperone proteins.
    • Chaperonins do not specify the final structure of a polypeptide but rather work to segregate and protect the polypeptide while it folds spontaneously.
  • At present, scientists use X-ray crystallography to determine protein conformation.
  • This technique requires the formation of a crystal of the protein being studied.
  • The pattern of diffraction of an X-ray by the atoms of the crystal can be used to determine the location of the atoms and to build a computer model of its structure.
  • Nuclear magnetic resonance (NMR) spectroscopy has recently been applied to this problem.
    • This method does not require protein crystallization.

Concept 5.5 Nucleic acids store and transmit hereditary information

  • The amino acid sequence of a polypeptide is programmed by a unit of inheritance known as a gene.
  • A gene consists of DNA, a polymer known as a nucleic acid.

    There are two types of nucleic acids: RNA and DNA.

  • There are two types of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).
    • These are the molecules that allow living organisms to reproduce their complex components from generation to generation.
  • DNA provides directions for its own replication.
  • DNA also directs RNA synthesis and, through RNA, controls protein synthesis.
  • Organisms inherit DNA from their parents.
    • Each DNA molecule is very long, consisting of hundreds to thousands of genes.
    • Before a cell reproduces itself by dividing, its DNA is copied. The copies are then passed to the next generation of cells.
  • While DNA encodes the information that programs all the cell’s activities, it is not directly involved in the day-to-day operations of the cell.
    • Proteins are responsible for implementing the instructions contained in DNA.
  • Each gene along a DNA molecule directs the synthesis of a specific type of messenger RNA molecule (mRNA).
  • The mRNA molecule interacts with the cell’s protein-synthesizing machinery to direct the ordering of amino acids in a polypeptide.
  • The flow of genetic information is from DNA -> RNA -> protein.
  • Protein synthesis occurs on cellular structures called ribosomes.
  • In eukaryotes, DNA is located in the nucleus, but most ribosomes are in the cytoplasm. mRNA functions as an intermediary, moving information and directions from the nucleus to the cytoplasm.
  • Prokaryotes lack nuclei but still use RNA as an intermediary to carry a message from DNA to the ribosomes.

    A nucleic acid strand is a polymer of nucleotides.

  • Nucleic acids are polymers made of nucleotide monomers.
  • Each nucleotide consists of three parts: a nitrogenous base, a pentose sugar, and a phosphate group.
  • The nitrogen bases are rings of carbon and nitrogen that come in two types: purines and pyrimidines.
    • Pyrimidines have a single six-membered ring.
      • There are three different pyrimidines: cytosine (C), thymine (T), and uracil (U).
    • Purines have a six-membered ring joined to a five-membered ring.
      • The two purines are adenine (A) and guanine (G).
  • The pentose joined to the nitrogen base is ribose in nucleotides of RNA and deoxyribose in DNA.
    • The only difference between the sugars is the lack of an oxygen atom on carbon two in deoxyribose.
    • Because the atoms in both the nitrogenous base and the sugar are numbered, the sugar atoms have a prime after the number to distinguish them.
    • Thus, the second carbon in the sugar ring is the 2’ (2 prime) carbon and the carbon that sticks up from the ring is the 5’ carbon.
    • The combination of a pentose and a nitrogenous base is a nucleoside.
  • The addition of a phosphate group creates a nucleoside monophosphate or nucleotide.
  • Polynucleotides are synthesized when adjacent nucleotides are joined by covalent bonds called phosphodiester linkages that form between the —OH group on the 3’ of one nucleotide and the phosphate on the 5’ carbon of the next.
    • This creates a repeating backbone of sugar-phosphate units, with appendages consisting of the nitrogenous bases.
  • The two free ends of the polymer are distinct.
    • One end has a phosphate attached to a 5’ carbon; this is the 5’ end.
    • The other end has a hydroxyl group on a 3’ carbon; this is the 3’ end.
  • The sequence of bases along a DNA or mRNA polymer is unique for each gene.
    • Because genes are normally hundreds to thousands of nucleotides long, the number of possible base combinations is virtually limitless.
  • The linear order of bases in a gene specifies the order of amino acids—the primary structure—of a protein, which in turn determines three-dimensional conformation and function.

Inheritance is based on replication of the DNA double helix.

  • An RNA molecule is a single polynucleotide chain.
  • DNA molecules have two polynucleotide strands that spiral around an imaginary axis to form a double helix.
    • The double helix was first proposed as the structure of DNA in 1953 by James Watson and Francis Crick.
  • The sugar-phosphate backbones of the two polynucleotides are on the outside of the helix.
    • The two backbones run in opposite 5’ -> 3’ directions from each other, an arrangement referred to as antiparallel.
  • Pairs of nitrogenous bases, one from each strand, connect the polynucleotide chains with hydrogen bonds.
  • Most DNA molecules have thousands to millions of base pairs.
  • Because of their shapes, only some bases are compatible with each other.
    • Adenine (A) always pairs with thymine (T) and guanine (G) with cytosine (C).
  • With these base-pairing rules, if we know the sequence of bases on one strand, we know the sequence on the opposite strand.
    • The two strands are complementary.
  • Prior to cell division, each of the strands serves as a template to order nucleotides into a new complementary strand.
    • This results in two identical copies of the original double-stranded DNA molecule, which are then distributed to the daughter cells.
  • This mechanism ensures that a full set of genetic information is transmitted whenever a cell reproduces.

    We can use DNA and proteins as tape measures of evolution.

  • Genes (DNA) and their products (proteins) document the hereditary background of an organism.
  • Because DNA molecules are passed from parents to offspring, siblings have greater similarity in their DNA and protein than do unrelated individuals of the same species.
  • This argument can be extended to develop a “molecular genealogy” to relationships between species.
  • Two species that appear to be closely related based on fossil and molecular evidence should also be more similar in DNA and protein sequences than are more distantly related species.
    • In fact, that is so.
      • For example, if we compare the sequence of 146 amino acids in a hemoglobin polypeptide, we find that humans and gorillas differ in just 1 amino acid.
        • Humans and gibbons differ in 2 amino acids.
        • Humans and rhesus monkeys differ in 8 amino acids.
      • More distantly related species have more differences.
        • Humans and mice differ in 27 amino acids.
        • Humans and frogs differ in 67 amino acids.
      • Molecular biology can be used to assess evolutionary kinship.

Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 5-1

Subject: 
Subject X2: 

Chapter 06 - A Tour of the Cell

Chapter 6 A Tour of the Cell
Lecture Outline

Overview: The Importance of Cells

  • All organisms are made of cells.
    • Many organisms are single-celled.
    • Even in multicellular organisms, the cell is the basic unit of structure and function.
  • The cell is the simplest collection of matter that can live.
  • All cells are related by their descent from earlier cells.

Concept 6.1 To study cells, biologists use microscopes and the tools of biochemistry

  • The discovery and early study of cells progressed with the invention of microscopes in 1590 and their improvement in the 17th century.
  • In a light microscope (LM), visible light passes through the specimen and then through glass lenses.
    • The lenses refract light such that the image is magnified into the eye or onto a video screen.
  • Microscopes vary in magnification and resolving power.
    • Magnification is the ratio of an object’s image to its real size.
    • Resolving power is a measure of image clarity.
      • It is the minimum distance two points can be separated and still be distinguished as two separate points.
      • Resolution is limited by the shortest wavelength of the radiation used for imaging.
  • The minimum resolution of a light microscope is about 200 nanometers (nm), the size of a small bacterium.
  • Light microscopes can magnify effectively to about 1,000 times the size of the actual specimen.
    • At higher magnifications, the image blurs.
  • Techniques developed in the 20th century have enhanced contrast and enabled particular cell components to be stained or labeled so they stand out.
  • While a light microscope can resolve individual cells, it cannot resolve much of the internal anatomy, especially the organelles.
  • To resolve smaller structures, we use an electron microscope (EM), which focuses a beam of electrons through the specimen or onto its surface.
    • Because resolution is inversely related to wavelength used, electron microscopes (whose electron beams have shorter wavelengths than visible light) have finer resolution.
    • Theoretically, the resolution of a modern EM could reach 0.002 nanometer (nm), but the practical limit is closer to about 2 nm.
  • Transmission electron microscopes (TEMs) are used mainly to study the internal ultrastructure of cells.
    • A TEM aims an electron beam through a thin section of the specimen.
    • The image is focused and magnified by electromagnets.
    • To enhance contrast, the thin sections are stained with atoms of heavy metals.
  • Scanning electron microscopes (SEMs) are useful for studying surface structures.
    • The sample surface is covered with a thin film of gold.
    • The beam excites electrons on the surface of the sample.
    • These secondary electrons are collected and focused on a screen.
    • The result is an image of the topography of the specimen.
    • The SEM has great depth of field, resulting in an image that seems three-dimensional.
  • Electron microscopes reveal organelles that are impossible to resolve with the light microscope.
    • However, electron microscopes can only be used on dead cells.
  • Light microscopes do not have as high a resolution, but they can be used to study live cells.
  • Microscopes are major tools in cytology, the study of cell structures.
  • Cytology combined with biochemistry, the study of molecules and chemical processes in metabolism, to produce modern cell biology.

Cell biologists can isolate organelles to study their functions.

  • The goal of cell fractionation is to separate the major organelles of the cells so their individual functions can be studied.
  • This process is driven by an ultracentrifuge, a machine that can spin at up to 130,000 revolutions per minute and apply forces of more than 1 million times gravity (1,000,000 g).
  • Fractionation begins with homogenization, gently disrupting the cell.
  • The homogenate is spun in a centrifuge to separate heavier pieces into the pellet while lighter particles remain in the supernatant.
    • As the process is repeated at higher speeds and for longer durations, smaller and smaller organelles can be collected in subsequent pellets.
  • Cell fractionation prepares isolates of specific cell components.
  • This enables the functions of these organelles to be determined, especially by the reactions or processes catalyzed by their proteins.
    • For example, one cellular fraction was enriched in enzymes that function in cellular respiration.
    • Electron microscopy revealed that this fraction is rich in mitochondria.
    • This evidence helped cell biologists determine that mitochondria are the site of cellular respiration.
  • Cytology and biochemistry complement each other in correlating cellular structure and function.

Concept 6.2 Eukaryotic cells have internal membranes that compartmentalize their functions

Prokaryotic and eukaryotic cells differ in size and complexity.

  • All cells are surrounded by a plasma membrane.
  • The semifluid substance within the membrane is the cytosol, containing the organelles.
  • All cells contain chromosomes that have genes in the form of DNA.
  • All cells also have ribosomes, tiny organelles that make proteins using the instructions contained in genes.
  • A major difference between prokaryotic and eukaryotic cells is the location of chromosomes.
  • In a eukaryotic cell, chromosomes are contained in a membrane-enclosed organelle, the nucleus.
  • In a prokaryotic cell, the DNA is concentrated in the nucleoid without a membrane separating it from the rest of the cell.
  • In eukaryote cells, the chromosomes are contained within a membranous nuclear envelope.
  • The region between the nucleus and the plasma membrane is the cytoplasm.
    • All the material within the plasma membrane of a prokaryotic cell is cytoplasm.
  • Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of specialized form and function.
    • These membrane-bound organelles are absent in prokaryotes.
  • Eukaryotic cells are generally much bigger than prokaryotic cells.
  • The logistics of carrying out metabolism set limits on cell size.
    • At the lower limit, the smallest bacteria, mycoplasmas, are between 0.1 to 1.0 micron.
    • Most bacteria are 1–10 microns in diameter.
    • Eukaryotic cells are typically 10–100 microns in diameter.
  • Metabolic requirements also set an upper limit to the size of a single cell.
  • As a cell increases in size, its volume increases faster than its surface area.
    • Smaller objects have a greater ratio of surface area to volume.
  • The plasma membrane functions as a selective barrier that allows the passage of oxygen, nutrients, and wastes for the whole volume of the cell.
  • The volume of cytoplasm determines the need for this exchange.
  • Rates of chemical exchange across the plasma membrane may be inadequate to maintain a cell with a very large cytoplasm.
  • The need for a surface sufficiently large to accommodate the volume explains the microscopic size of most cells.
  • Larger organisms do not generally have larger cells than smaller organisms—simply more cells.
  • Cells that exchange a lot of material with their surroundings, such as intestinal cells, may have long, thin projections from the cell surface called microvilli. Microvilli increase surface area without significantly increasing cell volume.

Internal membranes compartmentalize the functions of a eukaryotic cell.

  • A eukaryotic cell has extensive and elaborate internal membranes, which partition the cell into compartments.
  • These membranes also participate directly in metabolism, as many enzymes are built into membranes.
  • The compartments created by membranes provide different local environments that facilitate specific metabolic functions, allowing several incompatible processes to go on simultaneously in a cell.
  • The general structure of a biological membrane is a double layer of phospholipids.
  • Other lipids and diverse proteins are embedded in the lipid bilayer or attached to its surface.
  • Each type of membrane has a unique combination of lipids and proteins for its specific functions.
  • For example, enzymes embedded in the membranes of mitochondria function in cellular respiration.

Concept 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

  • The nucleus contains most of the genes in a eukaryotic cell.
    • Additional genes are located in mitochondria and chloroplasts.
  • The nucleus averages about 5 microns in diameter.
  • The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope.
    • The two membranes of the nuclear envelope are separated by 20–40 nm.
    • The envelope is perforated by pores that are about 100 nm in diameter.
    • At the lip of each pore, the inner and outer membranes of the nuclear envelope are fused to form a continuous membrane.
    • A protein structure called a pore complex lines each pore, regulating the passage of certain large macromolecules and particles.
  • The nuclear side of the envelope is lined by the nuclear lamina, a network of protein filaments that maintains the shape of the nucleus.
  • There is evidence that a framework of fibers called the nuclear matrix extends through the nuclear interior.
  • Within the nucleus, the DNA and associated proteins are organized into discrete units called chromosomes, structures that carry the genetic information.
  • Each chromosome is made up of fibrous material called chromatin, a complex of proteins and DNA.
    • Stained chromatin appears through light microscopes and electron microscopes as a diffuse mass.
  • As the cell prepares to divide, the chromatin fibers coil up and condense, becoming thick enough to be recognized as the familiar chromosomes.
  • Each eukaryotic species has a characteristic number of chromosomes.
    • A typical human cell has 46 chromosomes.
    • A human sex cell (egg or sperm) has only 23 chromosomes.
  • In the nucleus is a region of densely stained fibers and granules adjoining chromatin, the nucleolus.
    • In the nucleolus, ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm to form ribosomal subunits.
    • The subunits pass through the nuclear pores to the cytoplasm, where they combine to form ribosomes.
  • The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA).
    • The mRNA travels to the cytoplasm through the nuclear pores and combines with ribosomes to translate its genetic message into the primary structure of a specific polypeptide.

    Ribosomes build a cell’s proteins.

  • Ribosomes, containing rRNA and protein, are the organelles that carry out protein synthesis.
    • Cell types that synthesize large quantities of proteins (e.g., pancreas cells) have large numbers of ribosomes and prominent nucleoli.
  • Some ribosomes, free ribosomes, are suspended in the cytosol and synthesize proteins that function within the cytosol.
  • Other ribosomes, bound ribosomes, are attached to the outside of the endoplasmic reticulum or nuclear envelope.
    • These synthesize proteins that are either included in membranes or exported from the cell.
  • Ribosomes can shift between roles depending on the polypeptides they are synthesizing.

Concept 6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell

  • Many of the internal membranes in a eukaryotic cell are part of the endomembrane system.
  • These membranes are either directly continuous or connected via transfer of vesicles, sacs of membrane.
    • In spite of these connections, these membranes are diverse in function and structure.
    • The thickness, molecular composition and types of chemical reactions carried out by proteins in a given membrane may be modified several times during a membrane’s life.
  • The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane.

The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions.

  • The endoplasmic reticulum (ER) accounts for half the membranes in a eukaryotic cell.
  • The ER includes membranous tubules and internal, fluid-filled spaces called cisternae.
  • The ER membrane is continuous with the nuclear envelope, and the cisternal space of the ER is continuous with the space between the two membranes of the nuclear envelope.
  • There are two connected regions of ER that differ in structure and function.
    • Smooth ER looks smooth because it lacks ribosomes.
      • Rough ER looks rough because ribosomes (bound ribosomes) are attached to the outside, including the outside of the nuclear envelope.
    • The smooth ER is rich in enzymes and plays a role in a variety of metabolic processes.
      • Enzymes of smooth ER synthesize lipids, including oils, phospholipids, and steroids.
      • These include the sex hormones of vertebrates and adrenal steroids.
      • In the smooth ER of the liver, enzymes help detoxify poisons and drugs such as alcohol and barbiturates.
        • Frequent use of these drugs leads to the proliferation of smooth ER in liver cells, increasing the rate of detoxification.
        • This increases tolerance to the target and other drugs, so higher doses are required to achieve the same effect.
      • Smooth ER stores calcium ions.
        • Muscle cells have a specialized smooth ER that pumps calcium ions from the cytosol and stores them in its cisternal space.
        • When a nerve impulse stimulates a muscle cell, calcium ions rush from the ER into the cytosol, triggering contraction.
        • Enzymes then pump the calcium back, readying the cell for the next stimulation.
  • Rough ER is especially abundant in cells that secrete proteins.
    • As a polypeptide is synthesized on a ribosome attached to rough ER, it is threaded into the cisternal space through a pore formed by a protein complex in the ER membrane.
    • As it enters the cisternal space, the new protein folds into its native conformation.
    • Most secretory polypeptides are glycoproteins, proteins to which a carbohydrate is attached.
    • Secretory proteins are packaged in transport vesicles that carry them to their next stage.
  • Rough ER is also a membrane factory.
    • Membrane-bound proteins are synthesized directly into the membrane.
    • Enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol.
    • As the ER membrane expands, membrane can be transferred as transport vesicles to other components of the endomembrane system.

    The Golgi apparatus is the shipping and receiving center for cell products.

  • Many transport vesicles from the ER travel to the Golgi apparatus for modification of their contents.
  • The Golgi is a center of manufacturing, warehousing, sorting, and shipping.
  • The Golgi apparatus is especially extensive in cells specialized for secretion.
  • The Golgi apparatus consists of flattened membranous sacs—cisternae—looking like a stack of pita bread.
    • The membrane of each cisterna separates its internal space from the cytosol.
    • One side of the Golgi, the cis side, is located near the ER. The cis face receives material by fusing with transport vesicles from the ER.
    • The other side, the trans side, buds off vesicles that travel to other sites.
  • During their transit from the cis to the trans side, products from the ER are usually modified.
  • The Golgi can also manufacture its own macromolecules, including pectin and other noncellulose polysaccharides.
  • The Golgi apparatus is a very dynamic structure.
    • According to the cisternal maturation model, the cisternae of the Golgi progress from the cis to the trans face, carrying and modifying their protein cargo as they move.
  • Finally, the Golgi sorts and packages materials into transport vesicles.
    • Molecular identification tags are added to products to aid in sorting.
    • Products are tagged with identifiers such as phosphate groups. These act like ZIP codes on mailing labels to identify the product’s final destination.

    Lysosomes are digestive compartments.

  • A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to digest macromolecules.
  • Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids.
  • These enzymes work best at pH 5.
    • Proteins in the lysosomal membrane pump hydrogen ions from the cytosol into the lumen of the lysosomes.
    • Rupture of one or a few lysosomes has little impact on a cell because the lysosomal enzymes are not very active at the neutral pH of the cytosol.
    • However, massive rupture of many lysosomes can destroy a cell by autodigestion.
  • Lysosomal enzymes and membrane are synthesized by rough ER and then transferred to the Golgi apparatus for further modification.
  • Proteins on the inner surface of the lysosomal membrane are spared by digestion by their three-dimensional conformations, which protect vulnerable bonds from hydrolysis.
  • Lysosomes carry out intracellular digestion in a variety of circumstances.
  • Amoebas eat by engulfing smaller organisms by phagocytosis.
    • The food vacuole formed by phagocytosis fuses with a lysosome, whose enzymes digest the food.
    • As the polymers are digested, monomers pass to the cytosol to become nutrients for the cell.
  • Lysosomes can play a role in recycling of the cell’s organelles and macromolecules.
    • This recycling, or autophagy, renews the cell.
    • During autophagy, a damaged organelle or region of cytosol becomes surrounded by membrane.
    • A lysosome fuses with the resulting vesicle, digesting the macromolecules and returning the organic monomers to the cytosol for reuse.
  • The lysosomes play a critical role in the programmed destruction of cells in multicellular organisms.
    • This process plays an important role in development.
    • The hands of human embryos are webbed until lysosomes digest the cells in the tissue between the fingers.
    • This important process is called programmed cell death, or apoptosis.

    Vacuoles have diverse functions in cell maintenance.

  • Vesicles and vacuoles (larger versions) are membrane-bound sacs with varied functions.
    • Food vacuoles are formed by phagocytosis and fuse with lysosomes.
    • Contractile vacuoles, found in freshwater protists, pump excess water out of the cell to maintain the appropriate concentration of salts.
    • A large central vacuole is found in many mature plant cells.
      • The membrane surrounding the central vacuole, the tonoplast, is selective in its transport of solutes into the central vacuole.
      • The functions of the central vacuole include stockpiling proteins or inorganic ions, disposing of metabolic byproducts, holding pigments, and storing defensive compounds that defend the plant against herbivores.
      • Because of the large vacuole, the cytosol occupies only a thin layer between the plasma membrane and the tonoplast. The presence of a large vacuole increases surface area to volume ratio for the cell.

Concept 6.5 Mitochondria and chloroplasts change energy from one form to another

  • Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work.
  • Mitochondria are the sites of cellular respiration, generating ATP from the catabolism of sugars, fats, and other fuels in the presence of oxygen.
  • Chloroplasts, found in plants and algae, are the sites of photosynthesis.
    • They convert solar energy to chemical energy and synthesize new organic compounds such as sugars from CO2 and H2O.
  • Mitochondria and chloroplasts are not part of the endomembrane system.
    • In contrast to organelles of the endomembrane system, each mitochondrion or chloroplast has two membranes separating the innermost space from the cytosol.
    • Their membrane proteins are not made by the ER, but rather by free ribosomes in the cytosol and by ribosomes within the organelles themselves.
  • Both organelles have small quantities of DNA that direct the synthesis of the polypeptides produced by these internal ribosomes.
  • Mitochondria and chloroplasts grow and reproduce as semiautonomous organelles.
  • Almost all eukaryotic cells have mitochondria.
    • There may be one very large mitochondrion or hundreds to thousands of individual mitochondria.
    • The number of mitochondria is correlated with aerobic metabolic activity.
    • A typical mitochondrion is 1–10 microns long.
    • Mitochondria are quite dynamic: moving, changing shape, and dividing.
  • Mitochondria have a smooth outer membrane and a convoluted inner membrane with infoldings called cristae.
    • The inner membrane divides the mitochondrion into two internal compartments.
    • The first is the intermembrane space, a narrow region between the inner and outer membranes.
    • The inner membrane encloses the mitochondrial matrix, a fluid-filled space with DNA, ribosomes, and enzymes.
    • Some of the metabolic steps of cellular respiration are catalyzed by enzymes in the matrix.
    • The cristae present a large surface area for the enzymes that synthesize ATP.
  • The chloroplast is one of several members of a generalized class of plant structures called plastids.
    • Amyloplasts are colorless plastids that store starch in roots and tubers.
    • Chromoplasts store pigments for fruits and flowers.
    • Chloroplasts contain the green pigment chlorophyll as well as enzymes and other molecules that function in the photosynthetic production of sugar.
  • Chloroplasts measure about 2 microns × 5 microns and are found in leaves and other green organs of plants and algae.
  • The contents of the chloroplast are separated from the cytosol by an envelope consisting of two membranes separated by a narrow intermembrane space.
  • Inside the innermost membrane is a fluid-filled space, the stroma, in which float membranous sacs, the thylakoids.
    • The stroma contains DNA, ribosomes, and enzymes.
    • The thylakoids are flattened sacs that play a critical role in converting light to chemical energy. In some regions, thylakoids are stacked like poker chips into grana.
    • The membranes of the chloroplast divide the chloroplast into three compartments: the intermembrane space, the stroma, and the thylakoid space.
  • Like mitochondria, chloroplasts are dynamic structures.
    • Their shape is plastic, and they can reproduce themselves by pinching in two.
  • Mitochondria and chloroplasts are mobile and move around the cell along tracks of the cytoskeleton.

Peroxisomes generate and degrade H2O2 in performing various metabolic functions.

  • Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen.
    • An intermediate product of this process is hydrogen peroxide (H2O2), a poison.
    • The peroxisome contains an enzyme that converts H2O2 to water.
    • Some peroxisomes break fatty acids down to smaller molecules that are transported to mitochondria as fuel for cellular respiration.
    • Peroxisomes in the liver detoxify alcohol and other harmful compounds.
    • Specialized peroxisomes, glyoxysomes, convert the fatty acids in seeds to sugars, which the seedling can use as a source of energy and carbon until it is capable of photosynthesis.
  • Peroxisomes are bound by a single membrane.
  • They form not from the endomembrane system, but by incorporation of proteins and lipids from the cytosol.
  • They split in two when they reach a certain size.

Concept 6.6 The cytoskeleton is a network of fibers that organizes structures and activities in the cell

  • The cytoskeleton is a network of fibers extending throughout the cytoplasm.
  • The cytoskeleton organizes the structures and activities of the cell.

    The cytoskeleton provides support, motility, and regulation.

  • The cytoskeleton provides mechanical support and maintains cell shape.
  • The cytoskeleton provides anchorage for many organelles and cytosolic enzymes.
  • The cytoskeleton is dynamic and can be dismantled in one part and reassembled in another to change the shape of the cell.
  • The cytoskeleton also plays a major role in cell motility, including changes in cell location and limited movements of parts of the cell.
  • The cytoskeleton interacts with motor proteins to produce motility.
    • Cytoskeleton elements and motor proteins work together with plasma membrane molecules to move the whole cell along fibers outside the cell.
    • Motor proteins bring about movements of cilia and flagella by gripping cytoskeletal components such as microtubules and moving them past each other.
    • The same mechanism causes muscle cells to contract.
  • Inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton.
  • The cytoskeleton manipulates the plasma membrane to form food vacuoles during phagocytosis.
  • Cytoplasmic streaming in plant cells is caused by the cytoskeleton.
  • Recently, evidence suggests that the cytoskeleton may play a role in the regulation of biochemical activities in the cell.
  • There are three main types of fibers making up the cytoskeleton: microtubules, microfilaments, and intermediate filaments.
  • Microtubules, the thickest fibers, are hollow rods about 25 microns in diameter and 200 nm to 25 microns in length.
    • Microtubule fibers are constructed of the globular protein tubulin.
    • Each tubulin molecule is a dimer consisting of two subunits.
    • A microtubule changes in length by adding or removing tubulin dimers.
  • Microtubules shape and support the cell and serve as tracks to guide motor proteins carrying organelles to their destination.
  • Microtubules are also responsible for the separation of chromosomes during cell division.
  • In many cells, microtubules grow out from a centrosome near the nucleus.
    • These microtubules resist compression to the cell.
  • In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring.
    • Before a cell divides, the centrioles replicate.
  • A specialized arrangement of microtubules is responsible for the beating of cilia and flagella.
    • Many unicellular eukaryotic organisms are propelled through water by cilia and flagella.
    • Cilia or flagella can extend from cells within a tissue layer, beating to move fluid over the surface of the tissue.
      • For example, cilia lining the windpipe sweep mucus carrying trapped debris out of the lungs.
  • Cilia usually occur in large numbers on the cell surface.
    • They are about 0.25 microns in diameter and 2–20 microns long.
  • There are usually just one or a few flagella per cell.
    • Flagella are the same width as cilia, but 10–200 microns long.
  • Cilia and flagella differ in their beating patterns.
    • A flagellum has an undulatory movement that generates force in the same direction as the flagellum’s axis.
    • Cilia move more like oars with alternating power and recovery strokes that generate force perpendicular to the cilium’s axis.
  • In spite of their differences, both cilia and flagella have the same ultrastructure.
    • Both have a core of microtubules sheathed by the plasma membrane.
    • Nine doublets of microtubules are arranged in a ring around a pair at the center. This “9 + 2” pattern is found in nearly all eukaryotic cilia and flagella.
    • Flexible “wheels” of proteins connect outer doublets to each other and to the two central microtubules.
    • The outer doublets are also connected by motor proteins.
    • The cilium or flagellum is anchored in the cell by a basal body, whose structure is identical to a centriole.
  • The bending of cilia and flagella is driven by the arms of a motor protein, dynein.
    • Addition and removal of a phosphate group causes conformation changes in dynein.
    • Dynein arms alternately grab, move, and release the outer microtubules.
    • Protein cross-links limit sliding. As a result, the forces exerted by the dynein arms cause the doublets to curve, bending the cilium or flagellum.
  • Microfilaments are solid rods about 7 nm in diameter.
    • Each microfilament is built as a twisted double chain of actin subunits.
    • Microfilaments can form structural networks due to their ability to branch.
  • The structural role of microfilaments in the cytoskeleton is to bear tension, resisting pulling forces within the cell.
  • They form a three-dimensional network just inside the plasma membrane to help support the cell’s shape, giving the cell cortex the semisolid consistency of a gel.
  • Microfilaments are important in cell motility, especially as part of the contractile apparatus of muscle cells.
    • In muscle cells, thousands of actin filaments are arranged parallel to one another.
    • Thicker filaments composed of myosin interdigitate with the thinner actin fibers.
    • Myosin molecules act as motor proteins, walking along the actin filaments to shorten the cell.
  • In other cells, actin-myosin aggregates are less organized but still cause localized contraction.
    • A contracting belt of microfilaments divides the cytoplasm of animal cells during cell division.
    • Localized contraction brought about by actin and myosin also drives amoeboid movement.
      • Pseudopodia, cellular extensions, extend and contract through the reversible assembly and contraction of actin subunits into microfilaments.
        • Microfilaments assemble into networks that convert sol to gel.
        • According to a widely accepted model, filaments near the cell’s trailing edge interact with myosin, causing contraction.
        • The contraction forces the interior fluid into the pseudopodium, where the actin network has been weakened.
        • The pseudopodium extends until the actin reassembles into a network.
  • In plant cells, actin-myosin interactions and sol-gel transformations drive cytoplasmic streaming.
    • This creates a circular flow of cytoplasm in the cell, speeding the distribution of materials within the cell.
  • Intermediate filaments range in diameter from 8–12 nanometers, larger than microfilaments but smaller than microtubules.
  • Intermediate filaments are a diverse class of cytoskeletal units, built from a family of proteins called keratins.
    • Intermediate filaments are specialized for bearing tension.
  • Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes.
  • They reinforce cell shape and fix organelle location.

Concept 6.7 Extracellular components and connections between cells help coordinate cellular activities

Plant cells are encased by cell walls.

  • The cell wall, found in prokaryotes, fungi, and some protists, has multiple functions.
  • In plants, the cell wall protects the cell, maintains its shape, and prevents excessive uptake of water.
  • It also supports the plant against the force of gravity.
  • The thickness and chemical composition of cell walls differs from species to species and among cell types within a plant.
  • The basic design consists of microfibrils of cellulose embedded in a matrix of proteins and other polysaccharides. This is the basic design of steel-reinforced concrete or fiberglass.
  • A mature cell wall consists of a primary cell wall, a middle lamella with sticky polysaccharides that holds cells together, and layers of secondary cell wall.
  • Plant cell walls are perforated by channels between adjacent cells called plasmodesmata.

The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and regulation.

  • Though lacking cell walls, animal cells do have an elaborate extracellular matrix (ECM).
  • The primary constituents of the extracellular matrix are glycoproteins, especially collagen fibers, embedded in a network of glycoprotein proteoglycans.
  • In many cells, fibronectins in the ECM connect to integrins, intrinsic membrane proteins that span the membrane and bind on their cytoplasmic side to proteins attached to microfilaments of the cytoskeleton.
    • The interconnections from the ECM to the cytoskeleton via the fibronectin-integrin link permit the integration of changes inside and outside the cell.
  • The ECM can regulate cell behavior.
    • Embryonic cells migrate along specific pathways by matching the orientation of their microfilaments to the “grain” of fibers in the extracellular matrix.
    • The extracellular matrix can influence the activity of genes in the nucleus via a combination of chemical and mechanical signaling pathways.
      • This may coordinate the behavior of all the cells within a tissue.

    Intercellular junctions help integrate cells into higher levels of structure and function.

  • Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact.
  • Plant cells are perforated with plasmodesmata, channels allowing cytosol to pass between cells.
    • Water and small solutes can pass freely from cell to cell.
    • In certain circumstances, proteins and RNA can be exchanged.
  • Animals have 3 main types of intercellular links: tight junctions, desmosomes, and gap junctions.
  • In tight junctions, membranes of adjacent cells are fused, forming continuous belts around cells.
    • This prevents leakage of extracellular fluid.
  • Desmosomes (or anchoring junctions) fasten cells together into strong sheets, much like rivets.
    • Intermediate filaments of keratin reinforce desmosomes.
  • Gap junctions (or communicating junctions) provide cytoplasmic channels between adjacent cells.
    • Special membrane proteins surround these pores.
    • Ions, sugars, amino acids, and other small molecules can pass.
    • In embryos, gap junctions facilitate chemical communication during development.

    A cell is a living unit greater than the sum of its parts.

  • While the cell has many structures with specific functions, all these structures must work together.
    • For example, macrophages use actin filaments to move and extend pseudopodia to capture their bacterial prey.
    • Food vacuoles are digested by lysosomes, a product of the endomembrane system of ER and Golgi.
  • The enzymes of the lysosomes and proteins of the cytoskeleton are synthesized on the ribosomes.
  • The information for the proteins comes from genetic messages sent by DNA in the nucleus.
  • All of these processes require energy in the form of ATP, most of which is supplied by the mitochondria.
  • A cell is a living unit greater than the sum of its parts.

Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 6-1

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Chapter 6 A Tour of the Cell93 KB
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Chapter 07 - Membrane Structure and Function

Chapter 7 Membrane Structure and Function
Lecture Outline

Overview: Life at the Edge

  • The plasma membrane separates the living cell from its nonliving surroundings.
  • This thin barrier, 8 nm thick, controls traffic into and out of the cell.
  • Like all biological membranes, the plasma membrane is selectively permeable, allowing some substances to cross more easily than others.

Concept 7.1 Cellular membranes are fluid mosaics of lipids and proteins

  • The main macromolecules in membranes are lipids and proteins, but carbohydrates are also important.
  • The most abundant lipids are phospholipids.
  • Phospholipids and most other membrane constituents are amphipathic molecules.
    • Amphipathic molecules have both hydrophobic regions and hydrophilic regions.
  • The arrangement of phospholipids and proteins in biological membranes is described by the fluid mosaic model.

    Membrane models have evolved to fit new data.

  • Models of membranes were developed long before membranes were first seen with electron microscopes in the 1950s.
    • In 1915, membranes isolated from red blood cells were chemically analyzed and found to be composed of lipids and proteins.
    • In 1925, E. Gorter and F. Grendel reasoned that cell membranes must be a phospholipid bilayer two molecules thick.
    • The molecules in the bilayer are arranged such that the hydrophobic fatty acid tails are sheltered from water while the hydrophilic phosphate groups interact with water.
    • Actual membranes adhere more strongly to water than do artificial membranes composed only of phospholipids.
    • One suggestion was that proteins on the surface of the membrane increased adhesion.
    • In 1935, H. Davson and J. Danielli proposed a sandwich model in which the phospholipid bilayer lies between two layers of globular proteins.
    • Early images from electron microscopes seemed to support the Davson-Danielli model, and until the 1960s, it was widely accepted as the structure of the plasma membrane and internal membranes.
    • Further investigation revealed two problems.
      • First, not all membranes were alike. Membranes differ in thickness, appearance when stained, and percentage of proteins.
        • Membranes with different functions differ in chemical composition and structure.
      • Second, measurements showed that membrane proteins are not very soluble in water.
      • Membrane proteins are amphipathic, with hydrophobic and hydrophilic regions.
      • If membrane proteins were at the membrane surface, their hydrophobic regions would be in contact with water.
  • In 1972, S. J. Singer and G. Nicolson presented a revised model that proposed that the membrane proteins are dispersed and individually inserted into the phospholipid bilayer.
    • In this fluid mosaic model, the hydrophilic regions of proteins and phospholipids are in maximum contact with water, and the hydrophobic regions are in a nonaqueous environment within the membrane.
  • A specialized preparation technique, freeze-fracture, splits a membrane along the middle of the phospholipid bilayer.
  • When a freeze-fracture preparation is viewed with an electron microscope, protein particles are interspersed in a smooth matrix, supporting the fluid mosaic model.

    Membranes are fluid.

  • Membrane molecules are held in place by relatively weak hydrophobic interactions.
  • Most of the lipids and some proteins drift laterally in the plane of the membrane, but rarely flip-flop from one phospholipid layer to the other.
  • The lateral movements of phospholipids are rapid, about 2 microns per second. A phospholipid can travel the length of a typical bacterial cell in 1 second.
  • Many larger membrane proteins drift within the phospholipid bilayer, although they move more slowly than the phospholipids.
    • Some proteins move in a very directed manner, perhaps guided or driven by motor proteins attached to the cytoskeleton.
    • Other proteins never move and are anchored to the cytoskeleton.
  • Membrane fluidity is influenced by temperature. As temperatures cool, membranes switch from a fluid state to a solid state as the phospholipids pack more closely.
  • Membrane fluidity is also influenced by its components. Membranes rich in unsaturated fatty acids are more fluid that those dominated by saturated fatty acids because the kinks in the unsaturated fatty acid tails at the locations of the double bonds prevent tight packing.
  • The steroid cholesterol is wedged between phospholipid molecules in the plasma membrane of animal cells.
  • At warm temperatures (such as 37°C), cholesterol restrains the movement of phospholipids and reduces fluidity.
  • At cool temperatures, it maintains fluidity by preventing tight packing.
  • Thus, cholesterol acts as a “temperature buffer” for the membrane, resisting changes in membrane fluidity as temperature changes.
  • To work properly with active enzymes and appropriate permeability, membranes must be about as fluid as salad oil.
  • Cells can alter the lipid composition of membranes to compensate for changes in fluidity caused by changing temperatures.
    • For example, cold-adapted organisms such as winter wheat increase the percentage of unsaturated phospholipids in their membranes in the autumn.
    • This prevents membranes from solidifying during winter.

    Membranes are mosaics of structure and function.

  • A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer.
  • Proteins determine most of the membrane’s specific functions.
  • The plasma membrane and the membranes of the various organelles each have unique collections of proteins.
  • There are two major populations of membrane proteins.
    • Peripheral proteins are not embedded in the lipid bilayer at all.
      • Instead, they are loosely bound to the surface of the protein, often connected to integral proteins.
    • Integral proteins penetrate the hydrophobic core of the lipid bilayer, often completely spanning the membrane (as transmembrane proteins).
      • The hydrophobic regions embedded in the membrane’s core consist of stretches of nonpolar amino acids, often coiled into alpha helices.
      • Where integral proteins are in contact with the aqueous environment, they have hydrophilic regions of amino acids.
    • On the cytoplasmic side of the membrane, some membrane proteins connect to the cytoskeleton.
    • On the exterior side of the membrane, some membrane proteins attach to the fibers of the extracellular matrix.
  • The proteins of the plasma membrane have six major functions:
    1. Transport of specific solutes into or out of cells.
    2. Enzymatic activity, sometimes catalyzing one of a number of steps of a metabolic pathway.
    3. Signal transduction, relaying hormonal messages to the cell.
    4. Cell-cell recognition, allowing other proteins to attach two adjacent cells together.
    5. Intercellular joining of adjacent cells with gap or tight junctions.
    6. Attachment to the cytoskeleton and extracellular matrix, maintaining cell shape and stabilizing the location of certain membrane proteins.

    Membrane carbohydrates are important for cell-cell recognition.

  • The plasma membrane plays the key role in cell-cell recognition.
    • Cell-cell recognition, the ability of a cell to distinguish one type of neighboring cell from another, is crucial to the functioning of an organism.
    • This attribute is important in the sorting and organization of cells into tissues and organs during development.
    • It is also the basis for rejection of foreign cells by the immune system.
    • Cells recognize other cells by binding to surface molecules, often carbohydrates, on the plasma membrane.
  • Membrane carbohydrates are usually branched oligosaccharides with fewer than 15 sugar units.
  • They may be covalently bonded to lipids, forming glycolipids, or more commonly to proteins, forming glycoproteins.
  • The oligosaccharides on the external side of the plasma membrane vary from species to species, from individual to individual, and even from cell type to cell type within the same individual.
    • This variation distinguishes each cell type.
    • The four human blood groups (A, B, AB, and O) differ in the external carbohydrates on red blood cells.

    Membranes have distinctive inside and outside faces.

  • Membranes have distinct inside and outside faces. The two layers may differ in lipid composition. Each protein in the membrane has a directional orientation in the membrane.
  • The asymmetrical orientation of proteins, lipids and associated carbohydrates begins during the synthesis of membrane in the ER and Golgi apparatus.
  • Membrane lipids and proteins are synthesized in the endoplasmic reticulum. Carbohydrates are added to proteins in the ER, and the resulting glycoproteins are further modified in the Golgi apparatus. Glycolipids are also produced in the Golgi apparatus.
  • When a vesicle fuses with the plasma membrane, the outside layer of the vesicle becomes continuous with the inside layer of the plasma membrane. In that way, molecules that originate on the inside face of the ER end up on the outside face of the plasma membrane.

Concept 7.2 Membrane structure results in selective permeability

  • A steady traffic of small molecules and ions moves across the plasma membrane in both directions.
    • For example, sugars, amino acids, and other nutrients enter a muscle cell, and metabolic waste products leave.
    • The cell absorbs oxygen and expels carbon dioxide.
    • It also regulates concentrations of inorganic ions, such as Na+, K+, Ca2+, and Cl?, by shuttling them across the membrane.
  • However, substances do not move across the barrier indiscriminately; membranes are selectively permeable.
  • The plasma membrane allows the cell to take up many varieties of small molecules and ions and exclude others. Substances that move through the membrane do so at different rates.
  • Movement of a molecule through a membrane depends on the interaction of the molecule with the hydrophobic core of the membrane.
    • Hydrophobic molecules, such as hydrocarbons, CO2, and O2, can dissolve in the lipid bilayer and cross easily.
    • The hydrophobic core of the membrane impedes the direct passage of ions and polar molecules, which cross the membrane with difficulty.
      • This includes small molecules, such as water, and larger molecules, such as glucose and other sugars.
      • An ion, whether a charged atom or molecule, and its surrounding shell of water also has difficulty penetrating the hydrophobic core.
  • Proteins assist and regulate the transport of ions and polar molecules.
  • Specific ions and polar molecules can cross the lipid bilayer by passing through transport proteins that span the membrane.
    • Some transport proteins, called channel proteins, have a hydrophilic channel that certain molecules or ions can use as a tunnel through the membrane.
    • For example, the passage of water through the membrane can be greatly facilitated by channel proteins known as aquaporins.
    • Other transport proteins, called carrier proteins, bind to molecules and change shape to shuttle them across the membrane.
  • Each transport protein is specific as to the substances that it will translocate.
    • For example, the glucose transport protein in the liver will carry glucose into the cell but will not transport fructose, its structural isomer.

Concept 7.3 Passive transport is diffusion of a substance across a membrane with no energy investment

  • Diffusion is the tendency of molecules of any substance to spread out in the available space.
    • Diffusion is driven by the intrinsic kinetic energy (thermal motion or heat) of molecules.
  • Movements of individual molecules are random.
  • However, movement of a population of molecules may be directional.
  • Imagine a permeable membrane separating a solution with dye molecules from pure water. If the membrane has microscopic pores that are large enough, dye molecules will cross the barrier randomly.
  • The net movement of dye molecules across the membrane will continue until both sides have equal concentrations of the dye.
  • At this dynamic equilibrium, as many molecules cross one way as cross in the other direction.
  • In the absence of other forces, a substance will diffuse from where it is more concentrated to where it is less concentrated, down its concentration gradient.
  • No work must be done to move substances down the concentration gradient.
  • Diffusion is a spontaneous process that decreases free energy and increases entropy by creating a randomized mixture.
  • Each substance diffuses down its own concentration gradient, independent of the concentration gradients of other substances.
  • The diffusion of a substance across a biological membrane is passive transport because it requires no energy from the cell to make it happen.
    • The concentration gradient itself represents potential energy and drives diffusion.
  • Because membranes are selectively permeable, the interactions of the molecules with the membrane play a role in the diffusion rate.
  • Diffusion of molecules of limited permeability through the lipid bilayer may be assisted by transport proteins.

    Osmosis is the passive transport of water.

  • Differences in the relative concentration of dissolved materials in two solutions can lead to the movement of ions from one to the other.
    • The solution with the higher concentration of solutes is hypertonic relative to the other solution.
    • The solution with the lower concentration of solutes is hypotonic relative to the other solution.
    • These are comparative terms.
      • Tap water is hypertonic compared to distilled water but hypotonic compared to seawater.
    • Solutions with equal solute concentrations are isotonic.
  • Imagine that two sugar solutions differing in concentration are separated by a membrane that will allow water through, but not sugar.
  • The hypertonic solution has a lower water concentration than the hypotonic solution.
    • More of the water molecules in the hypertonic solution are bound up in hydration shells around the sugar molecules, leaving fewer unbound water molecules.
  • Unbound water molecules will move from the hypotonic solution, where they are abundant, to the hypertonic solution, where they are rarer. Net movement of water continues until the solutions are isotonic.
  • The diffusion of water across a selectively permeable membrane is called osmosis.
  • The direction of osmosis is determined only by a difference in total solute concentration.
    • The kinds of solutes in the solutions do not matter.
    • This makes sense because the total solute concentration is an indicator of the abundance of bound water molecules (and, therefore, of free water molecules).
  • When two solutions are isotonic, water molecules move at equal rates from one to the other, with no net osmosis.
  • The movement of water by osmosis is crucial to living organisms.

    Cell survival depends on balancing water uptake and loss.

  • An animal cell (or other cell without a cell wall) immersed in an isotonic environment experiences no net movement of water across its plasma membrane.
    • Water molecules move across the membrane but at the same rate in both directions.
    • The volume of the cell is stable.
  • The same cell in a hypertonic environment will lose water, shrivel, and probably die.
  • A cell in a hypotonic solution will gain water, swell, and burst.
  • For organisms living in an isotonic environment (for example, many marine invertebrates), osmosis is not a problem.
    • The cells of most land animals are bathed in extracellular fluid that is isotonic to the cells.
  • Organisms without rigid walls have osmotic problems in either a hypertonic or hypotonic environment and must have adaptations for osmoregulation, the control of water balance, to maintain their internal environment.
  • For example, Paramecium, a protist, is hypertonic to the pond water in which it lives.
    • In spite of a cell membrane that is less permeable to water than other cells, water still continually enters the Paramecium cell.
    • To solve this problem, Paramecium cells have a specialized organelle, the contractile vacuole, which functions as a bilge pump to force water out of the cell.
  • The cells of plants, prokaryotes, fungi, and some protists have walls that contribute to the cell’s water balance.
  • A plant cell in a hypotonic solution will swell until the elastic cell wall opposes further uptake.
    • At this point the cell is turgid (very firm), a healthy state for most plant cells.
  • Turgid cells contribute to the mechanical support of the plant.
  • If a plant cell and its surroundings are isotonic, there is no movement of water into the cell. The cell becomes flaccid (limp), and the plant may wilt.
  • The cell wall provides no advantages when a plant cell is immersed in a hypertonic solution. As the plant cell loses water, its volume shrinks. Eventually, the plasma membrane pulls away from the wall. This plasmolysis is usually lethal.

    Specific proteins facilitate passive transport of water and selected solutes.

  • Many polar molecules and ions that are normally impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane.
  • The passive movement of molecules down their concentration gradient via transport proteins is called facilitated diffusion.
  • Two types of transport proteins facilitate the movement of molecules or ions across membranes: channel proteins and carrier proteins.
  • Some channel proteins simply provide hydrophilic corridors for the passage of specific molecules or ions.
    • For example, water channel proteins, aquaporins, greatly facilitate the diffusion of water.
  • Many ion channels function as gated channels. These channels open or close depending on the presence or absence of a chemical or physical stimulus.
    • If chemical, the stimulus is a substance other than the one to be transported.
      • For example, stimulation of a receiving neuron by specific neurotransmitters opens gated channels to allow sodium ions into the cell.
      • When the neurotransmitters are not present, the channels are closed.
  • Some transport proteins do not provide channels but appear to actually translocate the solute-binding site and solute across the membrane as the transport protein changes shape.
    • These shape changes may be triggered by the binding and release of the transported molecule.
  • In certain inherited diseases, specific transport systems may be defective or absent.
    • Cystinuria is a human disease characterized by the absence of a protein that transports cysteine and other amino acids across the membranes of kidney cells.
    • An individual with cystinuria develops painful kidney stones as amino acids accumulate and crystallize in the kidneys.

Concept 7.4 Active transport uses energy to move solutes against their gradients

  • Some transport proteins can move solutes across membranes against their concentration gradient, from the side where they are less concentrated to the side where they are more concentrated.
  • This active transport requires the cell to expend metabolic energy.
  • Active transport enables a cell to maintain its internal concentrations of small molecules that would otherwise diffuse across the membrane.
  • Active transport is performed by specific proteins embedded in the membranes.
  • ATP supplies the energy for most active transport.
    • ATP can power active transport by transferring a phosphate group from ATP (forming ADP) to the transport protein.
    • This may induce a conformational change in the transport protein, translocating the solute across the membrane.
  • The sodium-potassium pump actively maintains the gradient of sodium ions (Na+) and potassium ions (K+) across the plasma membrane of animal cells.
    • Typically, K+ concentration is low outside an animal cell and high inside the cell, while Na+ concentration is high outside an animal cell and low inside the cell.
    • The sodium-potassium pump maintains these concentration gradients, using the energy of one ATP to pump three Na+ out and two K+ in.

    Some ion pumps generate voltage across membranes.

  • All cells maintain a voltage across their plasma membranes.
  • Voltage is electrical potential energy due to the separation of opposite charges.
    • The cytoplasm of a cell is negative in charge compared to the extracellular fluid because of an unequal distribution of cations and anions on opposite sides of the membrane.
    • The voltage across a membrane is called a membrane potential, and ranges from ?50 to ?200 millivolts (mV). The inside of the cell is negative compared to the outside.
  • The membrane potential acts like a battery.
  • The membrane potential favors the passive transport of cations into the cell and anions out of the cell.
  • Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane.
    • One is a chemical force based on an ion’s concentration gradient.
    • The other is an electrical force based on the effect of the membrane potential on the ion’s movement.
  • An ion does not simply diffuse down its concentration gradient but diffuses down its electrochemical gradient.
    • For example, there is a higher concentration of Na+ outside a resting nerve cell than inside.
    • When the neuron is stimulated, a gated channel opens and Na+ diffuse into the cell down their electrochemical gradient. The diffusion of Na+ is driven by their concentration gradient and by the attraction of cations to the negative side of the membrane.
  • Special transport proteins, electrogenic pumps, generate the voltage gradient across a membrane.
    • The sodium-potassium pump in animals restores the electrochemical gradient not only by the active transport of Na+ and K+, setting up a concentration gradient, but because it pumps two K+ inside for every three Na+ that it moves out, setting up a voltage across the membrane.
  • The sodium-potassium pump is the major electrogenic pump of animal cells.
  • In plants, bacteria, and fungi, a proton pump is the major electrogenic pump, actively transporting H+ out of the cell.
  • Proton pumps in the cristae of mitochondria and the thylakoids of chloroplasts concentrate H+ behind membranes.
  • These electrogenic pumps store energy that can be accessed for cellular work.

    In cotransport, a membrane protein couples the transport of two solutes.

  • A single ATP-powered pump that transports one solute can indirectly drive the active transport of several other solutes in a mechanism called cotransport.
  • As the solute that has been actively transported diffuses back passively through a transport protein, its movement can be coupled with the active transport of another substance against its concentration gradient.
  • Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive the active transport of amino acids, sugars, and other nutrients into the cell.
  • One specific transport protein couples the diffusion of protons out of the cell and the transport of sucrose into the cell. Plants use the mechanism of sucrose-proton cotransport to load sucrose into specialized cells in the veins of leaves for distribution to nonphotosynthetic organs such as roots.

Concept 7.5 Bulk transport across the plasma membrane occurs by exocytosis and endocytosis

  • Small molecules and water enter or leave the cell through the lipid bilayer or by transport proteins.
  • Large molecules, such as polysaccharides and proteins, cross the membrane via vesicles.
  • During exocytosis, a transport vesicle budded from the Golgi apparatus is moved by the cytoskeleton to the plasma membrane.
  • When the two membranes come in contact, the bilayers fuse and spill the contents to the outside.
  • Many secretory cells use exocytosis to export their products.
  • During endocytosis, a cell brings in macromolecules and particulate matter by forming new vesicles from the plasma membrane.
  • Endocytosis is a reversal of exocytosis, although different proteins are involved in the two processes.
    • A small area of the plasma membrane sinks inward to form a pocket.
    • As the pocket deepens, it pinches in to form a vesicle containing the material that had been outside the cell.
  • There are three types of endocytosis: phagocytosis (“cellular eating”), pinocytosis (“cellular drinking”), and receptor-mediated endocytosis.
  • In phagocytosis, the cell engulfs a particle by extending pseudopodia around it and packaging it in a large vacuole.
  • The contents of the vacuole are digested when the vacuole fuses with a lysosome.
  • In pinocytosis, a cell creates a vesicle around a droplet of extracellular fluid. All included solutes are taken into the cell in this nonspecific process.
  • Receptor-mediated endocytosis allows greater specificity, transporting only certain substances.
  • This process is triggered when extracellular substances, or ligands, bind to special receptors on the membrane surface. The receptor proteins are clustered in regions of the membrane called coated pits, which are lined on their cytoplasmic side by a layer of coat proteins.
  • Binding of ligands to receptors triggers the formation of a vesicle by the coated pit, bringing the bound substances into the cell.
  • Receptor-mediated endocytosis enables a cell to acquire bulk quantities of specific materials that may be in low concentrations in the environment.
    • Human cells use this process to take in cholesterol for use in the synthesis of membranes and as a precursor for the synthesis of steroids.
    • Cholesterol travels in the blood in low-density lipoproteins (LDL), complexes of protein and lipid.
    • These lipoproteins act as ligands to bind to LDL receptors and enter the cell by endocytosis.
    • In an inherited disease called familial hypercholesterolemia, the LDL receptors are defective, leading to an accumulation of LDL and cholesterol in the blood.
    • This contributes to early atherosclerosis.

Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 7-1

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Chapter 08 - An Introduction to Metabolism

Chapter 8 An Introduction to Metabolism
Lecture Outline

Overview: The Energy of Life

Concept 8.1 An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics

  • The totality of an organism’s chemical reactions is called metabolism.
  • Metabolism is an emergent property of life that arises from interactions between molecules within the orderly environment of the cell.

    The chemistry of life is organized into metabolic pathways.

  • Metabolic pathways begin with a specific molecule, which is then altered in a series of defined steps to form a specific product.
  • A specific enzyme catalyzes each step of the pathway.
  • Catabolic pathways release energy by breaking down complex molecules to simpler compounds.
    • A major pathway of catabolism is cellular respiration, in which the sugar glucose is broken down in the presence of oxygen to carbon dioxide and water.
  • Anabolic pathways consume energy to build complicated molecules from simpler compounds. They are also called biosynthetic pathways.
    • The synthesis of protein from amino acids is an example of anabolism.
  • The energy released by catabolic pathways can be stored and then used to drive anabolic pathways.
  • Energy is fundamental to all metabolic processes, and therefore an understanding of energy is key to understanding how the living cell works.
    • Bioenergetics is the study of how organisms manage their energy resources.

    Organisms transform energy.

  • Energy is the capacity to do work.
    • Energy exists in various forms, and cells transform energy from one type into another.
  • Kinetic energy is the energy associated with the relative motion of objects.
    • Objects in motion can perform work by imparting motion to other matter.
    • Photons of light can be captured and their energy harnessed to power photosynthesis in green plants.
    • Heat or thermal energy is kinetic energy associated with the random movement of atoms or molecules.
  • Potential energy is the energy that matter possesses because of its location or structure.
    • Chemical energy is a form of potential energy stored in molecules because of the arrangement of their atoms.
  • Energy can be converted from one form to another.
    • For example, as a boy climbs stairs to a diving platform, he is releasing chemical energy stored in his cells from the food he ate for lunch.
    • The kinetic energy of his muscle movement is converted into potential energy as he climbs higher.
    • As he dives, the potential energy is converted back to kinetic energy.
    • Kinetic energy is transferred to the water as he enters it.
    • Some energy is converted to heat due to friction.

    The energy transformations of life are subject to two laws of thermodynamics.

  • Thermodynamics is the study of energy transformations.
  • In this field, the term system refers to the matter under study and the surroundings include everything outside the system.
  • A closed system, approximated by liquid in a thermos, is isolated from its surroundings.
  • In an open system, energy and matter can be transferred between the system and its surroundings.
  • Organisms are open systems.
    • They absorb energy—light or chemical energy in the form of organic molecules—and release heat and metabolic waste products such as urea or CO2 to their surroundings.
  • The first law of thermodynamics states that energy can be transferred and transformed, but it cannot be created or destroyed.
    • The first law is also known as the principle of conservation of energy.
    • Plants do not produce energy; they transform light energy to chemical energy.
  • During every transfer or transformation of energy, some energy is converted to heat, which is the energy associated with the random movement of atoms and molecules.
  • A system can use heat to do work only when there is a temperature difference that results in heat flowing from a warmer location to a cooler one.
    • If temperature is uniform, as in a living cell, heat can only be used to warm the organism.
  • Energy transfers and transformations make the universe more disordered due to this loss of usable energy.
  • Entropy is a quantity used as a measure of disorder or randomness.
    • The more random a collection of matter, the greater its entropy.
  • The second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe.
    • While order can increase locally, there is an unstoppable trend toward randomization of the universe.
    • Much of the increased entropy of the universe takes the form of increasing heat, which is the energy of random molecular motion.
  • In most energy transformations, ordered forms of energy are converted at least partly to heat.
    • Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as heat.
    • Living cells unavoidably convert organized forms of energy to heat.
  • For a process to occur on its own, without outside help in the form of energy input, it must increase the entropy of the universe.
  • The word spontaneous describes a process that can occur without an input of energy.
    • Spontaneous processes need not occur quickly.
    • Some spontaneous processes are instantaneous, such as an explosion. Some are very slow, such as the rusting of an old car.
  • Another way to state the second law of thermodynamics is for a process to occur spontaneously, it must increase the entropy of the universe.
  • Living systems create ordered structures from less ordered starting materials.
    • For example, amino acids are ordered into polypeptide chains.
    • The structure of a multicellular body is organized and complex.
  • However, an organism also takes in organized forms of matter and energy from its surroundings and replaces them with less ordered forms.
    • For example, an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide and water.
  • Over evolutionary time, complex organisms have evolved from simpler ones.
    • This increase in organization does not violate the second law of thermodynamics.
    • The entropy of a particular system, such as an organism, may decrease as long as the total entropy of the universe—the system plus its surroundings—increases.
    • Organisms are islands of low entropy in an increasingly random universe.
    • The evolution of biological order is perfectly consistent with the laws of thermodynamics.

Concept 8.2 The free-energy change of a reaction tells us whether the reaction occurs spontaneously

  • How can we determine which reactions occur spontaneously and which ones require an input of energy?
  • The concept of free energy provides a useful function for measuring spontaneity of a system.
  • Free energy is the portion of a system’s energy that is able to perform work when temperature and pressure is uniform throughout the system, as in a living cell.
  • The free energy (G) in a system is related to the total enthalpy (in biological systems, equivalent to energy) (H) and the entropy (S) by this relationship:
    • G = H - TS, where T is temperature in Kelvin units.
    • Increases in temperature amplify the entropy term.
    • Not all the energy in a system is available for work because the entropy component must be subtracted from the enthalpy component.
    • What remains is the free energy that is available for work.
  • Free energy can be thought of as a measure of the stability of a system.
    • Systems that are high in free energy—compressed springs, separated charges, organic polymers—are unstable and tend to move toward a more stable state, one with less free energy.
    • Systems that tend to change spontaneously are those that have high enthalpy, low entropy, or both.
  • In any spontaneous process, the free energy of a system decreases.
  • We can represent this change in free energy from the start of a process until its finish by:
    • ΔG = Gfinal state - Gstarting state
    • Or ΔG = ΔH - TΔS
  • For a process to be spontaneous, the system must either give up enthalpy (decrease in H), give up order (increase in S), or both.
    • ΔG must be negative for a process to be spontaneous.
    • Every spontaneous process is characterized by a decrease in the free energy of the system.
    • Processes that have a positive or zero ΔG are never spontaneous.
  • The greater the decrease in free energy, the more work a spontaneous process can perform.
  • Nature runs “downhill.”
  • A system at equilibrium is at maximum stability.
    • In a chemical reaction at equilibrium, the rates of forward and backward reactions are equal, and there is no change in the concentration of products or reactants.
    • At equilibrium ΔG = 0, and the system can do no work.
    • A process is spontaneous and can perform work only when it is moving toward equilibrium.
    • Movements away from equilibrium are nonspontaneous and require the addition of energy from an outside energy source (the surroundings).
  • Chemical reactions can be classified as either exergonic or endergonic based on free energy.
  • An exergonic reaction proceeds with a net release of free energy; ΔG is negative.
  • The magnitude of ΔG for an exergonic reaction is the maximum amount of work the reaction can perform.
  • The greater the decrease in free energy, the greater the amount of work that can be done.
    • For the overall reaction of cellular respiration: C6H12O6 + 6O2 -> 6CO2 + 6H2O
      • ΔG = -686 kcal/mol
    • For each mole (180 g) of glucose broken down by respiration, 686 kcal of energy are made available to do work in the cell.
      • The products have 686 kcal less free energy than the reactants.
  • An endergonic reaction is one that absorbs free energy from its surroundings.
    • Endergonic reactions store energy in molecules; ΔG is positive.
    • Endergonic reactions are nonspontaneous, and the magnitude of ΔG is the quantity of energy required to drive the reaction.
  • If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must require an equivalent investment of energy.
    • For the conversion of carbon dioxide and water to sugar, ΔG = +686 kcal/mol.
  • Photosynthesis is strongly endergonic, powered by the absorption of light energy.
  • Reactions in a closed system eventually reach equilibrium and can do no work.
    • A cell that has reached metabolic equilibrium has a ΔG = 0 and is dead!
  • Metabolic disequilibrium is one of the defining features of life.
  • Cells maintain disequilibrium because they are open systems. The constant flow of materials into and out of the cell keeps metabolic pathways from ever reaching equilibrium.
    • A cell continues to do work throughout its life.
  • A catabolic process in a cell releases free energy in a series of reactions, not in a single step.
  • Some reversible reactions of respiration are constantly “pulled” in one direction, as the product of one reaction does not accumulate but becomes the reactant in the next step.
  • Sunlight provides a daily source of free energy for photosynthetic organisms.
  • Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.

Concept 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions

  • A cell does three main kinds of work:
    1. Mechanical work, such as the beating of cilia, contraction of muscle cells, and movement of chromosomes during cellular reproduction.
    2. Transport work, the pumping of substances across membranes against the direction of spontaneous movement.
    3. Chemical work, driving endergonic reactions such as the synthesis of polymers from monomers.
  • Cells manage their energy resources to do this work by energy coupling, the use of an exergonic process to drive an endergonic one.
  • In most cases, the immediate source of energy to power cellular work is ATP.
  • ATP (adenosine triphosphate) is a type of nucleotide consisting of the nitrogenous base adenine, the sugar ribose, and a chain of three phosphate groups.
  • The bonds between phosphate groups can be broken by hydrolysis.
    • Hydrolysis of the end phosphate group forms adenosine diphosphate.
      • ATP -> ADP + Pi
      • This reaction releases 7.3 kcal of energy per mole of ATP under standard conditions (1 M of each reactant and product, 25°C, pH 7).
    • In the cell, ΔG for hydrolysis of ATP is about -13 kcal/mol.
  • While the phosphate bonds of ATP are sometimes referred to as high-energy phosphate bonds, these are actually fairly weak covalent bonds.
    • However, they are unstable, and their hydrolysis yields energy because the products are more stable.
  • The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.
  • Why does the hydrolysis of ATP yield so much energy?
    • Each of the three phosphate groups has a negative charge.
    • These three like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule.
  • In the cell, the energy from the hydrolysis of ATP is directly coupled to endergonic processes by the transfer of the phosphate group to another molecule.
    • This recipient molecule is now phosphorylated.
    • This molecule is now more reactive (less stable) than the original unphosphorylated molecules.
  • Mechanical, transport, and chemical work in the cell are nearly always powered by the hydrolysis of ATP.
    • In each case, a phosphate group is transferred from ATP to another molecule and the phosphorylated molecule undergoes a change that performs work.
  • ATP is a renewable resource that can be regenerated by the addition of a phosphate group to ADP.
    • The energy to phosphorylate ADP comes from catabolic reactions in the cell.
    • A working muscle cell recycles its entire pool of ATP once each minute.
    • More than 10 million ATP molecules are consumed and regenerated per second per cell.
  • Regeneration of ATP is an endergonic process, requiring an investment of energy.
    • ΔG = 7.3 kcal/mol.
  • Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the exergonic regeneration of ATP.
  • The chemical potential energy temporarily stored in ATP drives most cellular work.

Concept 8.4 Enzymes speed up metabolic reactions by lowering energy barriers

  • Spontaneous chemical reactions may occur so slowly as to be imperceptible.
    • The hydrolysis of table sugar (sucrose) to glucose and fructose is exergonic.
      • ΔG = -7 kcal/mol
    • Despite this, your sugar sits in its bowl with no observable hydrolysis.
    • If we add a small amount of the enzyme catalyst sucrase to a solution of sugar, all the sucrose will be hydrolyzed within seconds.
  • A catalyst is a chemical agent that speeds up the rate of a reaction without being consumed by the reaction.
    • An enzyme is a catalytic protein.
  • Enzymes regulate metabolic pathways.
  • Every chemical reaction involves bond breaking and bond forming.
    • To hydrolyze sucrose, the bond between glucose and fructose must be broken and new bonds must form with hydrogen and hydroxyl ions from water.
  • To reach a state where bonds can break and reform, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat as the molecules assume stable shapes with lower energy.
  • The initial investment of energy for starting a reaction is the free energy of activation or activation energy (EA).
  • Activation energy is the amount of energy necessary to push the reactants over an energy barrier so that the reaction can proceed.
    • At the summit, the molecules are in an unstable condition, the transition state.
    • Activation energy may be supplied in the form of heat that the reactant molecules absorb from the surroundings.
    • The bonds of the reactants break only when the molecules have absorbed enough energy to become unstable and, therefore, more reactive.
    • The absorption of thermal energy increases the speed of the reactant molecules, so they collide more often and more forcefully.
    • Thermal agitation of the atoms in the molecules makes bonds more likely to break.
    • As the molecules settle into new, stable bonding arrangements, energy is released to the surroundings.
    • In exergonic reactions, the activation energy is released back to the surroundings, and additional energy is released with the formation of new bonds.
  • For some processes, EA is not high, and the thermal energy provided by room temperature is sufficient for many reactants to reach the transition state.
  • In many cases, EA is high enough that the transition state is rarely reached and that the reaction hardly proceeds at all. In these cases, the reaction will only occur at a noticeable rate if the reactants are heated.
    • A spark plug provides the energy to energize a gasoline-oxygen mixture and cause combustion.
    • Without that activation energy, the hydrocarbons of gasoline are too stable to react with oxygen.
  • Proteins, DNA, and other complex organic molecules are rich in free energy. Their hydrolysis is spontaneous, with the release of large amounts of energy.
    • However, there is not enough energy at the temperatures typical of the cell for the vast majority of organic molecules to make it over the hump of activation energy.
  • How are the barriers for selected reactions surmounted to allow cells to carry out the processes of life?
    • Heat would speed up reactions, but it would also denature proteins and kill cells.
  • Enzymes speed reactions by lowering EA.
    • The transition state can then be reached even at moderate temperatures.
  • Enzymes do not change ΔG.
    • They hasten reactions that would occur eventually.
    • Because enzymes are so selective, they determine which chemical processes will occur at any time.

    Enzymes are substrate specific.

  • The reactant that an enzyme acts on is the substrate.
  • The enzyme binds to a substrate, or substrates, forming an enzyme-substrate complex.
  • While the enzyme and substrate are bound, the catalytic action of the enzyme converts the substrate to the product or products.
  • The reaction catalyzed by each enzyme is very specific.
  • What accounts for this molecular recognition?
    • The specificity of an enzyme results from its three-dimensional shape.
  • Only a portion of the enzyme binds to the substrate.
    • The active site of an enzyme is typically a pocket or groove on the surface of the protein into which the substrate fits.
    • The active site is usually formed by only a few amino acids.
  • The specificity of an enzyme is due to the fit between the active site and the substrate.
  • As the substrate enters the active site, interactions between the substrate and the amino acids of the protein causes the enzyme to change shape slightly, leading to a tighter induced fit that brings chemical groups in position to catalyze the reaction.

    The active site is an enzyme’s catalytic center.

  • In most cases, substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds.
    • R groups of a few amino acids on the active site catalyze the conversion of substrate to product.
    • The product then leaves the active site.
  • A single enzyme molecule can catalyze thousands of reactions a second.
  • Enzymes are unaffected by the reaction and are reusable.
  • Most metabolic enzymes can catalyze a reaction in both the forward and reverse directions.
    • The actual direction depends on the relative concentrations of products and reactants.
    • Enzymes catalyze reactions in the direction of equilibrium.
  • Enzymes use a variety of mechanisms to lower activation energy and speed up a reaction.
    • In reactions involving more than one reactant, the active site brings substrates together in the correct orientation for the reaction to proceed.
    • As the active site binds the substrate, it may put stress on bonds that must be broken, making it easier for the reactants to reach the transition state.
    • R groups at the active site may create a microenvironment that is conducive to a specific reaction.
      • An active site may be a pocket of low pH, facilitating H+ transfer to the substrate as a key step in catalyzing the reaction.
    • Enzymes may briefly bind covalently to substrates.
      • Subsequent steps of the reaction restore the R groups within the active site to their original state.
  • The rate that a specific number of enzymes convert substrates to products depends in part on substrate concentrations.
    • At low substrate concentrations, an increase in substrate concentration speeds binding to available active sites.
    • However, there is a limit to how fast a reaction can occur.
    • At high substrate concentrations, the active sites on all enzymes are engaged.
      • The enzyme is saturated.
      • The rate of the reaction is determined by the speed at which the active site can convert substrate to product.
  • The only way to increase productivity at this point is to add more enzyme molecules.

    A cell’s physical and chemical environment affects enzyme activity.

  • The activity of an enzyme is affected by general environmental conditions, such as temperature and pH.
  • Each enzyme works best at certain optimal conditions, which favor the most active conformation for the enzyme molecule.
  • Temperature has a major impact on reaction rate.
    • As temperature increases, collisions between substrates and active sites occur more frequently as molecules move more rapidly.
    • As temperature increases further, thermal agitation begins to disrupt the weak bonds that stabilize the protein’s active conformation, and the protein denatures.
    • Each enzyme has an optimal temperature.
      • Most human enzymes have optimal temperatures of about 35–40°C.
      • Bacteria that live in hot springs contain enzymes with optimal temperatures of 70°C or above.
  • Each enzyme also has an optimal pH.
  • Maintenance of the active conformation of the enzyme requires a particular pH.
    • This falls between pH 6 and 8 for most enzymes.
    • However, digestive enzymes in the stomach are designed to work best at pH 2, while those in the intestine have an optimum of pH 8.
  • Many enzymes require nonprotein helpers, called cofactors, for catalytic activity.
    • Cofactors bind permanently or reversibly to the enzyme.
    • Some inorganic cofactors include zinc, iron, and copper.
  • Organic cofactors are called coenzymes.
    • Many vitamins are coenzymes.
  • Binding by inhibitors prevents enzymes from catalyzing reactions.
    • If inhibitors attach to the enzyme by covalent bonds, inhibition may be irreversible.
    • If inhibitors bind by weak bonds, inhibition may be reversible.
  • Some reversible inhibitors resemble the substrate and compete for binding to the active site.
    • These molecules are called competitive inhibitors.
    • Competitive inhibition can be overcome by increasing the concentration of the substrate.
  • Noncompetitive inhibitors impede enzymatic reactions by binding to another part of the molecule.
    • Binding by the inhibitor causes the enzyme to change shape, rendering the active site less effective at catalyzing the reaction.
  • Toxins and poisons are often irreversible enzyme inhibitors.
  • Sarin is the nerve gas that was released by terrorists in the Tokyo subway in 1995.
    • Sarin binds covalently to the R group on the amino acid serine.
    • Serine is found in the active site of acetylcholinesterase, an important nervous system enzyme.

Concept 8.5 Regulation of enzyme activity helps control metabolism

    Metabolic control often depends on allosteric regulation.

  • In many cases, the molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors.
  • Regulatory molecules often bind weakly to an allosteric site, a specific receptor on the enzyme away from the active site.
    • Binding by these molecules can either inhibit or stimulate enzyme activity.
  • Most allosterically regulated enzymes are constructed of two or more polypeptide chains.
    • Each subunit has its own active site.
    • Allosteric sites are often located where subunits join.
  • The binding of an activator stabilizes the conformation that has functional active sites, while the binding of an inhibitor stabilizes the inactive form of the enzyme.
  • As the chemical conditions in the cell shift, the pattern of allosteric regulation may shift as well.
  • By binding to key enzymes, reactants and products of ATP hydrolysis may play a major role in balancing the flow of traffic between anabolic and catabolic pathways.
    • For example, ATP binds to several catabolic enzymes allosterically, inhibiting their activity by lowering their affinity for substrate.
    • ADP functions as an activator of the same enzymes.
    • ATP and ADP also affect key enzymes in anabolic pathways.
    • In this way, allosteric enzymes control the rates of key reactions in metabolic pathways.
  • In enzymes with multiple catalytic subunits, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits, a process called cooperativity.
    • This mechanism amplifies the response of enzymes to substrates, priming the enzyme to accept additional substrates.
  • A common method of metabolic control is feedback inhibition in which an early step in a metabolic pathway is switched off by the pathway’s final product.
    • The product acts as an inhibitor of an enzyme in the pathway.
  • Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.

    The localization of enzymes within a cell helps order metabolism.

  • Structures within the cell help bring order to metabolic pathways.
  • A team of enzymes for several steps of a metabolic pathway may be assembled as a multienzyme complex.
  • The product from the first reaction can then pass quickly to the next enzyme until the final product is released.
  • Some enzymes and enzyme complexes have fixed locations within the cells as structural components of particular membranes.
    • Others are confined within membrane-enclosed eukaryotic organelles.
  • Metabolism, the intersecting set of chemical pathways characteristic of life, is a choreographed interplay of thousands of different kinds of cellular molecules.

    Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 8-1

Subject: 
Subject X2: 

Chapter 09 - Cellular Respiration: Harvesting Chemical Energy

Chapter 9 Cellular Respiration: Harvesting Chemical Energy
Lecture Outline

Overview: Life Is Work

  • To perform their many tasks, living cells require energy from outside sources.
  • Energy enters most ecosystems as sunlight and leaves as heat.
  • Photosynthesis generates oxygen and organic molecules that the mitochondria of eukaryotes use as fuel for cellular respiration.
  • Cells harvest the chemical energy stored in organic molecules and use it to regenerate ATP, the molecule that drives most cellular work.
  • Respiration has three key pathways: glycolysis, the citric acid cycle, and oxidative phosphorylation.

Concept 9.1 Catabolic pathways yield energy by oxidizing organic fuels

  • The arrangement of atoms of organic molecules represents potential energy.
  • Enzymes catalyze the systematic degradation of organic molecules that are rich in energy to simpler waste products with less energy.
  • Some of the released energy is used to do work; the rest is dissipated as heat.
  • Catabolic metabolic pathways release the energy stored in complex organic molecules.
  • One type of catabolic process, fermentation, leads to the partial degradation of sugars in the absence of oxygen.
  • A more efficient and widespread catabolic process, cellular respiration, consumes oxygen as a reactant to complete the breakdown of a variety of organic molecules.
    • In eukaryotic cells, mitochondria are the site of most of the processes of cellular respiration.
  • Cellular respiration is similar in broad principle to the combustion of gasoline in an automobile engine after oxygen is mixed with hydrocarbon fuel.
    • Food is the fuel for respiration. The exhaust is carbon dioxide and water.
  • The overall process is:
    • organic compounds + O2 --> CO2 + H2O + energy (ATP + heat).
  • Carbohydrates, fats, and proteins can all be used as the fuel, but it is most useful to consider glucose.
  • C6H12O6 + 6O2 --> 6CO2 + 6H2O + Energy (ATP + heat)
  • The catabolism of glucose is exergonic with a ? G of ?686 kcal per mole of glucose.
    • Some of this energy is used to produce ATP, which can perform cellular work.

    Redox reactions release energy when electrons move closer to electronegative atoms.

  • Catabolic pathways transfer the electrons stored in food molecules, releasing energy that is used to synthesize ATP.
  • Reactions that result in the transfer of one or more electrons from one reactant to another are oxidation-reduction reactions, or redox reactions.
    • The loss of electrons is called oxidation.
    • The addition of electrons is called reduction.
  • The formation of table salt from sodium and chloride is a redox reaction.
    • Na + Cl --> Na+ + Cl?
    • Here sodium is oxidized and chlorine is reduced (its charge drops from 0 to ?1).
  • More generally: Xe? + Y --> X + Ye?
    • X, the electron donor, is the reducing agent and reduces Y.
    • Y, the electron recipient, is the oxidizing agent and oxidizes X.
  • Redox reactions require both a donor and acceptor.
  • Redox reactions also occur when the transfer of electrons is not complete but involves a change in the degree of electron sharing in covalent bonds.
    • In the combustion of methane to form water and carbon dioxide, the nonpolar covalent bonds of methane (C—H) and oxygen (O=O) are converted to polar covalent bonds (C=O and O—H).
    • When methane reacts with oxygen to form carbon dioxide, electrons end up farther away from the carbon atom and closer to their new covalent partners, the oxygen atoms, which are very electronegative.
    • In effect, the carbon atom has partially “lost” its shared electrons. Thus, methane has been oxidized.
  • The two atoms of the oxygen molecule share their electrons equally. When oxygen reacts with the hydrogen from methane to form water, the electrons of the covalent bonds are drawn closer to the oxygen.
    • In effect, each oxygen atom has partially “gained” electrons, and so the oxygen molecule has been reduced.
    • Oxygen is very electronegative, and is one of the most potent of all oxidizing agents.
  • Energy must be added to pull an electron away from an atom.
  • The more electronegative the atom, the more energy is required to take an electron away from it.
  • An electron loses potential energy when it shifts from a less electronegative atom toward a more electronegative one.
  • A redox reaction that relocates electrons closer to oxygen, such as the burning of methane, releases chemical energy that can do work.

    The “fall” of electrons during respiration is stepwise, via NAD+ and an electron transport chain.

  • Cellular respiration does not oxidize glucose in a single step that transfers all the hydrogen in the fuel to oxygen at one time.
  • Rather, glucose and other fuels are broken down in a series of steps, each catalyzed by a specific enzyme.
    • At key steps, electrons are stripped from the glucose.
    • In many oxidation reactions, the electron is transferred with a proton, as a hydrogen atom.
  • The hydrogen atoms are not transferred directly to oxygen but are passed first to a coenzyme called NAD+ (nicotinamide adenine dinucleotide).
  • How does NAD+ trap electrons from glucose?
    • Dehydrogenase enzymes strip two hydrogen atoms from the fuel (e.g., glucose), oxidizing it.
    • The enzyme passes two electrons and one proton to NAD+.
    • The other proton is released as H+ to the surrounding solution.
  • By receiving two electrons and only one proton, NAD+ has its charge neutralized when it is reduced to NADH.
    • NAD+ functions as the oxidizing agent in many of the redox steps during the catabolism of glucose.
  • The electrons carried by NADH have lost very little of their potential energy in this process.
  • Each NADH molecule formed during respiration represents stored energy. This energy is tapped to synthesize ATP as electrons “fall” from NADH to oxygen.
  • How are electrons extracted from food and stored by NADH finally transferred to oxygen?
    • Unlike the explosive release of heat energy that occurs when H2 and O2 are combined (with a spark for activation energy), cellular respiration uses an electron transport chain to break the fall of electrons to O2 into several steps.
  • The electron transport chain consists of several molecules (primarily proteins) built into the inner membrane of a mitochondrion.
  • Electrons released from food are shuttled by NADH to the “top” higher-energy end of the chain.
  • At the “bottom” lower-energy end, oxygen captures the electrons along with H+ to form water.
  • Electron transfer from NADH to oxygen is an exergonic reaction with a free energy change of ?53 kcal/mol.
  • Electrons are passed to increasingly electronegative molecules in the chain until they reduce oxygen, the most electronegative receptor.
  • In summary, during cellular respiration, most electrons travel the following “downhill” route: food --> NADH --> electron transport chain --> oxygen.

    These are the stages of cellular respiration: a preview.

  • Respiration occurs in three metabolic stages: glycolysis, the citric acid cycle, and the electron transport chain and oxidative phosphorylation.
  • Glycolysis occurs in the cytoplasm.
    • It begins catabolism by breaking glucose into two molecules of pyruvate.
  • The citric acid cycle occurs in the mitochondrial matrix.
    • It completes the breakdown of glucose by oxidizing a derivative of pyruvate to carbon dioxide.
  • Several steps in glycolysis and the citric acid cycle are redox reactions in which dehydrogenase enzymes transfer electrons from substrates to NAD+, forming NADH.
  • NADH passes these electrons to the electron transport chain.
  • In the electron transport chain, the electrons move from molecule to molecule until they combine with molecular oxygen and hydrogen ions to form water.
  • As they are passed along the chain, the energy carried by these electrons is transformed in the mitochondrion into a form that can be used to synthesize ATP via oxidative phosphorylation.
  • The inner membrane of the mitochondrion is the site of electron transport and chemiosmosis, processes that together constitute oxidative phosphorylation.
    • Oxidative phosphorylation produces almost 90% of the ATP generated by respiration.
  • Some ATP is also formed directly during glycolysis and the citric acid cycle by substrate-level phosphorylation.
    • Here an enzyme transfers a phosphate group from an organic substrate to ADP, forming ATP.
  • For each molecule of glucose degraded to carbon dioxide and water by respiration, the cell makes up to 38 ATP, each with 7.3 kcal/mol of free energy.
  • Respiration uses the small steps in the respiratory pathway to break the large denomination of energy contained in glucose into the small change of ATP.
    • The quantity of energy in ATP is more appropriate for the level of work required in the cell.

Concept 9.2 Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

  • During glycolysis, glucose, a six carbon-sugar, is split into two three-carbon sugars.
  • These smaller sugars are oxidized and rearranged to form two molecules of pyruvate, the ionized form of pyruvic acid.
  • Each of the ten steps in glycolysis is catalyzed by a specific enzyme.
  • These steps can be divided into two phases: an energy investment phase and an energy payoff phase.
  • In the energy investment phase, the cell invests ATP to provide activation energy by phosphorylating glucose.
    • This requires 2 ATP per glucose.
  • In the energy payoff phase, ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released by the oxidation of glucose.
  • The net yield from glycolysis is 2 ATP and 2 NADH per glucose.
    • No CO2 is produced during glycolysis.
  • Glycolysis can occur whether O2 is present or not.

Concept 9.3 The citric acid cycle completes the energy-yielding oxidation of organic molecules

  • More than three-quarters of the original energy in glucose is still present in the two molecules of pyruvate.
  • If oxygen is present, pyruvate enters the mitochondrion where enzymes of the citric acid cycle complete the oxidation of the organic fuel to carbon dioxide.
  • After pyruvate enters the mitochondrion via active transport, it is converted to a compound called acetyl coenzyme A or acetyl CoA.
  • This step is accomplished by a multienzyme complex that catalyzes three reactions:
    1. A carboxyl group is removed as CO2.
    2. The remaining two-carbon fragment is oxidized to form acetate. An enzyme transfers the pair of electrons to NAD+ to form NADH.
    3. Acetate combines with coenzyme A to form the very reactive molecule acetyl CoA.
  • Acetyl CoA is now ready to feed its acetyl group into the citric acid cycle for further oxidation.
  • The citric acid cycle is also called the Krebs cycle in honor of Hans Krebs, who was largely responsible for elucidating its pathways in the 1930s.
  • The citric acid cycle oxidizes organic fuel derived from pyruvate.
    • The citric acid cycle has eight steps, each catalyzed by a specific enzyme.
    • The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate.
    • The next seven steps decompose the citrate back to oxaloacetate. It is the regeneration of oxaloacetate that makes this process a cycle.
    • Three CO2 molecules are released, including the one released during the conversion of pyruvate to acetyl CoA.
  • The cycle generates one ATP per turn by substrate-level phosphorylation.
    • A GTP molecule is formed by substrate-level phosphorylation.
    • The GTP is then used to synthesize an ATP, the only ATP generated directly by the citric acid cycle.
  • Most of the chemical energy is transferred to NAD+ and FAD during the redox reactions.
  • The reduced coenzymes NADH and FADH2 then transfer high-energy electrons to the electron transport chain.
  • Each cycle produces one ATP by substrate-level phosphorylation, three NADH, and one FADH2 per acetyl CoA.

Concept 9.4 During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis

    The inner mitochondrial membrane couples electron transport to ATP synthesis.

  • Only 4 of 38 ATP ultimately produced by respiration of glucose are produced by substrate-level phosphorylation.
    • Two are produced during glycolysis, and 2 are produced during the citric acid cycle.
  • NADH and FADH2 account for the vast majority of the energy extracted from the food.
    • These reduced coenzymes link glycolysis and the citric acid cycle to oxidative phosphorylation, which uses energy released by the electron transport chain to power ATP synthesis.
  • The electron transport chain is a collection of molecules embedded in the cristae, the folded inner membrane of the mitochondrion.
    • The folding of the cristae increases its surface area, providing space for thousands of copies of the chain in each mitochondrion.
    • Most components of the chain are proteins bound to prosthetic groups, nonprotein components essential for catalysis.
  • Electrons drop in free energy as they pass down the electron transport chain.
  • During electron transport along the chain, electron carriers alternate between reduced and oxidized states as they accept and donate electrons.
    • Each component of the chain becomes reduced when it accepts electrons from its “uphill” neighbor, which is less electronegative.
    • It then returns to its oxidized form as it passes electrons to its more electronegative “downhill” neighbor.
  • Electrons carried by NADH are transferred to the first molecule in the electron transport chain, a flavoprotein.
  • The electrons continue along the chain that includes several cytochrome proteins and one lipid carrier.
    • The prosthetic group of each cytochrome is a heme group with an iron atom that accepts and donates electrons.
  • The last cytochrome of the chain, cyt a3, passes its electrons to oxygen, which is very electronegative.
    • Each oxygen atom also picks up a pair of hydrogen ions from the aqueous solution to form water.
    • For every two electron carriers (four electrons), one O2 molecule is reduced to two molecules of water.
  • The electrons carried by FADH2 have lower free energy and are added at a lower energy level than those carried by NADH.
    • The electron transport chain provides about one-third less energy for ATP synthesis when the electron donor is FADH2 rather than NADH.
  • The electron transport chain generates no ATP directly.
  • Its function is to break the large free energy drop from food to oxygen into a series of smaller steps that release energy in manageable amounts.
  • How does the mitochondrion couple electron transport and energy release to ATP synthesis?
    • The answer is a mechanism called chemiosmosis.
  • A protein complex, ATP synthase, in the cristae actually makes ATP from ADP and Pi.
  • ATP uses the energy of an existing proton gradient to power ATP synthesis.
    • The proton gradient develops between the intermembrane space and the matrix.
  • The proton gradient is produced by the movement of electrons along the electron transport chain.
  • The chain is an energy converter that uses the exergonic flow of electrons to pump H+ from the matrix into the intermembrane space.
  • The protons pass back to the matrix through a channel in ATP synthase, using the exergonic flow of H+ to drive the phosphorylation of ADP.
  • Thus, the energy stored in a H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis.
  • From studying the structure of ATP synthase, scientists have learned how the flow of H+ through this large enzyme powers ATP generation.
  • ATP synthase is a multisubunit complex with four main parts, each made up of multiple polypeptides:
    1. A rotor in the inner mitochondrial membrane.
    2. A knob that protrudes into the mitochondrial matrix.
    3. An internal rod extending from the rotor into the knob.
    4. A stator, anchored next to the rotor, which holds the knob stationary.
  • Protons flow down a narrow space between the stator and rotor, causing the rotor and its attached rod to rotate.
    • The spinning rod causes conformational changes in the stationary knob, activating three catalytic sites in the knob where ADP and inorganic phosphate combine to make ATP.
  • How does the inner mitochondrial membrane generate and maintain the H+ gradient that drives ATP synthesis in the ATP synthase protein complex?
    • Creating the H+ gradient is the function of the electron transport chain.
    • The ETC is an energy converter that uses the exergonic flow of electrons to pump H+ across the membrane from the mitochondrial matrix to the intermembrane space.
    • The H+ has a tendency to diffuse down its gradient.
  • The ATP synthase molecules are the only place that H+ can diffuse back to the matrix.
    • The exergonic flow of H+ is used by the enzyme to generate ATP.
    • This coupling of the redox reactions of the electron transport chain to ATP synthesis is called chemiosmosis.
  • How does the electron transport chain pump protons?
    • Certain members of the electron transport chain accept and release H+ along with electrons.
    • At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution.
  • The electron carriers are spatially arranged in the membrane in such a way that protons are accepted from the mitochondrial matrix and deposited in the intermembrane space.
    • The H+ gradient that results is the proton-motive force.
    • The gradient has the capacity to do work.
  • Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work.
  • In mitochondria, the energy for proton gradient formation comes from exergonic redox reactions, and ATP synthesis is the work performed.
  • Chemiosmosis in chloroplasts also generates ATP, but light drives the electron flow down an electron transport chain and H+ gradient formation.
  • Prokaryotes generate H+ gradients across their plasma membrane.
    • They can use this proton-motive force not only to generate ATP, but also to pump nutrients and waste products across the membrane and to rotate their flagella.

    Here is an accounting of ATP production by cellular respiration.

  • During cellular respiration, most energy flows from glucose --> NADH --> electron transport chain --> proton-motive force --> ATP.
  • Let’s consider the products generated when cellular respiration oxidizes a molecule of glucose to six CO2 molecules.
  • Four ATP molecules are produced by substrate-level phosphorylation during glycolysis and the citric acid cycle.
  • Many more ATP molecules are generated by oxidative phosphorylation.
  • Each NADH from the citric acid cycle and the conversion of pyruvate contributes enough energy to the proton-motive force to generate a maximum of 3 ATP.
    • The NADH from glycolysis may also yield 3 ATP.
  • Each FADH2 from the citric acid cycle can be used to generate about 2 ATP.
  • Why is our accounting so inexact?
  • There are three reasons that we cannot state an exact number of ATP molecules generated by one molecule of glucose.
    1. Phosphorylation and the redox reactions are not directly coupled to each other, so the ratio of number of NADH to number of ATP is not a whole number.
      • One NADH results in 10 H+ being transported across the inner mitochondrial membrane.
      • Between 3 and 4 H+ must reenter the mitochondrial matrix via ATP synthase to generate 1 ATP.
      • Therefore, 1 NADH generates enough proton-motive force for synthesis of 2.5 to 3.3 ATP.
      • We round off and say that 1 NADH generates 3 ATP.
    2. The ATP yield varies slightly depending on the type of shuttle used to transport electrons from the cytosol into the mitochondrion.
      • The mitochondrial inner membrane is impermeable to NADH, so the two electrons of the NADH produced in glycolysis must be conveyed into the mitochondrion by one of several electron shuttle systems.
      • In some shuttle systems, the electrons are passed to NAD+, which generates 3 ATP. In others, the electrons are passed to FAD, which generates only 2 ATP.
    3. The proton-motive force generated by the redox reactions of respiration may drive other kinds of work, such as mitochondrial uptake of pyruvate from the cytosol.
      • If all the proton-motive force generated by the electron transport chain were used to drive ATP synthesis, one glucose molecule could generate a maximum of 34 ATP by oxidative phosphorylation plus 4 ATP (net) from substrate-level phosphorylation to give a total yield of 36–38 ATP (depending on the efficiency of the shuttle).
  • How efficient is respiration in generating ATP?
    • Complete oxidation of glucose releases 686 kcal/mol.
    • Phosphorylation of ADP to form ATP requires at least 7.3 kcal/mol.
    • Efficiency of respiration is 7.3 kcal/mol times 38 ATP/glucose divided by 686 kcal/mol glucose, which equals 0.4 or 40%.
    • Approximately 60% of the energy from glucose is lost as heat.
      • Some of that heat is used to maintain our high body temperature (37°C).
  • Cellular respiration is remarkably efficient in energy conversion.

Concept 9.5 Fermentation enables some cells to produce ATP without the use of oxygen

  • Without electronegative oxygen to pull electrons down the transport chain, oxidative phosphorylation ceases.
  • However, fermentation provides a mechanism by which some cells can oxidize organic fuel and generate ATP without the use of oxygen.
    • In glycolysis, glucose is oxidized to two pyruvate molecules with NAD+ as the oxidizing agent.
    • Glycolysis is exergonic and produces 2 ATP (net).
    • If oxygen is present, additional ATP can be generated when NADH delivers its electrons to the electron transport chain.
  • Glycolysis generates 2 ATP whether oxygen is present (aerobic) or not (anaerobic).
  • Anaerobic catabolism of sugars can occur by fermentation.
  • Fermentation can generate ATP from glucose by substrate-level phosphorylation as long as there is a supply of NAD+ to accept electrons.
    • If the NAD+ pool is exhausted, glycolysis shuts down.
    • Under aerobic conditions, NADH transfers its electrons to the electron transfer chain, recycling NAD+.
  • Under anaerobic conditions, various fermentation pathways generate ATP by glycolysis and recycle NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate.
  • In alcohol fermentation, pyruvate is converted to ethanol in two steps.
    • First, pyruvate is converted to a two-carbon compound, acetaldehyde, by the removal of CO2.
    • Second, acetaldehyde is reduced by NADH to ethanol.
    • Alcohol fermentation by yeast is used in brewing and winemaking.
  • During lactic acid fermentation, pyruvate is reduced directly by NADH to form lactate (the ionized form of lactic acid) without release of CO2.
    • Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt.
    • Human muscle cells switch from aerobic respiration to lactic acid fermentation to generate ATP when O2 is scarce.
      • The waste product, lactate, may cause muscle fatigue, but ultimately it is converted back to pyruvate in the liver.
  • Fermentation and cellular respiration are anaerobic and aerobic alternatives, respectively, for producing ATP from sugars.
    • Both use glycolysis to oxidize sugars to pyruvate with a net production of 2 ATP by substrate-level phosphorylation.
    • Both use NAD+ as an oxidizing agent to accept electrons from food during glycolysis.
  • The two processes differ in their mechanism for oxidizing NADH to NAD+.
    • In fermentation, the electrons of NADH are passed to an organic molecule to regenerate NAD+.
    • In respiration, the electrons of NADH are ultimately passed to O2, generating ATP by oxidative phosphorylation.
  • More ATP is generated from the oxidation of pyruvate in the citric acid cycle.
    • Without oxygen, the energy still stored in pyruvate is unavailable to the cell.
    • Under aerobic respiration, a molecule of glucose yields 38 ATP, but the same molecule of glucose yields only 2 ATP under anaerobic respiration.
  • Yeast and many bacteria are facultative anaerobes that can survive using either fermentation or respiration.
    • At a cellular level, human muscle cells can behave as facultative anaerobes.
  • For facultative anaerobes, pyruvate is a fork in the metabolic road that leads to two alternative routes.
    • Under aerobic conditions, pyruvate is converted to acetyl CoA and oxidation continues in the citric acid cycle.
    • Under anaerobic conditions, pyruvate serves as an electron acceptor to recycle NAD+.
  • The oldest bacterial fossils are more than 3.5 billion years old, appearing long before appreciable quantities of O2 accumulated in the atmosphere.
    • Therefore, the first prokaryotes may have generated ATP exclusively from glycolysis.
  • The fact that glycolysis is a ubiquitous metabolic pathway and occurs in the cytosol without membrane-enclosed organelles suggests that glycolysis evolved early in the history of life.

Concept 9.6 Glycolysis and the citric acid cycle connect to many other metabolic pathways

  • Glycolysis can accept a wide range of carbohydrates for catabolism.
    • Polysaccharides like starch or glycogen can be hydrolyzed to glucose monomers that enter glycolysis.
    • Other hexose sugars, such as galactose and fructose, can also be modified to undergo glycolysis.
  • The other two major fuels, proteins and fats, can also enter the respiratory pathways used by carbohydrates.
  • Proteins must first be digested to individual amino acids.
    • Amino acids that will be catabolized must have their amino groups removed via deamination.
    • The nitrogenous waste is excreted as ammonia, urea, or another waste product.
  • The carbon skeletons are modified by enzymes and enter as intermediaries into glycolysis or the citric acid cycle, depending on their structure.
  • Catabolism can also harvest energy stored in fats.
  • Fats must be digested to glycerol and fatty acids.
    • Glycerol can be converted to glyceraldehyde phosphate, an intermediate of glycolysis.
    • The rich energy of fatty acids is accessed as fatty acids are split into two-carbon fragments via beta oxidation.
    • These molecules enter the citric acid cycle as acetyl CoA.
  • A gram of fat oxides by respiration generates twice as much ATP as a gram of carbohydrate.
  • The metabolic pathways of respiration also play a role in anabolic pathways of the cell.
  • Intermediaries in glycolysis and the citric acid cycle can be diverted to anabolic pathways.
    • For example, a human cell can synthesize about half the 20 different amino acids by modifying compounds from the citric acid cycle.
    • Glucose can be synthesized from pyruvate; fatty acids can be synthesized from acetyl CoA.
  • Glycolysis and the citric acid cycle function as metabolic interchanges that enable cells to convert one kind of molecule to another as needed.
    • For example, excess carbohydrates and proteins can be converted to fats through intermediaries of glycolysis and the citric acid cycle.
  • Metabolism is remarkably versatile and adaptable.

    Feedback mechanisms control cellular respiration.

  • Basic principles of supply and demand regulate the metabolic economy.
    • If a cell has an excess of a certain amino acid, it typically uses feedback inhibition to prevent the diversion of intermediary molecules from the citric acid cycle to the synthesis pathway of that amino acid.
  • The rate of catabolism is also regulated, typically by the level of ATP in the cell.
    • If ATP levels drop, catabolism speeds up to produce more ATP.
  • Control of catabolism is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway.
  • One strategic point occurs in the third step of glycolysis, catalyzed by phosphofructokinase.
  • Allosteric regulation of phosphofructokinase sets the pace of respiration.
    • This enzyme catalyzes the earliest step that irreversibly commits the substrate to glycolysis.
    • Phosphofructokinase is an allosteric enzyme with receptor sites for specific inhibitors and activators.
    • It is inhibited by ATP and stimulated by AMP (derived from ADP).
      • When ATP levels are high, inhibition of this enzyme slows glycolysis.
      • As ATP levels drop and ADP and AMP levels rise, the enzyme becomes active again and glycolysis speeds up.
  • Citrate, the first product of the citric acid cycle, is also an inhibitor of phosphofructokinase.
    • This synchronizes the rate of glycolysis and the citric acid cycle.
  • If intermediaries from the citric acid cycle are diverted to other uses (e.g., amino acid synthesis), glycolysis speeds up to replace these molecules.
  • Metabolic balance is augmented by the control of other enzymes at other key locations in glycolysis and the citric acid cycle.
  • Cells are thrifty, expedient, and responsive in their metabolism.

    Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 9-1

Subject: 
Subject X2: 

Chapter 33 - Invertebrates

Chapter 33 Invertebrates
Lecture Outline

Overview: Life Without a Backbone

  • Invertebrates—animals without a backbone—account for 95% of known animal species and all but one of the roughly 35 animal phyla that have been described.
    • More than a million extant species of animals are known, and at least as many more will probably be identified by future biologists.
  • Invertebrates inhabit nearly all environments on Earth, from the scalding water of deep-sea hydrothermal vents to the rocky, frozen ground of Antarctica.

Concept 33.1 Sponges are sessile and have a porous body and choanocytes

  • Sponges (phylum Porifera) are so sedentary that they were mistaken for plants by the early Greeks.
  • Living in freshwater and marine environments, sponges are suspension feeders.
  • The body of a simple sponge resembles a sac perforated with holes.
    • Water is drawn through the pores into a central cavity, the spongocoel, and flows out through a larger opening, the osculum.
    • More complex sponges have folded body walls, and many contain branched water canals and several oscula.
  • Sponges range in height from about a few mm to 2 m and most are marine.
    • About 100 species live in fresh water.
  • Unlike eumetazoa, sponges lack true issues, groups of similar cells that form a functional unit.
  • The germ layers of sponges are loose federations of cells, which are not really tissues because the cells are relatively unspecialized.
    • The sponge body does contain different cell types.
  • Sponges collect food particles from water passing through food-trapping equipment.
    • Flagellated choanocytes, or collar cells, lining the spongocoel (internal water chambers) create a flow of water through the sponge with their flagella and trap food with their collars.
    • Based on both molecular evidence and the morphology of their choanocytes, sponges evolved from a colonial choanoflagellate ancestor.
  • The body of a sponge consists of two cell layers separated by a gelatinous region, the mesohyl.
  • Wandering though the mesohyl are amoebocytes.
    • They take up food from water and from choanocytes, digest it, and carry nutrients to other cells.
    • They also secrete tough skeletal fibers within the mesohyl.
      • In some groups of sponges, these fibers are sharp spicules of calcium carbonate or silica.
      • Other sponges produce more flexible fibers from a collagen protein called spongin.
        • ? We use these pliant, honeycombed skeletons as bath sponges.
  • Most sponges are sequential hermaphrodites, with each individual producing both sperm and eggs in sequence.
    • Gametes arise from choanocytes or amoebocytes.
    • The eggs are retained, but sperm are carried out the osculum by the water current.
    • Sperm are drawn into neighboring individuals and fertilize eggs in the mesohyl.
    • The zygotes develop into flagellated, swimming larvae that disperse from the parent.
    • When a larva finds a suitable substratum, it develops into a sessile adult.
  • Sponges produce a variety of antibiotics and other defensive compounds.
    • Researchers are now isolating these compounds, which may be useful in fighting human disease.

Concept 33.2 Cnidarians have radial symmetry, a gastrovascular cavity, and cnidocytes

  • All animals except sponges belong to the Eumetazoa, the animals with true tissues.
  • The cnidarians (hydras, jellies, sea anemones, and coral animals) have a relatively simple body construction.
    • They are a diverse group with more than 10,000 living species, most of which are marine.
    • They exhibit a relatively simple, diploblastic body plan that arose 570 million years ago.
  • The basic cnidarian body plan is a sac with a central digestive compartment, the gastrovascular cavity.
    • A single opening to this cavity functions as both mouth and anus.
  • This basic body plan has two variations: the sessile polyp and the floating medusa.
  • The cylindrical polyps, such as hydras and sea anemones, adhere to the substratum by the aboral end and extend their tentacles, waiting for prey.
  • Medusas (also called jellies) are flattened, mouth-down versions of polyps that move by drifting passively and by contracting their bell-shaped bodies.
    • The tentacles of a jelly dangle from the oral surface.
  • Some cnidarians exist only as polyps.
    • Others exist only as medusas.
    • Still others pass sequentially through both a medusa stage and a polyp stage in their life cycle.
  • Cnidarians are carnivores that use tentacles arranged in a ring around the mouth to capture prey and push the food into the gastrovascular chamber for digestion.
    • Batteries of cnidocytes on the tentacles defend the animal or capture prey.
      • Organelles called cnidae evert a thread that can inject poison into the prey, or stick to or entangle the target.
    • Cnidae called nematocysts are stinging capsules.
  • Muscles and nerves exist in their simplest forms in cnidarians.
  • Cells of the epidermis and gastrodermis have bundles of microfilaments arranged into contractile fibers.
    • True muscle tissue appears first in triploblastic animals.
    • When the animal closes its mouth, the gastrovascular cavity acts as a hydrostatic skeleton against which the contractile cells can work.
  • Movements are controlled by a noncentralized nerve net associated with simple sensory receptors that are distributed radially around the body.
  • The phylum Cnidaria is divided into four major classes: Hydrozoa, Scyphozoa, Cubozoa, and Anthozoa.
  • The four cnidarian classes show variations on the same body theme of polyp and medusa.
  • Most hydrozoans alternate polyp and medusa forms, as in the life cycle of Obelia.
    • The polyp stage, often a colony of interconnected polyps, is more conspicuous than the medusa.
  • Hydras, among the few freshwater cnidarians, are unusual members of the class Hydrozoa in that they exist only in the polyp form.
    • When environmental conditions are favorable, a hydra reproduces asexually by budding, the formation of outgrowths that pinch off from the parent to live independently.
    • When environmental conditions deteriorate, hydras form resistant zygotes that remain dormant until conditions improve.
  • The medusa generally prevails in the life cycle of class Scyphozoa.
    • The medusae of most species live among the plankton as jellies.
  • Most coastal scyphozoans go through small polyp stages during their life cycle.
    • Jellies that live in the open ocean generally lack the sessile polyp.
  • Cubozoans have a box-shaped medusa stage.
    • They can be distinguished from scyphozoans in other significant ways, such as having complex eyes in the fringe of the medusae.
  • Cubozoans, which generally live in tropical oceans, are often equipped with highly toxic cnidocytes.
  • Sea anemones and corals belong to the class Anthozoa.
    • They occur only as polyps.
    • Coral animals live as solitary or colonial forms and secrete a hard external skeleton of calcium carbonate.
    • Each polyp generation builds on the skeletal remains of earlier generations to form skeletons that we call coral.
  • In tropical seas, coral reefs provide habitat for a great diversity of invertebrates and fishes.
    • Coral reefs in many parts of the world are currently being destroyed by human activity.
    • Pollution, overfishing, and global warming are contributing to their demise.

Concept 33.3 Most animals have bilateral symmetry

  • The vast majority of animal species belong to the clade Bilateria, which consists of animals with bilateral symmetry and triploblastic development.
  • Most bilaterians are also coelomates.
  • The most recent common ancestor of living bilaterians probably lived in the later Proterozoic.
  • During the Cambrian explosion, most major groups of bilaterians emerged.

    Phylum Platyhelminthes: Flatworms are acoelomates with gastrovascular cavities.

  • Flatworms live in marine, freshwater, and damp terrestrial habitats.
    • They also include many parasitic species, such as the flukes and tapeworms.
  • Flatworms have thin bodies, ranging in size from nearly microscopic to tapeworms more than 20 m long.
  • Flatworms and other bilaterians are triploblastic, with a middle embryonic tissue layer, a mesoderm, which contributes to more complex organs and organ systems and to true muscle tissue.
  • While flatworms are structurally more complex than cnidarians, they are simpler than other bilaterians.
    • Like cnidarians, flatworms have a gastrovascular cavity with only one opening (and tapeworms lack a digestive system entirely and absorb nutrients across their body surface).
    • Unlike other bilaterians, flatworms lack a coelom.
  • The flat shape of a flatworm places all cells close to the surrounding water, enabling gas exchange and the elimination of nitrogenous wastes (ammonia) by diffusion across the body surface.
  • Flatworms have no specialized organs for gas exchange and circulation, and their relatively simple excretory apparatus functions mainly to maintain osmotic balance.
    • This apparatus consists of ciliated cells called flame bulbs that waft fluid through branched ducts that open to the outside.
  • Flatworms are divided into four classes: Turbellaria, Monogenia, Trematoda, and Cestoidea.
  • Turbellarians are nearly all free-living (nonparasitic) and most are marine.
    • Planarians, members of the genus Dugesia, are carnivores or scavengers in unpolluted ponds and streams.
  • Planarians move using cilia on the ventral epidermis, gliding along a film of mucus they secrete.
    • Some turbellarians use muscles for undulatory swimming.
  • A planarian has a head with a pair of eyespots to detect light, and lateral flaps that function mainly for smell.
    • The planarian nervous system is more complex and centralized than the nerve net of cnidarians.
      • Planarians can learn to modify their responses to stimuli.
    • Planarians reproduce asexually through regeneration.
      • The parent constricts in the middle, and each half regenerates the missing end.
    • Planarians can also reproduce sexually.
      • These hermaphrodites cross-fertilize.
    • The monogeneans (class Monogenea) and the trematodes (class Trematoda) live as parasites in or on other animals.
      • Many have suckers for attachment to their host.
      • A tough covering protects the parasites.
      • Reproductive organs nearly fill the interior of these worms.
    • Trematodes parasitize a wide range of hosts, and most species have complex life cycles with alternation of sexual and asexual stages.
      • Many require an intermediate host in which the larvae develop before infecting the final hosts (usually a vertebrate) where the adult worm lives.
      • The blood fluke Schistosoma infects 200 million people, leading to body pains and dysentery.
        • The intermediate host for Schistosoma is a snail.
    • Living within different hosts puts demands on trematodes that free-living animals do not face.
      • A blood fluke must evade the immune systems of two very different hosts.
      • By mimicking their host’s surface proteins, blood flukes create a partial immunological camouflage.
      • They also release molecules that manipulate the host’s immune system.
      • These defenses are so effective that individual flukes can survive in a human host for more than 40 years.
    • Most monogeneans are external parasites of fishes.
    • Their life cycles are simple, with a ciliated, free-living larva that starts an infection on a host.
    • While traditionally aligned with trematodes, some structural and chemical evidence suggests that they are more closely related to tapeworms.
  • Tapeworms (class Cestoidea) are also parasitic.
    • The adults live mostly in vertebrates, including humans.
  • Suckers and hooks on the head, or scolex, anchor the worm in the digestive tract of the host.
    • Tapeworms lack a gastrovascular cavity and absorb food particles from their hosts.
  • A long series of proglottids, sacs of sex organs, lie posterior to the scolex.
    • Mature proglottids, loaded with thousands of eggs, are released from the posterior end of the tapeworm and leave with the host’s feces.
    • In one type of cycle, tapeworm eggs in contaminated food or water are ingested by intermediary hosts, such as pigs or cattle.
    • The eggs develop into larvae that encyst in the muscles of their host.
    • Humans acquire the larvae by eating undercooked meat contaminated with cysts.
    • The larvae develop into mature adults within the human.

    Phylum Rotifera: Rotifers are pseudocoelomates with jaws, crowns of cilia, and complete digestive tracts.

  • Rotifers are tiny animals (5 µm to 2 mm), most of which live in freshwater.
    • Some live in the sea or in damp soil.
  • Rotifers are smaller than many protists but are truly multicellular, with specialized organ systems.
  • Rotifers have an alimentary canal, a digestive tract with a separate mouth and anus.
  • Internal organs lie in the pseudocoelom, a body cavity that is not completely lined with mesoderm.
    • The fluid in the pseudocoelom serves as a hydrostatic skeleton.
    • Through the movements of nutrients and wastes dissolved in the coelomic fluid, the pseudocoelom also functions as a circulatory system.
  • The word rotifer, “wheel-bearer,” refers to the crown of cilia that draws a vortex of water into the mouth.
    • Food particles drawn in by the cilia are captured by the jaws (trophi) in the pharynx and ground up.
  • Some rotifers exist only as females that produce more females from unfertilized eggs, a type of parthenogenesis.
  • Other species produce two types of eggs that develop by parthenogenesis.
    • One type forms females, and the other forms degenerate males that survive just long enough to fertilize eggs.
    • The zygote forms a resistant stage that can withstand environmental extremes until conditions improve.
    • The zygote then begins a new female generation that reproduces by parthenogenesis until conditions become unfavorable again.
  • It is puzzling that so many rotifers survive without males.
    • The vast majority of animals and plants reproduce sexually at least some of the time, and sexual reproduction has certain advantages over asexual reproduction.
    • For example, species that reproduce asexually tend to accumulate harmful mutations in their genomes faster than sexually reproducing species.
    • As a result, asexual species experience higher rates of extinction and lower rates of speciation.
  • A class of asexual rotifers called Bdelloidea consists of 360 species that all reproduce by parthenogenesis without males.
    • Thirty-five-million-year-old bdelloid rotifers have been found preserved in amber.
    • The morphology of these fossils resembles the female form.
    • DNA comparisons of bdelloids with their closest sexually reproducing rotifer relatives suggest that bdelloids have been asexual for far more than 35 million years.
  • Bdelloid rotifers raise interesting questions about the evolution of sex.

    The lophophorate phyla: ectoprocts, phoronids, and brachiopods are coelomates with ciliated tentacles around their mouths.

  • Bilaterians in three phyla—Ectoprocta, Phoronida, and Brachiopoda—are traditionally called lophophorate animals because they all have a lophophore.
    • The lophophore is a horseshoe-shaped or circular fold of the body wall bearing ciliated tentacles that surround and draw water toward the mouth.
    • The tentacles trap suspended food particles.
  • In addition to the lophophore, these three phyla share a U-shaped digestive tract and the absence of a head.
    • These may be adaptations to a sessile existence.
  • In contrast to flatworms, which lack a body cavity, and rotifers, which have a pseudocoelom, lophophorates have true coeloms completely lined with mesoderm.
  • Ectoprocts are colonial animals that superficially resemble plants.
    • In most species, the colony is encased in a hard exoskeleton.
    • The lophophores extend through pores in the exoskeleton.
  • Most ectoprocts are marine, where they are widespread and numerous sessile animals, with several species that can be important reef builders.
    • Ectoprocts also live in lakes and rivers.
  • Phoronids are tube-dwelling marine worms ranging from 1 mm to 50 cm in length.
    • Some live buried in the sand within chitinous tubes.
    • They extend the lophophore from the tube when feeding and pull it back in when threatened.
  • Brachiopods, or lampshells, superficially resemble clams and other bivalve molluscs.
    • However, the two halves of the brachiopod are dorsal and ventral to the animal, rather than lateral as in clams.
  • All brachiopods are marine.
    • Most live attached to the substratum by a stalk, opening their shell slightly to allow water to flow over the lophophore.
  • The living brachiopods are remnants of a richer past.
    • Thirty thousand species of brachiopod fossils have been described from the Paleozoic and Mesozoic eras.

    Phylum Nemertea: Proboscis worms are named for their prey-capturing apparatus.

  • The members of the Phylum Nemertea, proboscis worms or ribbon worms, have bodies much like those of flatworms.
    • However, they have a small fluid-filled sac that may be a reduced version of a true coelom.
    • The sac and fluid hydraulics operate an extensible proboscis, which the worm uses to capture prey.
  • Nemerteans range in length from less than 1 mm to several meters.
  • Nearly all nemerteans are marine, but a few species inhabit fresh water or damp soil.
    • Some are active swimmers, and others burrow into the sand.
  • Nemerteans and flatworms have similar excretory, sensory, and nervous systems.
  • However, nemerteans have an alimentary canal and a closed circulatory system in which the blood is contained in vessels.
    • Nemerteans have no heart, and the blood is propelled by muscles squeezing the vessels.

Concept 33.4 Molluscs have a muscular foot, a visceral mass, and a mantle

  • The phylum Mollusca includes many diverse forms, including snails and slugs, oysters and clams, and octopuses and squids.
  • Most molluscs are marine, though some inhabit fresh water, and some snails and slugs live on land.
  • Molluscs are soft-bodied animals, but most are protected by a hard shell of calcium carbonate.
    • Slugs, squids, and octopuses have reduced or lost their shells completely during their evolution.
  • Despite their apparent differences, all molluscs have a similar body plan with a muscular foot (typically for locomotion), a visceral mass with most of the internal organs, and a mantle.
    • The mantle, which secretes the shell, drapes over the visceral mass and creates a water-filled chamber, the mantle cavity, with gills, anus, and excretory pores.
    • Many molluscs feed by using a straplike rasping organ, a radula, to scrape up food.
  • Most molluscs have separate sexes, with gonads located in the visceral mass.
    • However, many snails are hermaphrodites.
  • The life cycle of many marine molluscs includes a ciliated larva, the trochophore.
    • This larva is also found in marine annelids (segmented worms) and some other lophotrochozoans.
  • The basic molluscan body plan has evolved in various ways in the eight classes of the phylum.
    • The four most prominent are the Polyplacophora (chitons), Gastropoda (snails and slugs), Bivalvia (clams, oysters, and other bivalves), and Cephalopoda (squids, octopuses, cuttlefish, and chambered nautiluses).
  • Chitons are marine animals with oval shapes and shells divided into eight dorsal plates.
    • The chiton body is unsegmented.
  • Chitons use their muscular foot to grip the rocky substrate tightly and to creep slowly over the rock surface.
  • Chitons are grazers that use their radulas to scrape and ingest algae.
  • Almost three-quarters of all living species of molluscs are gastropods.
    • Most gastropods are marine, but there are also many freshwater species.
    • Garden snails and slugs have adapted to land.
  • During embryonic development, gastropods undergo torsion in which the visceral mass is rotated up to 180 degrees, so the anus and mantle cavity are above the head in adults.
    • After torsion, some of the organs that were bilateral are reduced or lost on one side of the body.
  • Most gastropods are protected by single, spiral shells into which the animals can retreat if threatened.
    • Torsion and formation of the coiled shell are independent developmental processes.
  • While gastropod shells are typically conical, those of abalones and limpets are somewhat flattened.
  • Many gastropods have distinct heads with eyes at the tips of tentacles.
  • They move by a rippling motion of their foot or by means of cilia.
  • Most gastropods use their radula to graze on algae or plant material.
  • Some species are predators.
    • In these species, the radula is modified to bore holes in the shells of other organisms or to tear apart tough animal tissues.
    • In the tropical marine cone snails, teeth on the radula form separate poison darts, which penetrate and stun their prey, including fishes.
  • In place of the gills found in most aquatic gastropods, the lining of the mantle cavity of terrestrial snails functions as a lung.
  • The class Bivalvia includes clams, oysters, mussels, and scallops.
  • Bivalves have shells divided into two halves.
    • The two parts are hinged at the mid-dorsal line, and powerful adductor muscles close the shell tightly to protect the animal.
  • Bivalves have no distinct head, and the radula has been lost.
    • Some bivalves have eyes and sensory tentacles along the outer edge of the mantle.
  • The mantle cavity of a bivalve contains gills that are used for feeding and gas exchange.
  • Most bivalves are suspension feeders, trapping fine particles in mucus that coats the gills.
    • Cilia convey the particles to the mouth.
    • Water flows into the mantle cavity via the incurrent siphon, passes over the gills, and exits via the excurrent siphon.
  • Most bivalves live rather sedentary lives, a characteristic suited to suspension feeding.
    • Sessile mussels secrete strong threads that tether them to rocks, docks, boats, and the shells of other animals.
    • Clams can pull themselves into the sand or mud, using the muscular foot as an anchor.
    • Scallops can swim in short bursts to avoid predators by flapping their shells and jetting water out their mantle cavity.
  • Cephalopods are active predators that use rapid movements to dart toward their prey, which they capture with several long tentacles.
    • Squids and octopuses use beak-like jaws to bite their prey and then inject poison to immobilize the victim.
  • A mantle covers the visceral mass, but the shell is reduced and internal in squids, missing in many octopuses, and exists externally only in chambered nautiluses.
  • Fast movements by a squid occur when it contracts its mantle cavity and fires a stream of water through the excurrent siphon.
    • By pointing the siphon in different directions, the squid can rapidly move in different directions.
  • The foot of a cephalopod has been modified into the muscular siphon and parts of the tentacles and head.
  • Cephalopods are the only molluscs with a closed circulatory system.
    • They also have well-developed sense organs and a complex brain.
  • The ancestors of octopuses and squid were probably shelled molluscs that took up a predatory lifestyle.
  • Shelled cephalopods called ammonites were the dominant invertebrate predators of the seas for hundreds of millions of years until their disappearance in the mass extinctions at the end of the Cretaceous period.
  • Most squid are less than 75 cm long.
    • In 2003, a squid with a mantle 2.5 meters long was captured near Antarctica.
      • The specimen was possibly a juvenile, only half the size of an adult.
      • Large squid are thought to feed on large fish in the deep ocean, where sperm whales are their only natural predators.

Concept 33.5 Annelids are segmented worms

  • All annelids (“little rings”) have segmented bodies.
  • They range in length from less than 1 mm to 3 m for the giant Australian earthworm.
  • Annelids live in the sea, most freshwater habitats, and damp soil.
  • The phylum Annelida is divided into three classes: Oligochaeta (earthworms), Polychaeta (polychaetes), and Hirudinea (leeches).
  • Oligochaetes are named for their relatively sparse chaetae, or bristles made of chitin.
  • This class of segmented worms includes the earthworms and a variety of aquatic species.
  • Earthworms eat their way through soil, extracting nutrients as the soil passes through the alimentary canal.
    • Undigested material is egested as castings.
    • Earthworms till the soil, enriching it with their castings.
  • Earthworms are cross-fertilizing hermaphrodites.
    • Two earthworms exchange sperm and then separate.
    • The received sperm are stored while a special organ, the clitellum, secretes a mucous cocoon.
    • As the cocoon slides along the body, it picks up eggs and stored sperm and slides off the body into the soil.
  • Some earthworms can also reproduce asexually by fragmentation followed by regeneration.
  • Each segment of a polychaete (“many setae”) has a pair of paddlelike or ridgelike parapodia (“almost feet”) that function in locomotion.
    • Each parapodium has several chitinous setae.
    • In many polychaetes, the rich blood vessels in the parapodia function as gills.
  • Most polychaetes are marine.
    • Many crawl on or burrow in the seafloor, while a few drift and swim in the plankton.
    • Some live in tubes that the worms make by mixing mucus with sand and broken shells. Others construct tubes from their own secretions.
  • The majority of leeches inhabit fresh water, but land leeches move through moist vegetation.
  • Leeches range in size from about 1 to 30 cm.
  • Many leeches feed on other invertebrates, but some blood-sucking parasites feed by attaching temporarily to other animals, including humans.
    • Some parasitic species use blade-like jaws to slit the host’s skin, while others secrete enzymes that digest a hole through the skin.
    • The host is usually unaware of the attack because the leech secretes an anesthetic.
    • The leech also secretes hirudin, an anticoagulant, into the wound, allowing the leech to suck as much blood as it can hold.
  • Until the 20th century, leeches were frequently used by physicians for bloodletting.
    • Leeches are still used to drain blood that accumulates in tissues following injury or surgery.
    • Researchers are also investigating the potential use of hirudin to dissolve unwanted blood clots from surgery or heart disease.
    • A recombinant form of hirudin has been developed and is in clinical trials.

Concept 33.6 Nematodes are nonsegmented pseudocoelomates covered by a tough cuticle

  • Roundworms are found in most aquatic habitats, wet soil, moist tissues of plants, and the body fluids and tissues of animals.
  • They range in size from less than 1 mm to more than a meter.
  • The cylindrical bodies of roundworms are covered with a tough exoskeleton, the cuticle.
    • As the worm grows, it periodically sheds its old cuticle and secretes a new, larger one.
  • They have an alimentary tract and use the fluid in their pseudocoelom to transport nutrients since they lack a circulatory system.
  • Their thrashing motion is due to contraction of longitudinal muscles.
  • Nematodes usually reproduce sexually.
    • The sexes are separate in most species, and fertilization is internal.
    • Females may lay 100,000 or more fertilized eggs per day.
    • The zygotes of most nematodes are resistant cells that can survive harsh conditions.
  • Abundant, free-living nematodes live in moist soil and in decomposing organic matter on the bottom of lakes and oceans.
    • There are 25,000 described species, and perhaps ten times that number actually exist.
    • If nothing but nematodes remained, it has been said, they would still preserve the outline of the planet and many of its features.
    • They play a major role in decomposition and nutrient recycling.
      • The soil nematode, Caenorhabditis elegans, has become a model organism in developmental biology.
  • The nematodes include many species that are important agricultural pests that attack plant roots.
  • Other species parasitize animals.
    • More than 50 nematode species, including various pinworms and hookworms, parasitize humans.
    • Trichinella spiralis causes trichinosis when the nematode worms encyst in a variety of human organs, including skeletal muscle.
    • They are acquired by eating undercooked meat that has juvenile worms encysted in the muscle tissue.
  • Parasitic nematodes are able to hijack some of the cellular functions of their hosts.
    • Plant-parasitic nematodes produce molecules that induce the development of root cells that provide nutrients to the parasites.
    • Trichenella in human muscle cells controls the expression of muscle cell genes that code for proteins that make the cell elastic enough to house the nematode.
      • The muscle cell also releases signals to attract blood vessels, supplying the nematode with nutrients.

Concept 33.7 Arthropods are segmented coelomates that have an exoskeleton and jointed appendages

  • The world arthropod population has been estimated at a billion billion (1018) individuals.
  • Nearly a million arthropod species have been described.
    • Two out of every three known species are arthropods.
    • This phylum is represented in nearly all habitats in the biosphere.
  • On the criteria of species diversity, distribution, and sheer numbers, arthropods must be regarded as the most successful animal phylum.
  • The diversity and success of arthropods are largely due to three features: body segmentation, a hard exoskeleton, and jointed appendages.
    • Early arthropods such as the trilobites had pronounced segmentation, but little variation in their appendages.
  • Groups of segments and their appendages have become specialized for a variety of functions, permitting efficient division of labor among regions.
  • The body of an arthropod is completely covered by the cuticle, an exoskeleton constructed from layers of protein and chitin.
    • The exoskeleton protects the animal and provides points of attachment for the muscles that move appendages.
    • It is thick and inflexible in some regions, such as crab claws, and thin and flexible in others, such as joints.
  • The exoskeleton of arthropods is strong and relatively impermeable to water.
    • In order to grow, an arthropod must molt its old exoskeleton and secrete a larger one, a process called ecdysis that leaves the animal temporarily vulnerable to predators and other dangers.
  • The exoskeleton’s relative impermeability to water helped prevent desiccation and provided support on land.
    • Arthropods moved to land after the colonization of land by plants and fungi.
    • In 2004, an amateur fossil hunter found a 428-million-year-old fossil of a millipede. Fossilized arthropod tracks date from 450 million years ago.
  • Arthropods have well-developed sense organs, including eyes for vision, olfactory receptors for smell, and antennae for touch and smell.
    • Most sense organs are located at the anterior end of the animal, which shows extensive cephalization.
  • Arthropods have an open circulatory system in which hemolymph fluid is propelled by a heart through short arteries into sinuses (the hemocoel) surrounding tissues and organs.
    • Hemolymph returns to the heart through valved pores.
    • The hemocoel is not a coelom; the true coelom is much reduced in most arthropods.
    • Open circulatory systems evolved convergently in arthropods and molluscs.
  • Arthropods have evolved a variety of specialized organs for gas exchange.
    • Most aquatic species have gills with thin, feathery extensions that have an extensive surface area in contact with water.
    • Terrestrial arthropods generally have internal surfaces specialized for gas exchange.
      • For example, insects have tracheal systems, branched air ducts leading into the interior from pores in the cuticle.
  • Molecular systematics is suggesting new hypotheses about arthropod relationships.
    • Evidence shows that arthropods diverged early in their history into four main evolutionary lineages: cheliceriformes (sea spiders, horseshoe crabs, scorpions, ticks, spiders), myriapods (centipedes and millipedes), hexapods (insects and their wingless, six-legged relatives), and crustaceans (crabs, lobsters, shrimps, barnacles, and many others).
  • Cheliceriformes are named for their clawlike feeding appendages, chelicerae, which serve as pincers or fangs.
    • Cheliceriformes have an anterior cephalothorax and a posterior abdomen.
    • They lack sensory antennae, and most have simple eyes (eyes with a single lens).
    • The earliest cheliceriformes were eurypterids, or water scorpions, marine and freshwater predators that grew up to 3 m long.
    • Modern marine cheliceriformes include the sea spiders (pycnogonids) and the horseshoe crabs.
  • The majority of living cheliceriformes are arachnids, a group that includes scorpions, spiders, ticks, and mites.
  • Nearly all ticks are blood-sucking parasites on the body surfaces of reptiles or mammals.
    • Parasitic mites live on or in a wide variety of vertebrates, invertebrates, and plants.
  • The arachnid cephalothorax has six pairs of appendages.
    • There are four pairs of walking legs.
    • A pair of pedipalps function in sensing or feeding.
    • The chelicerae usually function in feeding.
  • Spiders inject poison from glands on the chelicerae to immobilize their prey and while chewing their prey, spill digestive juices into the tissues and suck up the liquid meal.
  • In most spiders, gas exchange is carried out by book lungs.
    • These are stacked plates contained in an internal chamber.
    • The plates present an extensive surface area, enhancing exchange of gases between the hemolymph and air.
  • A unique adaptation of many spiders is the ability to catch flying insects in webs of silk.
    • The silk protein is produced as a liquid by abdominal glands and spun by spinnerets into fibers that solidify.
    • Web designs are characteristic of each species.
    • Silk fibers have other functions as egg covers, drop lines for a rapid escape, and “gift wrapping” for nuptial gifts.
  • Millipedes and centipedes belong to the subphylum Myriapoda, the myriapods.
    • All living myriapods are terrestrial.
    • Millipedes (class Diplopoda) have two pairs of walking legs on each of their many trunk segments, formed by two fused segments.
    • They eat decaying leaves and plant matter.
    • They may have been among the earliest land animals.
  • Centipedes (class Chilopoda) are terrestrial carnivores.
    • The head has a pair of antennae and three pairs of appendages modified as mouth parts, including the jawlike mandibles.
    • Each segment in the trunk region has one pair of walking legs.
    • Centipedes have poison claws on the anteriormost trunk segment that paralyze prey and aid in defense.
  • Insects and their relatives (subphylum Hexapoda) are more species-rich than all other forms of life combined.
  • They live in almost every terrestrial habitat and in fresh water, and flying insects fill the air.
    • They are rare, but not absent, from the sea, where crustaceans dominate.
  • The oldest insect fossils date back to the Devonian period, about 416 million years ago.
    • When insect flight evolved in the Carboniferous and Permian periods, it sparked an explosion in insect varieties.
    • Diversification of mouthparts for feeding on gymnosperms and other Carboniferous plants also contributed to the adaptive radiation of insects.
    • In one widely held hypothesis, the radiation of flowering plants triggered the greatest diversification of insects in the Cretaceous and early Tertiary periods.
      • However, new research suggests that insects diversified first and, as pollinators and herbivores, may have caused the angiosperm radiation.
  • Flight is one key to the great success of insects.
    • Flying animals can escape many predators, find food and mates, and disperse to new habitats faster than organisms that must crawl on the ground.
  • Many insects have one or two pairs of wings that emerge from the dorsal side of the thorax.
    • Wings are extensions of the cuticle and are not true appendages.
  • Several hypotheses have been proposed for the evolution of wings.
    • In one hypothesis, wings first evolved as extensions of the cuticle that helped the insect absorb heat and were later modified for flight.
    • A second hypothesis argues that wings allowed animals to glide from vegetation to the ground.
    • Alternatively, wings may have served as gills in aquatic insects.
    • Still another hypothesis proposes that insect wings functioned for swimming before they functioned for flight.
  • Insect wings are also very diverse.
    • Dragonflies, among the first insects to fly, have two similar pairs of wings.
    • The wings of bees and wasps are hooked together and move as a single pair.
    • Butterfly wings operate similarly because the anterior wings overlap the posterior wings.
    • In beetles, the posterior wings function in flight, while the anterior wings act as covers that protect the flight wings when the beetle is on the ground or burrowing.
  • The internal anatomy of an insect includes several complex organ systems.
    • In the complete digestive system, there are regionally specialized organs with discrete functions.
    • Metabolic wastes are removed from the hemolymph by Malpighian tubules, outpockets of the digestive tract.
    • Respiration is accomplished by a branched, chitin-lined tracheal system that carries O2 from the spiracles directly to the cells.
  • The insect nervous system consists of a pair of ventral nerve cords with several segmental ganglia.
    • The two cords meet in the head, where the ganglia from several anterior segments are fused into a cerebral ganglion (brain).
    • This structure is close to the antennae, eyes, and other sense organs concentrated on the head.
  • Metamorphosis is central to insect development.
    • In incomplete metamorphosis (seen in grasshoppers and some other orders), the young resemble adults but are smaller and have different body proportions.
      • Through a series of molts, the young look more and more like adults until they reach full size.
    • In complete metamorphosis, larval stages specialized for eating and growing change morphology completely during the pupal stage and emerge as adults.
  • Reproduction in insects is usually sexual, with separate male and female individuals.
    • Coloration, sound, or odor bring together opposite sexes at the appropriate time.
    • In most species, sperm cells are deposited directly into the female’s vagina at the time of copulation.
      • In a few species, females pick up a sperm packet deposited by a male.
    • The females store sperm in the spermatheca, in some cases holding enough sperm from a single mating to last a lifetime.
    • After mating, females lay their eggs on a food source appropriate for the next generation.
  • Insects affect the lives of all other terrestrial organisms.
    • Insects are important natural and agricultural pollinators.
    • On the other hand, insects are carriers for many diseases, including malaria and African sleeping sickness.
    • Insects compete with humans for food, consuming crops intended to feed and clothe human populations.
      • Billions of dollars each year are spent by farmers on pesticides to minimize losses to insects.
      • In parts of Africa, insects claim about 75% of the crops.
  • While arachnids and insects thrive on land, most crustaceans remain in marine and freshwater environments.
  • Crustaceans typically have biramous (branched) appendages that are extensively specialized.
    • Lobsters and crayfish have 19 pairs of appendages, adapted to a variety of tasks.
    • In addition to two pairs of antennae, crustaceans have three or more pairs of mouthparts, including hard mandibles.
    • Walking legs are present on the thorax and other appendages for swimming or reproduction are found on the abdomen.
    • Crustaceans can regenerate lost appendages during molting.
  • Small crustaceans exchange gases across thin areas of the cuticle, but larger species have gills.
  • The circulatory system is open, with a heart pumping hemolymph into short arteries and then into sinuses that bathe the organs.
  • Nitrogenous wastes are excreted by diffusion through thin areas of the cuticle, but glands regulate the salt balance of the hemolymph.
  • Most crustaceans have separate sexes.
    • In lobsters and crayfish, males use a specialized pair of appendages to transfer sperm to the female’s reproductive pore.
    • Most aquatic species have several larval stages.
  • The isopods, with about 10,000 species, are one of the largest groups of crustaceans.
    • Most are small marine species, and some are abundant at the bottom of deep oceans.
    • Isopods also include the land-dwelling pill bugs, or wood lice, that live underneath moist logs and leaves.
  • Decapods, including lobsters, crayfish, crabs, and shrimp, are among the largest crustaceans.
    • The cuticle is hardened with calcium carbonate.
    • The exoskeleton over the cephalothorax forms a shield called the carapace.
    • While most decapods are marine, crayfish live in fresh water and some tropical crabs are terrestrial as adults.
  • Many small crustaceans are important members of marine and freshwater plankton communities.
    • Planktonic crustaceans include many species of copepods, which are among the most numerous of all animals.
    • Krill are shrimplike planktonic organisms that reach about 3 cm long.
    • A major food source for baleen whales and other ocean predators, they are now harvested extensively by humans for food and agricultural fertilizer.
  • Barnacles are primarily sessile crustaceans with parts of their cuticle hardened by calcium carbonate.
    • They anchor themselves to rocks, boat hulls, and pilings and strain food from the water by extending their appendages.
    • Their adhesive is as strong as any synthetic glue.

Concept 33.8 Echinoderms and chordates are deuterostomes

  • At first glance, sea stars and other echinoderms would seem to have little in common with the phylum Chordata, which includes the vertebrates.
  • However, these animals share the deuterostome characteristics of radial cleavage, type of development of the coelom from the archenteron, and formation of the anus from the blastopore.
  • Molecular systematics has reinforced the Deuterostomia as a clade of bilaterian animals.

    Phylum Echinodermata: Echinoderms have a water vascular system and secondary radial symmetry.

  • Sea stars and most other echinoderms are sessile or slow-moving marine animals.
  • A thin skin covers an endoskeleton of hard calcareous plates.
    • Most echinoderms are prickly from skeletal bumps and spines that have various functions.
  • Unique to echinoderms is the water vascular system, a network of hydraulic canals branching into extensions called tube feet.
    • These function in locomotion, feeding, and gas exchange.
  • Sexual reproduction in echinoderms usually involves the release of gametes by separate males and females into the seawater.
  • The internal and external parts of the animal radiate from the center, often as five spokes.
    • However, the radial anatomy of adult echinoderms is a secondary adaptation, as echinoderm larvae have bilateral symmetry.
    • The symmetry of adult echinoderms is not perfectly radial.
  • Living echinoderms are divided into six classes: Asteroidea (sea stars), Ophiuroidea (brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea lilies and feather stars), Holothuroidea (sea cucumbers), and Concentricycloidea (sea daisies).
  • Sea stars have multiple arms radiating from a central disk.
    • The undersides of the arms have rows of tube feet.
    • Each can act like a suction disk that is controlled by hydraulic and muscular action.
  • Sea stars use the tube feet to grasp the substrate, to creep slowly over the surface, or to capture prey.
    • When feeding on closed bivalves, the sea star grasps the bivalve tightly and everts its stomach through its mouth and into the narrow opening between the shells of the bivalve.
    • Enzymes from the sea star’s digestive organs then begin to digest the soft body of the bivalve inside its own shell.
  • Sea stars and some other echinoderms can regenerate lost arms and, in a few cases, even regrow an entire body from a single arm.
  • Brittle stars have a distinct central disk and long, flexible arms.
    • Their tube feet lack suckers.
    • They move by a serpentine lashing of their arms.
    • Some species are suspension feeders, and others are scavengers or predators.
  • Sea urchins and sand dollars have no arms, but they do have five rows of tube feet that are used for locomotion.
    • Sea urchins can also move by pivoting their long spines.
    • The mouth of an urchin is ringed by complex jawlike structures adapted for eating seaweed and other foods.
    • Sea urchins are roughly spherical, while sand dollars are flattened and disk-shaped.
  • Sea lilies are attached to the substratum by stalks, and feather stars crawl using their long, flexible arms.
    • Both use their arms for suspension feeding.
    • The arms circle the mouth, which is directed upward, away from the substrate.
    • Crinoids are an ancient class with very conservative evolution.
    • Fossilized sea lilies from 500 million years ago could pass for modern members of the class.
  • Sea cucumbers do not look much like other echinoderms.
    • They lack spines, the endoskeleton is much reduced, and the oral-aboral axis is elongated.
  • However, they do have five rows of tube feet, like other echinoderms, and other shared features.
    • Some tube feet around the mouth function as feeding tentacles for suspension feeding or deposit feeding
  • Sea daisies were discovered in 1986, and only two species are known.
    • Their armless bodies are disk-shaped with five-fold symmetry.
    • They are less than a centimeter in diameter.
  • Sea daisies absorb nutrients through the membrane surrounding their body.
    • Some taxonomists consider sea daisies to be highly derived sea stars.

    Phylum Chordata: The chordates include two invertebrate subphyla and all vertebrates.

  • The phylum to which we belong consists of two subphyla of invertebrate animals plus the hagfishes and vertebrates.
  • Both groups of deuterostomes, the echinoderms and chordates, have existed as distinct phyla for at least half a billion years.

Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 33-1

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Chapter 34 - Vertebrates

Chapter 34 Vertebrates
Lecture Outline

Overview: Half a Billion Years of Backbones

  • Vertebrates are named for vertebrae, the series of bones that make up the vertebral column or backbone.
  • There are about 52,000 species of vertebrates, far fewer than the 1 million insect species on Earth.
    • Plant-eating dinosaurs, at 40,000 kg, were the heaviest animals to walk on land.
    • The biggest animal that ever existed is the blue whale, at 100,000 kg.
    • Humans and our closest relatives are vertebrates.
  • This group includes other mammals, birds, lizards, snakes, turtles, amphibians, and the various classes of fishes.

Concept 34.1 Chordates have a notochord and a dorsal, hollow nerve cord

  • The vertebrates belong to one of the two major phyla in the Deuterostomia, the chordates.
    • Chordates are bilaterian animals, belonging to the Deuterostomia.
  • The phylum Chordata includes three subphyla, the vertebrates and two phyla of invertebrates—the urochordates and the cephalochordates.

    Four derived characters define the phylum Chordata.

  • Although chordates vary widely in appearance, all share the presence of four anatomical structures at some point in their lifetime.
  • These chordate characteristics are a notochord; a dorsal, hollow nerve cord; pharyngeal slits; and a muscular, post-anal tail.
    1. The notochord, present in all chordate embryos, is a longitudinal, flexible rod located between the digestive tube and the nerve cord.
      • It is composed of large, fluid-filled cells encased in fairly stiff, fibrous tissue.
      • It provides skeletal support throughout most of the length of the animal.
      • While the notochord persists in the adult stage of some invertebrate chordates and primitive vertebrates, it remains only as a remnant in vertebrates with a more complex, jointed skeleton.
      • For example, it is the gelatinous material of the disks between vertebrae in humans.
    2. The dorsal, hollow nerve cord of a chordate embryo develops from a plate of ectoderm that rolls into a tube dorsal to the notochord.
      • Other animal phyla have solid nerve cords, usually located ventrally.
      • The nerve cord of the chordate embryo develops into the central nervous system: the brain and spinal cord.
    3. The digestive tube of chordates extends from the mouth to the anus.
      • The region posterior to the mouth is the pharynx.
      • In all chordate embryos, a series of pouches separated by grooves forms along the sides of the pharynx.
      • In most chordates, these grooves (known as pharyngeal clefts) develop into pharyngeal gill slits that allow water that enters the mouth to exit without continuing through the entire digestive tract.
      • In many invertebrate chordates, the pharyngeal gill slits function as suspension-feeding devices.
      • The slits and the structures that support them have become modified for gas exchange (in aquatic vertebrates), jaw support, hearing, and other functions during vertebrate evolution.
    4. Most chordates have a muscular tail extending posterior to the anus.
      • In contrast, nonchordates have a digestive tract that extends nearly the whole length of the body.
      • The chordate tail contains skeletal elements and muscles.
      • It provides much of the propulsive force in many aquatic species.

    Invertebrate chordates provide clues to the origin of vertebrates.

  • Members of the subphylum Urochordata, commonly called tunicates, belong to the deepest-branching lineage of chordates.
    • They most resemble chordates during their larval stage, which may be brief.
  • The tunicate larva uses its tail muscles and notochord to swim through the water in search of a suitable substrate on which it can settle, guided by cues from light- and gravity-sensitive cells.
  • Tunicates undergo a radical metamorphosis to form a sessile adult with few chordate characteristics.
    • Its tail and notochord are resorbed, its nervous system degenerates, and its organs rotate 90 degrees.
  • Tunicates are suspension feeders.
    • Seawater passes inside the animal via an incurrent siphon, through the pharyngeal gill slits, and into a ciliated chamber, the atrium.
    • Food filtered from the water is trapped by a mucous net that is passed by cilia into the intestine.
    • Filtered water and feces exit through an anus that empties into an excurrent siphon.
  • Lancelets (members of the subphylum Cephalochordata) are blade-like in shape.
    • The notochord; dorsal, hollow nerve cord; numerous gill slits; and post-anal tail all persist in the adult stage.
    • Lancelets are up to 5 cm long.
    • They live with their posterior end buried in the sand and the anterior end exposed for feeding.
  • Adult lancelets retain key chordate characteristics.
  • Lancelets are suspension feeders, feeding by trapping tiny particles on mucous nets secreted across the pharyngeal slits.
    • Ciliary pumping creates a flow of water with suspended food particles into the mouth and out the gill slits.
    • In lancelets, the pharynx and gill slits are feeding structures and play only a minor role in respiration, which primarily occurs across the external body surface.
  • A lancelet frequently leaves its burrow to swim to a new location.
  • Though feeble swimmers, their swimming mechanism resembles that of fishes through the coordinated contraction of serial muscle blocks.
    • Contraction of chevron-shaped muscles flexes the notochord and produces lateral undulations that thrust the body forward.
    • The muscle segments develop from blocks of mesoderm, called somites, arranged serially along each side of the notochord of the embryo.
  • Tunicates and lancelets may provide clues about the evolutionary origin of the vertebrate body plan.
  • Tunicates display a number of chordate characteristics only as larvae, while lancelets retain those characters as adults.
    • Thus, an adult lancelet looks more like a larval tunicate than like an adult tunicate.
  • In the 1920s, biologist William Garstang suggested that tunicates represent an early stage in chordate evolution.
    • This stage may have occurred through paedogenesis, the precocious development of sexual maturity in a larva.
    • Garstang proposed that ancestral chordates became sexually mature while still in the larval stage.
  • The paedogenetic hypothesis is deduced from comparing modern forms, but the weight of evidence is against it.
  • The degenerate adult stage of tunicates appears to be a derived trait that evolved only after the tunicate lineage branched off from other chordates.
    • Even the tunicate larva appears to be highly derived.
    • Studies of Hox gene expression suggest that the tunicate larva does not develop the posterior part of its body axis.
      • Rather, the anterior region is elongated and contains a heart and digestive system.
  • Research on lancelets has revealed important clues about the evolution of the chordate brain.
    • Rather than a full-fledged brain, lancelets have only a slightly swollen tip on the anterior end of the dorsal nerve cord.
    • The same genes that organize major regions of the forebrain, midbrain, and hindbrain of vertebrates express themselves in a corresponding pattern in this small cluster of cells in the lancelet’s nerve cord.
    • The vertebrate brain apparently is an elaboration of an ancestral structure similar to the lancelet’s simple nerve cord tip.

Concept 34.2 Craniates are chordates that have a head

  • After the evolution of the basic chordate body plan, the next major transition was the appearance of a head.
  • Chordates with a head are known as craniates.
  • The origin of a head—with a brain at the anterior end of the dorsal nerve cord, eyes and other sensory organs, and a skull—opened up a new way of feeding for chordates: active predation.

    Living craniates have a set of derived characters.

  • Living craniates share a set of derived characters that distinguishes them from other chordates.
  • On the genetic level, they possess two clusters of Hox genes, while lancelets and chordates have only one.
    • Other important families of genes that produce signaling molecules and transcription factors are also duplicated in craniates.
    • This additional genetic complexity made a more complex morphology possible.
  • In craniates, a group of embryonic cells called the neural crest forms near the dorsal margins of the closing neural tube.
    • Neural crest cells disperse through the body and contribute to the formation of various structures, such as teeth, some of the bones and cartilages of the skull, the dermis of the face, several types of neurons, and the sensory capsules of the eyes and other sense organs.
    • The vertebrate cranium and brain (the enlarged anterior end of the dorsal, hollow nerve cord) and the anterior sensory organs are evidence of a high degree of cephalization, the concentration of sensory and neural equipment in the head.
  • In craniates, the pharyngeal clefts evolved into gill slits.
    • Unlike the pharyngeal slits of lancelets, which are used primarily for suspension feeding, gill slits are associated with muscles and nerves that allow water to be pumped through the slits.
    • This pumping sucks in food and facilitates gas exchange.

    Cambrian fossils provide clues to craniate origins.

  • Several recent fossil finds in China of early chordates have provided information about the origin of craniates.
    • They appear to be “missing links” that straddle the transition to craniates.
    • The most primitive of these fossils is a 3-cm-long animal called Haikouella.
      • This animal resembles a lancelet and was probably a suspension feeder.
      • Haikouella also had a small but well-formed brain, eyes, and muscular segments.
      • It also had hardened structures (“denticles”) in the pharynx that may have functioned somewhat like teeth.
      • However, Haikouella did not have a skull.
    • In other Cambrian rocks, paleontologists have found fossils of more advanced chordates, such as Haikouichthys.
      • Haikouichthys had a skull composed of cartilage and is the oldest known true craniate.
    • These fossils push craniate origins back to the Cambrian explosion.

    Class Myxini: Hagfishes are the least derived craniate lineage.

  • Hagfishes have a skull of cartilage but lack jaws and vertebrae.
    • They swim in a snakelike fashion by using their segmental muscles to exert force against their notochord, which they retain in adulthood as a strong, flexible rod of cartilage.
  • Hagfishes have a small brain, eyes, ears, and a nasal opening that connects with the pharynx.
    • They have toothlike formations made of keratin.
  • All of the 30 or so species of hagfishes are marine scavengers, feeding on worms and sick or dead fish.
    • Rows of slime glands along a hagfish’s body produce small amounts of slime perhaps to repulse other scavengers or larger amounts to deter a potential predator.
  • Vertebrate systematists do not consider hagfishes to be fish.
    • The taxonomic term fish refers only to a specific clade of vertebrates, the actinopterygians.

Concept 34.3 Vertebrates are craniates that have a backbone

  • During the Cambrian period, a lineage of craniates evolved into vertebrates.
  • With a more complex nervous system and a more elaborate skeleton, vertebrates became active predators.
  • After vertebrates branched off from other craniates, they underwent another genetic duplication, this one involving a group of transcription factor genes called the Dlx family.
  • This additional genetic complexity was associated with innovations in vertebrate nervous systems and skeletons, including a more extensive skull and a backbone composed of vertebrae.
  • In the majority of vertebrates, the vertebrae enclose the spinal cord and have taken over the biomechanical roles of the notochord.
  • Aquatic vertebrates also have a number of adaptations associated with faster swimming, including fins stiffened by fin rays and a more efficient gas exchange system in the gills.

    Class Cephalaspidomorphi: Lampreys are the oldest living lineage of vertebrates.

  • Like hagfishes, lampreys offer clues to early chordate evolution but also have acquired unique characters.
  • There are about 35 species of lampreys inhabiting both marine and freshwater environments.
    • Most lampreys are parasites that feed by clamping a round, jawless mouth onto a fish.
    • They use their rasping tongues to penetrate the skin of their fish prey and to ingest the prey’s blood.
  • Lampreys live as suspension-feeding larvae in streams for years before migrating to the sea or lakes as adults.
    • These larvae resemble lancelets and live partially buried in sediment.
  • Some species of lampreys feed only as larvae.
    • After metamorphosis, these lampreys attain sexual maturity, reproduce, and die within a few days.
  • The skeletons of lampreys are made of cartilage.
    • Unlike most vertebrate cartilage, lamprey cartilage contains no collagen. Instead, it is a stiff protein matrix.
  • The notochord persists as the main axial skeleton in adult lampreys.
    • Lampreys also have a cartilaginous pipe surrounding the rodlike notochord.
    • Pairs of cartilaginous projections extend dorsally, partially enclosing the nerve cord with what might be a vestige of an early-stage vertebral column.

    Many vertebrate lineages emerged early.

  • Conodonts were slender, soft-bodied vertebrates with prominent eyes.
    • At the anterior end of their mouth, they had a set of barbed hooks made of mineralized dental tissue.
  • Conodonts ranged in length from 3 to 30 cm.
    • They probably hunted with their large eyes and impaled their prey on hooks.
    • The food then passed to the pharynx, where a different set of dental elements crushed and sliced it.
  • Conodonts were very abundant for more than 300 million years.
  • Other vertebrates emerged during the Ordovician and Silurian periods.
    • These vertebrates had paired fins and an inner ear with two semicircular canals that provided a sense of balance.
  • Although they lacked jaws, they had a muscular pharynx that may have sucked in detritus or bottom-dwelling organisms.
  • They were armored with mineralized bone that offered protection from predators.
  • The vertebrate skeleton evolved initially as a structure of unmineralized cartilage.
    • Its mineralization began only after lampreys diverged from other vertebrates.
  • What initiated the process of mineralization in vertebrates?
    • Mineralization may have been associated with the transition to new feeding mechanisms.
  • The earliest known mineralized structures in vertebrates were conodont dental elements.
  • The armor seen in later jawless vertebrates was derived from dental mineralization.
    • Only in more derived vertebrates did the endoskeleton begin to mineralize, starting with the skull.

Concept 34.4 Gnathostomes are vertebrates that have jaws

  • The gnathostomes have true jaws, hinged structures that enable vertebrates to grasp food firmly.
    • According to one hypothesis, gnathostome jaws evolved by modification of the skeletal rods that had previously supported the anterior pharyngeal gill slits.
    • The remaining gill slits were no longer required for suspension feeding and remained as the major sites of respiratory gas exchange.

    Gnathostomes have a number of shared, derived characters.

  • Gnathostomes share other derived characters besides jaws.
  • The common ancestors of all gnathostomes underwent an additional duplication of the Hox genes, so that the single cluster present in early chordates became four.
    • Other gene clusters also duplicated, allowing further complexity in the development of gnathostome embryos.
  • The gnathostome forebrain is enlarged, in association with enhanced senses of vision and smell.
  • The lateral line system evolved as a row of microscopic organs sensitive to vibrations in the surrounding water.
  • The common ancestor of living gnathostomes had a mineralized axial skeleton, shoulder girdle, and two sets of paired appendages.
  • Gnathostomes appeared in the fossil record in the mid-Ordovician period, about 470 million years ago, and steadily diversified.
  • Gnathostome jaws and paired fins were major evolutionary breakthroughs.
    • Jaws, with the help of teeth, enable the animal to grip food items firmly and slice them up.
    • Paired fins, along with the tail, enable fishes to maneuver accurately while swimming.
  • With these adaptations, many fish species were active predators, allowing for the diversification of both lifestyles and nutrient sources.
  • The earliest gnathostomes in the fossil record are an extinct lineage of armored vertebrates called placoderms.
    • Most placoderms were less than a meter long, although some giants were more than 10 m long.
  • Another group of jawed vertebrates called acanthodians radiated in the Devonian.
  • Acanthodians were closely related to the ancestors of osteichthyans (ray-finned and lobe-finned fishes).
  • Both placoderms and acanthodians disappeared by the beginning of the Carboniferous period, 360 million years ago.

    Class Chondrichthyes: Sharks and rays have cartilaginous skeletons.

  • The class Chondrichthyes, sharks and their relatives, includes some of the biggest and most successful vertebrate predators in the oceans.
  • Chondrichthyes have relatively flexible endoskeletons of cartilage rather than bone.
    • In most species, parts of the skeleton are impregnated by calcium.
  • Conodonts and armored, jawless fishes show that mineralization of the vertebrate skeleton had begun before the chondrichthyan lineage branched off from other vertebrates.
    • Traces of bone can be found in living chondrichthyes, in their scales, at the base of their teeth and (in some sharks) in a thin layer on the surface of their vertebrae.
    • The loss of bone in chondrichthyes is a derived condition, which emerged after they diverged from other gnathostomes.
  • There are about 750 extant species, almost all in the subclass of sharks and rays, with a few dozen species in a second subclass of chimaeras or ratfishes.
    • All have well-developed jaws and paired fins.
  • The streamlined bodies of most sharks enable them to be swift, but not maneuverable, swimmers.
    • Powerful axial muscles power undulations of the body and caudal fin to drive the fish forward.
    • The dorsal fins provide stabilization.
    • While some buoyancy is provided by low-density oils in the large liver, the flow of water over the pectoral and pelvic fins also provides lift to keep the animal suspended in the water column.
  • Continual swimming also ensures that water flows into the mouth and out through the gills.
    • Some sharks and many skates and rays spend much time resting on the seafloor, using the muscles of their jaws and pharynx to pump water over the gills.
  • Most sharks are carnivores that swallow their prey whole or use their powerful jaws and sharp teeth to tear flesh from animals too large to swallow.
    • In contrast, the largest sharks and rays are suspension feeders that consume plankton.
    • Sharks have several rows of teeth that gradually move to the front of the mouth as old teeth are lost.
    • Within the intestine of a shark is a spiral valve, a corkscrew-shaped ridge that increases surface area and prolongs the passage of food along the short digestive tract.
  • Acute senses are adaptations that go along with the active, carnivorous lifestyle of sharks.
    • Sharks have sharp vision but cannot distinguish colors.
    • Their acute olfactory sense (smelling) occurs in a pair of nostrils that do not function in breathing.
    • Sharks can detect electrical fields, including those generated by the muscle contractions of nearby prey, through patches of specialized skin pores.
    • The lateral line system, a row of microscopic organs sensitive to pressure changes, can detect low-frequency vibrations.
    • In sharks, the whole body transmits sound to the hearing organs of the inner ear.
  • Shark eggs are fertilized internally.
    • Males transfer sperm via claspers on their pelvic fins to the reproductive tract of the female.
    • Oviparous sharks encase their eggs in protective cases and lay them outside the mother’s body.
      • These hatch months later as juveniles.
    • Ovoviviparous sharks retain fertilized eggs in the oviduct.
      • The embryo completes development in the uterus, nourished by the egg yolk.
    • A few sharks are viviparous, providing nutrients through a placenta to the developing offspring.
  • Rays are closely related to sharks, but they have adopted a very different lifestyle.
    • Most rays are flattened bottom dwellers that crush molluscs and crustaceans in their jaws.
    • The enlarged pectoral fins of rays are used like wings to propel the animal through the water.
    • The tail of many rays is whiplike and may bear venomous barbs for defense against threats.
  • Chondrichthyans have changed little in more than 300 million years.
    • They are severely threatened by overfishing.
    • In 2003, researchers reported that shark stocks in the northwest Atlantic declined 75% in 15 years.

    Osteichthyes: The extant classes of bony fishes are the ray-finned fishes, the lobe-finned fishes, and the lungfishes.

  • The vast majority of bony fishes belong to a clade of gnathostomes called the Osteichthyes (meaning “bony fish”).
  • Systematists today include tetrapods with bony fish in Osteichthyes, which otherwise would be paraphyletic.
  • Nearly all bony fishes have an ossified endoskeleton with a hard matrix of calcium phosphate.
    • It is not clear when the shift to a bony skeleton took place during gnathostome evolution.
  • Bony fishes breathe by drawing water over four or five pairs of gills located in chambers covered by a protective flap, the operculum.
    • Water is drawn into the mouth, through the pharynx, and out between the gills by movements of the operculum and muscles surrounding the gill chambers.
  • Most fishes have an internal, air-filled sac, the swim bladder.
    • The positive buoyancy provided by air counters the negative buoyancy of the tissues, enabling many fishes to be neutrally buoyant and remain suspended in the water.
    • The swim bladder evolved from balloonlike lungs that may have been used to breathe air when dissolved oxygen levels were low in stagnant shallow waters.
  • The skin of bony fishes is often covered with thin, flattened bony scales that differ in structure from the toothlike scales of sharks.
  • Glands in the skin secrete mucus that reduces drag in swimming.
  • Like sharks, aquatic osteichthyes have a lateral line system, which is evident as a row of tiny pits in the skin on either side of the body.
  • The reproduction of aquatic osteichthyes varies.
    • Most species are oviparous, reproducing by external fertilization after the female sheds large numbers of small eggs.
    • Internal fertilization and birthing characterize other species.
  • The most familiar families of fishes belong to the ray-finned fishes, members of class Actinopterygii.
    • This class includes bass, trout, perch, tuna, and herring.
    • In this group, the fins are supported by long, flexible rays.
    • The fins may be modified for maneuvering, defense, and other functions.
  • Bony fishes, including the ray-finned fishes, probably evolved in fresh water and then spread to the seas during their long history.
    • Many species of ray-finned fishes returned to fresh water at some point in their evolution.
    • Some ray-finned fishes, such as salmon, make a round-trip from fresh water to seawater and back to fresh water during their life cycle.
  • Ray-finned fishes evolved during the Devonian period, along with the lobe-finned fishes (Sarcopterygii).
  • The key derived character in lobe-fins is the presence of muscular pectoral and pelvic fins supported by extensions of the bony skeleton.
    • Many Devonian lobe-fins were large, bottom dwellers that may have used their paired, muscular fins to “walk” along the bottom.
    • By the end of the Devonian period, lobe-fin diversity was dwindling.
  • Today, only three lineages survive.
    • One lineage, the coelacanths (class Actinistia) probably originated as freshwater animals with lungs, but others shifted to the ocean, including the only living genus, Latimeria.
    • The second lineage of living lobe-fins is represented by three genera of lungfishes (class Dipnoi), which live today in the Southern Hemisphere.
      • They generally inhabit stagnant ponds and swamps.
      • They can gulp air into lungs connected to the pharynx of the digestive tract to provide oxygen for metabolism.
      • Lungfishes also have gills, which are the main organs for gas exchange in Australian lungfishes.
      • When ponds shrink during the dry season, some lungfishes can burrow into the mud and estivate.
    • The third lineage of lobe-fins that survives today is far more diverse than coelacanths or lungfishes.
  • During the mid-Devonian, the tetrapods adapted to life on land and gave rise to terrestrial vertebrates, including humans.

Concept 34.5 Tetrapods are gnathostomes that have limbs and feet

  • One of the most significant events in vertebrate history took place 360 million years ago, when the fins of some lobe-fins evolved into tetrapod limbs and feet.
  • The most significant character of tetrapods is the four limbs, which allow them to support their weight on land.
    • The feet of tetrapods have digits that allow them to transmit muscle-generated forces to the ground when they walk.
  • With the move to land, the bones of the pelvic girdle (to which the hind legs are attached) became fused to the backbone, permitting forces generated by the hind legs against the ground to be transferred to the rest of the body.
  • Living tetrapods do not have pharyngeal gill slits.
    • The ears are adapted to the detection of airborne sounds.
  • The Devonian coastal wetlands were home to a wide range of lobe-fins. Those that entered shallow, oxygen-poor water could use their lungs to breathe air.
  • Some species likely used their stout fins to move across the muddy bottom.
    • At the water’s edge, leglike appendages were probably better equipment than fins for paddling and crawling through the dense vegetation in shallow water.
    • The tetrapod body plan was thus a modification of a preexisting body plan.
  • In one lineage of lobe-fins, the fins became progressively more limb-like, while the rest of the body retained adaptations for aquatic life.
    • For example, fossils of Acanthostega from 365 million years ago had bony gill supports and rays in its tail to support propulsion in water, but it also had fully formed legs, ankles, and digits.
    • Acanthostega is representative of a period of vertebrate evolution when adaptations for shallow water allowed certain fishes to make a gradual transition to the terrestrial side of the water’s edge.
  • A great diversity of tetrapods emerged during the Carboniferous period.
    • Judging from the morphology and location of the fossils, most of these early tetrapods remained tied to water.

    Class Amphibia: Salamanders, frogs, and caecilians are the three extant amphibian orders.

  • Today the amphibians (class Amphibia) are represented by about 4,800 species of salamanders (order Urodela, “tailed ones”), frogs (order Anura, “tail-less ones”), and caecilians (order Apoda, “legless ones”).
  • Some of the 500 species of urodeles are entirely aquatic, but others live on land as adults or throughout life.
    • On land, most salamanders walk with a side-to-side bending of the body that may resemble the swagger of the early terrestrial tetrapods.
  • The 4,200 species of anurans are more specialized than urodeles for moving on land.
    • Adult frogs use powerful legs to hop along the terrain.
    • Frogs nab insects by flicking out their sticky tongues, which are attached to the front of the mouth.
  • Anurans may be camouflaged or secrete a distasteful, even poisonous, mucus from skin glands.
    • Many poisonous species are brightly colored, perhaps to warn predators who associate the coloration with danger.
  • Apodans, the caecilians (about 150 species), are legless and nearly blind.
    • The reduction of legs evolved secondarily from a legged ancestor.
  • Superficially resembling earthworms, most species burrow in moist forest soil in the tropics.
    • A few South American species live in freshwater ponds and streams.
  • Amphibian means “two lives,” a reference to the metamorphosis of many frogs from an aquatic stage, the tadpole, to the terrestrial adult.
    • Tadpoles are usually aquatic herbivores with gills and a lateral line system, and they swim by undulating their tails.
    • During metamorphosis, the tadpole develops legs, the lateral line disappears, and lungs replace gills.
    • Adult frogs are carnivorous hunters.
  • Many amphibians do not live a dualistic—aquatic and terrestrial—life.
    • There are some strictly aquatic, and some strictly terrestrial frogs, salamanders, and caecilians.
    • The larvae of salamanders and caecilians look like adults and are also carnivorous.
  • Paedomorphosis, the retention of some larval features in a sexually mature adult, is common among some groups of salamanders.
    • For example, the mudpuppy (Necturus) retains gills and other larval features when sexually mature.
  • Most amphibians retain close ties with water and are most abundant in damp habitats.
    • Those adapted to drier habitats spend much of their time in burrows or under moist leaves where the humidity is higher.
    • Most amphibians rely heavily on their moist skin to carry out gas exchange with the environment.
      • Some terrestrial species lack lungs entirely and breathe exclusively through their skin and oral cavity.
  • Amphibian eggs lack a shell and dehydrate quickly in dry air.
    • Most species have external fertilization, with eggs shed in ponds or swamps or at least in moist environments.
    • Some species lay vast numbers of eggs in temporary pools where mortality is high.
    • Others display various types of parental care and lay relatively few eggs.
      • In some species, males or females may house eggs on the back, in the mouth, or even in the stomach.
      • Some species are ovoviviparous or viviparous, retaining the developing eggs in the female reproductive tract until released as juveniles.
  • Many amphibians display complex and diverse social behavior, especially during the breeding season.
    • Then many male frogs fill the air with their mating calls as they defend breeding territories or attract females.
    • In some terrestrial species, migrations to specific breeding sites may involve vocal communication, celestial navigation, or chemical signaling.
  • For the past 25 years, zoologists have been documenting a rapid and alarming decline in amphibian populations throughout the world.
  • Several causes that have been proposed include habitat degradation, the spread of a pathogen (a chytrid fungus), and acid precipitation.
    • Acid precipitation is damaging to amphibians because of their dependence on wet places for completion of their life cycles.

Concept 34.6 Amniotes are tetrapods that have a terrestrially adapted egg

  • The amniote clade consists of the mammals and reptiles (including birds).
  • The evolution of amniotes from an amphibian ancestor involved many adaptations for terrestrial living.
  • The amniotic egg is the major derived character of the clade.
  • Inside the shell of the amniotic egg are several extraembryonic membranes that function in gas exchange, waste storage, and the transfer of stored nutrients to the embryo.
    • The amniotic egg is named for one of these membranes, the amnion, which encloses a fluid-filled “private pond” that bathes the embryo and acts as a hydraulic shock absorber.
  • The amniotic eggs enabled terrestrial vertebrates to complete their life cycles entirely on land.
    • In contrast to the shell-less eggs of amphibians, the amniotic eggs of most amniotes have a shell that retains water and can be laid in a dry place.
    • The calcareous shells of bird eggs are inflexible, while the leathery eggs of many reptiles are flexible.
    • Most mammals have dispensed with the shell.
      • The embryo implants in the wall of the uterus and obtains its nutrition from the mother.
  • Amniotes acquired other adaptations to terrestrial life, including less-permeable skin and the increasing use of the rib cage to ventilate the lungs.
  • Amniotes adopt a more elevated stance than earlier tetrapods and living amphibians.
  • The most recent common ancestor of living amphibians and amniotes lived about 340 million years ago, in the early Carboniferous period.
    • No fossils of amniotic eggs have been found from that time.
  • Early amniotes lived in drier environments than did earlier tetrapods.
  • Some were herbivores, with grinding teeth. Others were large and predatory.

    The reptile clade includes birds.

  • The reptile clade includes tuatara, lizards, snakes, turtles, crocodilians, and birds, as well as extinct groups such as dinosaurs.
  • Reptiles have several adaptations for terrestrial life not generally found in amphibians.
    • Scales containing the protein keratin waterproof the skin, preventing dehydration in dry air.
      • Crocodiles, which are adapted to water, have evolved more permeable scales called scutes.
    • Reptiles obtain all their oxygen with lungs, not through their dry skin.
      • As an exception, many turtles can use the moist surfaces of their cloaca for gas exchange.
  • Most reptiles lay shelled amniotic eggs on land.
    • Fertilization occurs internally, before the shell is secreted as the egg passes through the female’s reproductive tract.
    • Some species of lizards and snakes are viviparous, with their extraembryonic membranes forming a placenta that enables the embryo to obtain nutrients from its mother.
  • Nonbird reptiles are sometimes labeled “cold-blooded” because they do not use their metabolism extensively to control body temperature.
    • However, many nonbird reptiles regulate their body temperature behaviorally by basking in the sun when cool and seeking shade when hot.
  • Because they absorb external heat rather than generating much of their own, nonbird reptiles are more appropriately called ectotherms.
    • One advantage of this strategy is that an ectothermic reptile can survive on less than 10% of the calories required by a mammal of equivalent size.
  • The reptile clade is not entirely ectothermic.
    • Birds are endothermic, capable of keeping the body warm through metabolism.
  • The oldest reptilian fossils date back to the Carboniferous period, about 300 million years ago.
  • The first major group of reptiles to emerge was the parareptiles, large, stocky, quadrupedal herbivores.
    • Some parareptiles had dermal plates on their skin, which may have provided defense against predators.
  • Parareptiles died out 200 million years ago, at the end of the Triassic period.
  • As parareptiles were dwindling, an equally ancient clade of reptiles, the diapsids, was diversifying.
    • The most obvious derived character of diapsids is a pair of holes on each side of the skull, behind the eye socket.
  • The diapsids are composed of two main lineages.
    • One, the lepidosaurs, includes lizards, snakes, and tuataras.
      • This lineage also produced a number of marine reptiles including plesiosaurs and ichthyosaurs.
    • The archosaurs include crocodilians, and the extinct pterosaurs and dinosaurs.
  • Pterosaurs, which originated in the late Triassic, were the first flying tetrapods.
    • The pterosaur wing is formed from a bristle-covered membrane of skin that stretched between the hind leg and the tip of an elongated finger.
    • Well-preserved fossils show the presence of muscles, blood vessels, and nerves in the wing membrane, suggesting that pterosaurs could dynamically adjust their membranes to assist their flight.
  • Dinosaurs were an extremely diverse group varying in body shape, size, and habitat.
    • There were two main dinosaur lineages: the ornithischians, which were mostly herbivorous, and the saurischians, which included both long-necked giant herbivores and bipedal carnivorous theropods.
      • Theropods included the famous Tyrannosaurus rex as well as the ancestors of birds.
  • There is increasing evidence that many dinosaurs were agile; fast moving; and, in some species, social.
    • Paleontologists have discovered signs of parental care among dinosaurs.
  • There is continuing debate about whether dinosaurs were endothermic, capable of keeping their body warm through metabolism.
    • Some experts are skeptical.
    • In the warm, consistent Mesozoic climate, behavioral adaptations may have been sufficient for maintaining a suitable body temperature for terrestrial dinosaurs.
    • Also, the low surface-to-volume ratios would have reduced the effects of daily fluctuations in air temperature on the animal’s internal temperature.
    • Some anatomical evidence supports the hypothesis that at least some dinosaurs were endotherms.
      • Paleontologists have found fossils of dinosaurs in both Antarctica and the Arctic, although the climate in those areas was milder during the Mesozoic than today.
    • The dinosaur that gave rise to birds was certainly endothermic, as are all birds.
  • By the end of the Cretaceous, all dinosaurs (except birds) became extinct.
    • It is uncertain whether dinosaurs were declining before they were finished off by an asteroid or comet impact.
  • Lepidosaurs are represented by two living lineages.
  • One lineage includes the tuatara, two species of lizard-like reptiles found only on 30 islands off the coast of New Zealand.
    • Tuatara relatives lived at least 220 million years ago, when they thrived on every continent well into the Cretaceous period.
  • The other major living lineage of lepidosaurs are the squamates (lizards and snakes).
  • Lizards are the most numerous and diverse reptiles alive today.
    • Most are relatively small, but they range in length from 16 mm to 3 m.
  • Snakes are legless lepidosaurs that evolved from lizards closely related to the Komodo dragon.
  • It was once thought that snakes were descendents of lizards that adapted to a burrowing lifestyle through the loss of limbs.
    • However, recently discovered fossils of aquatic snakes with complete hind legs suggest that snakes likely evolved in water and then recolonized land.
    • Some species of snakes retain vestigial pelvic and limb bones, providing evidence of their ancestry.
  • Snakes are carnivorous, and a number of adaptations aid them in hunting and eating prey.
    • Snakes have acute chemical sensors and are sensitive to ground vibrations.
      • The flicking tongue fans odors toward olfactory organs on the roof of the mouth.
    • Heat-detecting organs of pit vipers, including rattlesnakes, enable these night hunters to locate warm animals.
    • Some poisonous snakes inject their venom through a pair of sharp, hollow or grooved teeth.
    • Loosely articulated jaws enable most snakes to swallow prey larger than the diameter of the snake itself.
  • Turtles are the most distinctive group of reptiles alive today.
  • All turtles have a boxlike shell made up of upper and lower shields that are fused to the vertebrae, clavicles, and ribs.
  • The earliest fossils of turtles are 220 million years old, with fully developed shells.
    • The origin of the turtle shell remains a puzzle.
      • Some paleontologists suggest that turtle shells evolved from the dermal shells of parareptiles.
    • Other studies link turtles to archosaurs or lepidosaurs.
    • There are two separate branches of turtles that have independently evolved mechanisms to retract their heads.
    • Turtles live in a variety of environments, from deserts to ponds to the sea.
  • Crocodiles and alligators (crocodilians) are among the largest living reptiles.
    • They spend most of their time in water, breathing air through upturned nostrils.
    • Crocodilians are confined to the tropics and subtropics.

    Birds evolved as feathered dinosaurs.

  • Like crocodilians, birds are archosaurs, but highly specialized for flight.
    • In addition to amniotic eggs and scales, modern birds have feathers and other distinctive flight equipment.
  • Almost every part of a typical bird’s anatomy is modified in some way to reduce weight and enhance flight.
    • One adaptation to reduce weight is the absence of some organs.
      • For instance, females have only one ovary.
    • Modern birds are toothless and grind their food in a muscular gizzard near the stomach.
  • The skeletons of birds have several adaptations that make them light and flexible, but strong.
    • The bones are air-filled and honeycombed to reduce weight without sacrificing much strength.
  • A bird’s feathers have a hollow, air-filled shaft that is light and strong.
    • Feathers are made of beta-keratin, a protein similar to the keratin of reptile scales.
  • The shape and arrangement of feathers forms wings into airfoils.
  • Power for flapping the wings comes from contractions of the pectoral muscles, anchored to a keel on the sternum.
  • The evolution of flight required radical alteration in body form but provides many benefits.
    • Flight enhances hunting and scavenging.
      • It enables many birds to exploit flying insects, an abundant, highly nutritious food resource.
    • Flight provides a ready escape from earthbound predators.
    • It enables many birds to migrate great distances to exploit different food resources and seasonal breeding areas.
  • Flying requires a great expenditure of energy with an active metabolism.
    • Birds are endothermic, using their own metabolic heat to maintain a constant body temperature.
      • Feathers and, in some species, a layer of fat provide insulation.
    • Efficient respiratory and circulatory systems with a four-chambered heart keep tissues well supplied with oxygen and nutrients.
      • The lungs have tiny tubes leading to and from elastic air sacs that help dissipate heat and reduce body density.
    • Birds have excellent vision and coordination, supported by well-developed areas of the brain.
      • The large brains of birds (proportionately larger than those of reptiles or amphibians) support very complex behavior.
    • During the breeding season, birds engage in elaborate courtship rituals.
      • This culminates in copulation, contact between the mates’ vents, the openings to their cloacae.
      • After eggs are laid, the avian embryo is kept warm through brooding by the mother, father, or both, depending on the species.
  • Cladistic analyses of fossilized skeletons support the hypothesis that the closest reptilian ancestors of birds were theropods.
  • In the late 1990s, Chinese paleontologists unearthed a treasure trove of feathered theropods that are shedding light on bird origins.
    • These fossils suggest that feathers evolved long before feathered flight, possibly for insulation or courtship.
  • Theropods may have evolved powered flight by one of two possible routes.
    1. Small ground-running dinosaurs chasing prey or evading predation may have used feathers to gain extra lift as they jumped into the air.
    2. Dinosaurs could have glided from trees, aided by feathers.
  • The most famous Mesozoic bird is Archaeopteryx, known from fossils from a German limestone quarry.
    • This ancient bird lived about 150 million years ago, during the late Jurassic period.
    • Archaeopteryx had clawed forelimbs, teeth, and a long tail containing vertebrae.
      • Without its feathers, Archaeopteryx would probably be classified as a theropod dinosaur.
      • Its skeletal anatomy indicates that it was a weak flyer, perhaps a tree-dwelling glider.
  • Neornithes, the clade that includes 28 orders of living birds, arose after the Cretaceous-Tertiary boundary, 65 million years ago.
  • Most birds can fly, but Neornithes includes a few flightless birds, the ratites, which lack both a breastbone and large pectoral muscles.
    • The ratites include the ostrich, kiwi, and emu.
  • The penguins make up the flightless order Sphenisciformes.
    • They have powerful pectoral muscles, which they use in swimming.
  • The demands of flight have rendered the general form of all flying birds similar to one another.
    • The beak of birds is very adaptable, taking on a great variety of shapes for different diets.

Concept 34.7 Mammals are amniotes that have hair and produce milk

    Mammals diversified extensively in the wake of the Cretaceous extinctions.

  • Mammals have a number of derived traits.
    • All mammalian mothers use mammary glands to nourish their babies with milk, a balanced diet rich in fats, sugars, proteins, minerals, and vitamins.
    • All mammals also have hair, made of keratin.
      • Hair and a layer of fat under the skin retain metabolic heat, contributing to endothermy in mammals.
    • Endothermy is supported by an active metabolism, made possible by efficient respiration and circulation.
      • Adaptations include a muscular diaphragm and a four-chambered heart.
  • Mammals generally have larger brains than other vertebrates of equivalent size.
    • Many species are capable of learning.
    • The relatively long period of parental care extends the time for offspring to learn important survival skills by observing their parents.
  • Feeding adaptations of the jaws and teeth are other important mammalian traits.
    • Unlike the uniform conical teeth of most reptiles, the teeth of mammals come in a variety of shapes and sizes adapted for processing many kinds of foods.
    • During the evolution of mammals from reptiles, two bones formerly in the jaw joint were incorporated into the mammalian ear and the jaw joint was remodeled.
  • Mammals belong to a group of amniotes known as synapsids.
    • Synapsids have a temporal fenestra behind the eye socket on each side of the skull.
  • Synapsids evolved into large herbivores and carnivores during the Permian period.
  • Mammal-like synapsids emerged by the end of the Triassic, 200 million years ago.
    • These animals were not mammals, but they were small and likely hairy, fed on insects at night, and had a higher metabolism that other synapsids.
    • They likely laid eggs.
  • The first true mammals arose in the Jurassic periods.
    • Early mammals diversified into a number of lineages, all about the size of a shrew.
  • During the Mesozoic, mammals coexisted with dinosaurs and underwent a great adaptive radiation in the Cenozoic in the wake of the Cretaceous extinctions.
    • Modern mammals are split into three groups: monotremes (egg-laying mammals), marsupials (mammals with pouches), and eutherian (placental) mammals.
  • Monotremes—the platypuses and the echidnas—are the only living mammals that lay eggs.
    • The reptile-like egg contains enough yolk to nourish the developing embryo.
  • Monotremes have hair, and females produce milk in specialized glands.
    • After hatching, the baby sucks milk from the mother’s fur because she lacks nipples.
  • Marsupials include opossums, kangaroos, bandicoots, and koalas.
  • In contrast to monotremes, marsupials have a higher metabolic rate, have nipples that produce milk, and give birth to live young.
  • A marsupial is born very early in development and, in most species, completes its embryonic development while nursing within a maternal pouch, the marsupium.
    • In most species, the tiny offspring climbs from the exit of the female’s reproductive tract to the mother’s pouch.
  • Marsupials existed worldwide throughout the Mesozoic area but now are restricted to Australia and the Americas.
    • In Australia, marsupials have radiated and filled niches occupied by eutherian mammals in other parts of the world.
      • Through convergent evolution, these diverse marsupials resemble eutherian mammals that occupy similar ecological roles.
  • While marsupial mammals diversified throughout the Tertiary in South America and Australia, the placental mammals began an adaptive radiation on the northern continents.
    • Australia’s isolation facilitated the diversification and survival of its marsupial fauna.
    • Invasions of placental mammals from North America impacted the marsupial fauna of South America about 12 million years ago and then again about 3 million years ago when the continents were connected by the Isthmus of Panama.
      • This mammalian biogeography is an example of the interplay between biological and geological evolution.
  • Compared to marsupials, eutherian mammals (placentals) have a longer period of pregnancy.
    • Young eutherians complete their embryonic development within the uterus, joined to the mother by the placenta.
    • Eutherians are commonly called placental mammals because their placentas are more complex than those of marsupials and provide a more intimate and long-lasting association between mother and young.

Concept 34.8 Humans are bipedal hominoids with a large brain

    Primate evolution provides a context for understanding human origins.

  • Primates include lemurs, monkeys, and apes.
  • Primates have large brains and short jaws.
  • Their eyes are forward-looking.
  • Most primates have hands and feet adapted for grasping.
  • Relative to other mammals, they have large brains and short jaws.
  • They have flat nails on their digits, rather than narrow claws.
  • Primates also have relatively well-developed parental care and relatively complex social behavior.
  • The earliest primates were probably tree dwellers, shaped by natural selection for arboreal life.
    • The grasping hands and feet of primates are adaptations for hanging on to tree branches.
      • All modern primates, except Homo, have a big toe that is widely separated from the other toes.
      • The thumb is relatively mobile and separate from the fingers in all primates, but a fully opposable thumb is found only in anthropoid primates.
      • The unique dexterity of humans, aided by distinctive bone structure at the thumb base, represents descent with modification from ancestral hands adapted for life in the trees.
  • Other primate features also originated as adaptations for tree dwelling.
    • The overlapping fields of vision of the two eyes enhance depth perception, an obvious advantage when brachiating.
    • Excellent hand-eye coordination is also important for arboreal maneuvering.
  • Primates are divided into two subgroups.
    • The Prosimii (prosimians) probably resemble early arboreal primates and include the lemurs of Madagascar and the lorises, pottos, and tarsiers of tropical Africa and southern Asia.
    • The Anthropoidea (anthropoids) include monkeys, apes, and humans.
  • The oldest known anthropoid fossils, from about 45 million years ago, support the hypothesis that tarsiers are the prosimians most closely related to anthropoids.
  • By the Oligocene, monkeys were established in Africa, Asia, and South America.
    • The Old World and New World monkeys underwent separate adaptive radiations.
    • All New World monkeys are arboreal, but Old World monkeys include arboreal and ground-dwelling species.
    • Most monkeys in both groups are diurnal, and usually live in bands held together by social behavior.
  • In addition to monkeys, the anthropoid suborder also includes four genera of apes: Hylobates (gibbons), Pongo (orangutans), Gorilla (gorillas), and Pan (chimpanzees and bonobos).
    • Modern apes are confined exclusively to the tropical regions of the Old World.
    • They evolved from Old World monkeys about 20–25 million years ago.
  • With the exception of gibbons, modern apes are larger than monkeys, with relatively long arms and short legs and no tails.
    • Only gibbons and orangutans are primarily arboreal.
  • Social organization varies among the genera, with gorillas and chimpanzees being highly social.
    • Apes have relatively larger brains than monkeys, and their behavior is more flexible.

    Humans are bipedal hominoids.

  • In the continuity of life spanning more than 3.5 billion years, humans and apes have shared ancestry for all but the past few million years.
  • Human evolution is marked by the evolution of several major features.
    • Humans stand upright and walk on two legs.
    • Humans have a much larger brain than other hominoids and are capable of language, symbolic thought, and tool use.
    • Humans have reduced jawbones and muscles and a shorter digestive tract.
    • Human and chimpanzee genomes are 99% identical.
      • Scientists are comparing the genomes of humans and chimpanzees to investigate the 1% difference.
  • Paleoanthropology is the study of human origins and evolution.
  • Paleoanthropologists have found fossils of 20 species of extinct hominoids that are more closely related to humans than to chimpanzees.
    • These species are known as hominids.
  • The oldest hominid is Sahelanthropus tchandensis, which lived 7 million years ago.
    • Sahelanthropus and other early hominids shared some of the derived characters of humans.
    • They had reduced canine teeth and relatively flat faces.
    • They were more upright and bipedal than other hominoids.
  • While early hominids were becoming bipedal, their brains remained small—about 400 to 450 cm3 in volume.
    • Early hominids were small in stature, with relatively large teeth and a protruding lower jaw.
  • Avoid three common sources of confusion:
    1. First, our ancestors were not chimpanzees or any other modern apes.
      • Chimpanzees and humans represent two divergent branches of the hominoid tree that evolved from a common ancestor that was neither a chimpanzee nor a human.
    2. Second, human evolution did not occur as a ladder with a series of steps leading directly from an ancestral hominoid to Homo sapiens.
      • If human evolution is a parade, then many splinter groups traveled down dead ends, and several different human species coexisted.
      • Human phylogeny is more like a multibranched bush with our species as the tip of the only surviving twig.
    3. Third, the various human characteristics, such as upright posture and an enlarged brain, did not evolve in unison.
    4. Different features evolved at different rates, called mosaic evolution.
    5. Our pedigree includes ancestors who walked upright but had brains much less developed than ours.
  • After dismissing some of the folklore on human evolution, we must admit that many questions about our own ancestry remain.
  • Hominid diversity increased dramatically between 4 and 2 million years ago.
  • The various pre-Homo hominids are classified in the genus Australopithecus (“southern ape”) and are known as australopiths.
    • The first australopith, A. africanus, was discovered in 1924 by Raymond Dart in a quarry in South Africa.
      • From this and other skeletons, it became clear that A. africanus probably walked fully erect and had humanlike hands and teeth.
      • However, the brain was only about one-third the size of a modern human’s brain.
    • In 1974, a new fossil, about 40% complete, was discovered in the Afar region of Ethiopia.
      • This fossil, nicknamed “Lucy,” was described as a new species, A. afarensis.
    • Based on this fossil and other discoveries, this species had a brain the size of a chimpanzee, a prognathous jaw, longer arms (for some level of arboreal locomotion), and sexual dimorphism more apelike than human.
      • However, the pelvis and skull bones and fossil tracks showed that A. afarensis walked bipedally.
      • Two lineages appeared after A. afarensis: the “robust” australopithecines with sturdy skulls and powerful jaws and teeth for grinding and chewing hard, tough foods; and the “gracile” australopithecines with lighter feeding equipment adapted for softer foods.
    • Combining evidence from the earliest hominids with the fossil record of australopiths makes it possible to consider hypotheses about trends in hominid evolution.
    • Why did hominids become bipedal?
      • Our anthropoid ancestors of 30–35 million years ago were tree dwelling.
        • Twenty million years ago, the forests contracted as the climate became drier.
        • The result was an increased savanna with few trees.
        • For decades, paleontologists thought that bipedalism was an adaptation to life on the savanna.
      • All early hominids show indications of bipedalism, but they lived in forests and open woodlands, not savanna.
      • An alternate hypothesis is that bipedalism allowed hominids to reach low-hanging fruits.
      • About 1.9 million years ago, hominids living in arid environments walked long distances on two legs.
    • The manufacture and use of complex tools is a derived human character.
      • When and why did tool use arise in the human lineage?
      • Other hominoids are capable of sophisticated tool use.
        • Orangutans can fashion probes from sticks for retrieving insects from their nests.
        • Chimps use rocks to smash open food and put leaves on their feet to walk over thorns.
      • The oldest generally accepted evidence of tool use is 2.5-million-year-old cut marks on animal bones found in Ethiopia.
        • The australopith fossils near the site had relatively small brains.
        • Perhaps tool use originated before large hominid brains evolved.
    • The earliest fossils that anthropologists place in our genus, Homo, are classified as Homo habilis.
      • These fossils range in age from 2.4 to 1.6 million years old.
      • This species had less prognathic jaws and larger brains (about 600–750 cm3) than australopiths.
      • In some cases, anthropologists have found sharp stone tools with these fossils, indicating that some hominids had started to use their brains and hands to fashion tools.
    • Fossils from 1.9 to 1.6 million years ago are recognized as a distinct species, Homo ergaster.
      • H. ergaster had a larger brain than Homo habilis, as well as long slender legs well adapted for long-distance walking.
      • This species lived in more-arid environments and was associated with more-sophisticated tool use.
      • Its reduced teeth suggest that it might have been able to cook or mash its food before eating it.
    • Specimens of early Homo show reduced sexual dimorphism, a trend that continued with our species.
      • Sexual dimorphism is reduced in pair-bonding species.
      • Male and female Homo ergaster may have engaged in more pair-bonding than earlier hominids, perhaps in order to provide long-term biparental care of babies.
    • Some paleontologists still think that Homo ergaster were merely early specimens of Homo erectus.
    • Homo erectus was the first hominid species to migrate out of Africa, colonizing Asia and Europe.
      • They lived from about 1.8 million to 500,000 years ago.
        • Fossils from Asia are known by such names as “Beijing man” and “Java Man.”
        • In Europe, Neanderthals arose from an earlier species, Homo heidelbergensis, which arose in Africa about 600,000 years ago and spread to Europe.
    • The term Neanderthal is now used for humans who lived throughout Europe from about 200,000 to 30,000 years ago.
      • Fossilized skulls indicate that Neanderthals had brains as large as ours, though somewhat different in shape.
      • They made hunting tools from stone and wood.
      • Neanderthals were generally more heavily built than modern humans.
    • Neanderthals apparently went extinct about 30,000 years ago, contributing little to the gene pool of modern humans.
    • Evidence of the extinction of Neanderthal can be found in their DNA.
      • Scientists have extracted DNA from four fossil Neanderthals living at different times and places in Europe.
        • All Neanderthals formed a clade, while modern Europeans were more closely related to modern Africans and Asians.
    • In 2003, researchers in Ethiopia found 160,000-year-old fossils of Homo sapiens, the oldest members of our species.
      • These early humans were slender and lacked brow ridges.
    • Evidence suggests that all living humans are more closely related to each other than to Neanderthals.
    • Europeans and Asians share a relatively recent common ancestor and many African lineages branched off from more ancient positions on the human family tree.
      • This is supported by analysis of mDNA and Y chromosomes of various populations.
    • These findings strongly suggest that all living humans arose from Africa and migrated from there 50,000 years ago.
    • Our ancestors emerged in one or more waves, spreading into Asia, then Europe, and Australia.
    • The rapid expansion of our species may have been spurred by the evolution of human cognition.
      • Neanderthals produced sophisticated tools, but had little creativity or capacity for symbolic thought.
    • In 2002, researchers found 77,000-year-old from South Africa.
    • By 36,000, humans were producing spectacular cave paintings.
    • Symbolic thought may have emerged along with full-blown human language, raising the reproductive fitness of humans by allowing them to construct new tools and teach others how to build them.
    • Population pressure may have driven humans to migrate into Asia and then Europe.
    • In 2002, geneticists found that FOXP2, a gene essential for human language, experienced intense natural selection after the ancestors of humans and chimps diverged.
      • Comparisons of flanking regions of the gene suggest that most changes took place within the past 200,000 years.
      • The evolutionary change in FOXP2 may be the first genetic clue about how our own species came to be.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 34-1

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    Chapter 35 - Plant Structure

    Chapter 35 Plant Structure, Growth, and Development
    Lecture Outline

    Overview: No Two Plants Are Alike

    • The fanwort, an aquatic weed, demonstrates the great developmental plasticity that is characteristic of plants. The fanwort has feathery underwater leaves and large, flat, floating surface leaves. Both leaf types have genetically identical cells, but the dissimilar environments in which they develop cause different genes involved in leaf formation to be turned on or off.
    • The form of any plant is controlled by environmental and genetic factors. As a result, no two plants are identical.
    • In addition to plastic structural responses of individual plants to specific environments, plant species have adaptive features that benefit them in their specific environments.
    • For example, cacti have leaves that are reduced as spines and a stem that serves as the primary site of photosynthesis. These adaptations reduce water loss in desert environments.
    • Angiosperms comprise 90% of plant species and are at the base of the food web of nearly every terrestrial ecosystem.
    • Most land animals, including humans, depend on angiosperms directly or indirectly for sustenance.

    Concept 35.1 The plant body has a hierarchy of organs, tissues, and cells

    • Plants, like multicellular animals, have organs that are composed of different tissues, and tissues are composed of different cell types.
      • A tissue is a group of cells with a common structure and function.
      • An organ consists of several types of tissues that work together to carry out particular functions.

      Vascular plants have three basic organs: roots, stems, and leaves.

    • The basic morphology of vascular plants reflects their evolutionary history as terrestrial organisms that inhabit and draw resources from two very different environments.
      • Plants obtain water and minerals from the soil.
      • They obtain CO2 and light above ground.
    • To obtain the resources they need, vascular plants have evolved two systems: a subterranean root system and an aerial shoot system of stems and leaves.
    • Each system depends on the other.
      • Lacking chloroplasts and living in the dark, roots would starve without the sugar and other organic nutrients imported from the photosynthetic tissues of the shoot system.
      • Conversely, the shoot system (and its reproductive tissues, flowers) depends on water and minerals absorbed from the soil by the roots.
    • A root is an organ that anchors a vascular plant in the soil, absorbs minerals and water, and stores food.
      • Most eudicots and gymnosperms have a taproot system, consisting of one large vertical root (the taproot) that produces many small lateral, or branch, roots.
        • In angiosperms, taproots often store food that supports flowering and fruit production later.
      • Seedless vascular plants and most monocots, including grasses, have fibrous root systems consisting of a mat of thin roots that spread out below the soil surface.
        • A fibrous root system is usually shallower than a taproot system.
        • Grass roots are concentrated in the upper few centimeters of soil. As a result, grasses make excellent ground cover for preventing erosion.
        • Sturdy, horizontal, underground stems called rhizomes anchor large monocots such as palms and bamboo.
      • The root system helps anchor a plant.
      • In both taproot and fibrous root systems, absorption of water and minerals occurs near the root tips, where vast numbers of tiny root hairs enormously increase the surface area.
      • Root hairs are extensions of individual epidermal cells on the root surface.
        • Absorption of water and minerals is also increased by mutualistic relationships between plant roots and bacteria and fungi.
      • Some plants have modified roots. Some arise from roots while adventitious roots arise aboveground from stems or even from leaves.
        • Some modified roots provide additional support and anchorage. Others store water and nutrients or absorb oxygen or water from the air.
    • A stem is an organ consisting of alternating nodes, the points at which leaves are attached, and internodes, the stem segments between nodes.
    • At the angle formed by each leaf and the stem is an axillary bud with the potential to form a lateral shoot or branch.
    • Growth of a young shoot is usually concentrated at its apex, where there is a terminal bud with developing leaves and a compact series of nodes and internodes.
    • The presence of a terminal bud is partly responsible for inhibiting the growth of axillary buds, a phenomenon called apical dominance.
      • By concentrating resources on growing taller, apical dominance is an evolutionary adaptation that increases the plant’s exposure to light.
      • In the absence of a terminal bud, the axillary buds break dominance and give rise to a vegetative branch complete with its own terminal bud, leaves, and axillary buds.
    • Modified shoots with diverse functions have evolved in many plants.
      • These shoots, which include stolons, rhizomes, tubers, and bulbs, are often mistaken for roots.
        • Stolons, such as the “runners” of strawberry plants, are horizontal stems that grow on the surface and enable a plant to colonize large areas asexually as plantlets form at nodes along each runner.
        • Rhizomes, like those of ginger, are horizontal stems that grow underground.
        • Tubers, including potatoes, are the swollen ends of rhizomes specialized for food storage.
        • Bulbs, such as onions, are vertical, underground shoots consisting mostly of the swollen bases of leaves that store food.
    • Leaves are the main photosynthetic organs of most plants, although green stems are also photosynthetic.
      • While leaves vary extensively in form, they generally consist of a flattened blade and a stalk, the petiole, which joins the leaf to a stem node.
      • Grasses and other monocots lack petioles. In these plants, the base of the leaf forms a sheath that envelops the stem.
    • Most monocots have parallel major veins that run the length of the blade, while eudicot leaves have a multibranched network of major veins.
    • Plant taxonomists use floral morphology, leaf shape, spatial arrangement of leaves, and the pattern of veins to help identify and classify plants.
      • For example, simple leaves have a single, undivided blade, while compound leaves have several leaflets attached to the petiole.
        • The leaflet of a compound leaf has no axillary bud at its base.
      • In a doubly compound leaf, each leaflet is divided into smaller leaflets.
    • Most leaves are specialized for photosynthesis.
      • Some plants have leaves that have become adapted for other functions.
      • These include tendrils that cling to supports, spines of cacti for defense, leaves modified for water storage, and brightly colored leaves that attract pollinators.

      Plant organs are composed of three tissue systems: dermal, vascular, and ground.

    • Each organ of a plant has three tissue systems: dermal, vascular, and ground.
      • Each system is continuous throughout the plant body.
    • The dermal tissue is the outer covering.
    • In nonwoody plants, it is a single layer of tightly packed cells, or epidermis, that covers and protects all young parts of the plant.
    • The epidermis has other specialized characteristics consistent with the function of the organ it covers.
      • For example, the root hairs are extensions of epidermal cells near the tips of the roots.
      • The epidermis of leaves and most stems secretes a waxy coating, the cuticle, which helps the aerial parts of the plant retain water.
    • In woody plants, protective tissues called periderm replace the epidermis in older regions of stems and roots.
    • Vascular tissue, continuous throughout the plant, is involved in the transport of materials between roots and shoots.
      • Xylem conveys water and dissolved minerals upward from roots into the shoots.
      • Phloem transports food made in mature leaves to the roots; to nonphotosynthetic parts of the shoot system; and to sites of growth, such as developing leaves and fruits.
      • The vascular tissue of a root or stem is called the stele.
        • In angiosperms, the vascular tissue of the root forms a solid central vascular cylinder, while stems and leaves have vascular bundles, strands consisting of xylem and phloem.
    • Ground tissue is tissue that is neither dermal tissue nor vascular tissue.
      • In eudicot stems, ground tissue is divided into pith, internal to vascular tissue, and cortex, external to the vascular tissue.
      • The functions of ground tissue include photosynthesis, storage, and support.
      • For example, the cortex of a eudicot stem typically consists of both fleshy storage cells and thick-walled support cells.

      Plant tissues are composed of three basic cell types: parenchyma, collenchyma, and sclerenchyma.

    • Plant cells are differentiated, with each type of plant cell possessing structural adaptations that make specific functions possible.
      • Cell differentiation may be evident within the protoplast, the cell contents exclusive of the cell wall.
      • Modifications of cell walls also play a role in plant cell differentiation.
    • We will consider the major types of differentiated plant cells: parenchyma, collenchyma, sclerenchyma, water-conducting cells of the xylem and sugar-conducting cells of the phloem.
    • Mature parenchyma cells have primary walls that are relatively thin and flexible, and most lack secondary walls.
      • The protoplast of a parenchyma cell usually has a large central vacuole.
      • Parenchyma cells are often depicted as “typical” plant cells because they generally are the least specialized, but there are exceptions.
      • For example, the highly specialized sieve-tube members of the phloem are parenchyma cells.
    • Parenchyma cells perform most of the metabolic functions of the plant, synthesizing and storing various organic products.
      • For example, photosynthesis occurs within the chloroplasts of parenchyma cells in the leaf.
      • Some parenchyma cells in the stems and roots have colorless plastids that store starch.
      • The fleshy tissue of most fruit is composed of parenchyma cells.
      • Most parenchyma cells retain the ability to divide and differentiate into other cell types under special conditions, such as the repair and replacement of organs after injury to the plant.
      • In the laboratory, it is possible to regenerate an entire plant from a single parenchyma cell.
    • Collenchyma cells have thicker primary walls than parenchyma cells, though the walls are unevenly thickened.
      • Grouped into strands or cylinders, collenchyma cells help support young parts of the plant shoot.
      • Young stems and petioles often have strands of collenchyma just below the epidermis, providing support without restraining growth.
      • Mature collenchyma cells are living and flexible and elongate with the stems and leaves they support.
    • Sclerenchyma cells have thick secondary walls usually strengthened by lignin and function as supporting elements of the plant.
      • They are much more rigid than collenchyma cells.
      • Unlike parenchyma cells, they cannot elongate.
      • Sclerenchyma cells occur in plant regions that have stopped lengthening.
    • Many sclerenchyma cells are dead at functional maturity, but they produce rigid secondary cells walls before the protoplast dies.
      • In parts of the plant that are still elongating, secondary walls are deposited in a spiral or ring pattern, enabling the cell wall to stretch like a spring as the cell grows.
    • Two types of sclerenchyma cells, fibers and sclereids, are specialized entirely for support.
      • Fibers are long, slender, and tapered, and usually occur in groups.
        • Those from hemp fibers are used for making rope, and those from flax are woven into linen.
      • Sclereids are irregular in shape and are shorter than fibers.
        • They have very thick, lignified secondary walls.
        • Sclereids impart hardness to nutshells and seed coats and the gritty texture to pear fruits.
    • The water-conducting elements of xylem, the tracheids and vessel elements, are elongated cells that are dead at functional maturity.
      • The thickened cell walls remain as a nonliving conduit through which water can flow.
    • Both tracheids and vessels have secondary walls interrupted by pits, thinner regions where only primary walls are present.
    • Tracheids are long, thin cells with tapered ends.
      • Water moves from cell to cell mainly through pits.
      • Because their secondary walls are hardened with lignin, tracheids function in support as well as transport.
    • Vessel elements are generally wider, shorter, thinner walled, and less tapered than tracheids.
      • Vessel elements are aligned end to end, forming long micropipes or xylem vessels.
      • The ends are perforated, enabling water to flow freely.
    • In the phloem, sucrose, other organic compounds, and some mineral ions move through tubes formed by chains of cells called sieve-tube members.
      • These are alive at functional maturity, although a sieve-tube member lacks a nucleus, ribosomes, and a distinct vacuole.
      • The end walls, the sieve plates, have pores that facilitate the flow of fluid between cells.
      • Each sieve-tube member has a nonconducting nucleated companion cell, which is connected to the sieve-tube member by numerous plasmodesmata.
      • The nucleus and ribosomes of the companion cell serve both that cell and the adjacent sieve-tube member.
      • In some plants, companion cells in leaves help load sugar into the sieve-tube members, which transport the sugars to other parts of the plant.

    Concept 35.2 Meristems generate cells for new organs

    • A major difference between plants and most animals is that plant growth is not limited to an embryonic period.
    • Most plants demonstrate indeterminate growth, growing as long as the plant lives.
    • In contrast, most animals and certain plant organs, such as flowers and leaves, undergo determinate growth, ceasing to grow after they reach a certain size.
    • Indeterminate growth does not mean immortality.
    • Annual plants complete their life cycle—from germination through flowering and seed production to death—in a single year or less.
      • Many wildflowers and important food crops, such as cereals and legumes, are annuals.
    • The life of a biennial plant spans two years.
      • Often, there is an intervening cold period between the vegetative growth season and the flowering season.
    • Plants such as trees, shrubs, and some grasses that live many years are perennials.
      • Perennials do not usually die from old age, but from an infection or some environmental trauma.
    • A plant is capable of indeterminate growth because it has perpetually embryonic tissues called meristems in its regions of growth.
      • These cells divide to generate additional cells, some of which remain in the meristematic region, while others become specialized and are incorporated into the tissues and organs of the growing plant.
      • Cells that remain as wellsprings of new cells in the meristem are called initials.
      • Those that are displaced from the meristem, derivatives, continue to divide for some time until the cells they produce differentiate within developing tissues.
    • The pattern of plant growth depends on the location of meristems.
    • Apical meristems, located at the tips of roots and in the buds of shoots, supply cells for the plant to grow in length.
      • This elongation, primary growth, enables roots to extend through the soil and shoots to increase their exposure to light and carbon dioxide.
      • In herbaceous plants, primary growth produces almost all of the plant body.
      • Woody plants also show secondary growth, progressive thickening of roots and shoots where primary growth has ceased.
        • Secondary growth is produced by lateral meristems, cylinders of dividing cells that extend along the length of roots and shoots.
        • The vascular cambium adds layers of vascular tissue called secondary xylem and phloem.
        • The cork cambium replaces the epidermis with thicker, tougher periderm.
    • In woody plants, primary growth produces young extensions of roots and shoots each growing season, while secondary growth thickens and strengthens the older parts of the plant.
    • At the tip of a winter twig of a deciduous tree is the dormant terminal bud, enclosed by bud scales that protect its apical meristem.
      • In the spring, the bud will shed its scales and begin a new spurt of primary growth.
      • Along each growth segment, nodes are marked by scars left when leaves fell in autumn.
      • Above each leaf scar is either an axillary bud or a branch twig.
    • Farther down the twig are whorls of scars left by the scales that enclosed the terminal bud during the previous winter.
    • Each spring and summer, as the primary growth extends the shoot, secondary growth thickens the parts of the shoot that formed in previous years.

    Concept 35.3 Primary growth lengthens roots and shoots

    • Primary growth produces the primary plant body, the parts of the root and shoot systems produced by apical meristems.
    • An herbaceous plant and the youngest parts of a woody plant represent the primary plant body.
    • Apical meristems lengthen both roots and shoots. However, there are important differences in the primary growth of these two systems.
    • The root tip is covered by a thimblelike root cap, which protects the meristem as the root pushes through the abrasive soil during primary growth.
      • The cap also secretes a polysaccharide slime that lubricates the soil around the growing root tip.
    • Growth in length is concentrated just behind the root tip, where three zones of cells at successive stages of primary growth are located.
      • These zones—the zone of cell division, the zone of elongation, and the zone of maturation—grade together.
    • The zone of cell division includes the root apical meristem and its derivatives.
      • New root cells are produced in this region, including the cells of the root cap.
    • The zone of cell division blends into the zone of elongation where cells elongate, sometimes to more than ten times their original length.
      • It is this elongation of cells that is mainly responsible for pushing the root tip, including the meristem, ahead.
      • The meristem sustains growth by continuously adding cells to the youngest end of the zone of elongation.
      • In the zone of maturation, cells become differentiated and become functionally mature.
    • The primary growth of roots consists of the epidermis, ground tissue, and vascular tissue.
    • Water and minerals absorbed from the soil must enter through the epidermis, a single layer of cells covering the root.
      • Root hairs greatly increase the surface area of epidermal cells.
      • Most roots have a solid core of xylem and phloem. The xylem radiates from the center in two or more spokes, with phloem developing in the wedges between the spokes.
      • In monocot roots, the vascular tissue consists of a central core of parenchyma surrounded by alternating patterns of xylem and phloem.
    • The ground tissue of roots consists of parenchyma cells that fill the cortex, the region between the vascular cylinder and the epidermis.
      • Cells within the ground tissue store food and are active in the uptake of minerals that enter the root with the soil solution.
    • The innermost layer of the cortex, the endodermis, is a cylinder one cell thick that forms a selective barrier between the cortex and the vascular cylinder.
    • An established root may sprout lateral roots from the outermost layer of the vascular cylinder, the pericycle.
      • The vascular tissue of the lateral root maintains its connection to the vascular tissue of the primary root.
    • The apical meristem of a shoot is a dome-shaped mass of dividing cells at the terminal bud.
      • Leaves arise as leaf primordia on the flanks of the apical meristem.
      • Axillary buds develop from islands of meristematic cells left by apical meristems at the bases of the leaf primordia.
    • Within a bud, leaf primordia are crowded close together because internodes are very short.
      • Most of the elongation of the shoot occurs by growth in length of slightly older internodes below the shoot apex.
      • This growth is due to cell division and cell elongation within the internode.
      • In some plants, including grasses, internodes continue to elongate all along the length of the shoot over a prolonged period.
        • These plants have meristematic regions called intercalary meristems at the base of each leaf.
        • This explains why grass continues to grow after being mowed.
    • Unlike their central position in a root, vascular tissue runs the length of a stem in strands called vascular bundles.
      • Because the vascular system of the stem is near the surface, branches can develop with connections to the vascular tissue without having to originate from deep within the main shoot.
    • In gymnosperms and most eudicots, the vascular bundles are arranged in a ring, with pith inside and cortex outside the ring.
      • The vascular bundles have xylem facing the pith and phloem facing the cortex.
    • In the stems of most monocots, the vascular bundles are scattered throughout the ground tissue rather than arranged in a ring.
    • In both monocots and eudicots, the stem’s ground tissue is mostly parenchyma.
    • Many stems are strengthened by collenchyma just beneath the epidermis.
      • Sclerenchyma fiber cells within vascular bundles also help support stems.
    • The leaf epidermis is composed of cells tightly locked together like pieces of a puzzle.
      • The leaf epidermis is the first line of defense against physical damage and pathogenic organisms, and its waxy cuticle is a barrier to water loss from the plant.
    • The epidermal barrier is interrupted only by the stomata, tiny pores flanked by specialized epidermal cells called guard cells.
      • Each stoma is an opening between a pair of guard cells that regulate the opening and closing of the pore.
      • The stomata regulate CO2 exchange between the surrounding air and the photosynthetic cells inside the leaf.
      • They are also the major avenues of evaporative water loss from the plant—a process called transpiration.
    • The ground tissue of the leaf, the mesophyll, is sandwiched between the upper and lower epidermis.
      • It consists mainly of parenchyma cells with many chloroplasts and specialized for photosynthesis.
      • In many eudicots, a layer or more of columnar palisade mesophyll lies over spongy mesophyll.
        • Carbon dioxide and oxygen circulate through the labyrinth of air spaces around the irregularly spaced cells of the spongy mesophyll.
        • The air spaces are particularly large near stomata, where gas exchange with the outside air occurs.
    • The vascular tissue of a leaf is continuous with the xylem and phloem of the stem.
      • Leaf traces, branches of vascular bundles in the stem, pass through petioles and into leaves.
      • Vascular bundles in the leaves are called veins. Each vein is enclosed in a protective bundle sheath consisting of one or more layers of parenchyma.
      • Within a leaf, veins subdivide repeatedly and branch throughout the mesophyll.
        • The xylem brings water and minerals to the photosynthetic tissues and the phloem carries sugars and other organic products to other parts of the plant.
        • The vascular infrastructure also functions to support and reinforce the shape of the leaf.

    Concept 35.4 Secondary growth adds girth to stems and roots in woody plants

    • The stems and roots of most eudicots increase in girth by secondary growth.
      • The secondary plant body consists of the tissues produced during this secondary growth in diameter.
      • Primary and secondary growth occur simultaneously but in different regions.
      • While elongation of the stem (primary growth) occurs at the apical meristem, increases in diameter (secondary growth) occur farther down the stem.
    • The vascular cambium is a cylinder of meristematic cells that forms secondary vascular tissue.
      • It forms successive layers of secondary xylem to its interior and secondary phloem to its exterior.
      • The accumulation of this tissue over the years accounts for most of the increase in diameter of a woody plant.
      • The vascular cambium develops from parenchyma cells that retain the capacity to divide.
      • This meristem forms in a layer between the primary xylem and primary phloem of each vascular bundle and in the ground tissue between the bundles.
    • The meristematic bands unite to form a continuous cylinder of dividing cells.
    • This ring of vascular cambium consists of regions of ray initials and fusiform initials.
      • The tapered, elongated cells of the fusiform initials form secondary xylem to the inside of the vascular cambium and secondary phloem to the outside.
      • Ray initials produce vascular rays that transfer water and nutrients laterally within the woody stem and also store starch and other reserves.
    • As secondary growth continues over the years, layer upon layer of secondary xylem accumulates, producing the tissue we call wood.
      • Wood consists mainly of tracheids, vessel elements (in angiosperms), and fibers.
      • These cells, dead at functional maturity, have thick, lignified walls that give wood its hardness and strength.
    • In temperate regions, secondary growth in perennial plants ceases during the winter.
      • The first tracheid and vessel cells formed in the spring (early wood) have larger diameters and thinner walls than cells produced later in the summer (late wood).
      • The structure of the early wood maximizes delivery of water to new, expanding leaves.
      • The thick-walled cells of later wood provide more physical support.
    • This pattern of growth—cambium dormancy, early wood production, and late wood production—produces annual growth rings.
    • As a tree or woody shrub ages, the older layers of secondary xylem, known as heartwood, no longer transport water and minerals.
    • The outer layers, known as sapwood, continue to transport xylem sap.
    • Only the youngest secondary phloem, closest to the vascular cambium, functions in sugar transport.
      • The older secondary phloem dies and is sloughed off as part of the bark.
    • The cork cambium acts as a meristem for a tough, thick covering for stems and roots that replaces the epidermis.
    • Early in secondary growth, the epidermis produced by primary growth splits, dries, and falls off the stem or root.
      • It is replaced by two tissues produced by the first cork cambium, which arises in the outer cortex of stems and in the outer layer of the pericycle of roots.
        • The first tissue, phelloderm, is a thin layer of parenchyma cells that forms to the interior of the cork cambium.
        • Cork cambium also produces cork cells, which accumulate at the cambium’s exterior.
        • Waxy material called suberin deposited in the cell walls of cork cells before they die acts as a barrier against water loss, physical damage, and pathogens.
    • The cork plus the cork cambium form the periderm, a protective layer that replaces the epidermis.
    • In areas called lenticels, spaces develop between the cork cells of the periderm.
      • These areas within the trunk facilitate gas exchange with the outside air.
    • Unlike the vascular cambium, cells of the cork cambium do not divide.
    • The thickening of a stem or root splits the first cork cambium, which loses its meristematic activity and differentiates into cork cells.
    • A new cork cambium forms to the inside, resulting in a new layer of periderm.
    • As this process continues, older layers of periderm are sloughed off.
      • This produces the cracked, peeling bark of many tree trunks.
    • Bark refers to all tissues external to the vascular cambium, including secondary phloem, cork cambium, and cork.

    Concept 35.5 Growth, morphogenesis, and differentiation produce the plant body

    • During plant development, a single cell, the zygote, gives rise to a multicellular plant of particular form with functionally integrated cells, tissues, and organs.
      • An increase in mass, or growth, results from cell division and cell expansion.
      • The development of body form and organization is called morphogenesis.
      • The specialization of cells with the same set of genetic instructions to produce a diversity of cell types is called differentiation.
    • Plants have tremendous developmental plasticity.
      • Plant form, including height, branching patterns, and reproductive output, is greatly influenced by environmental factors.
      • A broad range of morphologies can result from the same genotype as three developmental processes—growth, morphogenesis, and differentiation—transform a zygote into an adult plant.

      Molecular biology is revolutionizing the study of plants.

    • Modern molecular techniques allow plant biologists to investigate how growth, morphogenesis, and cellular differentiation give rise to a plant.
      • Much of this research has focused on Arabidopsis thaliana, a small weed in the mustard family.
      • Thousands of these small plants can be cultivated in a few square meters of lab space.
      • With a generation time of about six weeks, it is an excellent model for genetic studies.
    • The genome of Arabidopsis is among the tiniest of all known plants.
    • Arabidopsis was the first plant to have its genome sequenced, in a six-year multinational project.
    • Arabidopsis has a total of about 26,000 genes, with fewer than 15,000 different types of genes.
    • Now that the DNA sequence of Arabidopsis is known, plant biologists are working to identify the functions of every one of the plant’s genes by the year 2010.
      • To aid in this effort, biologists are attempting to create mutants for every gene in the plant’s genome.
      • Study of the function of these genes has already expanded our understanding of plant development.
      • By identifying each gene’s function, researchers aim to establish a blueprint for how plants are built.
      • One day it may be possible to create a computer-generated “virtual plant” that will enable researchers to visualize which plant genes are activated in different parts of the plant during the entire course of development.

      Growth involves both cell division and cell expansion.

    • Cell division in meristems increases cell number, increasing the potential for growth.
    • However, it is cell expansion that accounts for the actual increase in plant mass.
    • The plane (direction) and symmetry of cell division are important determinants of plant form.
      • If the planes of division by a single cell and its descendents are parallel to the plane of the first cell division, a single file of cells will be produced.
      • If the planes of cell division of the descendent cells vary at random, an unorganized clump of cells will result.
    • While mitosis results in symmetrical redistribution of chromosomes between daughter cells, cytokinesis may be asymmetrical.
      • Asymmetrical cell division, in which one cell receives more cytoplasm than the other, is common in plant cells and usually signals a key developmental event.
      • For example, guard cells form from an unspecialized epidermal cell through an asymmetrical cell division and a change in the plane of cell division.
    • The plane in which a cell will divide is determined during late interphase.
      • Microtubules in the outer cytoplasm become concentrated into a ring, the preprophase band.
      • While this disappears before metaphase, its “imprint” consists of an ordered array of actin microfilaments that remains after the microtubules disperse and signals the future plane of cell division.
      • Cell expansion in animal cells is quite different from cell expansion in plant cells.
      • Animal cells grow by synthesizing a protein-rich cytoplasm, a metabolically expensive process.
      • While growing plant cells add some organic material to their cytoplasm, water uptake by the large central vacuole accounts for 90% of a plant cell’s expansion.
        • This enables plants to grow economically and rapidly.
        • Bamboo shoots can elongate more than 2 m per week.
      • Rapid expansion of shoots and roots increases their exposure to light and soil, an important evolutionary adaptation to the immobile lifestyle of plants.
    • The greatest expansion of a plant cell is usually oriented along the plant’s main axis.
      • The orientations of cellulose microfibrils in the innermost layers of the cell wall cause this differential growth, as the cell expands mainly perpendicular to the “grain” of the microfibrils.
    • Studies of Arabidopsis mutants have confirmed the importance of cortical microtubules in both cell division and expansion.
    • For example, fass mutants have unusually squat cells, which follow seemingly random planes of cell division.
      • Their roots and stems lack the ordered cell files and layers.
    • Fass mutants develop into tiny adult plants with all their organs compressed longitudinally.
    • The cortical microtubular organization of fass mutants is abnormal.
      • Although the microtubules involved in chromosome movement and in cell plate deposition are normal, preprophase bands do not form prior to mitosis.
      • In interphase cells, the cortical microtubules are randomly positioned.
        • Therefore, the cellulose microfibrils deposited in the cell wall cannot be arranged to determine the direction of the cell’s elongation.
        • Cells with a fass mutation expand in all directions equally and divide in a haphazard arrangement, leading to stout stature and disorganized tissues.

      Morphogenesis depends on pattern formation.

    • Morphogenesis organizes dividing and expanding cells into multicellular tissues and organs.
      • The development of specific structures in specific locations is called pattern formation.
      • Pattern formation depends to a large extent on positional information, signals that continuously indicate each cell’s location within an embryonic structure.
      • Within a developing organ, each cell responds to positional information by differentiating into a particular cell type.
    • Developmental biologists are accumulating evidence that gradients of specific molecules, generally proteins or mRNAs, provide positional information.
      • For example, a substance diffusing from a shoot’s apical meristem may “inform” the cells below of their distance from the shoot tip.
      • A second chemical signal produced by the outermost cells may enable a cell to gauge their position relative to the radial axis of the developing organ.
      • Developmental biologists are testing the hypothesis that diffusible chemical signals provide plant cells with positional information.
    • One type of positional information is polarity, the identification of the root end and shoot end along a well-developed axis.
      • This polarity results in morphological and physiological differences, and it impacts the emergence of adventitious roots and shoots from the appropriate ends of plant cuttings.
      • The first division of the zygote is asymmetrical and may initiate the polarization of the plant body into root and shoot ends.
        • Once the polarity has been induced, it is very difficult to reverse experimentally.
        • The establishment of axial polarity is a critical step in plant morphogenesis.
      • In the gnom mutant of Arabidopsis, the first division is symmetrical, and the resulting ball-shaped plant lacks roots and leaves.
    • Other genes that regulate pattern formation and morphogenesis include the homeotic genes, which mediate many developmental events, such as organ initiation.
      • For example, the protein product of the KNOTTED-1 homeotic gene is important for the development of leaf morphology, including production of compound leaves.
      • Overexpression of this gene causes the compound leaves of a tomato plant to become “supercompound.”

      Cellular differentiation depends on the control of gene expression.

    • The diverse cell types of a plant, including guard cells, sieve-tube members, and xylem vessel elements, all descend from a common cell, the zygote, and share the same DNA.
    • The cloning of whole plants from single somatic cells demonstrates that the genome of a differentiated cell remains intact and can “dedifferentiate” to give rise to the diverse cell types of a plant.
      • Cellular differentiation depends, to a large extent, on control of gene expression.
      • Cells with the same genomes follow different developmental pathways because they selectively express certain genes at specific times during differentiation.
    • For example, two distinct cell types in Arabidopsis, root hair cells and hairless epidermal cells, develop from immature epidermal cells.
      • Cells in contact with one underlying cortical cell differentiate into mature, hairless cells, while those in contact with two underlying cortical cells differentiate into root hair cells.
      • The homeotic gene GLABRA-2 is normally expressed only in hairless cells. If it is rendered dysfunctional, every root epidermal cell develops a root hair.

      Clonal analysis of the shoot apex emphasizes the importance of a cell’s location in its developmental fate.

    • In the process of shaping a rudimentary organ, patterns of cell division and cell expansion affect the differentiation of cells by placing them in specific locations relative to other cells.
    • Thus, positional information underlies all the processes of development: growth, morphogenesis, and differentiation.
    • One approach to studying the relationship among these processes is clonal analysis, mapping the cell lineages (clones) derived from each cell in an apical meristem as organs develop.
    • Researchers induce some change in a cell that tags it in some way such that it (and its descendents) can be distinguished from its neighbors.
      • For example, a somatic mutation in an apical cell that prevents chlorophyll production will produce an “albino” cell.
        • This cell and all its descendants will appear as a linear file of colorless cells running down the long axis of the green shoot.
    • To some extent, the developmental fates of cells in the shoot apex are predictable.
      • For example, clonal mapping has shown that almost all the cells derived from division of the outermost meristematic cells become part of the dermal tissue of leaves and stems.
    • However, it is not possible to pinpoint precisely which cells of the meristem will give rise to specific tissues and organs because random changes in rates and planes of cell division can reorganize the meristem.
      • For example, the outermost cells usually divide in a plane parallel to the surface of the shoot apex.
      • Occasionally, an outer cell divides in a plane perpendicular to this layer, placing one daughter cell beneath the surface, among cells derived from different lineages.
    • In plants, a cell’s developmental fate is determined not by its membership in a particular lineage but by its final position in an emerging organ.

      Phase changes mark major shifts in development.

    • In plants, developmental changes can occur within the shoot apical meristem, leading to a phase change in the organs produced.
      • One example of a phase change is the gradual transition from a juvenile phase to an adult phase.
      • In some plants, the result of the phase change is a change in the morphology of the leaves.
      • The leaves of juvenile versus mature shoot regions differ in shape and other features.
      • Once the meristem has laid down the juvenile nodes and internodes, they retain that status even as the shoot continues to elongate and the meristem changes to the mature phase.
    • If axillary buds give rise to branches, those shoots reflect the developmental phase of the main shoot region from which they arise.
      • Though the main shoot apex may have made the transition to the mature phase, the older region of the shoot continues to give rise to branches bearing juvenile leaves if that shoot region was laid down when the main apex was still in the juvenile phase.
      • A branch with juvenile leaves may actually be older than a branch with mature leaves.
    • The juvenile-to-mature phase transition points to another difference in the development of plants versus animals.
      • In an animal, this transition occurs at the level of the entire organism, as a larva develops into an adult animal.
      • In plants, phase changes during the history of apical meristems can result in juvenile and mature regions coexisting along the axis of each shoot.

      Genes controlling transcription play key roles in a meristem’s change from a vegetative to a floral phase.

    • Another striking phase change in plant development is the transition from a vegetative shoot tip to a floral meristem.
      • This transition is triggered by a combination of environmental cues, such as day length, and internal signals, such as hormones.
    • Unlike vegetative growth, which is indeterminate, the production of a flower by an apical meristem terminates primary growth of that shoot tip as the apical meristem develops into the flower’s organs.
      • This transition is associated with the switching on of floral meristem identity genes.
      • The protein products of these genes are transcription factors that help activate the genes required for the development of the floral meristem.
    • Once a shoot meristem is induced to flower, positional information commits each primordium arising from the flanks of the shoot tip to develop into a specific flower organ.
      • Organ identity genes regulate positional information and function in the development of the floral pattern.
        • Mutations in these genes may lead to the substitution of one type of floral organ for the expected one.
    • Organ identity genes code for transcription factors.
      • Positional information determines which organ identity genes are expressed in which particular floral-organ primordium.
      • In Arabidopsis, three classes of organ identity genes interact to produce the spatial pattern of floral organs.
      • The ABC model of flower formation identifies how these genes direct the formation of four types of floral organs.
        • The model proposes that each class of organ identity genes is switched on in two specific whorls of the floral meristem.
        • A genes are switched on in the two outer whorls (sepals and petals), B genes are switched on in the two middle whorls (petals and stamens), and C genes are switched on in the two inner whorls (stamens and carpels).
          • Sepals arise in those parts of the floral meristems in which only A genes are active.
          • Petals arise in those parts of the floral meristems in which A and B genes are active.
          • Stamens arise in those parts of the floral meristems in which B and C genes are active.
          • Carpels arise in those parts of the floral meristems in which only C genes are active.
      • The ABC model can account for the phenotypes of mutants lacking A, B, or C gene activity.

    Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 35-1

    Subject: 
    Subject X2: 

    Chapter 10 - Photosynthesis

    Chapter 10 Photosynthesis
    Lecture Outline

    Overview: The Process That Feeds the Biosphere

    • Life on Earth is solar powered.
    • The chloroplasts of plants use a process called photosynthesis to capture light energy from the sun and convert it to chemical energy stored in sugars and other organic molecules.

      Plants and other autotrophs are the producers of the biosphere.

    • Photosynthesis nourishes almost all the living world directly or indirectly.
      • All organisms use organic compounds for energy and for carbon skeletons.
      • Organisms obtain organic compounds by one of two major modes: autotrophic nutrition or heterotrophic nutrition.
    • Autotrophs produce their organic molecules from CO2 and other inorganic raw materials obtained from the environment.
      • Autotrophs are the ultimate sources of organic compounds for all heterotrophic organisms.
      • Autotrophs are the producers of the biosphere.
    • Autotrophs can be separated by the source of energy that drives their metabolism.
      • Photoautotrophs use light as a source of energy to synthesize organic compounds.
        • Photosynthesis occurs in plants, algae, some other protists, and some prokaryotes.
        • Chemoautotrophs harvest energy from oxidizing inorganic substances, such as sulfur and ammonia.
          • Chemoautotrophy is unique to prokaryotes.
    • Heterotrophs live on organic compounds produced by other organisms.
      • These organisms are the consumers of the biosphere.
      • The most obvious type of heterotrophs feeds on other organisms.
        • Animals feed this way.
      • Other heterotrophs decompose and feed on dead organisms or on organic litter, like feces and fallen leaves.
        • Most fungi and many prokaryotes get their nourishment this way.
      • Almost all heterotrophs are completely dependent on photoautotrophs for food and for oxygen, a by-product of photosynthesis.

    Concept 10.1 Photosynthesis converts light energy to the chemical energy of food

    • All green parts of a plant have chloroplasts.
    • However, the leaves are the major site of photosynthesis for most plants.
      • There are about half a million chloroplasts per square millimeter of leaf surface.
    • The color of a leaf comes from chlorophyll, the green pigment in the chloroplasts.
      • Chlorophyll plays an important role in the absorption of light energy during photosynthesis.
    • Chloroplasts are found mainly in mesophyll cells forming the tissues in the interior of the leaf.
    • O2 exits and CO2 enters the leaf through microscopic pores called stomata in the leaf.
    • Veins deliver water from the roots and carry off sugar from mesophyll cells to nonphotosynthetic areas of the plant.
    • A typical mesophyll cell has 30–40 chloroplasts, each about 2–4 microns by 4–7 microns long.
    • Each chloroplast has two membranes around a central aqueous space, the stroma.
    • In the stroma is an elaborate system of interconnected membranous sacs, the thylakoids.
      • The interior of the thylakoids forms another compartment, the thylakoid space.
      • Thylakoids may be stacked into columns called grana.
    • Chlorophyll is located in the thylakoids.
      • Photosynthetic prokaryotes lack chloroplasts.
      • Their photosynthetic membranes arise from infolded regions of the plasma membranes, folded in a manner similar to the thylakoid membranes of chloroplasts.

      Evidence that chloroplasts split water molecules enabled researchers to track atoms through photosynthesis.

    • Powered by light, the green parts of plants produce organic compounds and O2 from CO2 and H2O.
    • The equation describing the process of photosynthesis is:
      • 6CO2 + 12H2O + light energy --> C6H12O6 + 6O2+ 6H2O
      • C6H12O6 is glucose.
    • Water appears on both sides of the equation because 12 molecules of water are consumed, and 6 molecules are newly formed during photosynthesis.
    • We can simplify the equation by showing only the net consumption of water:
      • 6CO2 + 6H2O + light energy --> C6H12O6 + 6O2
    • The overall chemical change during photosynthesis is the reverse of cellular respiration.
    • In its simplest possible form: CO2 + H2O + light energy --> [CH2O] + O2
      • [CH2O] represents the general formula for a sugar.
    • One of the first clues to the mechanism of photosynthesis came from the discovery that the O2 given off by plants comes from H2O, not CO2.
      • Before the 1930s, the prevailing hypothesis was that photosynthesis split carbon dioxide and then added water to the carbon:
        • Step 1: CO2 --> C + O2
        • Step 2: C + H2O --> CH2O
      • C. B. van Niel challenged this hypothesis.
      • In the bacteria that he was studying, hydrogen sulfide (H2S), not water, is used in photosynthesis.
      • These bacteria produce yellow globules of sulfur as a waste, rather than oxygen.
      • Van Niel proposed this chemical equation for photosynthesis in sulfur bacteria:
        • CO2 + 2H2S --> [CH2O] + H2O + 2S
    • He generalized this idea and applied it to plants, proposing this reaction for their photosynthesis:
      • CO2 + 2H2O --> [CH2O] + H2O + O2
    • Thus, van Niel hypothesized that plants split water as a source of electrons from hydrogen atoms, releasing oxygen as a byproduct.
    • Other scientists confirmed van Niel’s hypothesis twenty years later.
      • They used 18O, a heavy isotope, as a tracer.
      • They could label either C18O2 or H218O.
      • They found that the 18O label only appeared in the oxygen produced in photosynthesis when water was the source of the tracer.
    • Hydrogen extracted from water is incorporated into sugar, and oxygen is released to the atmosphere (where it can be used in respiration).
    • Photosynthesis is a redox reaction.
      • It reverses the direction of electron flow in respiration.
    • Water is split and electrons transferred with H+ from water to CO2, reducing it to sugar.
      • Because the electrons increase in potential energy as they move from water to sugar, the process requires energy.
      • The energy boost is provided by light.

      Here is a preview of the two stages of photosynthesis.

    • Photosynthesis is two processes, each with multiple stages.
    • The light reactions (photo) convert solar energy to chemical energy.
    • The Calvin cycle (synthesis) uses energy from the light reactions to incorporate CO2 from the atmosphere into sugar.
    • In the light reactions, light energy absorbed by chlorophyll in the thylakoids drives the transfer of electrons and hydrogen from water to NADP+ (nicotinamide adenine dinucleotide phosphate), forming NADPH.
      • NADPH, an electron acceptor, provides reducing power via energized electrons to the Calvin cycle.
      • Water is split in the process, and O2 is released as a by-product.
    • The light reaction also generates ATP using chemiosmosis, in a process called photophosphorylation.
    • Thus light energy is initially converted to chemical energy in the form of two compounds: NADPH and ATP.
    • The Calvin cycle is named for Melvin Calvin who, with his colleagues, worked out many of its steps in the 1940s.
    • The cycle begins with the incorporation of CO2 into organic molecules, a process known as carbon fixation.
    • The fixed carbon is reduced with electrons provided by NADPH.
    • ATP from the light reactions also powers parts of the Calvin cycle.
    • Thus, it is the Calvin cycle that makes sugar, but only with the help of ATP and NADPH from the light reactions.
    • The metabolic steps of the Calvin cycle are sometimes referred to as the light-independent reactions, because none of the steps requires light directly.
    • Nevertheless, the Calvin cycle in most plants occurs during daylight, because that is when the light reactions can provide the NADPH and ATP the Calvin cycle requires.
    • While the light reactions occur at the thylakoids, the Calvin cycle occurs in the stroma.

    Concept 10.2 The light reactions convert solar energy to the chemical energy of ATP and NADPH

    • The thylakoids convert light energy into the chemical energy of ATP and NADPH.
    • Light is a form of electromagnetic radiation.
    • Like other forms of electromagnetic energy, light travels in rhythmic waves.
    • The distance between crests of electromagnetic waves is called the wavelength.
      • Wavelengths of electromagnetic radiation range from less than a nanometer (gamma rays) to more than a kilometer (radio waves).
    • The entire range of electromagnetic radiation is the electromagnetic spectrum.
    • The most important segment for life is a narrow band between 380 to 750 nm, the band of visible light.
    • While light travels as a wave, many of its properties are those of a discrete particle, the photon.
      • Photons are not tangible objects, but they do have fixed quantities of energy.
    • The amount of energy packaged in a photon is inversely related to its wavelength.
      • Photons with shorter wavelengths pack more energy.
    • While the sun radiates a full electromagnetic spectrum, the atmosphere selectively screens out most wavelengths, permitting only visible light to pass in significant quantities.
      • Visible light is the radiation that drives photosynthesis.
    • When light meets matter, it may be reflected, transmitted, or absorbed.
      • Different pigments absorb photons of different wavelengths, and the wavelengths that are absorbed disappear.
      • A leaf looks green because chlorophyll, the dominant pigment, absorbs red and blue light, while transmitting and reflecting green light.
    • A spectrophotometer measures the ability of a pigment to absorb various wavelengths of light.
      • It beams narrow wavelengths of light through a solution containing the pigment and measures the fraction of light transmitted at each wavelength.
      • An absorption spectrum plots a pigment’s light absorption versus wavelength.
    • The light reaction can perform work with those wavelengths of light that are absorbed.
    • There are several pigments in the thylakoid that differ in their absorption spectra.
      • Chlorophyll a, the dominant pigment, absorbs best in the red and violet-blue wavelengths and least in the green.
      • Other pigments with different structures have different absorption spectra.
    • Collectively, these photosynthetic pigments determine an overall action spectrum for photosynthesis.
      • An action spectrum measures changes in some measure of photosynthetic activity (for example, O2 release) as the wavelength is varied.
    • The action spectrum of photosynthesis was first demonstrated in 1883 in an elegant experiment performed by Thomas Engelmann.
      • In this experiment, different segments of a filamentous alga were exposed to different wavelengths of light.
      • Areas receiving wavelengths favorable to photosynthesis produced excess O2.
      • Engelmann used the abundance of aerobic bacteria that clustered along the alga at different segments as a measure of O2 production.
    • The action spectrum of photosynthesis does not match exactly the absorption spectrum of any one photosynthetic pigment, including chlorophyll a.
    • Only chlorophyll a participates directly in the light reaction, but accessory photosynthetic pigments absorb light and transfer energy to chlorophyll a.
      • Chlorophyll b, with a slightly different structure than chlorophyll a, has a slightly different absorption spectrum and funnels the energy from these wavelengths to chlorophyll a.
      • Carotenoids can funnel the energy from other wavelengths to chlorophyll a and also participate in photoprotection against excessive light.
      • These compounds absorb and dissipate excessive light energy that would otherwise damage chlorophyll.
      • They also interact with oxygen to form reactive oxidative molecules that could damage the cell.
    • When a molecule absorbs a photon, one of that molecule’s electrons is elevated to an orbital with more potential energy.
      • The electron moves from its ground state to an excited state.
      • The only photons that a molecule can absorb are those whose energy matches exactly the energy difference between the ground state and excited state of this electron.
      • Because this energy difference varies among atoms and molecules, a particular compound absorbs only photons corresponding to specific wavelengths.
      • Thus, each pigment has a unique absorption spectrum.
    • Excited electrons are unstable.
    • Generally, they drop to their ground state in a billionth of a second, releasing heat energy.
    • Some pigments, including chlorophyll, can also release a photon of light in a process called fluorescence.
      • If a solution of chlorophyll isolated from chloroplasts is illuminated, it will fluoresce and give off heat.
    • Chlorophyll excited by absorption of light energy produces very different results in an intact chloroplast than it does in isolation.
    • In the thylakoid membrane, chlorophyll is organized along with proteins and smaller organic molecules into photosystems.
    • A photosystem is composed of a reaction center surrounded by a light-harvesting complex.
    • Each light-harvesting complex consists of pigment molecules (which may include chlorophyll a, chlorophyll b, and carotenoid molecules) bound to particular proteins.
    • Together, these light-harvesting complexes act like light-gathering “antenna complexes” for the reaction center.
    • When any antenna molecule absorbs a photon, it is transmitted from molecule to molecule until it reaches a particular chlorophyll a molecule, the reaction center.
    • At the reaction center is a primary electron acceptor, which accepts an excited electron from the reaction center chlorophyll a.
      • The solar-powered transfer of an electron from a special chlorophyll a molecule to the primary electron acceptor is the first step of the light reactions.
    • Each photosystem—reaction-center chlorophyll and primary electron acceptor surrounded by an antenna complex—functions in the chloroplast as a light-harvesting unit.
    • There are two types of photosystems in the thylakoid membrane.
      • Photosystem I (PS I) has a reaction center chlorophyll a that has an absorption peak at 700 nm.
      • Photosystem II (PS II) has a reaction center chlorophyll a that has an absorption peak at 680 nm.
      • The differences between these reaction centers (and their absorption spectra) lie not in the chlorophyll molecules, but in the proteins associated with each reaction center.
      • These two photosystems work together to use light energy to generate ATP and NADPH.
    • During the light reactions, there are two possible routes for electron flow: cyclic and noncyclic.
      • Noncyclic electron flow, the predominant route, produces both ATP and NADPH.
        1. Photosystem II absorbs a photon of light. One of the electrons of P680 is excited to a higher energy state.
        2. This electron is captured by the primary electron acceptor, leaving the reaction center oxidized.
        3. An enzyme extracts electrons from water and supplies them to the oxidized reaction center. This reaction splits water into two hydrogen ions and an oxygen atom that combines with another oxygen atom to form O2.
        4. Photoexcited electrons pass along an electron transport chain before ending up at an oxidized photosystem I reaction center.
        5. As these electrons “fall” to a lower energy level, their energy is harnessed to produce ATP.
        6. Meanwhile, light energy has excited an electron of PS I’s P700 reaction center. The photoexcited electron was captured by PS I’s primary electron acceptor, creating an electron “hole” in P700. This hole is filled by an electron that reaches the bottom of the electron transport chain from PS II.
        7. Photoexcited electrons are passed from PS I’s primary electron acceptor down a second electron transport chain through the protein ferredoxin (Fd).
        8. The enzyme NADP+ reductase transfers electrons from Fd to NADP+. Two electrons are required for NADP+’s reduction to NADPH. NADPH will carry the reducing power of these high-energy electrons to the Calvin cycle.
    • The light reactions use the solar power of photons absorbed by both photosystem I and photosystem II to provide chemical energy in the form of ATP and reducing power in the form of the electrons carried by NADPH.
    • Under certain conditions, photoexcited electrons from photosystem I, but not photosystem II, can take an alternative pathway, cyclic electron flow.
      • Excited electrons cycle from their reaction center to a primary acceptor, along an electron transport chain, and return to the oxidized P700 chlorophyll.
      • As electrons flow along the electron transport chain, they generate ATP by cyclic photophosphorylation.
      • There is no production of NADPH and no release of oxygen.
    • What is the function of cyclic electron flow?
    • Noncyclic electron flow produces ATP and NADPH in roughly equal quantities.
    • However, the Calvin cycle consumes more ATP than NADPH.
    • Cyclic electron flow allows the chloroplast to generate enough surplus ATP to satisfy the higher demand for ATP in the Calvin cycle.
    • Chloroplasts and mitochondria generate ATP by the same mechanism: chemiosmosis.
      • In both organelles, an electron transport chain pumps protons across a membrane as electrons are passed along a series of increasingly electronegative carriers.
      • This transforms redox energy to a proton-motive force in the form of an H+ gradient across the membrane.
      • ATP synthase molecules harness the proton-motive force to generate ATP as H+ diffuses back across the membrane.
    • Some of the electron carriers, including the cytochromes, are very similar in chloroplasts and mitochondria.
    • The ATP synthase complexes of the two organelles are also very similar.
    • There are differences between oxidative phosphorylation in mitochondria and photophosphorylation in chloroplasts.
    • Mitochondria transfer chemical energy from food molecules to ATP; chloroplasts transform light energy into the chemical energy of ATP.
    • The spatial organization of chemiosmosis also differs in the two organelles.
    • The inner membrane of the mitochondrion pumps protons from the mitochondrial matrix out to the intermembrane space. The thylakoid membrane of the chloroplast pumps protons from the stroma into the thylakoid space inside the thylakoid.
    • The thylakoid membrane makes ATP as the hydrogen ions diffuse down their concentration gradient from the thylakoid space back to the stroma through ATP synthase complexes, whose catalytic knobs are on the stroma side of the membrane.
    • The proton gradient, or pH gradient, across the thylakoid membrane is substantial.
      • When chloroplasts are illuminated, the pH in the thylakoid space drops to about 5 and the pH in the stroma increases to about 8, a thousandfold different in H+ concentration.
    • The light-reaction “machinery” produces ATP and NADPH on the stroma side of the thylakoid.
    • Noncyclic electron flow pushes electrons from water, where they have low potential energy, to NADPH, where they have high potential energy.
      • This process also produces ATP and oxygen as a by-product.

    Concept 10.3 The Calvin cycle uses ATP and NADPH to convert CO2 to sugar

    • The Calvin cycle regenerates its starting material after molecules enter and leave the cycle.
    • The Calvin cycle is anabolic, using energy to build sugar from smaller molecules.
    • Carbon enters the cycle as CO2 and leaves as sugar.
    • The cycle spends the energy of ATP and the reducing power of electrons carried by NADPH to make sugar.
    • The actual sugar product of the Calvin cycle is not glucose, but a three-carbon sugar, glyceraldehyde-3-phosphate (G3P).
    • Each turn of the Calvin cycle fixes one carbon.
    • For the net synthesis of one G3P molecule, the cycle must take place three times, fixing three molecules of CO2.
    • To make one glucose molecule requires six cycles and the fixation of six CO2 molecules.
    • The Calvin cycle has three phases.

      Phase 1: Carbon fixation

    • In the carbon fixation phase, each CO2 molecule is attached to a five-carbon sugar, ribulose bisphosphate (RuBP).
      • This is catalyzed by RuBP carboxylase or rubisco.
      • Rubisco is the most abundant protein in chloroplasts and probably the most abundant protein on Earth.
      • The six-carbon intermediate is unstable and splits in half to form two molecules of 3-phosphoglycerate for each CO2.

      Phase 2: Reduction

    • During reduction, each 3-phosphoglycerate receives another phosphate group from ATP to form 1,3-bisphosphoglycerate.
    • A pair of electrons from NADPH reduces each 1,3-bisphosphoglycerate to G3P.
      • The electrons reduce a carboxyl group to the aldehyde group of G3P, which stores more potential energy.
    • If our goal was the net production of one G3P, we would start with 3CO2 (3C) and three RuBP (15C).
    • After fixation and reduction, we would have six molecules of G3P (18C).
      • One of these six G3P (3C) is a net gain of carbohydrate.
        • This molecule can exit the cycle and be used by the plant cell.

      Phase 3: Regeneration

    • The other five G3P (15C) remain in the cycle to regenerate three RuBP. In a complex series of reactions, the carbon skeletons of five molecules of G3P are rearranged by the last steps of the Calvin cycle to regenerate three molecules of RuBP.
    • For the net synthesis of one G3P molecule, the Calvin cycle consumes nine ATP and six NADPH.
    • The light reactions regenerate ATP and NADPH.
    • The G3P from the Calvin cycle is the starting material for metabolic pathways that synthesize other organic compounds, including glucose and other carbohydrates.

    Concept 10.4 Alternative mechanisms of carbon fixation have evolved in hot, arid climates

    • One of the major problems facing terrestrial plants is dehydration.
    • At times, solutions to this problem require tradeoffs with other metabolic processes, especially photosynthesis.
    • The stomata are not only the major route for gas exchange (CO2 in and O2 out), but also for the evaporative loss of water.
    • On hot, dry days, plants close their stomata to conserve water. This causes problems for photosynthesis.
    • In most plants (C3 plants), initial fixation of CO2 occurs via rubisco, forming a three-carbon compound, 3-phosphoglycerate.
      • C3 plants include rice, wheat, and soybeans.
    • When their stomata partially close on a hot, dry day, CO2 levels drop as CO2 is consumed in the Calvin cycle.
    • At the same time, O2 levels rise as the light reaction converts light to chemical energy.
    • While rubisco normally accepts CO2, when the O2:CO2 ratio increases (on a hot, dry day with closed stomata), rubisco can add O2 to RuBP.
    • When rubisco adds O2 to RuBP, RuBP splits into a three-carbon piece and a two-carbon piece in a process called photorespiration.
      • The two-carbon fragment is exported from the chloroplast and degraded to CO2 by mitochondria and peroxisomes.
      • Unlike normal respiration, this process produces no ATP.
        • In fact, photorespiration consumes ATP.
      • Unlike photosynthesis, photorespiration does not produce organic molecules.
        • In fact, photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle.
    • A hypothesis for the existence of photorespiration is that it is evolutionary baggage.
    • When rubisco first evolved, the atmosphere had far less O2 and more CO2 than it does today.
      • The inability of the active site of rubisco to exclude O2 would have made little difference.
    • Today it does make a difference.
      • Photorespiration can drain away as much as 50% of the carbon fixed by the Calvin cycle on a hot, dry day.
    • Certain plant species have evolved alternate modes of carbon fixation to minimize photorespiration.
    • C4 plants first fix CO2 in a four-carbon compound.
      • Several thousand plants, including sugarcane and corn, use this pathway.
    • A unique leaf anatomy is correlated with the mechanism of C4 photosynthesis.
    • In C4 plants, there are two distinct types of photosynthetic cells: bundle-sheath cells and mesophyll cells.
      • Bundle-sheath cells are arranged into tightly packed sheaths around the veins of the leaf.
      • Mesophyll cells are more loosely arranged cells located between the bundle sheath and the leaf surface.
    • The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells.
    • However, the cycle is preceded by the incorporation of CO2 into organic molecules in the mesophyll.
    • The key enzyme, phosphoenolpyruvate carboxylase, adds CO2 to phosphoenolpyruvate (PEP) to form oxaloacetate.
      • PEP carboxylase has a very high affinity for CO2 and can fix CO2 efficiently when rubisco cannot (i.e., on hot, dry days when the stomata are closed).
    • The mesophyll cells pump these four-carbon compounds into bundle-sheath cells.
      • The bundle-sheath cells strip a carbon from the four-carbon compound as CO2, and return the three-carbon remainder to the mesophyll cells.
      • The bundle-sheath cells then use rubisco to start the Calvin cycle with an abundant supply of CO2.
    • In effect, the mesophyll cells pump CO2 into the bundle-sheath cells, keeping CO2 levels high enough for rubisco to accept CO2 and not O2.
    • C4 photosynthesis minimizes photorespiration and enhances sugar production.
    • C4 plants thrive in hot regions with intense sunlight.
    • A second strategy to minimize photorespiration is found in succulent plants, cacti, pineapples, and several other plant families.
      • These plants are known as CAM plants for crassulacean acid metabolism.
      • They open their stomata during the night and close them during the day.
        • Temperatures are typically lower at night, and humidity is higher.
      • During the night, these plants fix CO2 into a variety of organic acids in mesophyll cells.
      • During the day, the light reactions supply ATP and NADPH to the Calvin cycle, and CO2 is released from the organic acids.
    • Both C4 and CAM plants add CO2 into organic intermediates before it enters the Calvin cycle.
      • In C4 plants, carbon fixation and the Calvin cycle are spatially separated.
      • In CAM plants, carbon fixation and the Calvin cycle are temporally separated.
    • Both eventually use the Calvin cycle to make sugar from carbon dioxide.

      Here is a review of the importance of photosynthesis.

    • In photosynthesis, the energy that enters the chloroplasts as sunlight becomes stored as chemical energy in organic compounds.
    • Sugar made in the chloroplasts supplies the entire plant with chemical energy and carbon skeletons to synthesize all the major organic molecules of cells.
      • About 50% of the organic material is consumed as fuel for cellular respiration in plant mitochondria.
      • Carbohydrate in the form of the disaccharide sucrose travels via the veins to nonphotosynthetic cells.
        • There, it provides fuel for respiration and the raw materials for anabolic pathways, including synthesis of proteins and lipids and formation of the extracellular polysaccharide cellulose.
        • Cellulose, the main ingredient of cell walls, is the most abundant organic molecule in the plant, and probably on the surface of the planet.
    • Plants also store excess sugar by synthesis of starch.
      • Starch is stored in chloroplasts and in storage cells in roots, tubers, seeds, and fruits.
    • Heterotrophs, including humans, may completely or partially consume plants for fuel and raw materials.
    • On a global scale, photosynthesis is the most important process on Earth.
      • It is responsible for the presence of oxygen in our atmosphere.
      • Each year, photosynthesis synthesizes 160 billion metric tons of carbohydrate.

    Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 10-1

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    Chapter 11 - Cell Communication

    Chapter 11 Cell Communication
    Lecture Outline

    Overview: The Cellular Internet

    • Cell-to-cell communication is absolutely essential for multicellular organisms.
    • Cells must communicate to coordinate their activities.
    • Communication between cells is also important for many unicellular organisms.
    • Biologists have discovered universal mechanisms of cellular regulation involving the same small set of cell-signaling mechanisms.
      • The ubiquity of these mechanisms provides additional evidence for the evolutionary relatedness of all life.
    • Cells most often communicate by chemical signals, although signals may take other forms.

    Concept 11.1 External signals are converted into responses within the cell

    • What messages are passed from cell to cell? How do cells respond to these messages?
    • We will first consider communication in microbes, to gain insight into the evolution of cell signaling.

      Cell signaling evolved early in the history of life.

    • One topic of cell “conversation” is sex.
    • Saccharomyces cerevisiae, the yeast of bread, wine, and beer, identifies potential mates by chemical signaling.
      • There are two sexes, a and ?, each of which secretes a specific signaling molecule, a factor and ? factor, respectively.
      • These factors each bind to receptor proteins on the other mating type.
    • Once the mating factors have bound to the receptors, the two cells grow toward each other and undergo other cellular changes.
    • The two cells fuse, or mate, to form an a/? cell containing the genes of both cells.
    • The process by which a signal on a cell’s surface is converted into a specific cellular response is a series of steps called a signal-transduction pathway.
      • The molecular details of these pathways are strikingly similar in yeast and animal cells, even though their last common ancestor lived more than a billion years ago.
      • Signaling systems of bacteria and plants also share similarities.
    • These similarities suggest that ancestral signaling molecules evolved long ago in prokaryotes and have since been adopted for new uses by single-celled eukaryotes and multicellular descendents.

      Communicating cells may be close together or far apart.

    • Multicellular organisms release signaling molecules that target other cells.
    • Cells may communicate by direct contact.
      • Both animals and plants have cell junctions that connect to the cytoplasm of adjacent cells.
      • Signaling substances dissolved in the cytosol can pass freely between adjacent cells.
      • Animal cells can communicate by direct contact between membrane-bound cell surface molecules.
      • Such cell-cell recognition is important to such processes as embryonic development and the immune response.
    • In other cases, messenger molecules are secreted by the signaling cell.
      • Some transmitting cells release local regulators that influence cells in the local vicinity.
      • One class of local regulators in animals, growth factors, includes compounds that stimulate nearby target cells to grow and multiply.
      • This is an example of paracrine signaling, which occurs when numerous cells simultaneously receive and respond to growth factors produced by a single cell in their vicinity.
    • In synaptic signaling, a nerve cell produces a neurotransmitter that diffuses across a synapse to a single cell that is almost touching the sender.
      • The neurotransmitter stimulates the target cell.
      • The transmission of a signal through the nervous system can also be considered an example of long-distance signaling.
    • Local signaling in plants is not well understood. Because of their cell walls, plants must have different mechanisms from animals.
    • Plants and animals use hormones for long-distance signaling.
      • In animals, specialized endocrine cells release hormones into the circulatory system, by which they travel to target cells in other parts of the body.
      • Plant hormones, called growth regulators, may travel in vessels but more often travel from cell to cell or move through air by diffusion.
    • Hormones and local regulators range widely in size and type.
      • The plant hormone ethylene (C2H4), which promotes fruit ripening and regulates growth, is a hydrocarbon of only six atoms, capable of passing through cell walls.
      • Insulin, which regulates blood sugar levels in mammals, is a protein with thousands of atoms.
    • What happens when a cell encounters a signal?
      • The signal must be recognized by a specific receptor molecule, and the information it carries must be changed into another form, or transduced, inside the cell before the cell can respond.

      The three stages of cell signaling are reception, transduction, and response.

    • E. W. Sutherland and his colleagues pioneered our understanding of cell signaling.
      • Their work investigated how the animal hormone epinephrine stimulates breakdown of the storage polysaccharide glycogen in liver and skeletal muscle.
      • Breakdown of glycogen releases glucose derivatives that can be used for fuel in glycolysis or released as glucose in the blood for fuel elsewhere.
      • Thus one effect of epinephrine, which is released from the adrenal gland during times of physical or mental stress, is mobilization of fuel reserves.
    • Sutherland’s research team discovered that epinephrine activated a cytosolic enzyme, glycogen phosphorylase.
      • However, epinephrine did not activate the phosphorylase directly in vitro but could only act via intact cells.
      • Therefore, there must be an intermediate step or steps occurring inside the cell.
      • The plasma membrane must be involved in transmitting the epinephrine signal.
    • The process involves three stages: reception, transduction, and response.
      • In reception, a chemical signal binds to a cellular protein, typically at the cell’s surface or inside the cell.
      • In transduction, binding leads to a change in the receptor that triggers a series of changes in a series of different molecules along a signal-transduction pathway. The molecules in the pathway are called relay molecules.
      • In response, the transduced signal triggers a specific cellular activity.

    Concept 11.2 Reception: A signal molecule binds to a receptor protein, causing it to change shape

    • The cell targeted by a particular chemical signal has a receptor protein on or in the target cell that recognizes the signal molecule.
      • Recognition occurs when the signal binds to a specific site on the receptor that is complementary in shape to the signal.
    • The signal molecule behaves as a ligand, a small molecule that binds with specificity to a larger molecule.
    • Ligand binding causes the receptor protein to undergo a change in shape.
    • This may activate the receptor so that it can interact with other molecules.
      • For other receptors, this causes aggregation of receptor molecules, leading to further molecular events inside the cell.
    • Most signal receptors are plasma membrane proteins, whose ligands are large water-soluble molecules that are too large to cross the plasma membrane.

      Some receptor proteins are intracellular.

    • Some signal receptors are dissolved in the cytosol or nucleus of target cells.
      • To reach these receptors, the signals pass through the target cell’s plasma membrane.
      • Such chemical messengers are either hydrophobic enough or small enough to cross the phospholipid interior of the plasma membrane.
    • Hydrophobic messengers include the steroid and thyroid hormones of animals.
    • Nitric oxide (NO) is a gas whose small size allows it to pass between membrane phospholipids.
    • Testosterone is secreted by the testis and travels through the blood to enter cells throughout the body.
      • The cytosol of target cells contains receptor molecules that bind testosterone, activating the receptor.
      • These activated proteins enter the nucleus and turn on specific genes that control male sex characteristics.
    • How does the activated hormone-receptor complex turn on genes?
    • These activated proteins act as transcription factors.
    • Transcription factors control which genes are turned on—that is, which genes are transcribed into messenger RNA.
    • mRNA molecules leave the nucleus and carry information that directs the synthesis (translation) of specific proteins at the ribosome.
    • Other intracellular receptors (such as thyroid hormone receptors) are found in the nucleus and bind to the signal molecules there.

      Most signal receptors are plasma membrane proteins.

    • Most signal molecules are water-soluble and too large to pass through the plasma membrane.
    • They influence cell activities by binding to receptor proteins on the plasma membrane.
      • Binding leads to changes in the shape of the receptor or to the aggregation of receptors.
      • These cause changes in the intracellular environment.
    • There are three major types of membrane receptors: G-protein-linked receptors, receptor tyrosine kinases, and ion-channel receptors.
    • A G-protein-linked receptor consists of a receptor protein associated with a G protein on the cytoplasmic side.
      • Seven alpha helices span the membrane.
      • G-protein-linked receptors bind many different signal molecules, including yeast mating factors, epinephrine and many other hormones, and neurotransmitters.
    • The G protein acts as an on/off switch.
      • If GDP is bound to the G protein, the G protein is inactive.
      • When the appropriate signal molecule binds to the extracellular side of the receptor, the G protein binds GTP (instead of GDP) and becomes active.
      • The activated G protein dissociates from the receptor and diffuses along the membrane, where it binds to an enzyme, altering its activity.
      • The activated enzyme triggers the next step in a pathway leading to a cellular response.
    • The G protein can also act as a GTPase enzyme to hydrolyze GTP to GDP.
      • This change turns the G protein off.
    • Now inactive, the G protein leaves the enzyme, which returns to its original state.
    • The whole system can be shut down quickly when the extracellular signal molecule is no longer present.
    • G-protein receptor systems are extremely widespread and diverse in their functions.
      • They play important roles during embryonic development.
      • Vision and smell in humans depend on these proteins.
    • Similarities among G proteins and G-protein-linked receptors of modern organisms suggest that this signaling system evolved very early.
    • Several human diseases involve G-protein systems.
      • Bacterial infections causing cholera and botulism interfere with G-protein function.
    • The tyrosine-kinase receptor system is especially effective when the cell needs to trigger several signal transduction pathways and cellular responses at once.
      • This system helps the cell regulate and coordinate many aspects of cell growth and reproduction.
    • The tyrosine-kinase receptor belongs to a major class of plasma membrane receptors that have enzymatic activity.
      • A kinase is an enzyme that catalyzes the transfer of phosphate groups.
      • The cytoplasmic side of these receptors functions as a tyrosine kinase, transferring a phosphate group from ATP to tyrosine on a substrate protein.
    • An individual tyrosine-kinase receptor consists of several parts:
      • An extracellular signal-binding site.
      • A single alpha helix spanning the membrane.
      • An intracellular tail with several tyrosines.
    • The signal molecule binds to an individual receptor.
      • Ligands bind to two receptors, causing the two receptors to aggregate and form a dimer.
    • This dimerization activates the tyrosine-kinase section of the receptors, each of which then adds phosphate from ATP to the tyrosine tail of the other polypeptide.
    • The fully activated receptor proteins activate a variety of specific relay proteins that bind to specific phosphorylated tyrosine molecules.
      • One tyrosine-kinase receptor dimer may activate ten or more different intracellular proteins simultaneously.
      • These activated relay proteins trigger many different transduction pathways and responses.
    • A ligand-gated ion channel is a type of membrane receptor that can act as a gate when the receptor changes shape.
    • When a signal molecule binds as a ligand to the receptor protein, the gate opens to allow the flow of specific ions, such as Na+ or Ca2+, through a channel in the receptor.
      • Binding by a ligand to the extracellular side changes the protein’s shape and opens the channel.
      • When the ligand dissociates from the receptor protein, the channel closes.
    • The change in ion concentration within the cell may directly affect the activity of the cell.
    • Ligand-gated ion channels are very important in the nervous system.
      • For example, neurotransmitter molecules released at a synapse between two neurons bind as ligands to ion channels on the receiving cell, causing the channels to open.
      • Ions flow in and trigger an electrical signal that propagates down the length of the receiving cell.
    • Some gated ion channels respond to electrical signals, instead of ligands.

    Concept 11.3 Transduction: Cascades of molecular interactions relay signals from receptors to target molecules in the cell

    • The transduction stage of signaling is usually a multistep pathway.
    • These pathways often greatly amplify the signal.
      • If some molecules in a pathway transmit a signal to multiple molecules of the next component in the series, the result can be large numbers of activated molecules at the end of the pathway.
    • A small number of signal molecules can produce a large cellular response.
    • Also, multistep pathways provide more opportunities for coordination and regulation than do simpler systems.

      Pathways relay signals from receptors to cellular responses.

    • Signal-transduction pathways act like falling dominoes.
      • The signal-activated receptor activates another protein, which activates another, and so on, until the protein that produces the final cellular response is activated.
    • The relay molecules that relay a signal from receptor to response are mostly proteins.
      • The interaction of proteins is a major theme of cell signaling.
      • Protein interaction is a unifying theme of all cellular regulation.
    • The original signal molecule is not passed along the pathway and may not even enter the cell.
      • It passes on information.
      • At each step, the signal is transduced into a different form, often by a conformational change in a protein.
      • The conformational change is often brought about by phosphorylation.

      Protein phosphorylation, a common mode of regulation in cells, is a major mechanism of signal transduction.

    • The phosphorylation of proteins by a specific enzyme (a protein kinase) is a widespread cellular mechanism for regulating protein activity.
      • Most protein kinases act on other substrate proteins, unlike tyrosine kinases that act on themselves.
    • Most phosphorylation occurs at either serine or threonine amino acids of the substrate protein (unlike tyrosine phosphorylation in tyrosine kinases).
    • Many of the relay molecules in a signal-transduction pathway are protein kinases that act on other protein kinases to create a “phosphorylation cascade.”
    • Each protein phosphorylation leads to a conformational change because of the interaction between the newly added phosphate group and charged or polar amino acids on the protein.
    • Phosphorylation of a protein typically converts it from an inactive form to an active form.
      • Rarely, phosphorylation inactivates protein activity.
    • A single cell may have hundreds of different protein kinases, each specific for a different substrate protein.
      • Fully 2% of our genes are thought to code for protein kinases.
      • Together, they regulate a large proportion of the thousands of cell proteins.
    • Abnormal activity of protein kinases can cause abnormal cell growth and may contribute to the development of cancer.
    • The responsibility for turning off a signal-transduction pathway belongs to protein phosphatases.
      • These enzymes rapidly remove phosphate groups from proteins, a process called dephosphorylation.
      • Phosphatases also make the protein kinases available for reuse, enabling the cell to respond again to a signal.
    • At any given moment, the activity of a protein regulated by phosphorylation depends on the balance of active kinase molecules and active phosphatase molecules.
    • When the extracellular signal molecule is absent, active phosphatase molecules predominate, and the signaling pathway and cellular response are shut down.
    • The phosphorylation/dephosphorylation system acts as a molecular switch in the cell, turning activities on and off as required.

      Certain signal molecules and ions are key components of signaling pathways (second messengers).

    • Many signaling pathways involve small, water-soluble, nonprotein molecules or ions called second messengers.
      • These molecules rapidly diffuse throughout the cell.
    • Second messengers participate in pathways initiated by both G-protein-linked receptors and tyrosine-kinase receptors.
      • Two of the most widely used second messengers are cyclic AMP and Ca2+.
    • Once Sutherland knew that epinephrine caused glycogen breakdown without entering the cell, he looked for a second messenger inside the cell.
    • Binding by epinephrine leads to increases in the cytosolic concentration of cyclic AMP, or cAMP.
      • This occurs because the activated receptor activates adenylyl cyclase, which converts ATP to cAMP.
      • The normal cellular concentration of cAMP can be boosted twentyfold within seconds.
      • cAMP is short-lived, as phosphodiesterase converts it to AMP.
      • Another surge of epinephrine is needed to reboost the cytosolic concentration of cAMP.
    • Caffeine-containing beverages such as coffee provide an artificial way to keep the body alert.
      • Caffeine blocks the conversion of cAMP to AMP, maintaining the system in a state of activation in the absence of epinephrine.
    • Many hormones and other signal molecules trigger the formation of cAMP.
      • G-protein-linked receptors, G proteins, and protein kinases are other components of cAMP pathways.
      • cAMP diffuses through the cell and activates a serine/threonine kinase called protein kinase A.
      • The activated kinase phosphorylates various other proteins.
    • Regulation of cell metabolism is also provided by G-protein systems that inhibit adenylyl cyclase.
      • These use a different signal molecule to activate a different receptor that activates an inhibitory G protein.
    • Certain microbes cause disease by disrupting G-protein signaling pathways.
      • The cholera bacterium, Vibrio cholerae, may be present in water contaminated with human feces.
      • This bacterium colonizes the small intestine and produces a toxin that modifies a G protein that regulates salt and water secretion.
      • The modified G protein is unable to hydrolyze GTP to GDP and remains stuck in its active form, continuously stimulating adenylyl cyclase to make cAMP.
      • The resulting high concentration of cAMP causes the intestinal cells to secrete large amounts of water and salts into the intestines, leading to profuse diarrhea and death from loss of water and salts.
    • Treatments for certain human conditions involve signaling pathways.
      • One pathway uses cyclic GMP, or cGMP, as a signaling molecule. Its effects include the relaxation of smooth muscle cells in artery walls.
      • A compound was developed to treat chest pains. This compound inhibits the hydrolysis of cGMP to GMP, prolonging the signal and increasing blood flow to the heart muscle.
      • Under the trade name Viagra, this compound is now widely used as a treatment for erectile dysfunction. Viagra causes dilation of blood vessels, allowing increased blood flow to the penis.
    • Many signal molecules in animals induce responses in their target cells via signal-transduction pathways that increase the cytosolic concentration of Ca2+.
      • In animal cells, increases in Ca2+ may cause contraction of muscle cells, secretion of certain substances, and cell division.
      • In plant cells, increases in Ca2+ trigger responses such as the pathway for greening in response to light.
    • Cells use Ca2+ as a second messenger in both G-protein pathways and tyrosine-kinase pathways.
    • The Ca2+ concentration in the cytosol is typically much lower than that outside the cell, often by a factor of 10,000 or more.
      • Various protein pumps transport Ca2+ outside the cell or into the endoplasmic reticulum or other organelles.
      • As a result, the concentration of Ca2+ in the ER is usually much higher than the concentration in the cytosol.
    • Because cytosolic Ca2+ is so low, small changes in the absolute numbers of ions causes a relatively large percentage change in Ca2+ concentration.
    • Signal-transduction pathways trigger the release of Ca2+ from the cell’s ER.
    • The pathways leading to release involve still other second messengers, diacylglycerol (DAG) and inositol trisphosphate (IP3).
      • DAG and IP3 are created when a phospholipase cleaves membrane phospholipid PIP2.
      • The phospholipase may be activated by a G protein or by a tyrosine-kinase receptor.
      • IP3 activates a gated-calcium channel, releasing Ca2+ from the ER.
    • Calcium ions activate the next protein in a signal-transduction pathway.

    Concept 11.4 Response: Cell signaling leads to regulation of cytoplasmic activities or transcription

    • Ultimately, a signal-transduction pathway leads to the regulation of one or more cellular activities.
      • This may be the opening or closing of an ion channel or a change in cell metabolism.
      • For example, epinephrine helps regulate cellular energy metabolism by activating enzymes that catalyze the breakdown of glycogen.
    • The stimulation of glycogen breakdown by epinephrine involves a G-protein-linked receptor, a G protein, adenylyl cyclase, cAMP, and several protein kinases before glycogen phosphorylase is activated.
    • Other signaling pathways do not regulate the activity of enzymes but the synthesis of enzymes or other proteins.
    • Activated receptors may act as transcription factors that turn specific genes on or off in the nucleus.

      Elaborate pathways amplify and specify the cell’s response to signals.

    • Signaling pathways with multiple steps have two benefits.
      1. They amplify the response to a signal.
      2. They contribute to the specificity of the response.
    • At each catalytic step in a cascade, the number of activated products is much greater than in the preceding step.
      • In the epinephrine-triggered pathway, binding by a small number of epinephrine molecules can lead to the release of hundreds of millions of glucose molecules.
    • Various types of cells may receive the same signal but produce very different responses.
      • For example, epinephrine triggers liver or striated muscle cells to break down glycogen, but stimulates cardiac muscle cells to contract, leading to a rapid heartbeat.
    • The explanation for this specificity is that different kinds of cells have different collections of proteins.
      • The response of a particular cell to a signal depends on its particular collection of receptor proteins, relay proteins, and proteins needed to carry out the response.
      • Two cells that respond differently to the same signal differ in one or more of the proteins that handle and respond to the signal.
    • A signal may trigger a single pathway in one cell but trigger a branched pathway in another.
    • Two pathways may converge to modulate a single response.
    • Branching of pathways and interactions between pathways are important for regulating and coordinating a cell’s response to incoming information.
    • Rather than relying on diffusion of large relay molecules such as proteins, many signal pathways are linked together physically by scaffolding proteins.
      • Scaffolding proteins may themselves be relay proteins to which several other relay proteins attach.
      • This hardwiring enhances the speed, accuracy, and efficiency of signal transfer between cells.
    • The importance of relay proteins that serve as branch or intersection points in signaling pathways is underscored when these proteins are defective or missing.
      • The inherited disorder Wiskott-Aldrich syndrome (WAS) is caused by the absence of a single relay protein.
      • Symptoms include abnormal bleeding, eczema, and a predisposition to infections and leukemia, due largely to the absence of the protein in the cells of the immune system.
      • The WAS protein is located just beneath the cell surface, where it interacts with the microfilaments of the cytoskeleton and with several signaling pathways, including those that regulate immune cell proliferation.
      • When the WAS protein is absent, the cytoskeleton is not properly organized and signaling pathways are disrupted.
    • As important as activating mechanisms are inactivation mechanisms.
      • For a cell to remain alert and capable of responding to incoming signals, each molecular change in its signaling pathways must last only a short time.
      • If signaling pathway components become locked into one state, whether active or inactive, the proper function of the cell can be disrupted.
      • Binding of signal molecules to receptors must be reversible, allowing the receptors to return to their inactive state when the signal is released.
      • Similarly, activated signals (cAMP and phosphorylated proteins) must be inactivated by appropriate enzymes to prepare the cell for a fresh signal.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 11-1

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    Chapter 12 - The Cell Cycle

    Chapter 12 The Cell Cycle
    Lecture Outline

    Overview: The Key Roles of Cell Division

    • The ability of organisms to reproduce their kind is the one characteristic that best distinguishes living things from nonliving matter.
    • The continuity of life is based on the reproduction of cells, or cell division.

      Cell division functions in reproduction, growth, and repair.

    • The division of a unicellular organism reproduces an entire organism, increasing the population.
    • Cell division on a larger scale can produce progeny for some multicellular organisms.
    • This includes organisms that can grow by cuttings.
    • Cell division enables a multicellular organism to develop from a single fertilized egg or zygote.
    • In a multicellular organism, cell division functions to repair and renew cells that die from normal wear and tear or accidents.
    • Cell division is part of the cell cycle, the life of a cell from its origin in the division of a parent cell until its own division into two.

    Concept 12.1 Cell division results in genetically identical daughter cells

    • Cell division requires the distribution of identical genetic material—DNA—to two daughter cells.
    • What is remarkable is the fidelity with which DNA is passed along, without dilution, from one generation to the next.
    • A dividing cell duplicates its DNA, allocates the two copies to opposite ends of the cell, and then splits into two daughter cells.
    • A cell’s genetic information, packaged as DNA, is called its genome.
      • In prokaryotes, the genome is often a single long DNA molecule.
      • In eukaryotes, the genome consists of several DNA molecules.
    • A human cell must duplicate about 2 m of DNA and separate the two copies such that each daughter cell ends up with a complete genome.
    • DNA molecules are packaged into chromosomes.
      • Every eukaryotic species has a characteristic number of chromosomes in each cell nucleus.
        • Human somatic cells (body cells) have 46 chromosomes, made up of two sets of 23 (one from each parent).
        • Human gametes (sperm or eggs) have one set of 23 chromosomes, half the number in a somatic cell.
    • Eukaryotic chromosomes are made of chromatin, a complex of DNA and associated protein.
      • Each single chromosome contains one long, linear DNA molecule carrying hundreds or thousands of genes, the units that specify an organism’s inherited traits.
    • The associated proteins maintain the structure of the chromosome and help control gene activity.
    • When a cell is not dividing, each chromosome is in the form of a long, thin chromatin fiber.
    • Before cell division, chromatin condenses, coiling and folding to make a smaller package.
    • Each duplicated chromosome consists of two sister chromatids, which contain identical copies of the chromosome’s DNA.
      • The chromatids are initially attached by adhesive proteins along their lengths.
      • As the chromosomes condense, the region where the chromatids connect shrinks to a narrow area, the centromere.
    • Later in cell division, the sister chromatids are pulled apart and repackaged into two new nuclei at opposite ends of the parent cell.
      • Once the sister chromatids separate, they are considered individual chromosomes.
    • Mitosis, the formation of the two daughter nuclei, is usually followed by division of the cytoplasm, cytokinesis.
    • These processes start with one cell and produce two cells that are genetically identical to the original parent cell.
      • Each of us inherited 23 chromosomes from each parent: one set in an egg and one set in sperm.
      • The fertilized egg, or zygote, underwent cycles of mitosis and cytokinesis to produce a fully developed multicellular human made up of 200 trillion somatic cells.
      • These processes continue every day to replace dead and damaged cells.
      • Essentially, these processes produce clones—cells with identical genetic information.
    • In contrast, gametes (eggs or sperm) are produced only in gonads (ovaries or testes) by a variation of cell division called meiosis.
      • Meiosis yields four nonidentical daughter cells, each with half the chromosomes of the parent.
      • In humans, meiosis reduces the number of chromosomes from 46 to 23.
      • Fertilization fuses two gametes together and doubles the number of chromosomes to 46 again.

    Concept 12.2 The mitotic phase alternates with interphase in the cell cycle

    • The mitotic (M) phase of the cell cycle alternates with the much longer interphase.
      • The M phase includes mitosis and cytokinesis.
      • Interphase accounts for 90% of the cell cycle.
    • During interphase, the cell grows by producing proteins and cytoplasmic organelles, copies its chromosomes, and prepares for cell division.
    • Interphase has three subphases: the G1 phase (“first gap”), the S phase (“synthesis”), and the G2 phase (“second gap”).
      • During all three subphases, the cell grows by producing proteins and cytoplasmic organelles such as mitochondria and endoplasmic reticulum.
      • However, chromosomes are duplicated only during the S phase.
    • The daughter cells may then repeat the cycle.
    • A typical human cell might divide once every 24 hours.
      • Of this time, the M phase would last less than an hour, while the S phase might take 10–12 hours, or half the cycle.
      • The rest of the time would be divided between the G1 and G2 phases.
      • The G1 phase varies most in length from cell to cell.
    • Mitosis is a continuum of changes.
    • For convenience, mitosis is usually broken into five subphases: prophase, prometaphase, metaphase, anaphase, and telophase.
    • In late interphase, the chromosomes have been duplicated but are not condensed.
      • A nuclear membrane bounds the nucleus, which contains one or more nucleoli.
      • The centrosome has replicated to form two centrosomes.
      • In animal cells, each centrosome features two centrioles.
    • In prophase, the chromosomes are tightly coiled, with sister chromatids joined together.
      • The nucleoli disappear.
      • The mitotic spindle begins to form.
        • It is composed of centrosomes and the microtubules that extend from them.
      • The radial arrays of shorter microtubules that extend from the centrosomes are called asters.
      • The centrosomes move away from each other, apparently propelled by lengthening microtubules.
    • During prometaphase, the nuclear envelope fragments, and microtubules from the spindle interact with the condensed chromosomes.
      • Each of the two chromatids of a chromosome has a kinetochore, a specialized protein structure located at the centromere.
      • Kinetochore microtubules from each pole attach to one of two kinetochores.
      • Nonkinetochore microtubules interact with those from opposite ends of the spindle.
    • The spindle fibers push the sister chromatids until they are all arranged at the metaphase plate, an imaginary plane equidistant from the poles, defining metaphase.
    • At anaphase, the centromeres divide, separating the sister chromatids.
      • Each is now pulled toward the pole to which it is attached by spindle fibers.
      • By the end, the two poles have equivalent collections of chromosomes.
    • At telophase, daughter nuclei begin to form at the two poles.
      • Nuclear envelopes arise from the fragments of the parent cell’s nuclear envelope and other portions of the endomembrane system.
      • The chromosomes become less tightly coiled.
    • Cytokinesis, division of the cytoplasm, is usually well underway by late telophase.
    • In animal cells, cytokinesis involves the formation of a cleavage furrow, which pinches the cell in two.
    • In plant cells, vesicles derived from the Golgi apparatus produce a cell plate at the middle of the cell.

      The mitotic spindle distributes chromosomes to daughter cells: a closer look.

    • The mitotic spindle, fibers composed of microtubules and associated proteins, is a major driving force in mitosis.
    • As the spindle assembles during prophase, the elements come from partial disassembly of the cytoskeleton.
    • The spindle fibers elongate by incorporating more subunits of the protein tubulin.
    • Assembly of the spindle microtubules starts in the centrosome.
      • The centrosome (microtubule-organizing center) is a nonmembranous organelle that organizes the cell’s microtubules.
      • In animal cells, the centrosome has a pair of centrioles at the center, but the centrioles are not essential for cell division.
    • During interphase, the single centrosome replicates to form two centrosomes.
    • As mitosis starts, the two centrosomes are located near the nucleus.
      • As the spindle microtubules grow from them, the centrioles are pushed apart.
      • By the end of prometaphase, they are at opposite ends of the cell.
    • An aster, a radial array of short microtubules, extends from each centrosome.
    • The spindle includes the centrosomes, the spindle microtubules, and the asters.
    • Each sister chromatid has a kinetochore of proteins and chromosomal DNA at the centromere.
      • The kinetochores of the joined sister chromatids face in opposite directions.
    • During prometaphase, some spindle microtubules (called kinetochore microtubules) attach to the kinetochores.
    • When a chromosome’s kinetochore is “captured” by microtubules, the chromosome moves toward the pole from which those microtubules come.
    • When microtubules attach to the other pole, this movement stops and a tug-of-war ensues.
    • Eventually, the chromosome settles midway between the two poles of the cell, on the metaphase plate.
    • Nonkinetochore microtubules from opposite poles overlap and interact with each other.
    • By metaphase, the microtubules of the asters have grown and are in contact with the plasma membrane.
    • The spindle is now complete.
    • Anaphase commences when the proteins holding the sister chromatids together are inactivated.
      • Once the chromosomes are separate, full-fledged chromosomes, they move toward opposite poles of the cell.
    • How do the kinetochore microtubules function into the poleward movement of chromosomes?
    • One hypothesis is that the chromosomes are “reeled in” by the shortening of microtubules at the spindle poles.
    • Experimental evidence supports the hypothesis that motor proteins on the kinetochore “walk” the attached chromosome along the microtubule toward the nearest pole.
      • Meanwhile, the excess microtubule sections depolymerize at their kinetochore ends.
    • What is the function of the nonkinetochore microtubules?
    • Nonkinetochore microtubules are responsible for lengthening the cell along the axis defined by the poles.
      • These microtubules interdigitate and overlap across the metaphase plate.
      • During anaphase, the area of overlap is reduced as motor proteins attached to the microtubules walk them away from one another, using energy from ATP.
      • As microtubules push apart, the microtubules lengthen by the addition of new tubulin monomers to their overlapping ends, allowing continued overlap.

      Cytokinesis divides the cytoplasm: a closer look.

    • Cytokinesis, division of the cytoplasm, typically follows mitosis.
    • In animal cells, cytokinesis occurs by a process called cleavage.
    • The first sign of cleavage is the appearance of a cleavage furrow in the cell surface near the old metaphase plate.
    • On the cytoplasmic side of the cleavage furrow is a contractile ring of actin microfilaments associated with molecules of the motor protein myosin.
      • Contraction of the ring pinches the cell in two.
    • Cytokinesis in plants, which have cell walls, involves a completely different mechanism.
    • During telophase, vesicles from the Golgi coalesce at the metaphase plate, forming a cell plate.
      • The plate enlarges until its membranes fuse with the plasma membrane at the perimeter.
      • The contents of the vesicles form new cell wall material between the daughter cells.

      Mitosis in eukaryotes may have evolved from binary fission in bacteria.

    • Prokaryotes reproduce by binary fission, not mitosis.
    • Most bacterial genes are located on a single bacterial chromosome that consists of a circular DNA molecule and associated proteins.
    • While bacteria are smaller and simpler than eukaryotic cells, they still have large amounts of DNA that must be copied and distributed equally to two daughter cells.
    • The circular bacterial chromosome is highly folded and coiled in the cell.
    • In binary fission, chromosome replication begins at one point in the circular chromosome, the origin of replication site, producing two origins.
      • As the chromosome continues to replicate, one origin moves toward each end of the cell.
      • While the chromosome is replicating, the cell elongates.
      • When replication is complete, its plasma membrane grows inward to divide the parent cell into two daughter cells, each with a complete genome.
    • Researchers have developed methods to allow them to observe the movement of bacterial chromosomes.
      • The movement is similar to the poleward movements of the centromere regions of eukaryotic chromosomes.
      • However, bacterial chromosomes lack visible mitotic spindles or even microtubules.
    • The mechanism behind the movement of the bacterial chromosome is becoming clearer but is still not fully understood.
      • Several proteins have been identified and play important roles.
    • How did mitosis evolve?
      • There is evidence that mitosis had its origins in bacterial binary fission.
      • Some of the proteins involved in binary fission are related to eukaryotic proteins.
      • Two of these are related to eukaryotic tubulin and actin proteins.
    • As eukaryotes evolved, the ancestral process of binary fission gave rise to mitosis.
    • Possible intermediate evolutionary steps are seen in the division of two types of unicellular algae.
      • In dinoflagellates, replicated chromosomes are attached to the nuclear envelope.
      • In diatoms, the spindle develops within the nucleus.
    • In most eukaryotic cells, the nuclear envelope breaks down and a spindle separates the chromosomes.

    Concept 12.3 The cell cycle is regulated by a molecular control system

    • The timing and rates of cell division in different parts of an animal or plant are crucial for normal growth, development, and maintenance.
    • The frequency of cell division varies with cell type.
      • Some human cells divide frequently throughout life (skin cells).
      • Others have the ability to divide, but keep it in reserve (liver cells).
      • Mature nerve and muscle cells do not appear to divide at all after maturity.
    • Investigation of the molecular mechanisms regulating these differences provide important insights into the operation of normal cells, and may also explain cancer cells escape controls.

      Cytoplasmic signals drive the cell cycle.

    • The cell cycle appears to be driven by specific chemical signals present in the cytoplasm.
    • Some of the initial evidence for this hypothesis came from experiments in which cultured mammalian cells at different phases of the cell cycle were fused to form a single cell with two nuclei.
      • Fusion of an S phase cell and a G1 phase cell induces the G1 nucleus to start S phase.
        • This suggests that chemicals present in the S phase nucleus stimulated the fused cell.
      • Fusion of a cell in mitosis (M phase) with one in interphase (even G1 phase) induces the second cell to enter mitosis.
    • The sequential events of the cell cycle are directed by a distinct cell cycle control system.
      • Cyclically operating molecules trigger and coordinate key events in the cell cycle.
      • The control cycle has a built-in clock, but it is also regulated by external adjustments and internal controls.
    • A checkpoint in the cell cycle is a critical control point where stop and go-ahead signals regulate the cycle.
      • The signals are transmitted within the cell by signal transduction pathways.
      • Animal cells generally have built-in stop signals that halt the cell cycle at checkpoints until overridden by go-ahead signals.
      • Many signals registered at checkpoints come from cellular surveillance mechanisms.
      • These indicate whether key cellular processes have been completed correctly.
      • Checkpoints also register signals from outside the cell.
    • Three major checkpoints are found in the G1, G2, and M phases.
    • For many cells, the G1 checkpoint, the “restriction point” in mammalian cells, is the most important.
      • If the cell receives a go-ahead signal at the G1 checkpoint, it usually completes the cell cycle and divides.
      • If it does not receive a go-ahead signal, the cell exits the cycle and switches to a nondividing state, the G0 phase.
        • Most cells in the human body are in this phase.
        • Liver cells can be “called back” to the cell cycle by external cues, such as growth factors released during injury.
        • Highly specialized nerve and muscle cells never divide.
    • Rhythmic fluctuations in the abundance and activity of cell cycle control molecules pace the events of the cell cycle.
      • These regulatory molecules include protein kinases that activate or deactivate other proteins by phosphorylating them.
    • These kinases are present in constant amounts but require attachment of a second protein, a cyclin, to become activated.
      • Levels of cyclin proteins fluctuate cyclically.
      • Because of the requirement for binding of a cyclin, the kinases are called cyclin-dependent kinases, or Cdks.
    • Cyclin levels rise sharply throughout interphase, and then fall abruptly during mitosis.
    • Peaks in the activity of one cyclin-Cdk complex, MPF, correspond to peaks in cyclin concentration.
    • MPF (“maturation-promoting factor” or “M-phase-promoting-factor”) triggers the cell’s passage past the G2 checkpoint to the M phase.
      • MPF promotes mitosis by phosphorylating a variety of other protein kinases.
      • MPF stimulates fragmentation of the nuclear envelope by phosphorylation of various proteins of the nuclear lamina.
      • It also triggers the breakdown of cyclin, dropping cyclin and MPF levels during mitosis and inactivating MPF.
        • The noncyclin part of MPF, the Cdk, persists in the cell in inactive form until it associates with new cyclin molecules synthesized during the S and G2 phases of the next round of the cycle.
    • At least three Cdk proteins and several cyclins regulate the key G1 checkpoint.
    • Similar mechanisms are also involved in driving the cell cycle past the M phase checkpoint.

      Internal and external cues help regulate the cell cycle.

    • While research scientists know that active Cdks function by phosphorylating proteins, the identity of all these proteins is still under investigation.
    • Scientists do not yet know what Cdks actually do in most cases.
    • Some steps in the signaling pathways that regulate the cell cycle are clear.
      • Some signals originate inside the cell, others outside.
    • The M phase checkpoint ensures that all the chromosomes are properly attached to the spindle at the metaphase plate before anaphase.
      • This ensures that daughter cells do not end up with missing or extra chromosomes.
    • A signal to delay anaphase originates at kinetochores that have not yet attached to spindle microtubules.
      • This keeps the anaphase-promoting complex (APC) in an inactive state.
      • When all kinetochores are attached, the APC activates, triggering breakdown of cyclin and inactivation of proteins holding sister chromatids together.
    • A variety of external chemical and physical factors can influence cell division.
      • For example, cells fail to divide if an essential nutrient is left out of the culture medium.
    • Particularly important for mammalian cells are growth factors, proteins released by one group of cells that stimulate other cells to divide.
      • For example, platelet-derived growth factors (PDGF), produced by platelet blood cells, bind to tyrosine-kinase receptors of fibroblasts, a type of connective tissue cell.
      • This triggers a signal-transduction pathway that allows cells to pass the G1 checkpoint and divide.
    • Each cell type probably responds specifically to a certain growth factor or combination of factors.
    • The role of PDGF is easily seen in cell culture.
      • Fibroblasts in culture will only divide in the presence of a medium that also contains PDGF.
    • In a living organism, platelets release PDGF in the vicinity of an injury.
      • The resulting proliferation of fibroblasts helps heal the wound.
    • At least 50 different growth factors can trigger specific cells to divide.
    • The effect of an external physical factor on cell division can be seen in density-dependent inhibition of cell division.
      • Cultured cells normally divide until they form a single layer on the inner surface of the culture container.
      • If a gap is created, the cells will grow to fill the gap.
      • At high densities, the amount of growth factors and nutrients is insufficient to allow continued cell growth.
    • Most animal cells also exhibit anchorage dependence for cell division.
      • To divide, they must be anchored to a substratum, typically the extracellular matrix of a tissue.
      • Control appears to be mediated by pathways involving plasma membrane proteins and elements of the cytoskeleton linked to them.
    • Cancer cells exhibit neither density-dependent inhibition nor anchorage dependence.

      Cancer cells have escaped from cell cycle controls.

    • Cancer cells divide excessively and invade other tissues because they are free of the body’s control mechanisms.
      • Cancer cells do not stop dividing when growth factors are depleted.
      • This is either because a cancer cell manufactures its own growth factors, has an abnormality in the signaling pathway, or has an abnormal cell cycle control system.
    • If and when cancer cells stop dividing, they do so at random points, not at the normal checkpoints in the cell cycle.
    • Cancer cells may divide indefinitely if they have a continual supply of nutrients.
      • In contrast, nearly all mammalian cells divide 20 to 50 times under culture conditions before they stop, age, and die.
    • Cancer cells may be “immortal.”
      • HeLa cells from a tumor removed from a woman (Henrietta Lacks) in 1951 are still reproducing in culture.
    • The abnormal behavior of cancer cells begins when a single cell in a tissue undergoes a transformation that converts it from a normal cell to a cancer cell.
      • Normally, the immune system recognizes and destroys transformed cells.
      • However, cells that evade destruction proliferate to form a tumor, a mass of abnormal cells.
    • If the abnormal cells remain at the originating site, the lump is called a benign tumor.
      • Most do not cause serious problems and can be fully removed by surgery.
    • In a malignant tumor, the cells become invasive enough to impair the functions of one or more organs.
    • In addition to chromosomal and metabolic abnormalities, cancer cells often lose attachment to nearby cells, are carried by the blood and lymph system to other tissues, and start more tumors in an event called metastasis.
      • Cancer cells are abnormal in many ways.
      • They may have an unusual number of chromosomes, their metabolism may be disabled, and they may cease to function in any constructive way.
      • Cancer cells may secrete signal molecules that cause blood vessels to grow toward the tumor.
    • Treatments for metastasizing cancers include high-energy radiation and chemotherapy with toxic drugs.
      • These treatments target actively dividing cells.
      • Chemotherapeutic drugs interfere with specific steps in the cell cycle.
      • For example, Taxol prevents mitotic depolymerization, preventing cells from proceeding past metaphase.
      • The side effects of chemotherapy are due to the drug’s effects on normal cells.
    • Researchers are beginning to understand how a normal cell is transformed into a cancer cell.
      • The causes are diverse, but cellular transformation always involves the alteration of genes that influence the cell cycle control system.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 12-1

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    Chapter 12 The Cell Cycle82.5 KB
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    Chapter 13 - Meiosis and Sexual Life Cycles

    Chapter 13 Meiosis and Sexual Life Cycles
    Lecture Outline

    Overview: Hereditary Similarity and Variation

    • Living organisms are distinguished by their ability to reproduce their own kind.
    • Offspring resemble their parents more than they do less closely related individuals of the same species.
    • The transmission of traits from one generation to the next is called heredity or inheritance.
    • However, offspring differ somewhat from parents and siblings, demonstrating variation.
    • Farmers have bred plants and animals for desired traits for thousands of years, but the mechanisms of heredity and variation eluded biologists until the development of genetics in the 20th century.
    • Genetics is the scientific study of heredity and variation.

    Concept 13.1 Offspring acquire genes from parents by inheriting chromosomes

    • Parents endow their offspring with coded information in the form of genes.
      • Your genome is comprised of the tens of thousands of genes that you inherited from your mother and your father.
    • Genes program specific traits that emerge as we develop from fertilized eggs into adults.
    • Genes are segments of DNA. Genetic information is transmitted as specific sequences of the four deoxyribonucleotides in DNA.
      • This is analogous to the symbolic information of language in which words and sentences are translated into mental images.
      • Cells translate genetic “sentences” into freckles and other features with no resemblance to genes.
    • Most genes program cells to synthesize specific enzymes and other proteins whose cumulative action produces an organism’s inherited traits.
    • The transmission of hereditary traits has its molecular basis in the precise replication of DNA.
      • This produces copies of genes that can be passed from parents to offspring.
    • In plants and animals, sperm and ova (unfertilized eggs) transmit genes from one generation to the next.
    • After fertilization (fusion of a sperm cell and an ovum), genes from both parents are present in the nucleus of the fertilized egg, or zygote.
    • Almost all the DNA in a eukaryotic cell is subdivided into chromosomes in the nucleus.
      • Tiny amounts of DNA are also found in mitochondria and chloroplasts.
    • Every living species has a characteristic number of chromosomes.
      • Humans have 46 chromosomes in almost all of their cells.
    • Each chromosome consists of a single DNA molecule associated with various proteins.
    • Each chromosome has hundreds or thousands of genes, each at a specific location, its locus.

      Like begets like, more or less: a comparison of asexual and sexual reproduction.

    • Only organisms that reproduce asexually can produce offspring that are exact copies of themselves.
    • In asexual reproduction, a single individual is the sole parent to donate genes to its offspring.
      • Single-celled eukaryotes can reproduce asexually by mitotic cell division to produce two genetically identical daughter cells.
      • Some multicellular eukaryotes, like Hydra, can reproduce by budding, producing a mass of cells by mitosis.
    • An individual that reproduces asexually gives rise to a clone, a group of genetically identical individuals.
      • Members of a clone may be genetically different as a result of mutation.
    • In sexual reproduction, two parents produce offspring that have unique combinations of genes inherited from the two parents.
    • Unlike a clone, offspring produced by sexual reproduction vary genetically from their siblings and their parents.

    Concept 13.2 Fertilization and meiosis alternate in sexual life cycles

    • A life cycle is the generation-to-generation sequence of stages in the reproductive history of an organism.
    • It starts at the conception of an organism and continues until the organism produces its own offspring.

      Human cells contain sets of chromosomes.

    • In humans, each somatic cell (all cells other than sperm or ovum) has 46 chromosomes.
      • Each chromosome can be distinguished by size, position of the centromere, and pattern of staining with certain dyes.
    • Images of the 46 human chromosomes can be arranged in pairs in order of size to produce a karyotype display.
      • The two chromosomes comprising a pair have the same length, centromere position, and staining pattern.
      • These homologous chromosome pairs carry genes that control the same inherited characters.
    • Two distinct sex chromosomes, the X and the Y, are an exception to the general pattern of homologous chromosomes in human somatic cells.
    • The other 22 pairs are called autosomes.
    • The pattern of inheritance of the sex chromosomes determines an individual’s sex.
      • Human females have a homologous pair of X chromosomes (XX).
      • Human males have an X and a Y chromosome (XY).
    • Only small parts of the X and Y are homologous.
      • Most of the genes carried on the X chromosome do not have counterparts on the tiny Y.
      • The Y chromosome also has genes not present on the X.
    • The occurrence of homologous pairs of chromosomes is a consequence of sexual reproduction.
    • We inherit one chromosome of each homologous pair from each parent.
      • The 46 chromosomes in each somatic cell are two sets of 23, a maternal set (from your mother) and a paternal set (from your father).
    • The number of chromosomes in a single set is represented by n.
    • Any cell with two sets of chromosomes is called a diploid cell and has a diploid number of chromosomes, abbreviated as 2n.
    • Sperm cells or ova (gametes) have only one set of chromosomes—22 autosomes and an X (in an ovum) and 22 autosomes and an X or a Y (in a sperm cell).
    • A gamete with a single chromosome set is haploid, abbreviated as n.
    • Any sexually reproducing species has a characteristic haploid and diploid number of chromosomes.
      • For humans, the haploid number of chromosomes is 23 (n = 23), and the diploid number is 46 (2n = 46).

      Let’s discuss the role of meiosis in the human life cycle.

    • The human life cycle begins when a haploid sperm cell fuses with a haploid ovum.
    • These cells fuse (syngamy), resulting in fertilization.
    • The fertilized egg (zygote) is diploid because it contains two haploid sets of chromosomes bearing genes from the maternal and paternal family lines.
    • As an organism develops from a zygote to a sexually mature adult, mitosis generates all the somatic cells of the body.
      • Each somatic cell contains a full diploid set of chromosomes.
    • Gametes, which develop in the gonads (testes or ovaries), are not produced by mitosis.
      • If gametes were produced by mitosis, the fusion of gametes would produce offspring with four sets of chromosomes after one generation, eight after a second, and so on.
    • Instead, gametes undergo the process of meiosis in which the chromosome number is halved.
      • Human sperm or ova have a haploid set of 23 different chromosomes, one from each homologous pair.
    • Fertilization restores the diploid condition by combining two haploid sets of chromosomes.

      Organisms display a variety of sexual life cycles.

    • Fertilization and meiosis alternate in all sexual life cycles.
    • However, the timing of meiosis and fertilization does vary among species.
    • These variations can be grouped into three main types of life cycles.
    • In most animals, including humans, gametes are the only haploid cells.
      • Gametes do not divide but fuse to form a diploid zygote that divides by mitosis to produce a multicellular organism.
    • Plants and some algae have a second type of life cycle called alternation of generations.
      • This life cycle includes two multicellular stages, one haploid and one diploid.
      • The multicellular diploid stage is called the sporophyte.
      • Meiosis in the sporophyte produces haploid spores that develop by mitosis into the haploid gametophyte stage.
      • Gametes produced via mitosis by the gametophyte fuse to form the zygote, which grows into the sporophyte by mitosis.
    • Most fungi and some protists have a third type of life cycle.
      • Gametes fuse to form a zygote, which is the only diploid phase.
      • The zygote undergoes meiosis to produce haploid cells.
      • These haploid cells grow by mitosis to form the haploid multicellular adult organism.
      • The haploid adult produces gametes by mitosis.
    • Note that either haploid or diploid cells can divide by mitosis, depending on the type of life cycle. However, only diploid cells can undergo meiosis.
    • Although the three types of sexual life cycles differ in the timing of meiosis and fertilization, they share a fundamental feature: each cycle of chromosome halving and doubling contributes to genetic variation among offspring.

    Concept 13.3 Meiosis reduces the number of chromosome sets from diploid to haploid

    • Many steps of meiosis resemble steps in mitosis.
      • Both are preceded by the replication of chromosomes.
    • However, in meiosis, there are two consecutive cell divisions, meiosis I and meiosis II, resulting in four daughter cells.
      • The first division, meiosis I, separates homologous chromosomes.
      • The second, meiosis II, separates sister chromatids.
    • The four daughter cells have only half as many chromosomes as the parent cell.
    • Meiosis I is preceded by interphase, in which the chromosomes are replicated to form sister chromatids.
      • These are genetically identical and joined at the centromere.
      • The single centrosome is replicated, forming two centrosomes.
    • Division in meiosis I occurs in four phases: prophase I, metaphase I, anaphase I, and telophase I.

      Prophase I

    • Prophase I typically occupies more than 90% of the time required for meiosis.
    • During prophase I, the chromosomes begin to condense.
    • Homologous chromosomes loosely pair up along their length, precisely aligned gene for gene.
      • In crossing over, DNA molecules in nonsister chromatids break at corresponding places and then rejoin the other chromatid.
      • In synapsis, a protein structure called the synaptonemal complex forms between homologues, holding them tightly together along their length.
      • As the synaptonemal complex disassembles in late prophase, each chromosome pair becomes visible as a tetrad, or group of four chromatids.
      • Each tetrad has one or more chiasmata, sites where the chromatids of homologous chromosomes have crossed and segments of the chromatids have been traded.
      • Spindle microtubules form from the centrosomes, which have moved to the poles.
      • The breakdown of the nuclear envelope and nucleoli take place.
      • Kinetochores of each homologue attach to microtubules from one of the poles.

      Metaphase I

    • At metaphase I, the tetrads are all arranged at the metaphase plate, with one chromosome facing each pole.
      • Microtubules from one pole are attached to the kinetochore of one chromosome of each tetrad, while those from the other pole are attached to the other.

      Anaphase I

    • In anaphase I, the homologous chromosomes separate. One chromosome moves toward each pole, guided by the spindle apparatus.
      • Sister chromatids remain attached at the centromere and move as a single unit toward the pole.

      Telophase I and cytokinesis

    • In telophase I, movement of homologous chromosomes continues until there is a haploid set at each pole.
      • Each chromosome consists of two sister chromatids.
    • Cytokinesis usually occurs simultaneously, by the same mechanisms as mitosis.
      • In animal cells, a cleavage furrow forms. In plant cells, a cell plate forms.
    • No chromosome replication occurs between the end of meiosis I and the beginning of meiosis II, as the chromosomes are already replicated.

      Meiosis II

    • Meiosis II is very similar to mitosis.
      • During prophase II, a spindle apparatus forms and attaches to kinetochores of each sister chromatid.
        • Spindle fibers from one pole attach to the kinetochore of one sister chromatid, and those of the other pole attach to kinetochore of the other sister chromatid.
    • At metaphase II, the sister chromatids are arranged at the metaphase plate.
      • Because of crossing over in meiosis I, the two sister chromatids of each chromosome are no longer genetically identical.
      • The kinetochores of sister chromatids attach to microtubules extending from opposite poles.
    • At anaphase II, the centomeres of sister chromatids separate and two newly individual chromosomes travel toward opposite poles.
    • In telophase II, the chromosomes arrive at opposite poles.
      • Nuclei form around the chromosomes, which begin expanding, and cytokinesis separates the cytoplasm.
    • At the end of meiosis, there are four haploid daughter cells.

      There are key differences between mitosis and meiosis.

    • Mitosis and meiosis have several key differences.
      • The chromosome number is reduced from diploid to haploid in meiosis but is conserved in mitosis.
      • Mitosis produces daughter cells that are genetically identical to the parent and to each other.
      • Meiosis produces cells that are genetically distinct from the parent cell and from each other.
    • Three events, unique to meiosis, occur during the first division cycle.
      1. During prophase I of meiosis, replicated homologous chromosomes line up and become physically connected along their lengths by a zipperlike protein complex, the synaptonemal complex, in a process called synapsis. Genetic rearrangement between nonsister chromatids called crossing over also occurs. Once the synaptonemal complex is disassembled, the joined homologous chromosomes are visible as a tetrad. X-shaped regions called chiasmata are visible as the physical manifestation of crossing over. Synapsis and crossing over do not occur in mitosis.
      2. At metaphase I of meiosis, homologous pairs of chromosomes align along the metaphase plate. In mitosis, individual replicated chromosomes line up along the metaphase plate.
      3. At anaphase I of meiosis, it is homologous chromosomes, not sister chromatids, that separate and are carried to opposite poles of the cell. Sister chromatids of each replicated chromosome remain attached. In mitosis, sister chromatids separate to become individual chromosomes.
    • Meiosis I is called the reductional division because it halves the number of chromosome sets per cell—a reduction from the diploid to the haploid state.
    • The sister chromatids separate during the second meiosis division, meiosis II.

    Concept 13.4 Genetic variation produced in sexual life cycles contributes to evolution

    • What is the origin of genetic variation?
    • Mutations are the original source of genetic diversity.
    • Once different versions of genes arise through mutation, reshuffling during meiosis and fertilization produce offspring with their own unique set of traits.

      Sexual life cycles produce genetic variation among offspring.

    • The behavior of chromosomes during meiosis and fertilization is responsible for most of the variation that arises in each generation.
    • Three mechanisms contribute to genetic variation:
      1. Independent assortment of chromosomes.
      2. Crossing over.
      3. Random fertilization.
    • Independent assortment of chromosomes contributes to genetic variability due to the random orientation of homologous pairs of chromosomes at the metaphase plate during meiosis I.
      • There is a fifty-fifty chance that a particular daughter cell of meiosis I will get the maternal chromosome of a certain homologous pair and a fifty-fifty chance that it will receive the paternal chromosome.
    • Each homologous pair of chromosomes segregates independently of the other homologous pairs during metaphase I.
    • Therefore, the first meiotic division results in independent assortment of maternal and paternal chromosomes into daughter cells.
    • The number of combinations possible when chromosomes assort independently into gametes is 2n, where n is the haploid number of the organism.
      • If n = 3, there are 23 = 8 possible combinations.
      • For humans with n = 23, there are 223, or more than 8 million possible combinations of chromosomes.
    • Crossing over produces recombinant chromosomes, which combine genes inherited from each parent.
    • Crossing over begins very early in prophase I as homologous chromosomes pair up gene by gene.
    • In crossing over, homologous portions of two nonsister chromatids trade places.
      • For humans, this occurs an average of one to three times per chromosome pair.
    • Recent research suggests that, in some organisms, crossing over may be essential for synapsis and the proper assortment of chromosomes in meiosis I.
    • Crossing over, by combining DNA inherited from two parents into a single chromosome, is an important source of genetic variation.
    • At metaphase II, nonidentical sister chromatids sort independently from one another, increasing by even more the number of genetic types of daughter cells that are formed by meiosis.
    • The random nature of fertilization adds to the genetic variation arising from meiosis.
    • Any sperm can fuse with any egg.
      • The ovum is one of more than 8 million possible chromosome combinations.
      • The successful sperm is one of more than 8 million possibilities.
      • The resulting zygote could contain any one of more than 70 trillion possible combinations of chromosomes.
      • Crossing over adds even more variation to this.
    • Each zygote has a unique genetic identity.
    • The three sources of genetic variability in a sexually reproducing organism are:
      1. Independent assortment of homologous chromosomes during meiosis I and of nonidentical sister chromatids during meiosis II.
      2. Crossing over between homologous chromosomes during prophase I.
      3. Random fertilization of an ovum by a sperm.
    • All three mechanisms reshuffle the various genes carried by individual members of a population.

      Evolutionary adaptation depends on a population’s genetic variation.

    • Darwin recognized the importance of genetic variation in evolution.
      • A population evolves through the differential reproductive success of its variant members.
      • Those individuals best suited to the local environment leave the most offspring, transmitting their genes in the process.
    • This natural selection results in adaptation, the accumulation of favorable genetic variations.
    • If the environment changes or a population moves to a new environment, new genetic combinations that work best in the new conditions will produce more offspring, and these genes will increase.
      • The formerly favored genes will decrease.
    • Sex and mutation continually generate new genetic variability.
    • Although Darwin realized that heritable variation makes evolution possible, he did not have a theory of inheritance.
    • Gregor Mendel, a contemporary of Darwin’s, published a theory of inheritance that supported Darwin’s theory.
      • However, this work was largely unknown until 1900, after Darwin and Mendel had both been dead for more than 15 years.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 13-1

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    Chapter 14 - Mendel and the Gene Idea

    Chapter 14 Mendel and the Gene Idea
    Lecture Outline

    Overview: Drawing from the Deck of Genes

    • Every day we observe heritable variations (such as brown, green, or blue eyes) among individuals in a population.
    • These traits are transmitted from parents to offspring.
    • One possible explanation for heredity is a “blending” hypothesis.
      • This hypothesis proposes that genetic material contributed by each parent mixes in a manner analogous to the way blue and yellow paints blend to make green.
      • With blending inheritance, a freely mating population will eventually give rise to a uniform population of individuals.
      • Everyday observations and the results of breeding experiments tell us that heritable traits do not blend to become uniform.
    • An alternative model, “particulate” inheritance, proposes that parents pass on discrete heritable units, genes, that retain their separate identities in offspring.
      • Genes can be sorted and passed on, generation after generation, in undiluted form.
    • Modern genetics began in an abbey garden, where a monk named Gregor Mendel documented a particulate mechanism of inheritance.

    Concept 14.1 Mendel used the scientific approach to identify two laws of inheritance

    • Mendel discovered the basic principles of heredity by breeding garden peas in carefully planned experiments.
    • Mendel grew up on a small farm in what is today the Czech Republic.
    • In 1843, Mendel entered an Augustinian monastery.
    • He studied at the University of Vienna from 1851 to 1853, where he was influenced by a physicist who encouraged experimentation and the application of mathematics to science and by a botanist who stimulated Mendel’s interest in the causes of variation in plants.
    • These influences came together in Mendel’s experiments.
    • After university, Mendel taught at the Brunn Modern School and lived in the local monastery.
    • The monks at this monastery had a long tradition of interest in the breeding of plants, including peas.
    • Around 1857, Mendel began breeding garden peas to study inheritance.
    • Pea plants have several advantages for genetic study.
      • Pea plants are available in many varieties with distinct heritable features, or characters, with different variant traits.
      • Mendel could strictly control which plants mated with which.
      • Each pea plant has male (stamens) and female (carpal) sexual organs.
      • In nature, pea plants typically self-fertilize, fertilizing ova with the sperm nuclei from their own pollen.
      • However, Mendel could also use pollen from another plant for cross-pollination.
    • Mendel tracked only those characters that varied in an “either-or” manner, rather than a “more-or-less” manner.
      • For example, he worked with flowers that were either purple or white.
      • He avoided traits, such as seed weight, that varied on a continuum.
    • Mendel started his experiments with varieties that were true-breeding.
      • When true-breeding plants self-pollinate, all their offspring have the same traits.
    • In a typical breeding experiment, Mendel would cross-pollinate (hybridize) two contrasting, true-breeding pea varieties.
      • The true-breeding parents are the P generation, and their hybrid offspring are the F1 generation.
    • Mendel would then allow the F1 hybrids to self-pollinate to produce an F2 generation.
    • It was mainly Mendel’s quantitative analysis of F2 plants that revealed two fundamental principles of heredity: the law of segregation and the law of independent assortment.

      By the law of segregation, the two alleles for a character are separated during the formation of gametes.

    • If the blending model was correct, the F1 hybrids from a cross between purple-flowered and white-flowered pea plants would have pale purple flowers.
    • Instead, F1 hybrids all have purple flowers, just as purple as their purple-flowered parents.
    • When Mendel allowed the F1 plants to self-fertilize, the F2 generation included both purple-flowered and white-flowered plants.
      • The white trait, absent in the F1, reappeared in the F2.
    • Mendel used very large sample sizes and kept accurate records of his results.
      • Mendel recorded 705 purple-flowered F2 plants and 224 white-flowered F2 plants.
      • This cross produced a traits ratio of three purple to one white in the F2 offspring.
    • Mendel reasoned that the heritable factor for white flowers was present in the F1 plants, but did not affect flower color.
      • Purple flower color is a dominant trait, and white flower color is a recessive trait.
    • The reappearance of white-flowered plants in the F2 generation indicated that the heritable factor for the white trait was not diluted or “blended” by coexisting with the purple-flower factor in F1 hybrids.
    • Mendel found similar 3-to-1 ratios of two traits among F2 offspring when he conducted crosses for six other characters, each represented by two different traits.
    • For example, when Mendel crossed two true-breeding varieties, one producing round seeds and the other producing wrinkled seeds, all the F1 offspring had round seeds.
      • In the F2 plants, 75% of the seeds were round and 25% were wrinkled.
    • Mendel developed a hypothesis to explain these results that consisted of four related ideas. We will explain each idea with the modern understanding of genes and chromosomes.
      1. Alternative versions of genes account for variations in inherited characters.
        • The gene for flower color in pea plants exists in two versions, one for purple flowers and one for white flowers.
        • These alternate versions are called alleles.
        • Each gene resides at a specific locus on a specific chromosome.
        • The DNA at that locus can vary in its sequence of nucleotides.
        • The purple-flower and white-flower alleles are two DNA variations at the flower-color locus.
      2. For each character, an organism inherits two alleles, one from each parent.
        • A diploid organism inherits one set of chromosomes from each parent.
        • Each diploid organism has a pair of homologous chromosomes and, therefore, two copies of each gene.
        • These homologous loci may be identical, as in the true-breeding plants of the P generation.
        • Alternatively, the two alleles may differ.
      3. If the two alleles at a locus differ, then one, the dominant allele, determines the organism’s appearance. The other, the recessive allele, has no noticeable effect on the organism’s appearance.
        • In the flower-color example, the F1 plants inherited a purple-flower allele from one parent and a white-flower allele from the other.
        • They had purple flowers because the allele for that trait is dominant.
      4. Mendel’s law of segregation states that the two alleles for a heritable character separate and segregate during gamete production and end up in different gametes.
      • This segregation of alleles corresponds to the distribution of homologous chromosomes to different gametes in meiosis.
      • If an organism has two identical alleles for a particular character, then that allele is present as a single copy in all gametes.
      • If different alleles are present, then 50% of the gametes will receive one allele and 50% will receive the other.
    • Mendel’s law of segregation accounts for the 3:1 ratio that he observed in the F2 generation.
    • The F1 hybrids produce two classes of gametes, half with the purple-flower allele and half with the white-flower allele.
    • During self-pollination, the gametes of these two classes unite randomly.
    • This produces four equally likely combinations of sperm and ovum.
    • A Punnett square predicts the results of a genetic cross between individuals of known genotype.
    • Let us describe a Punnett square analysis of the flower-color example.
    • We will use a capital letter to symbolize the dominant allele and a lowercase letter to symbolize the recessive allele.
      • P is the purple-flower allele, and p is the white-flower allele.
    • What will be the physical appearance of the F2 offspring?
      • One in four F2 offspring will inherit two white-flower alleles and produce white flowers.
      • Half of the F2 offspring will inherit one white-flower allele and one purple-flower allele and produce purple flowers.
      • One in four F2 offspring will inherit two purple-flower alleles and produce purple flowers.
    • Mendel’s model accounts for the 3:1 ratio in the F2 generation.
    • An organism with two identical alleles for a character is homozygous for that character.
    • Organisms with two different alleles for a character is heterozygous for that character.
    • An organism’s traits are called its phenotype.
    • Its genetic makeup is called its genotype.
      • Two organisms can have the same phenotype but have different genotypes if one is homozygous dominant and the other is heterozygous.
    • For flower color in peas, the only individuals with white flowers are those that are homozygous recessive (pp) for the flower-color gene.
    • However, PP and Pp plants have the same phenotype (purple flowers) but different genotypes (homozygous dominant and heterozygous).
    • How can we tell the genotype of an individual with the dominant phenotype?
      • The organism must have one dominant allele, but could be homozygous dominant or heterozygous.
    • The answer is to carry out a testcross.
      • The mystery individual is bred with a homozygous recessive individual.
      • If any of the offspring display the recessive phenotype, the mystery parent must be heterozygous.

      By the law of independent assortment, each pair of alleles segregates independently into gametes.

    • Mendel’s first experiments followed only a single character, such as flower color.
      • All F1 progeny produced in these crosses were monohybrids, heterozygous for one character.
      • A cross between two heterozygotes is a monohybrid cross.
    • Mendel identified the second law of inheritance by following two characters at the same time.
    • In one such dihybrid cross, Mendel studied the inheritance of seed color and seed shape.
      • The allele for yellow seeds (Y) is dominant to the allele for green seeds (y).
      • The allele for round seeds (R) is dominant to the allele for wrinkled seeds (r).
    • Mendel crossed true-breeding plants that had yellow, round seeds (YYRR) with true-breeding plants that has green, wrinkled seeds (yyrr).
    • One possibility is that the two characters are transmitted from parents to offspring as a package.
      • The Y and R alleles and y and r alleles stay together.
    • If this were the case, the F1 offspring would produce yellow, round seeds.
    • The F2 offspring would produce two phenotypes (yellow + round; green + wrinkled) in a 3:1 ratio, just like a monohybrid cross.
      • This was not consistent with Mendel’s results.
    • An alternative hypothesis is that the two pairs of alleles segregate independently of each other.
      • The presence of a specific allele for one trait in a gamete has no impact on the presence of a specific allele for the second trait.
    • In our example, the F1 offspring would still produce yellow, round seeds.
    • However, when the F1s produced gametes, genes would be packaged into gametes with all possible allelic combinations.
      • Four classes of gametes (YR, Yr, yR, and yr) would be produced in equal amounts.
    • When sperm with four classes of alleles and ova with four classes of alleles combined, there would be 16 equally probable ways in which the alleles can combine in the F2 generation.
    • These combinations produce four distinct phenotypes in a 9:3:3:1 ratio.
    • This was consistent with Mendel’s results.
    • Mendel repeated the dihybrid cross experiment for other pairs of characters and always observed a 9:3:3:1 phenotypic ratio in the F2 generation.
    • Each character appeared to be inherited independently.
    • If you follow just one character in these crosses, you will observe a 3:1 F2 ratio, just as if this were a monohybrid cross.
    • The independent assortment of each pair of alleles during gamete formation is now called Mendel’s law of independent assortment.
    • Mendel’s law of independent assortment states that each pair of alleles segregates independently during gamete formation.
    • Strictly speaking, this law applies only to genes located on different, nonhomologous chromosomes.
    • Genes located near each other on the same chromosome tend to be inherited together and have more complex inheritance patterns than those predicted for the law of independent assortment.

    Concept 14.2 The laws of probability govern Mendelian inheritance

    • Mendel’s laws of segregation and independent assortment reflect the same laws of probability that apply to tossing coins or rolling dice.
    • The probability scale ranges from 0 (an event with no chance of occurring) to 1 (an event that is certain to occur).
      • The probability of tossing heads with a normal coin is 1/2.
      • The probability of rolling a 3 with a six-sided die is 1/6, and the probability of rolling any other number is 1 ? 1/6 = 5/6.
    • When tossing a coin, the outcome of one toss has no impact on the outcome of the next toss.
    • Each toss is an independent event, just like the distribution of alleles into gametes.
      • Like a coin toss, each ovum from a heterozygous parent has a 1/2 chance of carrying the dominant allele and a 1/2 chance of carrying the recessive allele.
      • The same odds apply to the sperm.
    • We can use the multiplication rule to determine the chance that two or more independent events will occur together in some specific combination.
      • Compute the probability of each independent event.
      • Multiply the individual probabilities to obtain the overall probability of these events occurring together.
      • The probability that two coins tossed at the same time will land heads up is 1/2 × 1/2 = 1/4.
      • Similarly, the probability that a heterozygous pea plant (Pp) will self-fertilize to produce a white-flowered offspring (pp) is the chance that a sperm with a white allele will fertilize an ovum with a white allele.
      • This probability is 1/2 × 1/2 = 1/4.
    • The rule of multiplication also applies to dihybrid crosses.
      • For a heterozygous parent (YyRr) the probability of producing a YR gamete is 1/2 × 1/2 = 1/4.
      • We can use this to predict the probability of a particular F2 genotype without constructing a 16-part Punnett square.
      • The probability that an F2 plant from heterozygous parents will have a YYRR genotype is 1/16 (1/4 chance for a YR ovum and 1/4 chance for a YR sperm).
    • The rule of addition also applies to genetic problems.
    • Under the rule of addition, the probability of an event that can occur two or more different ways is the sum of the separate probabilities of those ways.
      • For example, there are two ways that F1 gametes can combine to form a heterozygote.
        • The dominant allele could come from the sperm and the recessive from the ovum (probability = 1/4).
        • Or the dominant allele could come from the ovum and the recessive from the sperm (probability = 1/4).
        • The probability of obtaining a heterozygote is 1/4 + 1/4 = 1/2.
    • We can combine the rules of multiplication and addition to solve complex problems in Mendelian genetics.
    • Let’s determine the probability of an offspring having two recessive phenotypes for at least two of three traits resulting from a trihybrid cross between pea plants that are PpYyRr and Ppyyrr.
      • There are five possible genotypes that fulfill this condition: ppyyRr, ppYyrr, Ppyyrr, PPyyrr, and ppyyrr.
      • We can use the rule of multiplication to calculate the probability for each of these genotypes and then use the rule of addition to pool the probabilities for fulfilling the condition of at least two recessive traits.
    • The probability of producing a ppyyRr offspring:
      • The probability of producing pp = 1/2 × 1/2 = 1/4.
      • The probability of producing yy = 1/2 × 1 = 1/2.
      • The probability of producing Rr = 1/2 × 1 = 1/2.
      • Therefore, the probability of all three being present (ppyyRr) in one offspring is 1/4 × 1/2 × 1/2 = 1/16.
    • For ppYyrr: 1/4 × 1/2 × 1/2 = 1/16.
    • For Ppyyrr: 1/2 × 1/2 × 1/2 = 1/8 or 2/16.
    • For PPyyrr: 1/4 × 1/2 × 1/2 = 1/16.
    • For ppyyrr: 1/4 × 1/2 × 1/2 = 1/16.
    • Therefore, the chance that a given offspring will have at least two recessive traits is 1/16 + 2/16 + 1/16 + 1/16 = 6/16.

      Mendel discovered the particulate behavior of genes: a review.

    • While we cannot predict with certainty the genotype or phenotype of any particular seed from the F2 generation of a dihybrid cross, we can predict the probability that it will have a specific genotype or phenotype.
    • Mendel’s experiments succeeded because he counted so many offspring, was able to discern the statistical nature of inheritance, and had a keen sense of the rules of chance.
    • Mendel’s laws of independent assortment and segregation explain heritable variation in terms of alternative forms of genes that are passed along according to simple rules of probability.
    • These laws apply not just to garden peas, but to all diploid organisms that reproduce by sexual reproduction.
    • Mendel’s studies of pea inheritance endure not only in genetics, but as a case study of the power of scientific reasoning using the hypothetico-deductive approach.

    Concept 14.3 Inheritance patterns are often more complex than predicted by simple Mendelian genetics

    • In the 20th century, geneticists have extended Mendelian principles not only to diverse organisms, but also to patterns of inheritance more complex than Mendel described.
    • In fact, Mendel had the good fortune to choose a system that was relatively simple genetically.
      • Each character that Mendel studied is controlled by a single gene.
      • Each gene has only two alleles, one of which is completely dominant to the other.
    • The heterozygous F1 offspring of Mendel’s crosses always looked like one of the parental varieties because one allele was dominant to the other.
    • The relationship between genotype and phenotype is rarely so simple.
    • The inheritance of characters determined by a single gene deviates from simple Mendelian patterns when alleles are not completely dominant or recessive, when a gene has more than two alleles, or when a gene produces multiple phenotypes.
    • We will consider examples of each of these situations.
    • Alleles show different degrees of dominance and recessiveness in relation to each other.
    • One extreme is the complete dominance characteristic of Mendel’s crosses.
    • At the other extreme from complete dominance is codominance, in which two alleles affect the phenotype in separate, distinguishable ways.
      • For example, the M, N, and MN blood groups of humans are due to the presence of two specific molecules on the surface of red blood cells.
      • People of group M (genotype MM) have one type of molecule on their red blood cells, people of group N (genotype NN) have the other type, and people of group MN (genotype MN) have both molecules present.
      • The MN phenotype is not intermediate between M and N phenotypes but rather exhibits both the M and the N phenotype.
    • Some alleles show incomplete dominance, in which heterozygotes show a distinct intermediate phenotype not seen in homozygotes.
      • This is not blending inheritance because the traits are separable (particulate), as shown in further crosses.
      • Offspring of a cross between heterozygotes show three phenotypes: each parental and the heterozygote.
      • The phenotypic and genotypic ratios are identical: 1:2:1.
    • A clear example of incomplete dominance is seen in flower color of snapdragons.
      • A cross between a white-flowered plant and a red-flowered plant will produce all pink F1 offspring.
      • Self-pollination of the F1 offspring produces 25% white, 25% red, and 50% pink F2 offspring.
    • The relative effects of two alleles range from complete dominance of one allele, through incomplete dominance of either allele, to codominance of both alleles.
    • It is important to recognize that a dominant allele does not somehow subdue a recessive allele.
    • Alleles are simply variations in a gene’s nucleotide sequence.
      • When a dominant allele coexists with a recessive allele in a heterozygote, they do not interact at all.
    • To illustrate the relationship between dominance and phenotype, let us consider Mendel’s character of round versus wrinkled pea seed shape.
      • Pea plants with wrinkled seeds have two copies of the recessive allele.
      • The seeds are wrinkled due to the accumulation of monosaccharides because of the lack of a key enzyme that converts them to starch.
      • Excess water enters the seed due to the accumulation of monosaccharides.
        • The seeds wrinkle when the excess water dries.
      • Both homozygous dominants and heterozygotes produce enough enzymes to convert all the monosaccharides into starch.
      • As a result, they do not fill with excess water and form smooth seeds as they dry.
    • For any character, dominance/recessiveness relationships depend on the level at which we examine the phenotype.
      • For example, humans with Tay-Sachs disease lack a functioning enzyme to metabolize certain lipids. These lipids accumulate in the brain, harming brain cells, and ultimately leading to death.
      • Children with two Tay-Sachs alleles (homozygotes) have the disease.
      • Both heterozygotes with one working allele and homozygotes with two working alleles are healthy and normal at the organismal level.
      • The activity level of the lipid-metabolizing enzyme is reduced in heterozygotes. At the biochemical level, the alleles show incomplete dominance.
      • Heterozygous individuals produce equal numbers of normal and dysfunctional enzyme molecules. At the molecular level, the Tay-Sachs and functional alleles are codominant.
    • A dominant allele is not necessarily more common in a population than the recessive allele.
      • For example, one baby in 400 is born with polydactyly, a condition in which individuals are born with extra fingers or toes.
      • Polydactyly is due to a dominant allele.
      • However, the recessive allele is far more prevalent than the dominant allele.
        • 399 individuals out of 400 have five digits per appendage.
    • Many genes exist in populations in more than two allelic forms.
    • The ABO blood groups in humans are determined by three alleles, IA, IB, and i.
      • Both the IA and IB alleles are dominant to the i allele.
      • The IA and IB alleles are codominant to each other.
    • Because each individual carries two alleles, there are six possible genotypes and four possible blood types.
      • Individuals that are IAIA or IAi are type A and have type A carbohydrates on the surface of their red blood cells.
      • Individuals that are IBIB or IBi are type B and have type B carbohydrates on the surface of their red blood cells.
      • Individuals that are IAIB are type AB and have both type A and type B carbohydrates on the surface of their red blood cells.
      • Individuals that are ii are type O and have neither carbohydrate on the surface of their red blood cells.
    • Matching compatible blood groups is critical for blood transfusions because a person produces antibodies against foreign blood factors.
      • If the donor’s blood has an A or B carbohydrate that is foreign to the recipient, antibodies in the recipient’s blood will bind to the foreign molecules, cause the donated blood cells to clump together, and can kill the recipient.
    • The genes that we have covered so far affect only one phenotypic character.
    • However, most genes are pleiotropic, affecting more than one phenotypic character.
      • For example, the wide-ranging symptoms of sickle-cell disease are due to a single gene.
    • Considering the intricate molecular and cellular interactions responsible for an organism’s development, it is not surprising that a gene can affect a number of characteristics.
    • In epistasis, a gene at one locus alters the phenotypic expression of a gene at a second locus.
      • For example, in mice and many other mammals, coat color depends on two genes.
      • One, the epistatic gene, determines whether pigment will be deposited in hair or not.
        • Presence (C) is dominant to absence (c) of pigment.
      • The second gene determines whether the pigment to be deposited is black (B) or brown (b).
        • The black allele is dominant to the brown allele.
      • An individual that is cc has a white (albino) coat regardless of the genotype of the second gene.
    • A cross between two black mice that are heterozygous (BbCc) will follow the law of independent assortment.
    • However, unlike the 9:3:3:1 offspring ratio of a normal Mendelian experiment, the offspring ratio is nine black, three brown, and four white.
    • All cc mice will be albino, regardless of the alleles they inherit at the B gene.
    • Some characters cannot be classified as either-or, as Mendel’s genes were.
    • Quantitative characters vary in a population along a continuum.
    • These are usually due to polygenic inheritance, the additive effects of two or more genes on a single phenotypic character.
      • For example, skin color in humans is controlled by at least three independent genes.
      • Imagine that each gene has two alleles, one light and one dark, which demonstrate incomplete dominance.
      • An AABBCC individual is very dark; an aabbcc individual is very light.
    • A cross between two AaBbCc individuals (with intermediate skin shade) will produce offspring covering a wide range of shades.
      • Individuals with intermediate skin shades will be most common, but some very light and very dark individuals could be produced as well.
      • The range of phenotypes will form a normal distribution, if the number of offspring is great enough.
    • Phenotype depends on environment and genes.
      • A person becomes darker if they tan, despite their inherited skin color.
      • A single tree may have leaves that vary in size, shape, and greenness, depending on exposure to wind and sun.
      • For humans, nutrition influences height, exercise alters build, sun-tanning darkens skin, and experience improves performance on intelligence tests.
      • Even identical twins, who are genetically identical, accumulate phenotypic differences as a result of their unique experiences.
    • The relative importance of genes and the environment in influencing human characteristics is a very old and hotly contested debate.
    • The product of a genotype is generally not a rigidly defined phenotype, but a range of phenotypic possibilities, the norm of reaction, that are determined by the environment.
      • In some cases, the norm of reaction has no breadth, and a given genotype specifies a particular phenotype (for example, blood type).
      • In contrast, a person’s red and white blood cell count varies with factors such as altitude, customary exercise level, and presence of infection.
    • Norms of reaction are broadest for polygenic characters.
      • For these multifactorial characters, environment contributes to their quantitative nature.
    • A reductionist emphasis on single genes and single phenotypic characters presents an inadequate perspective on heredity and variation.
    • A more comprehensive theory of Mendelian genetics must view organisms as a whole.
    • The term phenotype can refer not only to specific characters such as flower color or blood group, but also to an organism in its entirety, including all aspects of its physical appearance.
    • Genotype can refer not just to a single genetic locus, but also to an organism’s entire genetic makeup.
    • An organism’s phenotype reflects its overall genotype and its unique environmental history.

    Concept 14.4 Many human traits follow Mendelian patterns of inheritance

    • While peas are convenient subjects for genetic research, humans are not.
      • The generation time is too long, fecundity is too low, and breeding experiments are unacceptable.
    • Yet humans are subject to the same rules governing inheritance as other organisms.
    • New techniques in molecular biology have led to many breakthrough discoveries in the study of human genetics.

      Pedigree analysis reveals Mendelian patterns in human inheritance.

    • Rather than manipulate mating patterns of people, geneticists analyze the results of matings that have already occurred.
    • In a pedigree analysis, information about the presence or absence of a particular phenotypic trait is collected from as many individuals in a family as possible, across generations.
    • The distribution of these characters is then mapped on the family tree.
      • For example, the occurrence of widow’s peak (W) is dominant to a straight hairline (w).
      • Phenotypes of family members and knowledge of dominant/recessive relations between alleles allow researchers to predict the genotypes of members of this family.
      • For example, if an individual in the third generation lacks a widow’s peak, but both her parents have widow’s peaks, then her parents must be heterozygous for that gene.
      • If some siblings in the second generation lack a widow’s peak and one of the grandparents (first generation) also lacks one, then we know the other grandparent must be heterozygous, and we can determine the genotype of many other individuals.
    • We can use the same family tree to trace the distribution of attached earlobes (f), a recessive characteristic.
    • Individuals with a dominant allele (F) have free earlobes.
    • Some individuals may be ambiguous, especially if they have the dominant phenotype and could be heterozygous or homozygous dominant.
    • A pedigree can help us understand the past and predict the future.
    • We can use normal Mendelian rules, including multiplication and addition, to predict the probability of specific phenotypes.
      • For example, these rules could be used to predict the probability that a child with WwFf parents will have a widow’s peak and attached earlobes.
        • The chance of having a widow’s peak is 3/4 (1/2 [WW] + 1/4 [Ww]).
        • The chance of having attached earlobes is 1/4 [ff].
        • This combination has a probability of 3/4 × 1/4 = 3/16.

      Many human disorders follow Mendelian patterns of inheritance.

    • Thousands of genetic disorders, including disabling or deadly hereditary diseases, are inherited as simple recessive traits.
    • These conditions range from relatively mild (albinism) to life-threatening (cystic fibrosis).
    • The recessive behavior of the alleles causing these conditions occurs because the allele codes for a malfunctioning protein or for no protein at all.
      • Heterozygotes have a normal phenotype because one normal allele produces enough of the required protein.
    • A recessively inherited disorder shows up only in homozygous individuals who inherit a recessive allele from each parent.
    • Individuals who lack the disorder are either homozygous dominant or heterozygotes.
    • While heterozygotes may lack obvious phenotypic effects, they are carriers who may transmit a recessive allele to their offspring.
    • Most people with recessive disorders are born to carriers with normal phenotypes.
      • Two carriers have a 1/4 chance of having a child with the disorder, 1/2 chance of having a child who is a carrier, and 1/4 chance of having a child without a defective allele.
    • Genetic disorders are not evenly distributed among all groups of humans.
    • This results from the different genetic histories of the world’s people during times when populations were more geographically and genetically isolated.
    • Cystic fibrosis strikes one of every 2,500 whites of European descent.
      • One in 25 people of European descent is a carrier for this condition.
      • The normal allele for this gene codes for a membrane protein that transports Cl? between cells and extracellular fluid.
      • If these channels are defective or absent, there are abnormally high extracellular levels of chloride.
      • This causes the mucus coats of certain cells to become thicker and stickier than normal.
      • This mucus buildup in the pancreas, lungs, digestive tract, and elsewhere causes poor absorption of nutrients, chronic bronchitis, and bacterial infections.
      • Without treatment, affected children die before five, but with treatment, they can live past their late 20s or even 30s.
    • Tay-Sachs disease is another lethal recessive disorder.
      • It is caused by a dysfunctional enzyme that fails to break down specific brain lipids.
      • The symptoms begin with seizures, blindness, and degeneration of motor and mental performance a few months after birth.
      • Inevitably, the child dies after a few years.
      • Among Ashkenazic Jews (those from central Europe), this disease occurs in one of 3,600 births, about 100 times greater than the incidence among non-Jews or Mediterranean (Sephardic) Jews.
    • The most common inherited disease among people of African descent is sickle-cell disease, which affects one of 400 African-Americans.
      • Sickle-cell disease is caused by the substitution of a single amino acid in hemoglobin.
      • When oxygen levels in the blood of an affected individual are low, sickle-cell hemoglobin aggregate into long rods that deform red blood cells into a sickle shape.
      • This sickling creates a cascade of symptoms, demonstrating the pleiotropic effects of this allele, as sickled cells clump and clog capillaries throughout the body.
    • Doctors can use regular blood transfusions to prevent brain damage and new drugs to prevent or treat other problems.
    • At the organismal level, the nonsickle allele is incompletely dominant to the sickle-cell allele.
      • Carriers are said to have sickle-cell trait.
      • These individuals are usually healthy, although some suffer some symptoms of sickle-cell disease under blood oxygen stress.
    • At the molecular level, the two alleles are codominant as both normal and abnormal (sickle-cell) hemoglobins are synthesized.
    • About one in ten African-Americans has sickle-cell trait.
      • The high frequency of heterozygotes is unusual for an allele with severe detrimental effects in homozygotes.
      • Individuals with one sickle-cell allele have increased resistance to malaria, a parasite that spends part of its life cycle in red blood cells.
      • In tropical Africa, where malaria is common, the sickle-cell allele is both a boon and a bane.
        • Homozygous normal individuals die of malaria and homozygous recessive individuals die of sickle-cell disease, while carriers are relatively free of both.
    • The relatively high frequency of sickle-cell trait in African-Americans is a vestige of their African roots.
    • Normally it is relatively unlikely that two carriers of the same rare, harmful allele will meet and mate.
    • However, consanguineous matings between close relatives increase the risk.
      • Individuals who share a recent common ancestor are more likely to carry the same recessive alleles.
    • Most societies and cultures have laws or taboos forbidding marriages between close relatives.
    • Although most harmful alleles are recessive, a number of human disorders are due to dominant alleles.
    • For example, achondroplasia, a form of dwarfism, has an incidence of one case in 25,000 people.
      • Heterozygous individuals have the dwarf phenotype.
      • Those who are not achondroplastic dwarfs, 99.99% of the population, are homozygous recessive for this trait.
      • This provides another example of a trait for which the recessive allele is far more prevalent than the dominant allele.
    • Lethal dominant alleles are much less common than lethal recessives.
      • If a lethal dominant kills an offspring before it can mature and reproduce, the allele will not be passed on to future generations.
      • In contrast, a lethal recessive allele can be passed on by heterozygous carriers who have normal phenotypes.
    • A lethal dominant allele can escape elimination if it causes death at a relatively advanced age, after the individual has already passed on the lethal allele to his or her children.
    • One example is Huntington’s disease, a degenerative disease of the nervous system.
      • The dominant lethal allele has no obvious phenotypic effect until an individual is about 35 to 45 years old.
      • The deterioration of the nervous system is irreversible and inevitably fatal.
    • Any child born to a parent who has the allele for Huntington’s disease has a 50% chance of inheriting the disease and the disorder.
    • In the United States, this devastating disease afflicts one in 10,000 people.
    • Recently, molecular geneticists have used pedigree analysis of affected families to track the Huntington’s allele to a locus near the tip of chromosome 4.
      • This has led to the development of a test that can detect the presence of the Huntington’s allele in an individual’s genome.
    • While some diseases are inherited in a simple Mendelian fashion due to alleles at a single locus, many other disorders have a multifactorial basis.
      • These may have a genetic component plus a significant environmental influence.
      • Multifactorial disorders include heart disease; diabetes; cancer; alcoholism; and certain mental illnesses, such as schizophrenia and manic-depressive disorder.
      • The genetic component of such disorders is typically polygenic.
    • At present, little is understood about the genetic contribution to most multifactorial diseases.
      • The best public health strategy is education about relevant environmental factors and promotion of healthy behavior.

      Technology is providing new tools for genetic testing and counseling.

    • A preventive approach to simple Mendelian disorders is sometimes possible.
    • The risk that a particular genetic disorder will occur can sometimes be assessed before a child is conceived or early in pregnancy.
    • Many hospitals have genetic counselors to provide information to prospective parents who are concerned about a family history of a specific disease.
    • Consider a hypothetical couple, John and Carol, who are planning to have their first child.
    • In both of their families’ histories, a recessive lethal disorder is present. Both John and Carol had brothers who died of the disease.
      • While not one of John, Carol, or their parents have the disease, their parents must have been carriers (Aa × Aa).
      • John and Carol each have a 2/3 chance of being carriers and a 1/3 chance of being homozygous dominant.
      • The probability that their first child will have the disease is 2/3 (chance that John is a carrier) × 2/3 (chance that Carol is a carrier) × 1/4 (chance that the offspring of two carriers is homozygous recessive) = 1/9.
      • If their first child is born with the disease, we know that John and Carol’s genotype must be Aa and they are both carriers.
      • In that case, the chance that their next child will also have the disease is 1/4.
    • Mendel’s laws are simply the rules of probability applied to heredity.
      • Because chance has no memory, the genotype of each child is unaffected by the genotypes of older siblings.
      • The chance that John and Carol’s first three children will have the disorder is 1/4 × 1/4 × 1/4 = 1/64. Should that outcome happen, the likelihood that a fourth child will also have the disorder is still 1/4.
    • Because most children with recessive disorders are born to parents with a normal phenotype, the key to assessing risk is identifying whether prospective parents are carriers of the recessive trait.
    • Recently developed tests for several disorders can distinguish normal phenotypes in heterozygotes from homozygous dominants.
      • These results allow individuals with a family history of a genetic disorder to make informed decisions about having children.
      • However, issues of confidentiality, discrimination, and counseling may arise.
    • Tests are also available to determine in utero if a child has a particular disorder.
    • One technique, amniocentesis, can be used from the 14th to 16th week of pregnancy to assess whether the fetus has a specific disease.
      • Fetal cells extracted from amniotic fluid are cultured and karyotyped to identify some disorders.
      • Other disorders can be identified from chemicals in the amniotic fluids.
    • A second technique, chorionic villus sampling (CVS) allows faster karyotyping and can be performed as early as the eighth to tenth week of pregnancy.
      • This technique extracts a sample of fetal tissue from the chorionic villi of the placenta.
      • This technique is not suitable for tests requiring amniotic fluid.
    • Other techniques, ultrasound and fetoscopy, allow fetal health to be assessed visually in utero.
      • Both fetoscopy and amniocentesis cause complications such as maternal bleeding or fetal death in about 1% of cases.
      • Therefore, these techniques are usually reserved for cases in which the risk of a genetic disorder or other type of birth defect is relatively great.
    • If fetal tests reveal a serious disorder, the parents face the difficult choice of terminating the pregnancy or preparing to care for a child with a genetic disorder.
    • Some genetic traits can be detected at birth by simple tests that are now routinely performed in hospitals.
    • One test can detect the presence of a recessively inherited disorder, phenylketonuria (PKU).
      • This disorder occurs in one in 10,000 to 15,000 births.
      • Individuals with this disorder accumulate the amino acid phenylalanine and its derivative phenylpyruvate in the blood to toxic levels.
        • This leads to mental retardation.
      • If the disorder is detected, a special diet low in phenylalanine usually promotes normal development.
      • Unfortunately, few other genetic diseases are so treatable.

    Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 14-1

    Subject: 
    Subject X2: 

    Chapter 15 - The Chromosomal Basis of Inheritance

    Chapter 15 The Chromosomal Basis of Inheritance
    Lecture Outline

    Overview: Locating Genes on Chromosomes

    • Today we know that genes—Gregor Mendel’s “hereditary factors”—are located on chromosomes.
    • A century ago, the relationship of genes and chromosomes was not so obvious.
    • Many biologists were skeptical about Mendel’s laws of segregation and independent assortment until evidence mounted that they had a physical basis in the behavior of chromosomes.

    Concept 15.1 Mendelian inheritance has its physical basis in the behavior of chromosomes

    • Around 1900, cytologists and geneticists began to see parallels between the behavior of chromosomes and the behavior of Mendel’s factors.
      • Using improved microscopy techniques, cytologists worked out the process of mitosis in 1875 and meiosis in the 1890s.
      • Chromosomes and genes are both present in pairs in diploid cells.
      • Homologous chromosomes separate and alleles segregate during meiosis.
      • Fertilization restores the paired condition for both chromosomes and genes.
    • Around 1902, Walter Sutton, Theodor Boveri, and others noted these parallels and a chromosome theory of inheritance began to take form:
      • Genes occupy specific loci on chromosomes.
      • Chromosomes undergo segregation during meiosis.
      • Chromosomes undergo independent assortment during meiosis.
    • The behavior of homologous chromosomes during meiosis can account for the segregation of the alleles at each genetic locus to different gametes.
    • The behavior of nonhomologous chromosomes can account for the independent assortment of alleles for two or more genes located on different chromosomes.

      Morgan traced a gene to a specific chromosome.

    • In the early 20th century, Thomas Hunt Morgan was the first geneticist to associate a specific gene with a specific chromosome.
    • Like Mendel, Morgan made an insightful choice in his experimental animal. Morgan worked with Drosophila melanogaster, a fruit fly that eats fungi on fruit.
      • Fruit flies are prolific breeders and have a generation time of two weeks.
      • Fruit flies have three pairs of autosomes and a pair of sex chromosomes (XX in females, XY in males).
    • Morgan spent a year looking for variant individuals among the flies he was breeding.
      • He discovered a single male fly with white eyes instead of the usual red.
    • The normal character phenotype is the wild type.
    • Alternative traits are called mutant phenotypes because they are due to alleles that originate as mutations in the wild-type allele.
      • When Morgan crossed his white-eyed male with a red-eyed female, all the F1 offspring had red eyes, suggesting that the red allele was dominant to the white allele.
    • Crosses between the F1 offspring produced the classic 3:1 phenotypic ratio in the F2 offspring.
    • Surprisingly, the white-eyed trait appeared only in F2 males.
      • All the F2 females and half the F2 males had red eyes.
    • Morgan concluded that a fly’s eye color was linked to its sex.
    • Morgan deduced that the gene with the white-eyed mutation is on the X chromosome, with no corresponding allele present on the Y chromosome.
      • Females (XX) may have two red-eyed alleles and have red eyes or may be heterozygous and have red eyes.
      • Males (XY) have only a single allele. They will be red-eyed if they have a red-eyed allele or white-eyed if they have a white-eyed allele.

    Concept 15.2 Linked genes tend to be inherited together because they are located near each other on the same chromosome

    • Each chromosome has hundreds or thousands of genes.
    • Genes located on the same chromosome that tend to be inherited together are called linked genes.
    • Results of crosses with linked genes deviate from those expected according to independent assortment.
    • Morgan observed this linkage and its deviations when he followed the inheritance of characters for body color and wing size.
      • The wild-type body color is gray (b+), and the mutant is black (b).
      • The wild-type wing size is normal (vg+), and the mutant has vestigial wings (vg).
    • The mutant alleles are recessive to the wild-type alleles.
    • Neither gene is on a sex chromosome.
    • Morgan crossed F1 heterozygous females (b+bvg+vg) with homozygous recessive males (bbvgvg).
    • According to independent assortment, this should produce 4 phenotypes in a 1:1:1:1 ratio.
    • Surprisingly, Morgan observed a large number of wild-type (gray-normal) and double-mutant (black-vestigial) flies among the offspring.
      • These phenotypes are those of the parents.
    • Morgan reasoned that body color and wing shape are usually inherited together because the genes for these characters are on the same chromosome.
    • The other two phenotypes (gray-vestigial and black-normal) were fewer than expected from independent assortment (but totally unexpected from dependent assortment).
    • What led to this genetic recombination, the production of offspring with new combinations of traits?

      Independent assortment of chromosomes and crossing over produce genetic recombinants.

    • Genetic recombination can result from independent assortment of genes located on nonhomologous chromosomes or from crossing over of genes located on homologous chromosomes.
    • Mendel’s dihybrid cross experiments produced offspring that had a combination of traits that did not match either parent in the P generation.
      • If the P generation consists of a yellow-round seed parent (YYRR) crossed with a green-wrinkled seed parent (yyrr), all F1 plants have yellow-round seeds (YyRr).
      • A cross between an F1 plant and a homozygous recessive plant (a testcross) produces four phenotypes.
      • Half are the parental types, with phenotypes that match the original P parents, with either yellow-round seeds or green-wrinkled seeds.
      • Half are recombinants, new combinations of parental traits, with yellow-wrinkled or green-round seeds.
    • A 50% frequency of recombination is observed for any two genes located on different (nonhomologous) chromosomes.
    • The physical basis of recombination between unlinked genes is the random orientation of homologous chromosomes at metaphase I of meiosis, which leads to the independent assortment of alleles.
    • The F1 parent (YyRr) produces gametes with four different combinations of alleles: YR, Yr, yR, and yr.
      • The orientation of the tetrad containing the seed-color gene has no bearing on the orientation of the tetrad with the seed-shape gene.
    • In contrast, linked genes, genes located on the same chromosome, tend to move together through meiosis and fertilization.
    • Under normal Mendelian genetic rules, we would not expect linked genes to recombine into assortments of alleles not found in the parents.
      • If the seed color and seed coat genes were linked, we would expect the F1 offspring to produce only two types of gametes, YR and yr, when the tetrads separate.
      • One homologous chromosome carries the Y and R alleles on the same chromosome, and the other homologous chromosome carries the y and r alleles.
    • The results of Morgan’s testcross for body color and wing shape did not conform to either independent assortment or complete linkage.
      • Under independent assortment, the testcross should produce a 1:1:1:1 phenotypic ratio.
      • If completely linked, we should expect to see a 1:1:0:0 ratio with only parental phenotypes among offspring.
    • Most of the offspring had parental phenotypes, suggesting linkage between the genes.
    • However, 17% of the flies were recombinants, suggesting incomplete linkage.
    • Morgan proposed that some mechanism must occasionally break the physical connection between genes on the same chromosome.
    • This process, called crossing over, accounts for the recombination of linked genes.
    • Crossing over occurs while replicated homologous chromosomes are paired during prophase of meiosis I.
      • One maternal and one paternal chromatid break at corresponding points and then rejoin with each other.
    • The occasional production of recombinant gametes during meiosis accounts for the occurrence of recombinant phenotypes in Morgan’s testcross.
    • The percentage of recombinant offspring, the recombination frequency, is related to the distance between linked genes.

      Geneticists can use recombination data to map a chromosome’s genetic loci.

    • One of Morgan’s students, Alfred Sturtevant, used crossing over of linked genes to develop a method for constructing a genetic map, an ordered list of the genetic loci along a particular chromosome.
    • Sturtevant hypothesized that the frequency of recombinant offspring reflected the distance between genes on a chromosome.
    • He assumed that crossing over is a random event, and that the chance of crossing over is approximately equal at all points on a chromosome.
    • Sturtevant predicted that the farther apart two genes are, the higher the probability that a crossover will occur between them, and therefore, the higher the recombination frequency.
      • The greater the distance between two genes, the more points there are between them where crossing over can occur.
    • Sturtevant used recombination frequencies from fruit fly crosses to map the relative position of genes along chromosomes.
    • A genetic map based on recombination frequencies is called a linkage map.
    • Sturtevant used the testcross design to map the relative position of three fruit fly genes, body color (b), wing size (vg), and eye color (cn).
      • The recombination frequency between cn and b is 9%.
      • The recombination frequency between cn and vg is 9.5%.
      • The recombination frequency between b and vg is 17%.
      • The only possible arrangement of these three genes places the eye color gene between the other two.
    • Sturtevant expressed the distance between genes, the recombination frequency, as map units.
      • One map unit (called a centimorgan) is equivalent to a 1% recombination frequency.
    • You may notice that the three recombination frequencies in our mapping example are not quite additive: 9% (b-cn) + 9.5% (cn-vg) > 17% (b-vg).
    • This results from multiple crossing over events.
      • A second crossing over “cancels out” the first and reduces the observed number of recombinant offspring.
      • Genes father apart (for example, b-vg) are more likely to experience multiple crossing over events.
    • Some genes on a chromosome are so far apart that a crossover between them is virtually certain.
    • In this case, the frequency of recombination reaches its maximum value of 50% and the genes behave as if found on separate chromosomes.
      • In fact, two genes studied by Mendel—for seed color and flower color—are located on the same chromosome but still assort independently.
    • Genes located far apart on a chromosome are mapped by adding the recombination frequencies between the distant genes and the intervening genes.
    • Sturtevant and his colleagues were able to map the linear positions of genes in Drosophila into four groups, one for each chromosome.
    • A linkage map provides an imperfect picture of a chromosome.
    • Map units indicate relative distance and order, not precise locations of genes.
      • The frequency of crossing over is not actually uniform over the length of a chromosome.
    • A linkage map does portray the order of genes along a chromosome, but does not accurately portray the precise location of those genes.
    • Combined with other methods like chromosomal banding, geneticists can develop cytogenetic maps of chromosomes.
      • These indicate the positions of genes with respect to chromosomal features.
    • Recent techniques show the physical distances between gene loci in DNA nucleotides.

    Concept 15.3 Sex-linked genes exhibit unique patterns of inheritance

      The chromosomal basis of sex varies with the organism.

    • Although the anatomical and physiological differences between women and men are numerous, the chromosomal basis of sex is rather simple.
    • In humans and other mammals, there are two varieties of sex chromosomes, X and Y.
      • An individual who inherits two X chromosomes usually develops as a female.
      • An individual who inherits an X and a Y chromosome usually develops as a male.
    • Other animals have different methods of sex determination.
      • The X-0 system is found in some insects. Females are XX, males are X.
      • In birds, some fishes, and some insects, females are ZW and males are ZZ.
      • In bees and ants, females are diploid and males are haploid.
    • In the X-Y system, the Y chromosome is much smaller than the X chromosome.
    • Only relatively short segments at either end of the Y chromosome are homologous with the corresponding regions of the X chromosome.
      • The X and Y rarely cross over.
    • In both testes (XY) and ovaries (XX), the two sex chromosomes segregate during meiosis, and each gamete receives one.
      • Each ovum receives an X chromosome.
      • Half the sperm cells receive an X chromosome, and half receive a Y chromosome.
    • Because of this, each conception has about a fifty-fifty chance of producing a particular sex.
      • If a sperm cell bearing an X chromosome fertilizes an ovum, the resulting zygote is female (XX).
      • If a sperm cell bearing a Y chromosome fertilizes an ovum, the resulting zygote is male (XY).
    • In humans, the anatomical signs of sex first appear when the embryo is about two months old.
    • In 1990, a British research team identified a gene on the Y chromosome required for the development of testes.
      • They named the gene SRY (sex-determining region of the Y chromosome).
    • In individuals with the SRY gene, the generic embryonic gonads develop into testes.
      • Activity of the SRY gene triggers a cascade of biochemical, physiological, and anatomical features because it regulates many other genes.
      • Other genes on the Y chromosome are necessary for the production of functional sperm.
      • In the absence of these genes, an XY individual is male but does not produce normal sperm.
    • In individuals lacking the SRY gene, the generic embryonic gonads develop into ovaries.

      Sex-linked genes have unique patterns of inheritance.

    • In addition to their role in determining sex, the sex chromosomes, especially the X chromosome, have genes for many characters unrelated to sex.
    • A gene located on either sex chromosome is called a sex-linked gene.
    • In humans, the term refers to a gene on the X chromosome.
    • Human sex-linked genes follow the same pattern of inheritance as Morgan’s white-eye locus in Drosophila.
      • Fathers pass sex-linked alleles to all their daughters but none of their sons.
      • Mothers pass sex-linked alleles to both sons and daughters.
    • If a sex-linked trait is due to a recessive allele, a female will express this phenotype only if she is homozygous.
      • Heterozygous females are carriers for the recessive trait.
      • Because males have only one X chromosome (hemizygous), any male receiving the recessive allele from his mother will express the recessive trait.
      • The chance of a female inheriting a double dose of the mutant allele is much less than the chance of a male inheriting a single dose.
      • Therefore, males are far more likely to exhibit sex-linked recessive disorders than are females.
    • For example, color blindness is a mild disorder inherited as a sex-linked trait.
      • A color-blind daughter may be born to a color-blind father whose mate is a carrier.
      • However, the odds of this are fairly low.
    • Several serious human disorders are sex-linked.
    • Duchenne muscular dystrophy affects one in 3,500 males born in the United States.
      • Affected individuals rarely live past their early 20s.
      • This disorder is due to the absence of an X-linked gene for a key muscle protein called dystrophin.
      • The disease is characterized by a progressive weakening of the muscles and a loss of coordination.
    • Hemophilia is a sex-linked recessive disorder defined by the absence of one or more proteins required for blood clotting.
      • These proteins normally slow and then stop bleeding.
      • Individuals with hemophilia have prolonged bleeding because a firm clot forms slowly.
      • Bleeding in muscles and joints can be painful and can lead to serious damage.
    • Today, people with hemophilia can be treated with intravenous injections of the missing protein.
    • Although female mammals inherit two X chromosomes, only one X chromosome is active.
    • Therefore, males and females have the same effective dose (one copy) of genes on the X chromosome.
      • During female development, one X chromosome per cell condenses into a compact object called a Barr body.
      • Most of the genes on the Barr-body chromosome are not expressed.
    • The condensed Barr-body chromosome is reactivated in ovarian cells that produce ova.
    • Mary Lyon, a British geneticist, demonstrated that selection of which X chromosome will form the Barr body occurs randomly and independently in embryonic cells at the time of X inactivation.
    • As a consequence, females consist of a mosaic of two types of cells, some with an active paternal X chromosome, others with an active maternal X chromosome.
      • After an X chromosome is inactivated in a particular cell, all mitotic descendants of that cell will have the same inactive X.
      • If a female is heterozygous for a sex-linked trait, approximately half her cells will express one allele, and the other half will express the other allele.
    • In humans, this mosaic pattern is evident in women who are heterozygous for an X-linked mutation that prevents the development of sweat glands.
      • A heterozygous woman will have patches of normal skin and skin patches lacking sweat glands.
    • Similarly, the orange-and-black pattern on tortoiseshell cats is due to patches of cells expressing an orange allele while other patches have a nonorange allele.
    • X inactivation involves modification of the DNA by attachment of methyl (—CH3) groups to cytosine nucleotides on the X chromosome that will become the Barr body.
    • Researchers have discovered a gene called XIST (X-inactive specific transcript).
      • This gene is active only on the Barr-body chromosome and produces multiple copies of an RNA molecule that attach to the X chromosome on which they were made.
      • This initiates X inactivation.
      • The mechanism that connects XIST RNA and DNA methylation is unknown.
    • What determines which of the two X chromosomes has an active XIST gene is also unknown.

    Concept 15.4 Alterations of chromosome number or structure cause some genetic disorders

    • Physical and chemical disturbances can damage chromosomes in major ways.
    • Errors during meiosis can alter chromosome number in a cell.
    • Plants tolerate genetic defects to a greater extent that do animals.
    • Nondisjunction occurs when problems with the meiotic spindle cause errors in daughter cells.
      • This may occur if tetrad chromosomes do not separate properly during meiosis I.
      • Alternatively, sister chromatids may fail to separate during meiosis II.
    • As a consequence of nondisjunction, one gamete receives two of the same type of chromosome, and another gamete receives no copy.
    • Offspring resulting from fertilization of a normal gamete with one produced by nondisjunction will have an abnormal chromosome number, a condition known as aneuploidy.
      • Trisomic cells have three copies of a particular chromosome type and have 2n + 1 total chromosomes.
      • Monosomic cells have only one copy of a particular chromosome type and have 2n ? 1 chromosomes.
    • If the organism survives, aneuploidy typically leads to a distinct phenotype.
    • Aneuploidy can also occur during failures of the mitotic spindle.
    • If this happens early in development, the aneuploid condition will be passed along by mitosis to a large number of cells.
      • This is likely to have a substantial effect on the organism.
    • Organisms with more than two complete sets of chromosomes are polyploid.
    • This may occur when a normal gamete fertilizes another gamete in which there has been nondisjunction of all its chromosomes.
      • The resulting zygote would be triploid (3n).
    • Alternatively, if a 2n zygote failed to divide after replicating its chromosomes, a tetraploid (4n) embryo would result from subsequent successful cycles of mitosis.
    • Polyploidy is relatively common among plants and much less common among animals, although it is known to occur in fishes and amphibians.
      • The spontaneous origin of polyploid individuals plays an important role in the evolution of plants.
      • Both fishes and amphibians have polyploid species.
      • Recently, researchers in Chile have identified a new rodent species that may be tetraploid.
    • Polyploids are more nearly normal in phenotype than aneuploids.
      • One extra or missing chromosome apparently upsets the genetic balance during development more than does an entire extra set of chromosomes.
    • Breakage of a chromosome can lead to four types of changes in chromosome structure.
      • A deletion occurs when a chromosome fragment lacking a centromere is lost during cell division.
        • This chromosome will be missing certain genes.
      • A duplication occurs when a fragment becomes attached as an extra segment to a sister chromatid.
        • Alternatively, a detached fragment may attach to a nonsister chromatid of a homologous chromosome.
        • In this case, the duplicated segments will not be identical if the homologues carry different alleles.
      • An inversion occurs when a chromosomal fragment reattaches to the original chromosome, but in the reverse orientation.
      • In translocation, a chromosomal fragment joins a nonhomologous chromosome.
    • Deletions and duplications are especially likely to occur during meiosis.
      • Homologous chromatids may break and rejoin at incorrect places during crossing over, so that one chromatid loses more genes than it receives.
      • The products of such a nonreciprocal crossover are one chromosome with a deletion and one chromosome with a duplication.
    • A diploid embryo that is homozygous for a large deletion or a male with a large deletion to its single X chromosome is usually missing many essential genes.
      • This is usually lethal.
    • Duplications and translocations are typically harmful.
    • Reciprocal translocation or inversion can alter phenotype because a gene’s expression is influenced by its location among neighboring genes.

      Human disorders are due to chromosome alterations.

    • Several serious human disorders are due to alterations of chromosome number and structure.
    • Although the frequency of aneuploid zygotes may be quite high in humans, most of these alterations are so disastrous to development that the embryos are spontaneously aborted long before birth.
      • Severe developmental problems result from an imbalance among gene products.
    • Certain aneuploid conditions upset the balance less, making survival to birth and beyond possible.
      • Surviving individuals have a set of symptoms—a syndrome—characteristic of the type of aneuploidy.
      • Genetic disorders caused by aneuploidy can be diagnosed before birth by fetal testing.
    • One aneuploid condition, Down syndrome, is due to three copies of chromosome 21 or trisomy 21.
      • It affects one in 700 children born in the United States.
    • Although chromosome 21 is the smallest human chromosome, trisomy 21 severely alters an individual’s phenotype in specific ways.
      • Individuals with Down syndrome have characteristic facial features, short stature, heart defects, susceptibility to respiratory infection, mental retardation, and increased risk of developing leukemia and Alzheimer’s disease.
      • Most are sexually underdeveloped and sterile.
    • Most cases of Down syndrome result from nondisjunction during gamete production in one parent.
    • The frequency of Down syndrome increases with the age of the mother.
      • This may be linked to some age-dependent abnormality in the spindle checkpoint during meiosis I, leading to nondisjunction.
    • Trisomies of other chromosomes also increase in incidence with maternal age, but it is rare for infants with these autosomal trisomies to survive for long.
    • Nondisjunction of sex chromosomes produces a variety of aneuploid conditions in humans.
    • This aneuploidy upsets the genetic balance less severely that autosomal aneuploidy.
      • This may be because the Y chromosome contains relatively few genes and because extra copies of the X chromosome become inactivated as Barr bodies in somatic cells.
    • An XXY male has Klinefelter’s syndrome, which occurs once in every 2,000 live births.
      • These individuals have male sex organs, but have abnormally small testes and are sterile.
      • Although the extra X is inactivated, some breast enlargement and other female characteristics are common.
      • Affected individuals have normal intelligence.
    • Males with an extra Y chromosome (XYY) tend to be somewhat taller than average.
    • Trisomy X (XXX), which occurs once in every 2,000 live births, produces healthy females.
    • Monosomy X or Turner syndrome (X0) occurs once in every 5,000 births.
      • This is the only known viable monosomy in humans.
      • X0 individuals are phenotypically female but are sterile because their sex organs do not mature.
      • When provided with estrogen replacement therapy, girls with Turner syndrome develop secondary sex characteristics.
      • Most are of normal intelligence.
    • Structural alterations of chromosomes can also cause human disorders.
    • Deletions, even in a heterozygous state, can cause severe problems.
    • One syndrome, cri du chat, results from a specific deletion in chromosome 5.
      • These individuals are mentally retarded, have small heads with unusual facial features, and have a cry like the mewing of a distressed cat.
      • This syndrome is fatal in infancy or early childhood.
    • Chromosomal translocations between nonhomologous chromosomes are also associated with human disorders.
    • Chromosomal translocations have been implicated in certain cancers, including chronic myelogenous leukemia (CML).
      • CML occurs when a large fragment of chromosome 22 switches places with a small fragment from the tip of chromosome 9.
      • The resulting short, easily recognized chromosome 22 is called the Philadelphia chromosome.

    Concept 15.5 Some inheritance patterns are exceptions to the standard chromosome theory

      The phenotypic effects of some mammalian genes depend on whether they are inherited from the mother or the father.

    • For most genes, it is a reasonable assumption that a specific allele will have the same effect regardless of whether it is inherited from the mother or father.
    • However, for a few dozen mammalian traits, phenotype varies depending on which parent passed along the alleles for those traits.
      • The genes involved are not necessarily sex linked and may or may not lie on the X chromosome.
    • Variation in phenotype depending on whether an allele is inherited from the male or female parent is called genomic imprinting.
    • Genomic imprinting occurs during formation of gametes and results in the silencing of certain genes.
      • Imprinted genes are not expressed.
    • Because different genes are imprinted in sperm and ova, some genes in a zygote are maternally imprinted, and others are paternally imprinted.
      • These maternal and paternal imprints are transmitted to all body cells during development.
      • For a maternally imprinted gene, only the paternal allele is expressed.
      • For a paternally imprinted gene, only the maternal allele is expressed.
    • Patterns of imprinting are characteristic of a given species.
    • The gene for insulin-like growth factor 2 (Igf2) is one of the first imprinted genes to be identified.
    • Although the growth factor is required for normal prenatal growth, only the paternal allele is expressed.
    • Evidence that the Igf2 allele is imprinted initially came from crosses between wild-type mice and dwarf mice homozygous for a recessive mutation in the Igf2 gene.
      • The phenotypes of heterozygous offspring differ, depending on whether the mutant allele comes from the mother or the father.
      • The Igf2 allele is imprinted in eggs, turning off expression of the imprinted allele.
      • In sperm, the Igf2 allele is not imprinted and functions normally.
    • What exactly is a genomic imprint?
    • In many cases, it consists of methyl (—CH3) groups that are added to the cytosine nucleotides of one of the alleles.
    • The hypothesis that methylation directly silences an allele is consistent with the evidence that heavily methylated genes are usually inactive.
      • Other mechanisms may lead to silencing of imprinted genes.
    • Most of the known imprinted genes are critical for embryonic development.
    • In experiments with mice, embryos engineered to inherit both copies of certain chromosomes from the same parent die before birth, whether their lone parent is male or female.
    • Normal development requires that embryonic cells have one active copy of certain genes.
    • Aberrant imprinting is associated with abnormal development and certain cancers.

      Extranuclear genes exhibit a non-Mendelian pattern of inheritance.

    • Not all of a eukaryote cell’s genes are located on nuclear chromosomes, or even in the nucleus.
    • Extranuclear genes are found in small circles of DNA in mitochondria and chloroplasts.
    • These organelles reproduce themselves and transmit their genes to daughter organelles.
      • Their cytoplasmic genes do not display Mendelian inheritance, because they are not distributed to offspring according to the same rules that direct distribution of nuclear chromosomes during meiosis.
    • Karl Correns first observed cytoplasmic genes in plants in 1909 when he studied the inheritance of patches of yellow or white on the leaves of an otherwise green plant.
      • He determined that the coloration of the offspring was determined by only the maternal parent.
      • These coloration patterns are due to genes in the plastids that are inherited only via the ovum, not via the sperm nucleus in the pollen.
    • Because a zygote inherits all its mitochondria from the ovum, all mitochondrial genes in mammals demonstrate maternal inheritance.
    • Several rare human disorders are produced by mutations to mitochondrial DNA.
      • These primarily impact ATP supply by producing defects in the electron transport chain or ATP synthase.
      • Tissues that require high energy supplies (the nervous system and muscles) may suffer energy deprivation from these defects.
      • For example, a person with mitochondrial myopathy suffers weakness, intolerance of exercise, and muscle deterioration.
      • Other mitochondrial mutations may contribute to diabetes, heart disease, and other diseases of aging.

    Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 15-1

    Subject: 
    Subject X2: 

    Chapter 16 - The Molecular Basis of Inheritance

    Chapter 16 The Molecular Basis of Inheritance
    Lecture Outline

    Overview: Life’s Operating Instructions

    • In April 1953, James Watson and Francis Crick shook the scientific world with an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA.
    • Your genetic endowment is the DNA you inherited from your parents.
    • Nucleic acids are unique in their ability to direct their own replication.
    • The resemblance of offspring to their parents depends on the precise replication of DNA and its transmission from one generation to the next.
    • It is this DNA program that directs the development of your biochemical, anatomical, physiological, and (to some extent) behavioral traits.

    Concept 16.1 DNA is the genetic material

      The search for genetic material led to DNA.

    • Once T. H. Morgan’s group showed that genes are located on chromosomes, the two constituents of chromosomes—proteins and DNA—were the candidates for the genetic material.
    • Until the 1940s, the great heterogeneity and specificity of function of proteins seemed to indicate that proteins were the genetic material.
    • However, this was not consistent with experiments with microorganisms, such as bacteria and viruses.
    • The discovery of the genetic role of DNA began with research by Frederick Griffith in 1928.
    • He studied Streptococcus pneumoniae, a bacterium that causes pneumonia in mammals.
      • One strain, the R strain, was harmless.
      • The other strain, the S strain, was pathogenic.
    • Griffith mixed heat-killed S strain with live R strain bacteria and injected this into a mouse.
      • The mouse died, and he recovered the pathogenic strain from the mouse’s blood.
    • Griffith called this phenomenon transformation, a phenomenon now defined as a change in genotype and phenotype due to the assimilation of foreign DNA by a cell.
    • For the next 14 years, scientists tried to identify the transforming substance.
    • Finally in 1944, Oswald Avery, Maclyn McCarty, and Colin MacLeod announced that the transforming substance was DNA.
    • Still, many biologists were skeptical.
      • Proteins were considered better candidates for the genetic material.
      • There was also a belief that the genes of bacteria could not be similar in composition and function to those of more complex organisms.
    • Further evidence that DNA was the genetic material was derived from studies that tracked the infection of bacteria by viruses.
    • Viruses consist of DNA (or sometimes RNA) enclosed by a protective coat of protein.
      • To replicate, a virus infects a host cell and takes over the cell’s metabolic machinery.
      • Viruses that specifically attack bacteria are called bacteriophages or just phages.
    • In 1952, Alfred Hershey and Martha Chase showed that DNA was the genetic material of the phage T2.
    • The T2 phage, consisting almost entirely of DNA and protein, attacks Escherichia coli (E. coli), a common intestinal bacteria of mammals.
    • This phage can quickly turn an E. coli cell into a T2-producing factory that releases phages when the cell ruptures.
    • To determine the source of genetic material in the phage, Hershey and Chase designed an experiment in which they could label protein or DNA and then track which entered the E. coli cell during infection.
      • They grew one batch of T2 phage in the presence of radioactive sulfur, marking the proteins but not DNA.
      • They grew another batch in the presence of radioactive phosphorus, marking the DNA but not proteins.
      • They allowed each batch to infect separate E. coli cultures.
      • Shortly after the onset of infection, they spun the cultured infected cells in a blender, shaking loose any parts of the phage that remained outside the bacteria.
      • The mixtures were spun in a centrifuge, which separated the heavier bacterial cells in the pellet from lighter free phages and parts of phage in the liquid supernatant.
      • They then tested the pellet and supernatant of the separate treatments for the presence of radioactivity.
    • Hershey and Chase found that when the bacteria had been infected with T2 phages that contained radiolabeled proteins, most of the radioactivity was in the supernatant that contained phage particles, not in the pellet with the bacteria.
    • When they examined the bacterial cultures with T2 phage that had radiolabeled DNA, most of the radioactivity was in the pellet with the bacteria.
    • Hershey and Chase concluded that the injected DNA of the phage provides the genetic information that makes the infected cells produce new viral DNA and proteins to assemble into new viruses.
    • The fact that cells double the amount of DNA in a cell prior to mitosis and then distribute the DNA equally to each daughter cell provided some circumstantial evidence that DNA was the genetic material in eukaryotes.
    • Similar circumstantial evidence came from the observation that diploid sets of chromosomes have twice as much DNA as the haploid sets in gametes of the same organism.
    • By 1947, Erwin Chargaff had developed a series of rules based on a survey of DNA composition in organisms.
      • He already knew that DNA was a polymer of nucleotides consisting of a nitrogenous base, deoxyribose, and a phosphate group.
      • The bases could be adenine (A), thymine (T), guanine (G), or cytosine (C).
    • Chargaff noted that the DNA composition varies from species to species.
    • In any one species, the four bases are found in characteristic, but not necessarily equal, ratios.
    • He also found a peculiar regularity in the ratios of nucleotide bases that are known as Chargaff’s rules.
    • In all organisms, the number of adenines was approximately equal to the number of thymines (%T = %A).
    • The number of guanines was approximately equal to the number of cytosines (%G = %C).
    • Human DNA is 30.9% adenine, 29.4% thymine, 19.9% guanine, and 19.8% cytosine.
    • The basis for these rules remained unexplained until the discovery of the double helix.

      Watson and Crick discovered the double helix by building models to conform to X-ray data.

    • By the beginnings of the 1950s, the race was on to move from the structure of a single DNA strand to the three-dimensional structure of DNA.
      • Among the scientists working on the problem were Linus Pauling in California and Maurice Wilkins and Rosalind Franklin in London.
    • Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure of DNA.
      • In this technique, X-rays are diffracted as they passed through aligned fibers of purified DNA.
      • The diffraction pattern can be used to deduce the three-dimensional shape of molecules.
    • James Watson learned from their research that DNA was helical in shape, and he deduced the width of the helix and the spacing of nitrogenous bases.
      • The width of the helix suggested that it was made up of two strands, contrary to a three-stranded model that Linus Pauling had recently proposed.
    • Watson and his colleague Francis Crick began to work on a model of DNA with two strands, the double helix.
    • Using molecular models made of wire, they placed the sugar-phosphate chains on the outside and the nitrogenous bases on the inside of the double helix.
      • This arrangement put the relatively hydrophobic nitrogenous bases in the molecule’s interior.
    • The sugar-phosphate chains of each strand are like the side ropes of a rope ladder.
      • Pairs of nitrogenous bases, one from each strand, form rungs.
      • The ladder forms a twist every ten bases.
    • The nitrogenous bases are paired in specific combinations: adenine with thymine and guanine with cytosine.
    • Pairing like nucleotides did not fit the uniform diameter indicated by the X-ray data.
      • A purine-purine pair is too wide, and a pyrimidine-pyrimidine pairing is too short.
      • Only a pyrimidine-purine pairing produces the 2-nm diameter indicated by the X-ray data.
    • In addition, Watson and Crick determined that chemical side groups of the nitrogenous bases would form hydrogen bonds, connecting the two strands.
      • Based on details of their structure, adenine would form two hydrogen bonds only with thymine, and guanine would form three hydrogen bonds only with cytosine.
      • This finding explained Chargaff’s rules.
    • The base-pairing rules dictate the combinations of nitrogenous bases that form the “rungs” of DNA.
    • However, this does not restrict the sequence of nucleotides along each DNA strand.
    • The linear sequence of the four bases can be varied in countless ways.
    • Each gene has a unique order of nitrogenous bases.
    • In April 1953, Watson and Crick published a succinct, one-page paper in Nature reporting their double helix model of DNA.

    Concept 16.2 Many proteins work together in DNA replication and repair

    • The specific pairing of nitrogenous bases in DNA was the flash of inspiration that led Watson and Crick to the correct double helix.
    • The possible mechanism for the next step, the accurate replication of DNA, was clear to Watson and Crick from their double helix model.

      During DNA replication, base pairing enables existing DNA strands to serve as templates for new complementary strands.

    • In a second paper, Watson and Crick published their hypothesis for how DNA replicates.
      • Essentially, because each strand is complementary to the other, each can form a template when separated.
      • The order of bases on one strand can be used to add complementary bases and therefore duplicate the pairs of bases exactly.
    • When a cell copies a DNA molecule, each strand serves as a template for ordering nucleotides into a new complementary strand.
      • One at a time, nucleotides line up along the template strand according to the base-pairing rules.
      • The nucleotides are linked to form new strands.
    • Watson and Crick’s model, semiconservative replication, predicts that when a double helix replicates, each of the daughter molecules will have one old strand and one newly made strand.
    • Other competing models, the conservative model and the dispersive model, were also proposed.
    • Experiments in the late 1950s by Matthew Meselson and Franklin Stahl supported the semiconservative model proposed by Watson and Crick over the other two models.
      • In their experiments, they labeled the nucleotides of the old strands with a heavy isotope of nitrogen (15N), while any new nucleotides were indicated by a lighter isotope (14N).
      • Replicated strands could be separated by density in a centrifuge.
      • Each model—the semiconservative model, the conservative model, and the dispersive model—made specific predictions about the density of replicated DNA strands.
      • The first replication in the 14N medium produced a band of hybrid (15N-14N) DNA, eliminating the conservative model.
      • A second replication produced both light and hybrid DNA, eliminating the dispersive model and supporting the semiconservative model.

      A large team of enzymes and other proteins carries out DNA replication.

    • It takes E. coli 25 minutes to copy each of the 5 million base pairs in its single chromosome and divide to form two identical daughter cells.
    • A human cell can copy its 6 billion base pairs and divide into daughter cells in only a few hours.
    • This process is remarkably accurate, with only one error per ten billion nucleotides.
    • More than a dozen enzymes and other proteins participate in DNA replication.
    • Much more is known about replication in bacteria than in eukaryotes.
      • The process appears to be fundamentally similar for prokaryotes and eukaryotes.
    • The replication of a DNA molecule begins at special sites, origins of replication.
    • In bacteria, this is a specific sequence of nucleotides that is recognized by the replication enzymes.
      • These enzymes separate the strands, forming a replication “bubble.”
      • Replication proceeds in both directions until the entire molecule is copied.
    • In eukaryotes, there may be hundreds or thousands of origin sites per chromosome.
      • At the origin sites, the DNA strands separate, forming a replication “bubble” with replication forks at each end.
      • The replication bubbles elongate as the DNA is replicated, and eventually fuse.
    • DNA polymerases catalyze the elongation of new DNA at a replication fork.
    • As nucleotides align with complementary bases along the template strand, they are added to the growing end of the new strand by the polymerase.
      • The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells.
    • In E. coli, two different DNA polymerases are involved in replication: DNA polymerase III and DNA polymerase I.
    • In eukaryotes, at least 11 different DNA polymerases have been identified so far.
    • Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate.
      • Each has a nitrogenous base, deoxyribose, and a triphosphate tail.
      • ATP is a nucleoside triphosphate with ribose instead of deoxyribose.
    • Like ATP, the triphosphate monomers used for DNA synthesis are chemically reactive, partly because their triphosphate tails have an unstable cluster of negative charge.
    • As each nucleotide is added to the growing end of a DNA strand, the last two phosphate groups are hydrolyzed to form pyrophosphate.
      • The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules drives the polymerization of the nucleotide to the new strand.
    • The strands in the double helix are antiparallel.
    • The sugar-phosphate backbones run in opposite directions.
      • Each DNA strand has a 3’ end with a free hydroxyl group attached to deoxyribose and a 5’ end with a free phosphate group attached to deoxyribose.
      • The 5’ --> 3’ direction of one strand runs counter to the 3’ --> 5’ direction of the other strand.
    • DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand.
      • A new DNA strand can only elongate in the 5’ --> 3’ direction.
    • Along one template strand, DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5’ --> 3’ direction.
      • The DNA strand made by this mechanism is called the leading strand.
    • The other parental strand (5’ --> 3’ into the fork), the lagging strand, is copied away from the fork.
      • Unlike the leading strand, which elongates continuously, the lagging stand is synthesized as a series of short segments called Okazaki fragments.
    • Okazaki fragments are about 1,000–2,000 nucleotides long in E. coli and 100–200 nucleotides long in eukaryotes.
    • Another enzyme, DNA ligase, eventually joins the sugar-phosphate backbones of the Okazaki fragments to form a single DNA strand.
    • DNA polymerases cannot initiate synthesis of a polynucleotide.
      • They can only add nucleotides to the 3’ end of an existing chain that is base-paired with the template strand.
    • The initial nucleotide chain is called a primer.
    • In the initiation of the replication of cellular DNA, the primer is a short stretch of RNA with an available 3’ end.
      • The primer is 5–10 nucleotides long in eukaryotes.
    • Primase, an RNA polymerase, links ribonucleotides that are complementary to the DNA template into the primer.
      • RNA polymerases can start an RNA chain from a single template strand.
    • After formation of the primer, DNA pol III adds a deoxyribonucleotide to the 3’ end of the RNA primer and continues adding DNA nucleotides to the growing DNA strand according to the base-pairing rules.
    • Returning to the original problem at the replication fork, the leading strand requires the formation of only a single primer as the replication fork continues to separate.
    • For synthesis of the lagging strand, each Okazaki fragment must be primed separately.
      • Another DNA polymerase, DNA polymerase I, replaces the RNA nucleotides of the primers with DNA versions, adding them one by one onto the 3’ end of the adjacent Okazaki fragment.
    • The primers are converted to DNA before DNA ligase joins the fragments together.
    • In addition to primase, DNA polymerases, and DNA ligases, several other proteins have prominent roles in DNA synthesis.
    • Helicase untwists the double helix and separates the template DNA strands at the replication fork.
      • This untwisting causes tighter twisting ahead of the replication fork, and topoisomerase helps relieve this strain.
    • Single-strand binding proteins keep the unpaired template strands apart during replication.
    • To summarize, at the replication fork, the leading strand is copied continuously into the fork from a single primer.
      • The lagging strand is copied away from the fork in short segments, each requiring a new primer.
    • It is conventional and convenient to think of the DNA polymerase molecules as moving along a stationary DNA template.
    • In reality, the various proteins involved in DNA replication form a single large complex, a DNA replication “machine.”
    • Many protein-protein interactions facilitate the efficiency of this machine.
      • For example, helicase works much more rapidly when it is in contact with primase.
    • The DNA replication machine is probably stationary during the replication process.
    • In eukaryotic cells, multiple copies of the machine may anchor to the nuclear matrix, a framework of fibers extending through the interior of the nucleus.
    • The DNA polymerase molecules “reel in” the parental DNA and “extrude” newly made daughter DNA molecules.

      Enzymes proofread DNA during its replication and repair damage in existing DNA.

    • Mistakes during the initial pairing of template nucleotides and complementary nucleotides occur at a rate of one error per 100,000 base pairs.
    • DNA polymerase proofreads each new nucleotide against the template nucleotide as soon as it is added.
    • If there is an incorrect pairing, the enzyme removes the wrong nucleotide and then resumes synthesis.
    • The final error rate is only one per ten billion nucleotides.
    • DNA molecules are constantly subject to potentially harmful chemical and physical agents.
      • Reactive chemicals, radioactive emissions, X-rays, and ultraviolet light can change nucleotides in ways that can affect encoded genetic information.
      • DNA bases may undergo spontaneous chemical changes under normal cellular conditions.
    • Mismatched nucleotides that are missed by DNA polymerase or mutations that occur after DNA synthesis is completed can often be repaired.
      • Each cell continually monitors and repairs its genetic material, with 100 repair enzymes known in E. coli and more than 130 repair enzymes identified in humans.
    • In mismatch repair, special enzymes fix incorrectly paired nucleotides.
      • A hereditary defect in one of these enzymes is associated with a form of colon cancer.
    • In nucleotide excision repair, a nuclease cuts out a segment of a damaged strand.
      • DNA polymerase and ligase fill in the gap.
    • The importance of the proper functioning of repair enzymes is clear from the inherited disorder xeroderma pigmentosum.
      • These individuals are hypersensitive to sunlight.
      • Ultraviolet light can produce thymine dimers between adjacent thymine nucleotides.
      • This buckles the DNA double helix and interferes with DNA replication.
      • In individuals with this disorder, mutations in their skin cells are left uncorrected and cause skin cancer.

      The ends of DNA molecules are replicated by a special mechanism.

    • Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes.
    • The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands.
      • Repeated rounds of replication produce shorter and shorter DNA molecules.
    • Prokaryotes do not have this problem because they have circular DNA molecules without ends.
    • The ends of eukaryotic chromosomal DNA molecules, the telomeres, have special nucleotide sequences.
    • Telomeres do not contain genes. Instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence.
      • In human telomeres, this sequence is typically TTAGGG, repeated between 100 and 1,000 times.
    • Telomeres protect genes from being eroded through multiple rounds of DNA replication.
      • Telomeric DNA tends to be shorter in dividing somatic cells of older individuals and in cultured cells that have divided many times.
    • It is possible that the shortening of telomeres is somehow connected with the aging process of certain tissues and perhaps to aging in general.
    • Telomeric DNA and specific proteins associated with it also prevents the staggered ends of the daughter molecule from activating the cell’s system for monitoring DNA damage.
    • Eukaryotic cells have evolved a mechanism to restore shortened telomeres in germ cells, which give rise to gametes.
      • If the chromosomes of germ cells became shorter with every cell cycle, essential genes would eventually be lost.
    • An enzyme called telomerase catalyzes the lengthening of telomeres in eukaryotic germ cells, restoring their original length.
    • Telomerase uses a short molecule of RNA as a template to extend the 3’ end of the telomere.
      • There is now room for primase and DNA polymerase to extend the 5’ end.
      • It does not repair the 3’-end “overhang,” but it does lengthen the telomere.
    • Telomerase is not present in most cells of multicellular organisms.
    • Therefore, the DNA of dividing somatic cells and cultured cells tends to become shorter.
      • Telomere length may be a limiting factor in the life span of certain tissues and of the organism.
    • Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo.
      • Cells from large tumors often have unusually short telomeres, because they have gone through many cell divisions.
    • Active telomerase has been found in some cancerous somatic cells.
      • This overcomes the progressive shortening that would eventually lead to self-destruction of the cancer.
      • Immortal strains of cultured cells are capable of unlimited cell division.
    • Telomerase may provide a useful target for cancer diagnosis and chemotherapy.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 16-1

    Subject: 
    Subject X2: 

    Chapter 17 - From Gene to Protein

    Chapter 17 From Gene to Protein
    Lecture Outline

    Overview: The Flow of Genetic Information

    • The information content of DNA is in the form of specific sequences of nucleotides along the DNA strands.
    • The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins.
    • Gene expression, the process by which DNA directs protein synthesis, includes two stages called transcription and translation.
    • Proteins are the links between genotype and phenotype.
      • For example, Mendel’s dwarf pea plants lack a functioning copy of the gene that specifies the synthesis of a key protein, gibberellin.
      • Gibberellins stimulate the normal elongation of stems.

    Concept 17.1 Genes specify proteins via transcription and translation

      The study of metabolic defects provided evidence that genes specify proteins.

    • In 1909, Archibald Gerrod was the first to suggest that genes dictate phenotype through enzymes that catalyze specific chemical reactions in the cell.
      • He suggested that the symptoms of an inherited disease reflect a person’s inability to synthesize a particular enzyme.
      • He referred to such diseases as “inborn errors of metabolism.”
    • Gerrod speculated that alkaptonuria, a hereditary disease, was caused by the absence of an enzyme that breaks down a specific substrate, alkapton.
      • Research conducted several decades later supported Gerrod’s hypothesis.
    • Progress in linking genes and enzymes rested on the growing understanding that cells synthesize and degrade most organic molecules in a series of steps, a metabolic pathway.
    • In the 1930s, George Beadle and Boris Ephrussi speculated that each mutation affecting eye color in Drosophila blocks pigment synthesis at a specific step by preventing production of the enzyme that catalyzes that step.
      • However, neither the chemical reactions nor the enzymes that catalyze them were known at the time.
    • Beadle and Edward Tatum were finally able to establish the link between genes and enzymes in their exploration of the metabolism of a bread mold, Neurospora crassa.
      • They bombarded Neurospora with X-rays and screened the survivors for mutants that differed in their nutritional needs.
      • Wild-type Neurospora can grow on a minimal medium of agar, inorganic salts, glucose, and the vitamin biotin.
    • Beadle and Tatum identified mutants that could not survive on minimal medium, because they were unable to synthesize certain essential molecules from the minimal ingredients.
      • However, most of these nutritional mutants can survive on a complete growth medium that includes all 20 amino acids and a few other nutrients.
    • One type of mutant required only the addition of arginine to the minimal growth medium.
      • Beadle and Tatum concluded that this mutant was defective somewhere in the biochemical pathway that normally synthesizes arginine.
      • They identified three classes of arginine-deficient mutants, each apparently lacking a key enzyme at a different step in the synthesis of arginine.
      • They demonstrated this by growing these mutant strains in media that provided different intermediate molecules.
      • Their results provided strong evidence for the one gene–one enzyme hypothesis.
    • Later research refined the one gene–one enzyme hypothesis.
    • First, not all proteins are enzymes.
      • Keratin, the structural protein of hair, and insulin, a hormone, both are proteins and gene products.
    • This tweaked the hypothesis to one gene–one protein.
    • Later research demonstrated that many proteins are composed of several polypeptides, each of which has its own gene.
    • Therefore, Beadle and Tatum’s idea has been restated as the one gene–one polypeptide hypothesis.
    • Some genes code for RNA molecules that play important roles in cells although they are never translated into protein.

      Transcription and translation are the two main processes linking gene to protein.

    • Genes provide the instructions for making specific proteins.
    • The bridge between DNA and protein synthesis is the nucleic acid RNA.
    • RNA is chemically similar to DNA, except that it contains ribose as its sugar and substitutes the nitrogenous base uracil for thymine.
      • An RNA molecule almost always consists of a single strand.
    • In DNA or RNA, the four nucleotide monomers act like the letters of the alphabet to communicate information.
    • The specific sequence of hundreds or thousands of nucleotides in each gene carries the information for the primary structure of proteins, the linear order of the 20 possible amino acids.
    • To get from DNA, written in one chemical language, to protein, written in another, requires two major stages: transcription and translation.
    • During transcription, a DNA strand provides a template for the synthesis of a complementary RNA strand.
      • Just as a DNA strand provides a template for the synthesis of each new complementary strand during DNA replication, it provides a template for assembling a sequence of RNA nucleotides.
    • Transcription of many genes produces a messenger RNA (mRNA) molecule.
    • During translation, there is a change of language.
      • The site of translation is the ribosome, complex particles that facilitate the orderly assembly of amino acids into polypeptide chains.
    • Why can’t proteins be translated directly from DNA?
      • The use of an RNA intermediate provides protection for DNA and its genetic information.
      • Using an RNA intermediate allows more copies of a protein to be made simultaneously, since many RNA transcripts can be made from one gene.
        • Also, each gene transcript can be translated repeatedly.
    • The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes.
    • Because bacteria lack nuclei, their DNA is not segregated from ribosomes and other protein-synthesizing equipment.
      • This allows the coupling of transcription and translation.
      • Ribosomes attach to the leading end of an mRNA molecule while transcription is still in progress.
    • In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs at ribosomes in the cytoplasm.
      • The transcription of a protein-coding eukaryotic gene results in pre-mRNA.
      • The initial RNA transcript of any gene is called a primary transcript.
      • RNA processing yields the finished mRNA.
    • To summarize, genes program protein synthesis via genetic messages in the form of messenger RNA.
    • The molecular chain of command in a cell is DNA --> RNA --> protein.

      In the genetic code, nucleotide triplets specify amino acids.

    • If the genetic code consisted of a single nucleotide or even pairs of nucleotides per amino acid, there would not be enough combinations (4 and 16, respectively) to code for all 20 amino acids.
    • Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids.
    • With a triplet code, three consecutive bases specify an amino acid, creating 43 (64) possible code words.
    • The genetic instructions for a polypeptide chain are written in DNA as a series of nonoverlapping three-nucleotide words.
    • During transcription, one DNA strand, the template strand, provides a template for ordering the sequence of nucleotides in an RNA transcript.
      • A given DNA strand can be the template strand for some genes along a DNA molecule, while for other genes in other regions, the complementary strand may function as the template.
    • The complementary RNA molecule is synthesized according to base-pairing rules, except that uracil is the complementary base to adenine.
    • Like a new strand of DNA, the RNA molecule is synthesized in an antiparallel direction to the template strand of DNA.
    • The mRNA base triplets are called codons, and they are written in the 5’ --> 3’ direction.
    • During translation, the sequence of codons along an mRNA molecule is translated into a sequence of amino acids making up the polypeptide chain.
      • During translation, the codons are read in the 5’ --> 3’ direction along the mRNA.
      • Each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide.
    • Because codons are base triplets, the number of nucleotides making up a genetic message must be three times the number of amino acids making up the protein product.
      • It takes at least 300 nucleotides to code for a polypeptide that is 100 amino acids long.
    • The task of matching each codon to its amino acid counterpart began in the early 1960s.
    • Marshall Nirenberg determined the first match: UUU coded for the amino acid phenylalanine.
      • He created an artificial mRNA molecule entirely of uracil and added it to a test tube mixture of amino acids, ribosomes, and other components for protein synthesis.
      • This “poly-U” translated into a polypeptide containing a single amino acid, phenylalanine, in a long chain.
    • AAA, GGG, and CCC were solved in the same way.
    • Other more elaborate techniques were required to decode mixed triplets such as AUA and CGA.
    • By the mid-1960s the entire code was deciphered.
      • Sixty-one of 64 triplets code for amino acids.
      • The codon AUG not only codes for the amino acid methionine, but also indicates the “start” of translation.
      • Three codons do not indicate amino acids but are “stop” signals marking the termination of translation.
    • There is redundancy in the genetic code but no ambiguity.
      • Several codons may specify the same amino acid, but no codon specifies more than one amino acid.
      • The redundancy in the code is not random. In many cases, codons that are synonyms for a particular amino acid differ only in the third base of the triplet.
    • To extract the message from the genetic code requires specifying the correct starting point.
      • This establishes the reading frame; subsequent codons are read in groups of three nucleotides.
      • The cell’s protein-synthesizing machinery reads the message as a series of nonoverlapping three-letter words.
    • In summary, genetic information is encoded as a sequence of nonoverlapping base triplets, or codons, each of which is translated into a specific amino acid during protein synthesis.

      The genetic code must have evolved very early in the history of life.

    • The genetic code is nearly universal, shared by organisms from the simplest bacteria to the most complex plants and animals.
    • In laboratory experiments, genes can be transcribed and translated after they are transplanted from one species to another.
      • This has permitted bacteria to be programmed to synthesize certain human proteins after insertion of the appropriate human genes.
    • Such applications are exciting developments in biotechnology.
    • Exceptions to the universality of the genetic code exist in certain unicellular eukaryotes and in the organelle genes of some species.
      • Some prokaryotes can translate stop codons into one of two amino acids not found in most organisms.
    • The evolutionary significance of the near universality of the genetic code is clear.
      • A language shared by all living things arose very early in the history of life—early enough to be present in the common ancestors of all modern organisms.
    • A shared genetic vocabulary is a reminder of the kinship that bonds all life on Earth.

    Concept 17.2 Transcription is the DNA-directed synthesis of RNA: a closer look

    • Messenger RNA, the carrier of information from DNA to the cell’s protein-synthesizing machinery, is transcribed from the template strand of a gene.
    • RNA polymerase separates the DNA strands at the appropriate point and bonds the RNA nucleotides as they base-pair along the DNA template.
      • Like DNA polymerases, RNA polymerases can only assemble a polynucleotide in its 5’ --> 3’ direction.
      • Unlike DNA polymerases, RNA polymerases are able to start a chain from scratch; they don’t need a primer.
    • Specific sequences of nucleotides along the DNA mark where gene transcription begins and ends.
      • RNA polymerase attaches and initiates transcription at the promoter.
      • In prokaryotes, the sequence that signals the end of transcription is called the terminator.
    • Molecular biologists refer to the direction of transcription as “downstream” and the other direction as “upstream.”
    • The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit.
    • Bacteria have a single type of RNA polymerase that synthesizes all RNA molecules.
    • In contrast, eukaryotes have three RNA polymerases (I, II, and III) in their nuclei.
      • RNA polymerase II is used for mRNA synthesis.
    • Transcription can be separated into three stages: initiation, elongation, and termination of the RNA chain.
    • The presence of a promoter sequence determines which strand of the DNA helix is the template.
      • Within the promoter is the starting point for the transcription of a gene.
      • The promoter also includes a binding site for RNA polymerase several dozen nucleotides “upstream” of the start point.
    • In prokaryotes, RNA polymerase can recognize and bind directly to the promoter region.
    • In eukaryotes, proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription.
    • Only after certain transcription factors are attached to the promoter does RNA polymerase II bind to it.
    • The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex.
      • A crucial promoter DNA sequence is called a TATA box.
    • RNA polymerase then starts transcription.
    • As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at time.
      • The enzyme adds nucleotides to the 3’ end of the growing strand.
    • Behind the point of RNA synthesis, the double helix re-forms and the RNA molecule peels away.
      • Transcription progresses at a rate of 60 nucleotides per second in eukaryotes.
    • A single gene can be transcribed simultaneously by several RNA polymerases at a time.
    • A growing strand of RNA trails off from each polymerase.
      • The length of each new strand reflects how far along the template the enzyme has traveled from the start point.
    • The congregation of many polymerase molecules simultaneously transcribing a single gene increases the amount of mRNA transcribed from it.
    • This helps the cell make the encoded protein in large amounts.
    • Transcription proceeds until after the RNA polymerase transcribes a terminator sequence in the DNA.
      • In prokaryotes, RNA polymerase stops transcription right at the end of the terminator.
        • Both the RNA and DNA are then released.
      • In eukaryotes, the pre-mRNA is cleaved from the growing RNA chain while RNA polymerase II continues to transcribe the DNA.
        • Specifically, the polymerase transcribes a DNA sequence called the polyadenylation signal sequence that codes for a polyadenylation sequence (AAUAAA) in the pre-mRNA.
        • At a point about 10 to 35 nucleotides past this sequence, the pre-mRNA is cut from the enzyme.
        • The polymerase continues transcribing for hundreds of nucleotides.
        • Transcription is terminated when the polymerase eventually falls off the DNA.

    Concept 17.3 Eukaryotic cells modify RNA after transcription

    • Enzymes in the eukaryotic nucleus modify pre-mRNA before the genetic messages are dispatched to the cytoplasm.
      • During RNA processing, both ends of the primary transcript are usually altered.
      • Certain interior parts of the molecule are cut out and the remaining parts spliced together.
    • At the 5’ end of the pre-mRNA molecule, a modified form of guanine is added, the 5’ cap.
    • At the 3’ end, an enzyme adds 50 to 250 adenine nucleotides, the poly-A tail.
    • These modifications share several important functions.
      • They seem to facilitate the export of mRNA from the nucleus.
      • They help protect mRNA from hydrolytic enzymes.
      • They help the ribosomes attach to the 5’ end of the mRNA.
    • The most remarkable stage of RNA processing occurs during the removal of a large portion of the RNA molecule in a cut-and-paste job of RNA splicing.
    • Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides.
      • Noncoding segments of nucleotides called intervening regions, or introns, lie between coding regions.
      • The final mRNA transcript includes coding regions, exons, which are translated into amino acid sequences, plus the leader and trailer sequences.
    • RNA splicing removes introns and joins exons to create an mRNA molecule with a continuous coding sequence.
    • This splicing is accomplished by a spliceosome.
      • Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites.
      • snRNPs are located in the cell nucleus and are composed of RNA and protein molecules.
      • Each snRNP has several protein molecules and a small nuclear RNA molecule (snRNA).
        • Each snRNA is about 150 nucleotides long.
    • The spliceosome interacts with certain sites along an intron, releasing the introns and joining together the two exons that flanked the introns.
      • snRNAs appear to play a major role in catalytic processes, as well as spliceosome assembly and splice site recognition.
    • The idea of a catalytic role for snRNA arose from the discovery of ribozymes, RNA molecules that function as enzymes.
      • In some organisms, splicing occurs without proteins or additional RNA molecules.
      • The intron RNA functions as a ribozyme and catalyzes its own excision.
      • For example, in the protozoan Tetrahymena, self-splicing occurs in the production of ribosomal RNA (rRNA), a component of the organism’s ribosomes.
      • The pre-rRNA actually removes its own introns.
    • The discovery of ribozymes rendered obsolete the statement, “All biological catalysts are proteins.”
    • The fact that RNA is single-stranded plays an important role in allowing certain RNA molecules to function as ribozymes.
    • A region of the RNA molecule may base-pair with a complementary region elsewhere in the same molecule, thus giving the RNA a specific 3-D structure that is key to its ability to catalyze reactions.
    • Introns and RNA splicing appear to have several functions.
      • Some introns play a regulatory role in the cell. These introns contain sequences that control gene activity in some way.
      • Splicing itself may regulate the passage of mRNA from the nucleus to the cytoplasm.
      • One clear benefit of split genes is to enable one gene to encode for more than one polypeptide.
    • Alternative RNA splicing gives rise to two or more different polypeptides, depending on which segments are treated as exons.
      • Sex differences in fruit flies may be due to differences in splicing RNA transcribed from certain genes.
      • Early results of the Human Genome Project indicate that this phenomenon may be common in humans, and may explain why we have a relatively small number of genes.
    • Proteins often have a modular architecture with discrete structural and functional regions called domains.
    • The presence of introns in a gene may facilitate the evolution of new and potentially useful proteins as a result of a process known as exon shuffling.
      • In many cases, different exons code for different domains of a protein.
    • The presence of introns increases the probability of potentially beneficial crossing over between genes.
      • Introns increase the opportunity for recombination between two alleles of a gene.
        • This raises the probability that a crossover will switch one version of an exon for another version found on the homologous chromosome.
      • There may also be occasional mixing and matching of exons between completely different genes.
      • Either way, exon shuffling can lead to new proteins through novel combinations of functions.

    Concept 17.4 Translation is the RNA-directed synthesis of a polypeptide: a closer look

    • In the process of translation, a cell interprets a series of codons along an mRNA molecule and builds a polypeptide.
    • The interpreter is transfer RNA (tRNA), which transfers amino acids from the cytoplasmic pool to a ribosome.
      • A cell has all 20 amino acids available in its cytoplasm, either by synthesizing them from scratch or by taking them up from the surrounding solution.
    • The ribosome adds each amino acid carried by tRNA to the growing end of the polypeptide chain.
    • During translation, each type of tRNA links an mRNA codon with the appropriate amino acid.
    • Each tRNA arriving at the ribosome carries a specific amino acid at one end and has a specific nucleotide triplet, an anticodon, at the other.
    • The anticodon base-pairs with a complementary codon on mRNA.
      • If the codon on mRNA is UUU, a tRNA with an AAA anticodon and carrying phenylalanine will bind to it.
    • Codon by codon, tRNAs deposit amino acids in the prescribed order, and the ribosome joins them into a polypeptide chain.
    • The tRNA molecule is a translator, because it can read a nucleic acid word (the mRNA codon) and translate it to a protein word (the amino acid).
    • Like other types of RNA, tRNA molecules are transcribed from DNA templates in the nucleus.
    • Once it reaches the cytoplasm, each tRNA is used repeatedly, picking up its designated amino acid in the cytosol, depositing the amino acid at the ribosome, and returning to the cytosol to pick up another copy of that amino acid.
    • A tRNA molecule consists of a strand of about 80 nucleotides that folds back on itself to form a three-dimensional structure.
      • It includes a loop containing the anticodon and an attachment site at the 3’ end for an amino acid.
    • If each anticodon had to be a perfect match to each codon, we would expect to find 61 types of tRNA, but the actual number is about 45.
    • The anticodons of some tRNAs recognize more than one codon.
    • This is possible because the rules for base pairing between the third base of the codon and anticodon are relaxed (called wobble).
      • At the wobble position, U on the anticodon can bind with A or G in the third position of a codon.
      • Wobble explains why the synonymous codons for a given amino acid can differ in their third base, but not usually in their other bases.
    • Each amino acid is joined to the correct tRNA by aminoacyl-tRNA synthetase.
    • The 20 different synthetases match the 20 different amino acids.
      • Each has active sites for only a specific tRNA-and-amino-acid combination.
      • The synthetase catalyzes a covalent bond between them in a process driven by ATP hydrolysis.
        • The result is an aminoacyl-tRNA or activated amino acid.
    • Ribosomes facilitate the specific coupling of the tRNA anticodons with mRNA codons during protein synthesis.
      • Each ribosome is made up of a large and a small subunit.
      • The subunits are composed of proteins and ribosomal RNA (rRNA), the most abundant RNA in the cell.
    • In eukaryotes, the subunits are made in the nucleolus.
      • After rRNA genes are transcribed to rRNA in the nucleus, the rRNA and proteins are assembled to form the subunits with proteins from the cytoplasm.
    • The subunits exit the nucleus via nuclear pores.
    • The large and small subunits join to form a functional ribosome only when they attach to an mRNA molecule.
    • While very similar in structure and function, prokaryotic and eukaryotic ribosomes have enough differences that certain antibiotic drugs (like tetracycline) can paralyze prokaryotic ribosomes without inhibiting eukaryotic ribosomes.
    • Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.
      • The P site holds the tRNA carrying the growing polypeptide chain.
      • The A site carries the tRNA with the next amino acid to be added to the chain.
      • Discharged tRNAs leave the ribosome at the E (exit) site.
    • The ribosome holds the tRNA and mRNA in close proximity and positions the new amino acid for addition to the carboxyl end of the growing polypeptide.
      • It then catalyzes the formation of the peptide bond.
      • As the polypeptide becomes longer, it passes through an exit tunnel in the ribosome’s large unit and is released to the cytosol.
    • Recent advances in our understanding of the structure of the ribosome strongly support the hypothesis that rRNA, not protein, carries out the ribosome’s functions.
      • RNA is the main constituent at the interphase between the two subunits and of the A and P sites.
      • It is the catalyst for peptide bond formation.
      • A ribosome can be regarded as one colossal ribozyme.
    • Translation can be divided into three stages: initiation, elongation, and termination.
    • All three phases require protein “factors” that aid in the translation process.
    • Both initiation and chain elongation require energy provided by the hydrolysis of GTP.
    • Initiation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits.
      • First, a small ribosomal subunit binds with mRNA and a special initiator tRNA, which carries methionine and attaches to the start codon.
      • The small subunit then moves downstream along the mRNA until it reaches the start codon, AUG, which signals the start of translation.
        • This establishes the reading frame for the mRNA.
        • The initiator tRNA, already associated with the complex, then hydrogen-bonds with the start codon.
      • Proteins called initiation factors bring in the large subunit so that the initiator tRNA occupies the P site.
    • Elongation involves the participation of several protein elongation factors, and consists of a series of three-step cycles as each amino acid is added to the proceeding one.
      • During codon recognition, an elongation factor assists hydrogen bonding between the mRNA codon under the A site with the corresponding anticodon of tRNA carrying the appropriate amino acid.
        • This step requires the hydrolysis of two GTP.
      • During peptide bond formation, an rRNA molecule catalyzes the formation of a peptide bond between the polypeptide in the P site with the new amino acid in the A site.
        • This step separates the tRNA at the P site from the growing polypeptide chain and transfers the chain, now one amino acid longer, to the tRNA at the A site.
      • During translocation, the ribosome moves the tRNA with the attached polypeptide from the A site to the P site.
        • Because the anticodon remains bonded to the mRNA codon, the mRNA moves along with it.
        • The next codon is now available at the A site.
        • The tRNA that had been in the P site is moved to the E site and then leaves the ribosome.
        • Translocation is fueled by the hydrolysis of GTP.
        • Effectively, translocation ensures that the mRNA is “read” 5’ --> 3’ codon by codon.
        • The three steps of elongation continue to add amino acids codon by codon until the polypeptide chain is completed.
    • Termination occurs when one of the three stop codons reaches the A site.
      • A release factor binds to the stop codon and hydrolyzes the bond between the polypeptide and its tRNA in the P site.
      • This frees the polypeptide, and the translation complex disassembles.
    • Typically a single mRNA is used to make many copies of a polypeptide simultaneously.
      • Multiple ribosomes, polyribosomes, may trail along the same mRNA.
      • Polyribosomes can be found in prokaryotic and eukaryotic cells.
    • A ribosome requires less than a minute to translate an average-sized mRNA into a polypeptide.
    • During and after synthesis, a polypeptide coils and folds to its three-dimensional shape spontaneously.
      • The primary structure, the order of amino acids, determines the secondary and tertiary structure.
    • Chaperone proteins may aid correct folding.
    • In addition, proteins may require posttranslational modifications before doing their particular job.
      • This may require additions such as sugars, lipids, or phosphate groups to amino acids.
      • Enzymes may remove some amino acids or cleave whole polypeptide chains.
      • Two or more polypeptides may join to form a protein.

      Signal peptides target some eukaryotic polypeptides to specific destinations in the cell.

    • Two populations of ribosomes, free and bound, are active participants in protein synthesis.
    • Free ribosomes are suspended in the cytosol and synthesize proteins that reside in the cytosol.
    • Bound ribosomes are attached to the cytosolic side of the endoplasmic reticulum.
      • They synthesize proteins of the endomembrane system as well as proteins secreted from the cell.
    • While bound and free ribosomes are identical in structure, their location depends on the type of protein that they are synthesizing.
    • Translation in all ribosomes begins in the cytosol, but a polypeptide destined for the endomembrane system or for export has a specific signal peptide region at or near the leading end.
      • This consists of a sequence of about 20 amino acids.
    • A signal recognition particle (SRP) binds to the signal peptide and attaches it and its ribosome to a receptor protein in the ER membrane.
      • The SRP consists of a protein-RNA complex.
    • After binding, the SRP leaves and protein synthesis resumes with the growing polypeptide snaking across the membrane into the cisternal space via a protein pore.
      • An enzyme usually cleaves the signal polypeptide.
    • Secretory proteins are released entirely into the cisternal space, but membrane proteins remain partially embedded in the ER membrane.
    • Other kinds of signal peptides are used to target polypeptides to mitochondria, chloroplasts, the nucleus, and other organelles that are not part of the endomembrane system.
      • In these cases, translation is completed in the cytosol before the polypeptide is imported into the organelle.
      • While the mechanisms of translocation vary, each of these polypeptides has a “ZIP code” that ensures its delivery to the correct cellular location.
    • Prokaryotes also employ signal sequences to target proteins for secretion.

    Concept 17.5 RNA plays multiple roles in the cell: a review

    • The cellular machinery of protein synthesis and ER targeting is dominated by various kinds of RNA.
      • In addition to mRNA, these include tRNA; rRNA; and in eukaryotes, snRNA and SRP RNA.
      • A type of RNA called small nucleolar RNA (snoRNA) aids in processing pre-rRNA transcripts in the nucleolus, a process necessary for ribosome formation.
      • Recent research has also revealed the presence of small, single-stranded and double-stranded RNA molecules that play important roles in regulating which genes get expressed.
        • These types of RNA include small interfering RNA (siRNA) and microRNA (miRNA).
      • The diverse functions of RNA are based, in part, on its ability to form hydrogen bonds with other nucleic acid molecules (DNA or RNA).
      • It can also assume a specific three-dimensional shape by forming hydrogen bonds between bases in different parts of its polynucleotide chain.
    • DNA may be the genetic material of all living cells today, but RNA is much more versatile.
    • The diverse functions of RNA range from structural to informational to catalytic.

    Concept 17.6 Comparing gene expression in prokaryotes and eukaryotes reveals key differences

    • Although prokaryotes and eukaryotes carry out transcription and translation in very similar ways, they do have differences in cellular machinery and in details of the processes.
      • Eukaryotic RNA polymerases differ from those of prokaryotes and require transcription factors.
      • They differ in how transcription is terminated.
      • Their ribosomes also are different.
    • One major difference is that prokaryotes can transcribe and translate the same gene simultaneously.
      • The new protein quickly diffuses to its operating site.
    • In eukaryotes, the nuclear envelope segregates transcription from translation.
      • In addition, extensive RNA processing is carried out between these processes.
      • This provides additional steps whose regulation helps coordinate the elaborate activities of a eukaryotic cell.
    • Eukaryotic cells also have complicated mechanisms for targeting proteins to the appropriate organelle.

    Concept 17.7 Point mutations can affect protein structure and function

    • Mutations are changes in the genetic material of a cell (or virus).
    • These include large-scale mutations in which long segments of DNA are affected (for example, translocations, duplications, and inversions).
    • A chemical change in just one base pair of a gene causes a point mutation.
    • If these occur in gametes or cells producing gametes, they may be transmitted to future generations.
    • For example, sickle-cell disease is caused by a mutation of a single base pair in the gene that codes for one of the polypeptides of hemoglobin.
      • A change in a single nucleotide from T to A in the DNA template leads to an abnormal protein.
    • A point mutation that results in the replacement of a pair of complementary nucleotides with another nucleotide pair is called a base-pair substitution.
    • Some base-pair substitutions have little or no impact on protein function.
      • In silent mutations, altered nucleotides still code for the same amino acids because of redundancy in the genetic code.
      • Other changes lead to switches from one amino acid to another with similar properties.
      • Still other mutations may occur in a region where the exact amino acid sequence is not essential for function.
    • Other base-pair substitutions cause a readily detectable change in a protein.
      • These are usually detrimental but can occasionally lead to an improved protein or one with novel capabilities.
      • Changes in amino acids at crucial sites, especially active sites, are likely to impact function.
    • Missense mutations are those that still code for an amino acid but a different one.
    • Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein.
    • Insertions and deletions are additions or losses of nucleotide pairs in a gene.
      • These have a disastrous effect on the resulting protein more often than substitutions do.
    • Unless insertion or deletion mutations occur in multiples of three, they cause a frameshift mutation.
      • All the nucleotides downstream of the deletion or insertion will be improperly grouped into codons.
      • The result will be extensive missense, ending sooner or later in nonsense—premature termination.
    • Mutations can occur in a number of ways.
      • Errors can occur during DNA replication, DNA repair, or DNA recombination.
      • These can lead to base-pair substitutions, insertions, or deletions, as well as mutations affecting longer stretches of DNA.
      • These are called spontaneous mutations.
    • Rough estimates suggest that about 1 nucleotide in every 1010 is altered and inherited by daughter cells.
    • Mutagens are chemical or physical agents that interact with DNA to cause mutations.
    • Physical agents include high-energy radiation like X-rays and ultraviolet light.
    • Chemical mutagens fall into several categories.
      • Some chemicals are base analogues that may be substituted into DNA, but they pair incorrectly during DNA replication.
      • Other mutagens interfere with DNA replication by inserting into DNA and distorting the double helix.
      • Still others cause chemical changes in bases that change their pairing properties.
    • Researchers have developed various methods to test the mutagenic activity of different chemicals.
      • These tests are often used as a preliminary screen of chemicals to identify those that may cause cancer.
      • This makes sense because most carcinogens are mutagenic and most mutagens are carcinogenic.

      What is a gene? We revisit the question.

    • The Mendelian concept of a gene views it as a discrete unit of inheritance that affects phenotype.
      • Morgan and his colleagues assigned genes to specific loci on chromosomes.
      • We can also view a gene as a specific nucleotide sequence along a region of a DNA molecule.
        • We can define a gene functionally as a DNA sequence that codes for a specific polypeptide chain.
    • All these definitions are useful in certain contexts.
    • Even the one gene–one polypeptide definition must be refined and applied selectively.
      • Most eukaryotic genes contain large introns that have no corresponding segments in polypeptides.
      • Promoters and other regulatory regions of DNA are not transcribed either, but they must be present for transcription to occur.
      • Our molecular definition must also include the various types of RNA that are not translated into polypeptides, such as rRNA, tRNA, and other RNAs.
    • This is our definition of a gene: A gene is a region of DNA whose final product is either a polypeptide or an RNA molecule.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 17-1

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    Chapter 18 - The Genetics of Viruses and Bacteria

    Chapter 18 The Genetics of Viruses and Bacteria
    Lecture Outline

    Overview: Microbial Model Systems

    • Viruses and bacteria are the simplest biological systems—microbial models in which scientists find life’s fundamental molecular mechanisms in their most basic, accessible forms.
    • Molecular biology was born in the laboratories of microbiologists studying viruses and bacteria.
      • Microbes such as E. coli and its viruses are called model systems because of their use in studies that reveal broad biological principles.
      • Microbiologists provided most of the evidence that genes are made of DNA, and they worked out most of the major steps in DNA replication, transcription, and translation.
      • Techniques enabling scientists to manipulate genes and transfer them from one organism to another were developed in microbes.
    • In addition, viruses and bacteria have unique genetic features with implications for understanding the diseases that they cause.
    • Bacteria are prokaryotic organisms, with cells that are much smaller and more simply organized than those of eukaryotes, such as plants and animals.
    • Viruses are smaller and simpler still, lacking the structure and metabolic machinery of cells.
      • Most viruses are little more than aggregates of nucleic acids and protein—genes in a protein coat.

    Concept 18.1 A virus has a genome but can reproduce only within a host cell

      Researchers discovered viruses by studying a plant disease.

    • The story of how viruses were discovered begins in 1883 with research on the cause of tobacco mosaic disease by Adolf Mayer.
      • This disease stunts tobacco plant growth and mottles plant leaves.
      • Mayer concluded that the disease was infectious when he found that he could transmit the disease by rubbing sap from diseased leaves onto healthy plants.
      • He concluded that the disease must be caused by an extremely small bacterium.
      • Ten years later, Dimitri Ivanovsky demonstrated that the sap was still infectious even after passing through a filter designed to remove bacteria.
    • In 1897, Martinus Beijerinck ruled out the possibility that the disease was due to a filterable toxin produced by a bacterium by demonstrating that the infectious agent could reproduce.
      • The sap from one generation of infected plants could be used to infect a second generation of plants that could infect subsequent generations.
      • Beijerinck also determined that the pathogen could reproduce only within the host, could not be cultivated on nutrient media, and was not inactivated by alcohol, generally lethal to bacteria.
    • In 1935, Wendell Stanley crystallized the pathogen, the tobacco mosaic virus (TMV).

      A virus is a genome enclosed in a protective coat.

    • Stanley’s discovery that some viruses could be crystallized was puzzling because not even the simplest cells can aggregate into regular crystals.
    • However, viruses are not cells.
    • They are infectious particles consisting of nucleic acid encased in a protein coat and, in some cases, a membranous envelope.
      • The tiniest viruses are only 20 nm in diameter—smaller than a ribosome.
    • The genome of viruses may consist of double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA, depending on the kind of virus.
      • A virus is called a DNA virus or an RNA virus, according to the kind of nucleic acid that makes up its genome.
      • The viral genome is usually organized as a single linear or circular molecule of nucleic acid.
      • The smallest viruses have only four genes, while the largest have several hundred.
    • The capsid is the protein shell enclosing the viral genome.
    • Capsids are built of a large number of protein subunits called capsomeres.
      • The number of different kinds of proteins making up the capsid is usually small.
      • The capsid of the tobacco mosaic virus has more than 1,000 copies of the same protein.
      • Adenoviruses have 252 identical proteins arranged into a polyhedral capsid—as an icosahedron.
    • Some viruses have accessory structures to help them infect their hosts.
    • A membranous envelope surrounds the capsids of flu viruses.
      • These viral envelopes are derived from the membrane of the host cell.
      • They also have some host cell viral proteins and glycoproteins, as well as molecules of viral origin.
      • Some viruses carry a few viral enzyme molecules within their capsids.
    • The most complex capsids are found in viruses that infect bacteria, called bacteriophages or phages.
    • The T-even phages (T2, T4, T6) that infect Escherichia coli have elongated icosahedral capsid heads that enclose their DNA and a protein tailpiece that attaches the phage to the host and injects the phage DNA inside.

      Viruses can reproduce only within a host cell.

    • Viruses are obligate intracellular parasites.
    • They can reproduce only within a host cell.
    • An isolated virus is unable to reproduce—or do anything else, except infect an appropriate host.
    • Viruses lack the enzymes for metabolism and the ribosomes for protein synthesis.
    • An isolated virus is merely a packaged set of genes in transit from one host cell to another.
    • Each type of virus can infect and parasitize only a limited range of host cells, called its host range.
      • This host specificity depends on the evolution of recognition systems by the virus.
      • Viruses identify host cells by a “lock and key” fit between proteins on the outside of the virus and specific receptor molecules on the host’s surface (which evolved for functions that benefit the host).
    • Some viruses have a broad enough host range to infect several species, while others infect only a single species.
      • West Nile virus can infect mosquitoes, birds, horses, and humans.
      • Measles virus can infect only humans.
    • Most viruses of eukaryotes attack specific tissues.
      • Human cold viruses infect only the cells lining the upper respiratory tract.
      • The AIDS virus binds only to certain white blood cells.
    • A viral infection begins when the genome of the virus enters the host cell.
    • Once inside, the viral genome commandeers its host, reprogramming the cell to copy viral nucleic acid and manufacture proteins from the viral genome.
      • The host provides nucleotides, ribosomes, tRNAs, amino acids, ATP, and other components for making the viral components dictated by viral genes.
    • Most DNA viruses use the DNA polymerases of the host cell to synthesize new genomes along the templates provided by the viral DNA.
      • RNA viruses use special virus-encoded polymerases that can use RNA as a template.
    • The nucleic acid molecules and capsomeres then self-assemble into viral particles and exit the cell.
      • Tobacco mosaic virus RNA and capsomeres can be assembled to form complete viruses if the components are mixed together under the right conditions.
    • The simplest type of viral reproductive cycle ends with the exit of many viruses from the infected host cell, a process that usually damages or destroys the host cell.

      Phages reproduce using lytic or lysogenic cycles.

    • While phages are the best understood of all viruses, some of them are also among the most complex.
    • Research on phages led to the discovery that some double-stranded DNA viruses can reproduce by two alternative mechanisms: the lytic cycle and the lysogenic cycle.
    • In the lytic cycle, the phage reproductive cycle culminates in the death of the host.
      • In the last stage, the bacterium lyses (breaks open) and releases the phages produced within the cell to infect others.
      • Each of these phages can infect a healthy cell.
    • Virulent phages reproduce only by a lytic cycle.
    • While phages have the potential to wipe out a bacterial colony in just hours, bacteria have defenses against phages.
      • Natural selection favors bacterial mutants with receptor sites that are no longer recognized by a particular type of phage.
      • Bacteria produce restriction endonucleases, or restriction enzymes, that recognize and cut up foreign DNA, including certain phage DNA.
        • Chemical modifications to the bacteria’s own DNA prevent its destruction by restriction nucleases.
      • Natural selection also favors phage mutants that are resistant to restriction enzymes.
    • In the lysogenic cycle, the phage genome replicates without destroying the host cell.
      • Temperate phages, like phage lambda, use both lytic and lysogenic cycles.
    • The lambda phage that infects E. coli demonstrates the cycles of a temperate phage.
    • Infection of an E. coli by phage lambda begins when the phage binds to the surface of the cell and injects its DNA.
      • What happens next depends on the reproductive mode: lytic or lysogenic cycle.
    • During a lytic cycle, the viral genes turn the host cell into a lambda phage-producing factory, and the cell lyses and releases its viral products.
    • During a lysogenic cycle, the viral DNA molecule is incorporated by genetic recombination into a specific site on the host cell’s chromosome.
    • In this prophage stage, one of the viral genes codes for a protein that represses most other prophage genes.
      • As a result, the phage genome is largely silent.
      • A few other prophage genes may also be expressed during lysogenic cycles.
      • Expression of these genes may alter the host’s phenotype, which can have medical significance.
    • Every time the host divides, it copies the phage DNA and passes the copies to daughter cells.
      • The viruses propagate without killing the host cells on which they depend.
    • The term lysogenic implies that prophages are capable of giving rise to active phages that lyse their host cells.
    • That happens when the viral genome exits the bacterial chromosome and initiates a lytic cycle.

      Animal viruses are diverse in their modes of infection and replication.

    • Many variations on the basic scheme of viral infection and reproduction are represented among animal viruses.
      • One key variable is the type of nucleic acid that serves as a virus’s genetic material.
      • Another variable is the presence or absence of a membranous envelope derived from the host cell membrane.
      • Most animal viruses with RNA genomes have an envelope, as do some with DNA genomes.
    • Viruses equipped with an outer envelope use the envelope to enter the host cell.
      • Glycoproteins on the envelope bind to specific receptors on the host’s membrane.
      • The envelope fuses with the host’s membrane, transporting the capsid and viral genome inside.
      • The viral genome duplicates and directs the host’s protein synthesis machinery to synthesize capsomeres with free ribosomes and glycoproteins with bound ribosomes.
      • After the capsid and viral genome self-assemble, they bud from the host cell covered with an envelope derived from the host’s plasma membrane, including viral glycoproteins.
    • The viral envelope is thus derived from the host’s plasma membrane, although viral genes specify some of the molecules in the membrane.
    • These enveloped viruses do not necessarily kill the host cell.
    • Some viruses have envelopes that are not derived from plasma membrane.
      • The envelope of the herpesvirus is derived from the nuclear envelope of the host.
      • These double-stranded DNA viruses reproduce within the cell nucleus using viral and cellular enzymes to replicate and transcribe their DNA.
      • In some cases, copies of the herpesvirus DNA remain behind as minichromosomes in the nuclei of certain nerve cells.
      • There they remain for life until triggered by physical or emotional stress to leave the genome and initiate active viral production.
      • The infection of other cells by these new viruses causes cold or genital sores.
    • The viruses that use RNA as the genetic material are quite diverse, especially those that infect animals.
      • In some with single-stranded RNA (class IV), the genome acts as mRNA and is translated directly.
      • In others (class V), the RNA genome serves as a template for complementary RNA strands, which function both as mRNA and as templates for the synthesis of additional copies of genome RNA.
      • All viruses that require RNA --> RNA synthesis to make mRNA use a viral enzyme that is packaged with the genome inside the capsid.
    • Retroviruses (class VI) have the most complicated life cycles.
      • These carry an enzyme called reverse transcriptase that transcribes DNA from an RNA template.
        • This provides RNA --> DNA information flow.
      • The newly made DNA is inserted as a provirus into a chromosome in the animal cell.
      • The host’s RNA polymerase transcribes the viral DNA into more RNA molecules.
        • These can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell.
    • Human immunodeficiency virus (HIV), the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus.
    • The reproductive cycle of HIV illustrates the pattern of infection and replication in a retrovirus.
    • The viral particle includes an envelope with glycoproteins for binding to specific types of red blood cells, a capsid containing two identical RNA strands as its genome, and two copies of reverse transcriptase.
    • After HIV enters the host cell, reverse transcriptase molecules are released into the cytoplasm and catalyze synthesis of viral DNA.
    • The host’s polymerase transcribes the proviral DNA into RNA molecules that can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell.
    • Transcription produces more copies of the viral RNA that are translated into viral proteins, which self-assemble into a virus particle and leave the host.

      Viruses may have evolved from other mobile genetic elements.

    • Viruses do not fit our definition of living organisms.
    • An isolated virus is biologically inert, and yet it has a genetic program written in the universal language of life.
    • Although viruses are obligate intracellular parasites that cannot reproduce independently, it is hard to deny their evolutionary connection to the living world.
    • Because viruses depend on cells for their own propagation, it is reasonable to assume that they evolved after the first cells appeared.
    • Most molecular biologists favor the hypothesis that viruses originated from fragments of cellular nucleic acids that could move from one cell to another.
      • A viral genome usually has more in common with the genome of its host than with those of viruses infecting other hosts.
      • However, some viruses have genetic sequences that are quite similar to seemingly distantly related viruses.
        • This genetic similarity may reflect the persistence of groups of viral genes that were evolutionarily successful during the early evolution of viruses and their eukaryotic host cells.
    • Perhaps the earliest viruses were naked bits of nucleic acids that passed between cells via injured cell surfaces.
      • The evolution of capsid genes may have facilitated the infection of undamaged cells.
    • Candidates for the original sources of viral genomes include plasmids and transposable elements.
      • Plasmids are small, circular DNA molecules that are separate from chromosomes.
      • Plasmids, found in bacteria and in eukaryote yeast, can replicate independently of the rest of the cell and are occasionally transferred between cells.
      • Transposable elements are DNA segments that can move from one location to another within a cell’s genome.
    • Both plasmids and transposable elements are mobile genetic elements.
    • The ongoing evolutionary relationship between viruses and the genomes of their hosts is an association that makes viruses very useful model systems in molecular biology.

    Concept 18.2 Viruses, viroids, and prions are formidable pathogens in animals and plants

    • The link between viral infection and the symptoms it produces is often obscure.
      • Some viruses damage or kill cells by triggering the release of hydrolytic enzymes from lysosomes.
      • Some viruses cause the infected cell to produce toxins that lead to disease symptoms.
      • Others have molecular components, such as envelope proteins, that are toxic.
    • In some cases, viral damage is easily repaired (respiratory epithelium after a cold), but in others, infection causes permanent damage (nerve cells after polio).
    • Many of the temporary symptoms associated with a viral infection result from the body’s own efforts at defending itself against infection.
    • The immune system is a complex and critical part of the body’s natural defense mechanism against viral and other infections.
    • Modern medicine has developed vaccines, harmless variants or derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen.
      • Vaccination has eradicated smallpox.
      • Effective vaccines are available against polio, measles, rubella, mumps, hepatitis B, and a number of other viral diseases.
    • Medical technology can do little to cure viral diseases once they occur.
    • Antibiotics, which can kill bacteria by inhibiting enzymes or processes specific to bacteria, are powerless against viruses, which have few or no enzymes of their own.
      • Most antiviral drugs resemble nucleosides and interfere with viral nucleic acid synthesis.
      • An example is acyclovir, which impedes herpesvirus reproduction by inhibiting the viral polymerase that synthesizes viral DNA.
      • Azidothymidine (AZT) curbs HIV reproduction by interfering with DNA synthesis by reverse transcriptase.
      • Currently, multidrug “cocktails” are the most effective treatment for HIV.

      New viral diseases are emerging.

    • In recent years, several emerging viruses have risen to prominence.
      • HIV, the AIDS virus, seemed to appear suddenly in the early 1980s.
      • Each year new strains of influenza virus cause millions to miss work or class, and deaths are not uncommon.
      • The deadly Ebola virus has caused hemorrhagic fevers in central Africa periodically since 1976.
      • West Nile virus appeared for the first time in North America in 1999.
      • A more recent viral disease is severe acute respiratory syndrome (SARS).
        • Researchers identified the disease agent causing SARS as a coronavirus, a class IV virus with a single-stranded RNA genome.
    • The emergence of these new viral diseases is due to three processes: mutation; spread of existing viruses from one species to another; and dissemination of a viral disease from a small, isolated population.
    • Mutation of existing viruses is a major source of new viral diseases.
      • RNA viruses tend to have high mutation rates because replication of their nucleic acid lacks proofreading.
      • Some mutations create new viral strains with sufficient genetic differences from earlier strains that they can infect individuals who had acquired immunity to these earlier strains.
        • This is the case in flu epidemics.
    • Another source of new viral diseases is the spread of existing viruses from one host species to another.
    • It is estimated that about three-quarters of new human diseases originated in other animals.
      • For example, hantavirus, which killed dozens of people in 1993, normally infects rodents, especially deer mice.
      • In 1993, unusually wet weather in the southwestern United States increased the mice’s food, exploding the population.
      • Humans acquired hantavirus when they inhaled dust-containing traces of urine and feces from infected mice.
      • The source of the SARS-causing virus is still undetermined, but candidates include the exotic animal markets in China.
      • In early 2004, the first cases of a new bird flu were reported in southeast Asia.
        • If this disease evolves to spread from person to person, the potential for a major human outbreak is great.
    • Finally, a viral disease can spread from a small, isolated population to a widespread epidemic.
      • For example, AIDS went unnamed and virtually unnoticed for decades before spreading around the world.
      • Technological and social factors, including affordable international travel, blood transfusion technology, sexual promiscuity, and the abuse of intravenous drugs allowed a previously rare disease to become a global scourge.
    • These emerging viruses are generally not new. Rather, they are existing viruses that mutate, spread to new host species, or expand their host territory.
    • Changes in host behavior and environmental changes can increase the viral traffic responsible for emerging disease.
      • Destruction of forests to expand cropland may bring humans into contact with other animals that may host viruses that can infect humans.

      Plant viruses are serious agricultural pests.

    • More than 2,000 types of viral diseases of plants are known.
      • These diseases account for an annual loss of $15 billion worldwide.
    • Plant viruses can stunt plant growth and diminish crop yields.
    • Most are RNA viruses with rod-shaped or polyhedral capsids.
    • Plant viral diseases are spread by two major routes.
    • In horizontal transmission, a plant is infected with the virus by an external source.
      • Plants are more susceptible if their protective epidermis is damaged, perhaps by wind, chilling, injury, or insects.
      • Insects are often carriers of viruses, transmitting disease from plant to plant.
    • In vertical transmission, a plant inherits a viral infection from a parent.
      • This may occur by asexual propagation or in sexual reproduction via infected seeds.
    • Once a virus starts reproducing inside a plant cell, viral particles can spread throughout the plant by passing through plasmodesmata.
      • These cytoplasmic connections penetrate the walls between adjacent cells.
      • Proteins encoded by viral genes can alter the diameter of plasmodesmata to allow passage of viral proteins or genomes.
    • Agricultural scientists have focused their efforts largely on reducing the incidence and transmission of viral disease and in breeding resistant plant varieties.

      Viroids and prions are the simplest infectious agents.

    • Viroids, smaller and simpler than even viruses, consist of tiny molecules of naked circular RNA that infect plants.
    • Their several hundred nucleotides do not encode for proteins but can be replicated by the host’s cellular enzymes.
    • These small RNA molecules can disrupt plant metabolism and stunt plant growth, perhaps by causing errors in the regulatory systems that control plant growth.
    • Viroids show that molecules can act as infectious agents to spread disease.
    • Prions are infectious proteins that spread disease.
      • They appear to cause several degenerative brain diseases including scrapie in sheep, “mad cow disease,” and Creutzfeldt-Jakob disease in humans.
    • Prions are likely transmitted in food.
    • They have two alarming characteristics.
      • They are very slow-acting agents. The incubation period is around ten years.
      • Prions are virtually indestructible. They are not destroyed or deactivated by heating to normal cooking temperatures.
    • How can a nonreplicating protein be a transmissible pathogen?
    • According to the leading hypothesis, a prion is a misfolded form of a normal brain protein.
    • When the prion gets into a cell with the normal form of the protein, the prion can convert the normal protein into the prion version, creating a chain reaction that increases their numbers.

    Concept 18.3 Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria

    • Bacteria are very valuable as microbial models in genetics research.
      • As prokaryotes, bacteria allow researchers to study molecular genetics in simple organisms.
      • With the advent of large-scale genome sequencing, information about many prokaryotes has accumulated.
      • The best-studied bacterium is Escherichia coli, “the laboratory rat of molecular biology.”
    • The major component of the bacterial genome is one double-stranded, circular DNA molecule that is associated with a small amount of protein.
      • For E. coli, the chromosomal DNA consists of about 4.6 million nucleotide pairs with about 4,400 genes.
      • This is 100 times more DNA than in a typical virus and 1,000 times less than in a typical eukaryote cell.
      • Tight coiling of DNA results in a dense region of DNA, called the nucleoid, which is not bound by a membrane.
    • In addition, many bacteria have plasmids, much smaller circles of DNA.
      • Each plasmid has only a small number of genes, from just a few to several dozen.
    • Bacterial cells divide by binary fission.
      • This is preceded by replication of the bacterial chromosome from a single origin of replication.
    • Bacteria proliferate very rapidly in a favorable natural or laboratory environment.
      • Under optimal laboratory conditions, E. coli can divide every 20 minutes, producing a colony of 107 to 108 bacteria in as little as 12 hours.
      • In the human colon, E. coli grows more slowly and can double every 12 hours.
      • It does reproduce rapidly enough to replace the 2 × 1010 bacteria lost each day in feces.
    • Through binary fission, most of the bacteria in a colony are genetically identical to the parent cell.
      • However, the spontaneous mutation rate of E. coli is 1 × 10?7 mutations per gene per cell division.
      • This produces about 2,000 bacteria per day in the human colon that have a mutation in any one gene.
      • About 9 million mutant E. coli are produced in the human gut each day.
    • New mutations, though individually rare, can have a significant impact on genetic diversity when reproductive rates are very high because of short generation spans.
    • Individual bacteria that are genetically well equipped for the local environment clone themselves more prolifically than do less fit individuals.
    • In contrast, organisms with slower reproduction rates (like humans) create genetic variation not by novel alleles produced through new mutations, but primarily by sexual recombination of existing alleles.

      Genetic recombination produces new bacterial strains.

    • In addition to mutation, genetic recombination generates diversity within bacterial populations.
    • Here, recombination is defined as the combining of DNA from two individuals into a single genome.
    • Bacterial recombination occurs through three processes: transformation, transduction, and conjugation.
    • Recombination can be observed when two mutant E. coli strains are combined.
      • If each is unable to synthesize one of its required amino acids, neither can grow on a minimal medium.
      • However, if they are combined, numerous colonies will be created that started from cells that acquired the missing genes for amino acid synthesis from the other strain.
      • Some of these capable cells may have resulted from mutation. However, most acquired the missing genes by genetic recombination.
    • Transformation is the alteration of a bacterial cell’s genotype by the uptake of naked, foreign DNA from the surrounding environment.
      • For example, harmless Streptococcus pneumoniae bacteria can be transformed to pneumonia-causing cells.
      • This occurs when a live nonpathogenic cell takes up a piece of DNA that happens to include the allele for pathogenicity from dead, broken-open pathogenic cells.
      • The foreign allele replaces the native allele in the bacterial chromosome by genetic recombination.
      • The resulting cell is now recombinant, with DNA derived from two different cells.
    • Years after transformation was discovered in laboratory cultures, most biologists believed that the process was too rare and haphazard to play an important role in natural bacterial populations.
    • Researchers have since learned that many bacterial species have surface proteins that are specialized for the uptake of naked DNA.
      • These proteins recognize and transport DNA from closely related bacterial species into the cell, which can then incorporate the foreign DNA into the genome.
      • While E. coli lacks this specialized mechanism, it can be induced to take up small pieces of DNA if cultured in a medium with a relatively high concentration of calcium ions.
      • In biotechnology, this technique has been used to introduce foreign DNA into E. coli.
    • Transduction occurs when a phage carries bacterial genes from one host cell to another as a result of aberrations in the phage reproductive cycle.
    • In generalized transduction, bacterial genes are randomly transferred from one bacterial cell to another.
    • Occasionally, a small piece of the host cell’s degraded DNA, rather than the phage genome, is packaged within a phage capsid.
      • When this phage attaches to another bacterium, it will inject this foreign DNA into its new host.
      • Some of this DNA can subsequently replace the homologous region of the second cell.
      • This type of transduction transfers bacterial genes at random.
    • Specialized transduction occurs via a temperate phage.
      • When the prophage viral genome is excised from the chromosome, it sometimes takes with it a small region of adjacent bacterial DNA.
      • These bacterial genes are injected along with the phage’s genome into the next host cell.
      • Specialized transduction only transfers those genes near the prophage site on the bacterial chromosome.
    • Both generalized and specialized transduction use phage as a vector to transfer genes between bacteria.
    • Sometimes known as bacterial “sex,” conjugation transfers genetic material between two bacterial cells that are temporarily joined.
    • The transfer is one-way. One cell (“male”) donates DNA and its “mate” (“female”) receives the genes.
      • A sex pilus from the male initially joins the two cells and creates a cytoplasmic mating bridge between cells.
    • “Maleness,” the ability to form a sex pilus and donate DNA, results from an F (for fertility) factor as a section of the bacterial chromosome or as a plasmid.
      • Plasmids, including the F plasmid, are small, circular, self-replicating DNA molecules.
    • A genetic element that can replicate either as part of the bacterial chromosome or independently of it is called an episome.
      • Episomes such as the F plasmid can undergo reversible incorporation into the cell’s chromosome.
    • Temperate viruses are also episomes.
    • Plasmids usually have only a few genes, which are not required for normal survival and reproduction of the bacterium.
      • However, plasmid genes may be advantageous in stressful conditions.
        • The F plasmid facilitates genetic recombination when environmental conditions no longer favor existing strains.
    • The F factor or its F plasmid consists of about 25 genes, most required for the production of sex pili.
      • Cells with either the F factor or the F plasmid are called F+ and they pass this condition to their offspring.
      • Cells lacking either form of the F factor, are called F?, and they function as DNA recipients.
    • When an F+ and F? cell meet, the F+ cell passes a copy of the F plasmid to the F? cell, converting it.
    • The plasmid form of the F factor can become integrated into the bacterial chromosome.
    • A cell with the F factor built into its chromosome is called an Hfr cell (for High frequency of recombination).
    • Hfr cells function as males during conjugation.
    • The Hfr cell initiates DNA replication at a point on the F factor DNA and begins to transfer the DNA copy from that point to its F? partner.
    • Random movements almost always disrupt conjugation long before an entire copy of the Hfr chromosome can be passed to the F? cell.
    • In the partially diploid cell, the newly acquired DNA aligns with the homologous region of the F? chromosome.
    • Recombination exchanges segments of DNA.
    • The resulting recombinant bacterium has genes from two different cells.
    • In the 1950s, Japanese physicians began to notice that some bacterial strains had evolved antibiotic resistance.
      • Mutations may reduce the ability of the pathogen’s cell-surface proteins to transport antibiotics into the bacterial cell.
      • Some of these genes code for enzymes that specifically destroy certain antibiotics, like tetracycline or ampicillin.
    • The genes conferring resistance are carried by plasmids, specifically the R plasmid (R for resistance).
    • When a bacterial population is exposed to an antibiotic, individuals with the R plasmid will survive and increase in the overall population.
    • Because R plasmids also have genes that encode for sex pili, they can be transferred from one cell to another by conjugation.
    • The DNA of a single cell can also undergo recombination due to movement of transposable genetic elements or transposable elements within the cell’s genome.
    • Unlike plasmids or prophages, transposable elements never exist independently but are always part of chromosomal or plasmid DNA.
      • During transposition, the transposable element moves from one location to another in a cell’s genome.
      • In bacteria, the movement may be within the chromosome, from a plasmid to a chromosome (or vice versa), or between plasmids.
      • Transposable elements may move by a “copy and paste” mechanism, in which the transposable element replicates at its original site, and the copy inserts elsewhere.
      • In other words, the transposable element is added at a new site without being lost from the old site.
    • Most transposable elements can move to many alternative locations in the DNA, potentially moving genes to a site where genes of that sort have never before existed.
    • The simplest transposable elements, called insertion sequences, exist only in bacteria.
    • An insertion sequence contains a single gene that codes for transposase, an enzyme that catalyzes movement of the insertion sequence from one site to another within the genome.
    • The insertion sequence consists of the transposase gene, flanked by a pair of inverted repeat sequences.
      • The 20 to 40 nucleotides of the inverted repeat on one side are repeated in reverse along the opposite DNA strand at the other end of the transposable element.
    • The transposase enzyme recognizes the inverted repeats as the edges of the transposable element.
    • Transposase cuts the transposable elements from its initial site and inserts it into the target site.
    • Insertion sequences cause mutations when they happen to land within the coding sequence of a gene or within a DNA region that regulates gene expression.
    • Insertion sequences account for 1.5% of the E. coli genome, but a mutation in a particular gene by transposition is rare, occurring about once in every 10 million generations.
      • This is about the same rate as spontaneous mutations from external factors.
    • Transposable elements longer and more complex than insertion sequences, called transposons, also move about in the bacterial genome.
    • In addition to the DNA required for transposition, transposons include extra genes that “go along for the ride,” such as genes for antibiotic resistance.
    • In some bacterial transposons, the extra genes are sandwiched between two insertion sequences.
    • While insertion sequences may not benefit bacteria in any specific way, transposons may help bacteria adapt to new environments.
      • For example, a single R plasmid may carry several genes for resistance to different antibiotics.
      • This is explained by transposons, which can add a gene for antibiotic resistance to a plasmid already carrying genes for resistance to other antibiotics.
      • The transmission of this composite plasmid to other bacterial cells by cell division or conjugation can spread resistance to a variety of antibiotics throughout a bacterial population.
      • In an antibiotic-rich environment, natural selection factors bacterial clones that have built up R plasmids with multiple antibiotic resistance through a series of transpositions.
    • Transposable elements are also important components of eukaryotic genomes.

    Concept 18.4 Individual bacteria respond to environmental change by regulating their gene expression

    • An individual bacterium, locked into the genome that it has inherited, can cope with environmental fluctuations by exerting metabolic control.
      • First, cells can vary the number of specific enzyme molecules they make by regulating gene expression.
      • Second, cells can adjust the activity of enzymes already present (for example, by feedback inhibition).
    • The tryptophan biosynthesis pathway demonstrates both levels of control.
      • If tryptophan levels are high, some of the tryptophan molecules can inhibit the first enzyme in the pathway.
      • If the abundance of tryptophan continues, the cell can stop synthesizing additional enzymes in this pathway by blocking transcription of the genes for these enzymes.
    • The basic mechanism for this control of gene expression in bacteria, the operon model, was discovered in 1961 by François Jacob and Jacques Monod.
    • E. coli synthesizes tryptophan from a precursor molecule in a series of steps, with each reaction catalyzed by a specific enzyme.
      • The five genes coding for these enzymes are clustered together on the bacterial chromosome, served by a single promoter.
      • Transcription gives rise to one long mRNA molecule that codes for all five enzymes in the tryptophan pathway.
      • The mRNA is punctuated with start and stop codons that signal where the coding sequence for each polypeptide begins and ends.
    • A key advantage of grouping genes of related functions into one transcription unit is that a single “on-off switch” can control a cluster of functionally related genes.
    • When an E. coli cell must make tryptophan for itself, all the enzymes are synthesized at one time.
    • The switch is a segment of DNA called an operator.
    • The operator, located between the promoter and the enzyme-coding genes, controls the access of RNA polymerase to the genes.
    • The operator, the promoter, and the genes they control constitute an operon.
    • By itself, an operon is on and RNA polymerase can bind to the promoter and transcribe the genes.
    • However, if a repressor protein, a product of a regulatory gene, binds to the operator, it can prevent transcription of the operon’s genes.
      • Each repressor protein recognizes and binds only to the operator of a certain operon.
      • Regulatory genes are transcribed continuously at low rates.
    • Binding by the repressor to the operator is reversible.
      • The number of active repressor molecules available determines the on or off mode of the operator.
    • Repressors contain allosteric sites that change shape depending on the binding of other molecules.
      • In the case of the trp, or tryptophan, operon, when concentrations of tryptophan in the cell are high, some tryptophan molecules bind as a corepressor to the repressor protein.
      • This activates the repressor and turns the operon off.
      • At low levels of tryptophan, most of the repressors are inactive, and the operon is transcribed.
    • The trp operon is an example of a repressible operon, one that is inhibited when a specific small molecule binds allosterically to a regulatory protein.
    • In contrast, an inducible operon is stimulated when a specific small molecule interacts with a regulatory protein.
      • In inducible operons, the regulatory protein is active (inhibitory) as synthesized, and the operon is off.
      • Allosteric binding by an inducer molecule makes the regulatory protein inactive, and the operon is turned on.
    • The lac operon contains a series of genes that code for enzymes that play a major role in the hydrolysis and metabolism of lactose (milk sugar).
      • In the absence of lactose, this operon is off, as an active repressor binds to the operator and prevents transcription.
    • Lactose metabolism begins with hydrolysis of lactose into its component monosaccharides, glucose and galactose.
    • This reaction is catalyzed by the enzyme ß-galactosidase.
      • Only a few molecules of this enzyme are present in an E. coli cell grown in the absence of lactose.
      • If lactose is added to the bacterium’s environment, the number of ß-galactosidase increases by a thousandfold within 15 minutes.
    • The gene for ß-galactosidase is part of the lac operon, which includes two other genes coding for enzymes that function in lactose metabolism.
    • The regulatory gene, lacI, located outside the operon, codes for an allosteric repressor protein that can switch off the lac operon by binding to the operator.
    • Unlike the trp operon, the lac repressor is active all by itself, binding to the operator and switching the lac operon off.
      • An inducer inactivates the repressor.
    • When lactose is present in the cell, allolactose, an isomer of lactose, binds to the repressor.
      • This inactivates the repressor, and the lac operon can be transcribed.
    • Repressible enzymes generally function in anabolic pathways, synthesizing end products from raw materials.
      • When the end product is present in sufficient quantities, the cell can allocate its resources to other uses.
    • Inducible enzymes usually function in catabolic pathways, digesting nutrients to simpler molecules.
      • By producing the appropriate enzymes only when the nutrient is available, the cell avoids making proteins that have nothing to do.
    • Both repressible and inducible operons demonstrate negative control because active repressors switch off the active form of the repressor protein.
    • Positive gene control occurs when an activator molecule interacts directly with the genome to switch transcription on.
    • Even if the lac operon is turned on by the presence of allolactose, the degree of transcription depends on the concentrations of other substrates.
      • If glucose levels are low, then cyclic AMP (cAMP) accumulates.
    • The regulatory protein catabolite activator protein (CAP) is an activator of transcription.
      • When cAMP is abundant, it binds to CAP, and the regulatory protein assumes its active shape and can bind to a specific site at the upstream end of the lac promoter.
    • The attachment of CAP to the promoter directly stimulates gene expression.
    • Thus, this mechanism qualifies as positive regulation.
    • The cellular metabolism is biased toward the use of glucose.
    • If glucose levels are sufficient and cAMP levels are low (lots of ATP), then the CAP protein has an inactive shape and cannot bind upstream of the lac promoter.
      • The lac operon will be transcribed but at a low level.
    • For the lac operon, the presence/absence of lactose (allolactose) determines if the operon is on or off.
    • Overall energy levels in the cell determine the level of transcription, a “volume” control, through CAP.
    • CAP works on several operons that encode enzymes used in catabolic pathways.
      • If glucose is present and CAP is inactive, then the synthesis of enzymes that catabolize other compounds is slowed.
      • If glucose levels are low and CAP is active, then the genes that produce enzymes that catabolize whichever other fuel is present will be transcribed at high levels.

    Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 18-1

    Subject: 
    Subject X2: 

    Chapter 19 - Eukaryotic Genomes

    Chapter 19 Eukaryotic Genomes
    Lecture Outline

    Overview: How Eukaryotic Genomes Work and Evolve

    • Two features of eukaryotic genomes present a major information-processing challenge.
      • First, the typical multicellular eukaryotic genome is much larger than that of a prokaryotic cell.
      • Second, cell specialization limits the expression of many genes to specific cells.
    • The estimated 25,000 genes in the human genome include an enormous amount of DNA that does not code for RNA or protein.
    • This DNA is elaborately organized.
      • Not only is the DNA associated with protein, but also this DNA-protein complex called chromatin is organized into higher structural levels than the DNA-protein complex in prokaryotes.

    Concept 19.1 Chromatin structure is based on successive levels of DNA packing

    • While the single circular chromosome of bacteria is coiled and looped in a complex but orderly manner, eukaryotic chromatin is far more complex.
    • Eukaryotic DNA is precisely combined with large amounts of protein.
      • The resulting chromatin undergoes striking changes in the course of the cell cycle.
    • During interphase of the cell cycle, chromatin fibers are usually highly extended within the nucleus.
    • As a cell prepares for meiosis, its chromatin condenses, forming a characteristic number of short, thick chromosomes that can be distinguished with a light microscope.
    • Eukaryotic chromosomes contain an enormous amount of DNA relative to their condensed length.
      • Each human chromosome averages about 1.5 × 108 nucleotide pairs.
      • If extended, each DNA molecule would be about 4 cm long, thousands of times longer than the cell diameter.
      • This chromosome and 45 other human chromosomes fit into the nucleus.
      • This occurs through an elaborate, multilevel system of DNA packing.
    • Histone proteins are responsible for the first level of DNA packaging.
      • The mass of histone in chromatin is approximately equal to the mass of DNA.
      • Their positively charged amino acids bind tightly to negatively charged DNA.
      • The five types of histones are very similar from one eukaryote to another, and similar proteins are found in prokaryotes.
      • The conservation of histone genes during evolution reflects their pivotal role in organizing DNA within cells.
    • Unfolded chromatin has the appearance of beads on a string.
      • In this configuration, a chromatin fiber is 10 nm in diameter (the 10-nm fiber).
    • Each bead of chromatin is a nucleosome, the basic unit of DNA packing.
      • The “string” between the beads is called linker DNA.
    • A nucleosome consists of DNA wound around a protein core composed of two molecules each of four types of histone: H2A, H2B, H3, and H4.
      • The amino acid (N-terminus) of each histone protein (the histone tail) extends outward from the nucleosome.
      • A molecule of a fifth histone, H1, attaches to the DNA near the nucleosome.
    • The beaded string seems to remain essentially intact throughout the cell cycle.
    • Histones leave the DNA only transiently during DNA replication.
    • They stay with the DNA during transcription.
      • By changing shape and position, nucleosomes allow RNA-synthesizing polymerases to move along the DNA.
    • The next level of packing is due to the interactions between the histone tails of one nucleosome and the linker DNA and nucleosomes to either side.
      • With the aid of histone H1, these interactions cause the 10-nm to coil to form the 30-nm chromatin fiber.
    • This fiber forms looped domains attached to a scaffold of nonhistone proteins to make up a 300-nm fiber.
    • In a mitotic chromosome, the looped domains coil and fold to produce the characteristic metaphase chromosome.
    • These packing steps are highly specific and precise, with particular genes located in the same places on metaphase chromosomes.
    • Interphase chromatin is generally much less condensed than the chromatin of mitotic chromosomes, but it shows several of the same levels of higher-order packing.
      • Much of the chromatin is present as a 10-nm fiber, and some is compacted into a 30-nm fiber, which in some regions is folded into looped domains.
      • An interphase chromosome lacks an obvious scaffold, but its looped domains seem to be attached to the nuclear lamina on the inside of the nuclear envelope, and perhaps also to fibers of the nuclear matrix.
    • The chromatin of each chromosome occupies a specific restricted area within the interphase nucleus.
    • Interphase chromosomes have highly condensed areas, heterochromatin, and less compacted areas, euchromatin.
    • Heterochromatin DNA is largely inaccessible to transcription enzymes.
      • Looser packing of euchromatin makes its DNA accessible to enzymes and available for transcription.

    Concept 19.2 Gene expression can be regulated at any stage, but the key step is transcription

    • Like unicellular organisms, the tens of thousands of genes in the cells of multicellular eukaryotes are continually turned on and off in response to signals from their internal and external environments.
    • Gene expression must be controlled on a long-term basis during cellular differentiation, the divergence in form and function as cells in a multicellular organism specialize.
      • A typical human cell probably expresses about 20% of its genes at any given time.
        • Highly specialized cells, such as nerves or muscles, express only a tiny fraction of their genes.
        • Although all the cells in an organism contain an identical genome, the subset of genes expressed in the cells of each type is unique.
        • The differences between cell types are due to differential gene expression, the expression of different genes by cells with the same genome.
    • The genomes of eukaryotes may contain tens of thousands of genes.
      • For quite a few species, only a small amount of the DNA—1.5% in humans—codes for protein.
      • Of the remaining DNA, a very small fraction consists of genes for rRNA and tRNA.
      • Most of the rest of the DNA seems to be largely noncoding, although researchers have found that a significant amount of it is transcribed into RNAs of unknown function.
    • Problems with gene expression and control can lead to imbalance and diseases, including cancers.
    • Our understanding of the mechanisms controlling gene expression in eukaryotes has been enhanced by new research methods, including advances in DNA technology.
    • In all organisms, the expression of specific genes is most commonly regulated at transcription, often in response to signals coming from outside the cell.
      • The term gene expression is often equated with transcription.
      • With their greater complexity, eukaryotes have opportunities for controlling gene expression at additional stages.
    • Each stage in the entire process of gene expression provides a potential control point where gene expression can be turned on or off, sped up or slowed down.
      • A web of control connects different genes and their products.
    • These levels of control include chromatin packing, transcription, RNA processing, translation, and various alterations to the protein product.

      Chromatin modifications affect the availability of genes for transcription.

    • In addition to its role in packing DNA inside the nucleus, chromatin organization regulates gene expression.
      • Genes of densely condensed heterochromatin are usually not expressed, presumably because transcription proteins cannot reach the DNA.
      • A gene’s location relative to nucleosomes and to attachment sites to the chromosome scaffold or nuclear lamina can affect transcription.
    • Chemical modifications of chromatin play a key role in chromatin structure and gene expression.
    • Chemical modifications of histones play a direct role in the regulation of gene transcription.
    • The N-terminus of each histone molecule in a nucleosome protrudes outward from the nucleosome.
      • These histone tails are accessible to various modifying enzymes, which catalyze the addition or removal of specific chemical groups.
    • Histone acetylation (addition of an acetyl group —COCH3) and deacetylation appear to play a direct role in the regulation of gene transcription.
      • Acetylated histones grip DNA less tightly, providing easier access for transcription proteins in this region.
      • Some of the enzymes responsible for acetylation or deacetylation are associated with or are components of transcription factors that bind to promoters.
      • Thus histone acetylation enzymes may promote the initiation of transcription not only by modifying chromatin structure, but also by binding to and recruiting components of the transcription machinery.
    • DNA methylation is the attachment by specific enzymes of methyl groups (—CH3) to DNA bases after DNA synthesis.
    • Inactive DNA is generally highly methylated compared to DNA that is actively transcribed.
      • For example, the inactivated mammalian X chromosome in females is heavily methylated.
    • Genes are usually more heavily methylated in cells where they are not expressed.
      • Demethylating certain inactive genes turns them on.
      • However, there are exceptions to this pattern.
    • DNA methylation proteins recruit histone deacetylation enzymes, providing a mechanism by which DNA methylation and histone deacetylation cooperate to repress transcription.
    • In some species, DNA methylation is responsible for long-term inactivation of genes during cellular differentiation.
      • Once methylated, genes usually stay that way through successive cell divisions.
      • Methylation enzymes recognize sites on one strand that are already methylated and correctly methylate the daughter strand after each round of DNA replication.
    • This methylation patterns accounts for genomic imprinting in which methylation turns off either the maternal or paternal alleles of certain genes at the start of development.
    • The chromatin modifications just discussed do not alter DNA sequence, and yet they may be passed along to future generations of cells.
      • Inheritance of traits by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance.
    • Researchers are amassing more and more evidence for the importance of epigenetic information in the regulation of gene expression.
      • Enzymes that modify chromatin structure are integral parts of the cell’s machinery for regulating transcription.

      Transcription initiation is controlled by proteins that interact with DNA and with each other.

    • Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more available or less available for transcription.
    • A cluster of proteins called a transcription initiation complex assembles on the promoter sequence at the “upstream” end of the gene.
      • One component, RNA polymerase II, transcribes the gene, synthesizing a primary RNA transcript or pre-mRNA.
      • RNA processing includes enzymatic addition of a 5’ cap and a poly-A tail, as well as splicing out of introns to yield a mature mRNA.
    • Multiple control elements are associated with most eukaryotic genes.
      • Control elements are noncoding DNA segments that regulate transcription by binding certain proteins.
      • These control elements and the proteins they bind are critical to the precise regulation of gene expression in different cell types.
    • To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors.
      • General transcription factors are essential for the transcription of all protein-coding genes.
      • Only a few general transcription factors independently bind a DNA sequence such as the TATA box within the promoter.
      • Others in the initiation complex are involved in protein-protein interactions, binding each other and RNA polymerase II.
    • The interaction of general transcription factors and RNA polymerase II with a promoter usually leads to only a low rate of initiation and production of few RNA transcripts.
    • In eukaryotes, high levels of transcription of particular genes depend on the interaction of control elements with specific transcription factors.
    • Some control elements, named proximal control elements, are located close to the promoter.
    • Distant control elements, enhancers, may be thousands of nucleotides away from the promoter or even downstream of the gene or within an intron.
    • A given gene may have multiple enhancers, each active at a different time or in a different cell type or location in the organism.
    • An activator is a protein that binds to an enhancer to stimulate transcription of a gene.
      • Protein-mediated bending of DNA brings bound activators in contact with a group of mediator proteins that interact with proteins at the promoter.
      • This helps assemble and position the initiation complex on the promoter.
    • Eukaryotic genes also have repressor proteins to inhibit expression of a gene.
      • Eukaryotic repressors can cause inhibition of gene expression by blocking the binding of activators to their control elements or to components of the transcription machinery or by turning off transcription even in the presence of activators.
    • Some activators and repressors act indirectly to influence chromatin structure.
      • Some activators recruit proteins that acetylate histones near the promoters of specific genes, promoting transcription.
      • Some repressors recruit proteins that deacetylate histones, reducing transcription or silencing the gene.
      • Recruitment of chromatin-modifying proteins seems to be the most common mechanism of repression in eukaryotes.
    • The number of nucleotide sequences found in control elements is surprisingly small.
    • For many genes, the particular combination of control elements associated with the gene may be more important than the presence of a single unique control element in regulating transcription of the gene.
    • Even with only a dozen control element sequences, a large number of combinations are possible.
    • A particular combination of control elements will be able to activate transcription only when the appropriate activator proteins are present, such as at a precise time during development or in a particular cell type.
      • The use of different combinations of control elements allows fine regulation of transcription with a small set of control elements.
    • In prokaryotes, coordinately controlled genes are often clustered into an operon with a single promoter and other control elements upstream.
      • The genes of the operon are transcribed into a single mRNA and translated together.
    • In contrast, very few eukaryotic genes are organized this way.
    • Recent studies of the genomes of several eukaryotic species have found that some coexpressed genes are clustered near each other on the same chromosome.
      • Each eukaryotic gene in these clusters has its own promoter and is individually transcribed.
      • The coordinate regulation of clustered genes in eukaryotic cells is thought to involve changes in the chromatin structure that makes the entire group of genes either available or unavailable for transcription.
    • More commonly, genes coding for the enzymes of a metabolic pathway are scattered over different chromosomes.
    • Coordinate gene expression in eukaryotes depends on the association of a specific control element or combination of control elements with every gene of a dispersed group.
    • A common group of transcription factors binds to all the genes in the group, promoting simultaneous gene transcription.
      • For example, a steroid hormone enters a cell and binds to a specific receptor protein in the cytoplasm or nucleus, forming a hormone-receptor complex that serves as a transcription activator.
      • Every gene whose transcription is stimulated by that steroid hormone has a control element recognized by that hormone-receptor complex.
      • Other signal molecules control gene expression indirectly by triggering signal-transduction pathways that lead to activation of transcription.
    • Systems for coordinating gene regulation probably arose early in evolutionary history and evolved by the duplication and distribution of control elements within the genome.

      Post-transcriptional mechanisms play supporting roles in the control of gene expression.

    • Gene expression may be blocked or stimulated by any posttranscriptional step.
    • By using regulatory mechanisms that operate after transcription, a cell can rapidly fine-tune gene expression in response to environmental changes without altering its transcriptional patterns.
    • RNA processing in the nucleus and the export of mRNA to the cytoplasm provide opportunities for gene regulation that are not available in bacteria.
    • In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.
      • Regulatory proteins specific to a cell type control intron-exon choices by binding to regulatory sequences within the primary transcript.
    • The life span of an mRNA molecule is an important factor in determining the pattern of protein synthesis.
    • Prokaryotic mRNA molecules may be degraded after only a few minutes.
    • Eukaryotic mRNAs typically last for hours, days, or weeks.
      • In red blood cells, mRNAs for hemoglobin polypeptides are unusually stable and are translated repeatedly.
    • A common pathway of mRNA breakdown begins with enzymatic shortening of the poly-A tail.
      • This triggers the enzymatic removal of the 5’ cap.
      • This is followed by rapid degradation of the mRNA by nucleases.
    • Nucleotide sequences in the untranslated trailer region at the 3’ end affect mRNA stability.
      • Transferring such a sequence from a short-lived mRNA to a normally stable mRNA results in quick mRNA degradation.
    • During the past few years, researchers have found small single-stranded RNA molecules called microRNAs, or miRNAs, that bind to complementary sequences in mRNA molecules.
      • miRNAs are formed from longer RNA precursors that fold back on themselves, forming a long hairpin structure stabilized by hydrogen bonding.
      • An enzyme called Dicer cuts the double-stranded RNA into short fragments.
      • One of the two strands is degraded. The other miRNA strand associates with a protein complex and directs the complex to any mRNA molecules with a complementary sequence.
      • The miRNA-protein complex then degrades the target mRNA or blocks its translation.
    • The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi).
      • Small interfering RNAs (siRNAs) are similar in size and function to miRNAs and are generated by similar mechanisms in eukaryotic cells.
    • Cellular RNAi pathways lead to the destruction of RNAs and may have originated as a natural defense against infection by RNA viruses.
      • Whatever their origin, RNAi plays an important role in regulating gene expression in the cell.
    • Translation of specific mRNAs can be blocked by regulatory proteins that bind to specific sequences or structures within the 5’ leader region of mRNA.
      • This prevents attachment of ribosomes.
    • mRNAs may be stored in egg cells without poly-A tails of sufficient size to allow translation initiation.
      • At the appropriate time during development, a cytoplasmic enzyme adds more A residues, allowing translation to begin.
    • Protein factors required to initiate translation in eukaryotes offer targets for simultaneously controlling translation of all mRNAs in a cell.
      • This allows the cell to shut down translation if environmental conditions are poor (for example, shortage of a key constituent) or until the appropriate conditions exist (for example, after fertilization in an egg or during daylight in plants).
    • Finally, eukaryotic polypeptides must often be processed to yield functional proteins.
      • This may include cleavage, chemical modifications, and transport to the appropriate destination.
    • The cell limits the lifetimes of normal proteins by selective degradation.
      • Many proteins, like the cyclins in the cell cycle, must be short-lived to function appropriately.
    • Proteins intended for degradation are marked by the attachment of ubiquitin proteins.
    • Giant protein complexes called proteasomes recognize the ubiquitin and degrade the tagged protein.
      • Mutations making cell cycle proteins impervious to proteasome degradation can lead to cancer.

    Concept 19.3 Cancer results from genetic changes that affect cell cycle control

    • Cancer is a disease in which cells escape the control methods that normally regulate cell growth and division.
      • The gene regulation systems that go wrong during cancer are the very same systems that play important roles in embryonic development, the immune response, and other biological processes.
    • The genes that normally regulate cell growth and division during the cell cycle include genes for growth factors, their receptors, and the intracellular molecules of signaling pathways.
      • Mutations altering any of these genes in somatic cells can lead to cancer.
    • The agent of such changes can be random spontaneous mutations or environmental influences such as chemical carcinogens, X-rays, or certain viruses.
    • In 1911, Peyton Rous discovered a virus that causes cancer in chickens.
      • Since then, scientists have recognized a number of tumor viruses that cause cancer in various animals, including humans.
      • All tumor viruses transform cells into cancer cells through the integration of viral nucleic acid into host cell DNA.
    • Cancer-causing genes, oncogenes, were initially discovered in retroviruses, but close counterparts, proto-oncogenes, have been found in other organisms.
    • The products of proto-oncogenes are proteins that stimulate normal cell growth and division and play essential functions in normal cells.
    • A proto-oncogene becomes an oncogene following genetic changes that lead to an increase in the proto-oncogene’s protein production or the activity of each protein molecule.
      • These genetic changes include movements of DNA within the genome, amplification of the proto-oncogene, and point mutations in the control element of the proto-oncogene.
    • Cancer cells frequently have chromosomes that have been broken and rejoined incorrectly.
      • This may translocate a fragment to a location near an active promoter or other control element.
      • Movement of transposable elements may also place a more active promoter near a proto-oncogene, increasing its expression.
    • Amplification increases the number of copies of the proto-oncogene in the cell.
    • A point mutation in the promoter or enhancer of a proto-oncogene may increase its expression.
      • A point mutation in the coding sequence may lead to translation of a protein that is more active or longer-lived.
    • Mutations to tumor-suppressor genes, whose normal products inhibit cell division, also contribute to cancer.
    • Any decrease in the normal activity of a tumor-suppressor protein may contribute to cancer.
      • Some tumor-suppressor proteins normally repair damaged DNA, preventing the accumulation of cancer-causing mutations.
      • Others control the adhesion of cells to each other or to an extracellular matrix, crucial for normal tissues and often absent in cancers.
      • Still others are components of cell-signaling pathways that inhibit the cell cycle.

      Oncogene proteins and faulty tumor-suppressor proteins interfere with normal signaling pathways.

    • The proteins encoded by many proto-oncogenes and tumor-suppressor genes are components of cell-signaling pathways.
    • Mutations in the products of two key genes, the ras proto-oncogene, and the p53 tumor suppressor gene occur in 30% and 50% of human cancers, respectively.
    • Both the Ras protein and the p53 protein are components of signal-transduction pathways that convey external signals to the DNA in the cell’s nucleus.
    • Ras, the product of the ras gene, is a G protein that relays a growth signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases.
      • At the end of the pathway is the synthesis of a protein that stimulates the cell cycle.
      • Many ras oncogenes have a point mutation that leads to a hyperactive version of the Ras protein that can issue signals on its own, resulting in excessive cell division.
    • The p53 gene, named for its 53,000-dalton protein product, is often called the “guardian angel of the genome.”
    • Damage to the cell’s DNA acts as a signal that leads to expression of the p53 gene.
    • The p53 protein is a transcription factor for several genes.
      • It can activate the p21 gene, which halts the cell cycle.
      • It can turn on genes involved in DNA repair.
      • When DNA damage is irreparable, the p53 protein can activate “suicide genes” whose protein products cause cell death by apoptosis.
    • A mutation that knocks out the p53 gene can lead to excessive cell growth and cancer.

      Multiple mutations underlie the development of cancer.

    • More than one somatic mutation is generally needed to produce the changes characteristic of a full-fledged cancer cell.
    • If cancer results from an accumulation of mutations, and if mutations occur throughout life, then the longer we live, the more likely we are to develop cancer.
    • Colorectal cancer, with 135,000 new cases and 60,000 deaths in the United States each year, illustrates a multistep cancer path.
    • The first sign is often a polyp, a small benign growth in the colon lining.
      • The cells of the polyp look normal but divide unusually frequently.
    • Through gradual accumulation of mutations that activate oncogenes and knock out tumor-suppressor genes, the polyp can develop into a malignant tumor.
    • About a half dozen DNA changes must occur for a cell to become fully cancerous.
    • These usually include the appearance of at least one active oncogene and the mutation or loss of several tumor-suppressor genes.
      • Since mutant tumor-suppressor alleles are usually recessive, mutations must knock out both alleles.
      • Most oncogenes behave as dominant alleles and require only one mutation.
    • In many malignant tumors, the gene for telomerase is activated, removing a natural limit on the number of times the cell can divide.
    • Viruses, especially retroviruses, play a role in about 15% of human cancer cases worldwide.
      • These include some types of leukemia, liver cancer, and cancer of the cervix.
    • Viruses promote cancer development by integrating their DNA into that of infected cells.
      • By this process, a retrovirus may donate an oncogene to the cell.
    • Alternatively, insertion of viral DNA may disrupt a tumor-suppressor gene or convert a proto-oncogene to an oncogene.
    • Some viruses produce proteins that inactivate p53 and other tumor-suppressor proteins, making the cell more prone to becoming cancerous.
    • The fact that multiple genetic changes are required to produce a cancer cell helps explain the predispositions to cancer that run in some families.
      • An individual inheriting an oncogene or a mutant allele of a tumor-suppressor gene will be one step closer to accumulating the necessary mutations for cancer to develop.
    • Geneticists are devoting much effort to finding inherited cancer alleles so that predisposition to certain cancers can be detected early in life.
      • About 15% of colorectal cancers involve inherited mutations, especially to DNA repair genes or to the tumor-suppressor gene adenomatous polyposis coli, or APC.
        • Normal functions of the APC gene include regulation of cell migration and adhesion.
        • Even in patients with no family history of the disease, APC is mutated in about 60% of colorectal cancers.
      • Between 5–10% of breast cancer cases show an inherited predisposition.
        • This is the second most common type of cancer in the United States, striking more than 180,000 women annually and leading to 40,000 annual deaths.
        • Mutations to one of two tumor-suppressor genes, BRCA1 and BRCA2, increase the risk of breast and ovarian cancer.
      • A woman who inherits one mutant BRCA1 allele has a 60% probability of developing breast cancer before age 50 (versus a 2% probability in an individual with two normal alleles).
      • BRCA1 and BRCA2 are considered tumor-suppressor genes because their wild-type alleles protect against breast cancer and because their mutant alleles are recessive.
      • Recent evidence suggests that the BRCA2 protein is directly involved in repairing breaks that occur in both strands of DNA.

    Concept 19.4 Eukaryotic genomes can have many noncoding DNA sequences in addition to genes

    • Several trends are evident when we compare the genomes of prokaryotes to those of eukaryotes.
    • There is a general trend from smaller to larger genomes, but with fewer genes in a given length of DNA.
      • Humans have 500 to 1,500 times as many base pairs in their genome as most prokaryotes, but only 5 to 15 times as many genes.
    • Most of the DNA in a prokaryote genome codes for protein, tRNA, or rRNA.
      • The small amount of noncoding DNA consists mainly of regulatory sequences.
    • In eukaryotes, most of the DNA (98.5% in humans) does not code for protein or RNA.
      • Gene-related regulatory sequences and introns account for 24% of the human genome.
        • Introns account for most of the difference in average length of eukaryotic (27,000 base pairs) and prokaryotic genes (1,000 base pairs).
      • Most intergenic DNA is repetitive DNA, present in multiple copies in the genome.
        • Transposable elements and related sequences make up 44% of the entire human genome.
    • The first evidence for transposable elements came from geneticist Barbara McClintock’s breeding experiments with Indian corn (maize) in the 1940s and 1950s.
    • Eukaryotic transposable elements are of two types: transposons, which move within a genome by means of a DNA intermediate, and retrotransposons, which move by means of an RNA intermediate, a transcript of the retrotransposon DNA.
      • Transposons can move by a “cut and paste” mechanism, which removes the element from its original site, or by a “copy and paste” mechanism, which leaves a copy behind.
      • Retrotransposons always leave a copy at the original site, since they are initially transcribed into an RNA intermediate.
    • Most transposons are retrotransposons, in which the transcribed RNA includes the code for an enzyme that catalyzes the insertion of the retrotransposon and may include a gene for reverse transcriptase.
      • Reverse transcriptase uses the RNA molecule originally transcribed from the retrotransposon as a template to synthesize a double-stranded DNA copy.
    • Multiple copies of transposable elements and related sequences are scattered throughout eukaryotic genomes.
      • A single unit is hundreds or thousands of base pairs long, and the dispersed “copies” are similar but not identical to one another.
      • Some of the copies are transposable elements and some are related sequences that have lost the ability to move.
      • Transposable elements and related sequences make up 25–50% of most mammalian genomes, and an even higher percentage in amphibians and angiosperms.
    • In primates, a large portion of transposable element–related DNA consists of a family of similar sequences called Alu elements.
      • These sequences account for approximately 10% of the human genome.
      • Alu elements are about 300 nucleotides long, shorter than most functional transposable elements, and they do not code for protein.
      • Many Alu elements are transcribed into RNA molecules.
      • However, their cellular function is unknown.
    • Repetitive DNA that is not related to transposable elements probably arose by mistakes that occurred during DNA replication or recombination.
      • Repetitive DNA accounts for about 15% of the human genome.
      • Five percent of the human genome consists of large-segment duplications in which 10,000 to 300,000 nucleotide pairs seem to have been copied from one chromosomal location to another.
    • Simple sequence DNA contains many copies of tandemly repeated short sequences of 15–500 nucleotides.
      • There may be as many as several hundred thousand repetitions of a nucleotide sequence.
      • Simple sequence DNA makes up 3% of the human genome.
      • Much of the genome’s simple sequence DNA is located at chromosomal telomeres and centromeres, suggesting that it plays a structural role.
        • The DNA at centromeres is essential for the separation of chromatids in cell division and may also help to organize the chromatin within the interphase nucleus.
        • Telomeric DNA prevents gene loss as DNA shortens with each round of replication and also binds proteins that protect the ends of a chromosome from degradation or attachment to other chromosomes.

      Gene families have evolved by duplication of ancestral genes.

    • Sequences coding for proteins and structural RNAs compose a mere 1.5% of the human genome.
      • If introns and regulatory sequences are included, gene-related DNA makes up 25% of the human genome.
    • In humans, solitary genes present in one copy per haploid set of chromosomes make up only half of the total coding DNA.
    • The rest occurs in multigene families, collections of identical or very similar genes.
    • Some multigene families consist of identical DNA sequences that may be clustered tandemly.
      • These code for RNA products or for histone proteins.
      • For example, the three largest rRNA molecules are encoded in a single transcription unit that is repeated tandemly hundreds to thousands of times.
      • This transcript is cleaved to yield three rRNA molecules that combine with proteins and one other kind of rRNA to form ribosomal subunits.
    • Two related families of nonidentical genes encode globins, a group of proteins that include the α (alpha) and β (beta) polypeptide sequences of hemoglobin.
    • The different versions of each globin subunit are expressed at different times in development, allowing hemoglobin to function effectively in the changing environment of the developing animal.
      • Within both the ? and ? families are sequences that are expressed during the embryonic, fetal, and/or adult stage of development.
      • In humans, the embryonic and fetal hemoglobins have higher affinity for oxygen than do adult forms, ensuring transfer of oxygen from mother to developing fetus.
      • Also found in the globin gene family clusters are several pseudogenes, DNA sequences similar to real genes that do not yield functional proteins.

    Concept 19.5 Duplications, rearrangements, and mutations of DNA contribute to genome evolution

    • The earliest forms of life likely had a minimal number of genes, including only those necessary for survival and reproduction.
    • The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification.
    • An accident in meiosis can result in one or more extra sets of chromosomes, a condition known as polyploidy.
      • In a polyploid organism, one complete set of genes can provide essential functions for the organism.
      • The genes in the extra set may diverge by accumulating mutations.
        • These variations may persist if the organism carrying them survives and reproduces.
      • In this way, genes with novel functions may evolve.
    • Errors during meiosis due to unequal crossing over during Prophase I can lead to duplication of individual genes.
    • Slippage during DNA replication can result in deletion or duplication of DNA regions.
      • Such errors can lead to regions of repeats, such as simple sequence DNA.
    • Major rearrangements of at least one set of genes occur during immune system differentiation.
    • Duplication events can lead to the evolution of genes with related functions, such as the a-globin and b-globin gene families.
      • A comparison of gene sequences within a multigene family indicates that they all evolved from one common ancestral globin gene, which was duplicated and diverged about 450–500 million years ago.
    • After the duplication events, the differences between the genes in the d family arose from mutations that accumulated in the gene copies over many generations.
      • The necessary function provided by an ?-globin protein was fulfilled by one gene, while other copies of the ?-globin gene accumulated random mutations.
      • Some mutations may have altered the function of the protein product in ways that were beneficial to the organism without changing its oxygen-carrying function.
    • The similarity in the amino acid sequences of the various ?-globin and ?-globin proteins supports this model of gene duplication and mutation.
      • Random mutations accumulating over time in the pseudogenes have destroyed their function.
      • In other gene families, one copy of a duplicated gene can undergo alterations that lead to a completely new function for the protein product.
      • The genes for lysozyme and ?-lactalbumin are good examples.
        • Lysozyme is an enzyme that helps prevent infection by hydrolyzing bacterial cell walls.
        • ??????-lactalbumin is a nonenzymatic protein that plays a role in mammalian milk production.
      • Both genes are found in mammals, while only lysozyme is found in birds.
        • The two proteins are similar in their amino acids sequences and 3-D structures.
      • These findings suggest that at some time after the bird and mammalian lineage had separated, the lysozyme gene underwent a duplication event in the mammalian lineage but not in the avian lineage.
        • Subsequently, one copy of the duplicated lysozyme gene evolved into a gene encoding ?-lactalbumin, a protein with a completely different function.
      • Rearrangement of existing DNA sequences has also contributed to genome evolution.
        • The presence of introns in eukaryotic genes may have promoted the evolution of new and potentially useful proteins by facilitating the duplication or repositioning of exons in the genome.
        • A particular exon within a gene could be duplicated on one chromosome and deleted from the homologous chromosome.
        • The gene with the duplicated exon would code for a protein with a second copy of the encoded domain.
      • This change in the protein’s structure could augment its function by increasing its stability or altering its ability to bind a particular ligand.
      • Mixing and matching of different exons within or between genes owing to errors in meiotic recombination is called exon shuffling and could lead to new proteins with novel combinations of functions.
      • The persistence of transposable elements as a large percentage of eukaryotic genomes suggests that they play an important role in shaping a genome over evolutionary time.
      • These elements can contribute to evolution of the genome by promoting recombination, disrupting cellular genes or control elements, and carrying entire genes or individual exons to new locations.
      • The presence of homologous transposable element sequences scattered throughout the genome allows recombination to take place between different chromosomes.
        • Most of these alterations are likely detrimental, causing chromosomal translocations and other changes in the genome that may be lethal to the organism.
        • Over the course of evolutionary time, an occasional recombination may be advantageous.
        • The movement of transposable elements around the genome can have several direct consequences.
          • If a transposable element “jumps” into the middle of a coding sequence of a protein-coding gene, it prevents the normal functioning of that gene.
          • If a transposable element inserts within a regulatory sequence, it may increase or decrease protein production.
        • During transposition, a transposable element may transfer genes to a new position on the genome or may insert an exon from one gene into another gene.
        • Transposable elements can lead to new coding sequences when an Alu element hops into introns to create a weak alternative splice site in the RNA transcript.
          • Splicing will usually occur at the regular splice sites, producing the original protein.
          • Occasionally, splicing will occur at the new weak site.
        • In this way, alternative genetic combinations can be “tried out” while the function of the original gene product is retained.
        • These processes produce no effect or harmful effects in most individual cases.
        • However, over long periods of time, the generation of genetic diversity provides more raw material for natural selection to work on during evolution.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 19-1

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    Chapter 19 Eukaryotic Genomes90.5 KB
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    Chapter 20 - DNA Technology and Genomics

    Chapter 20 DNA Technology and Genomics
    Lecture Outline

    Overview: Understanding and Manipulating Genomes

    • One of the great achievements of modern science has been the sequencing of the human genome, which was largely completed by 2003.
    • Progress began with the development of techniques for making recombinant DNA, in which genes from two different sources—and often different species—are combined in vitro into the same molecule.
    • The methods for making recombinant DNA are central to genetic engineering, the direct manipulation of genes for practical purposes.
      • Applications include the introduction of a desired gene into the DNA of a host that will produce the desired protein.
    • DNA technology has launched a revolution in biotechnology, the manipulation of organisms or their components to make useful products.
      • Practices that go back centuries, such as the use of microbes to make wine and cheese and the selective breeding of livestock, are examples of biotechnology.
        • These techniques exploit naturally occurring mutations and genetic recombination.
    • Biotechnology based on the manipulation of DNA in vitro differs from earlier practices by enabling scientists to modify specific genes and move them between organisms as distinct as bacteria, plants, and animals.
    • DNA technology is now applied in areas ranging from agriculture to criminal law, but its most important achievements are in basic research.

    Concept 20.1 DNA cloning permits production of multiple copies of a specific gene or other DNA segment

    • To study a particular gene, scientists needed to develop methods to isolate the small, well-defined portion of a chromosome containing the gene of interest.
    • Techniques for gene cloning enable scientists to prepare multiple identical copies of gene-sized pieces of DNA.
    • One basic cloning technique begins with the insertion of a foreign gene into a bacterial plasmid.
      • E. coli and its plasmids are commonly used.
      • First, a foreign gene is inserted into a bacterial plasmid to produce a recombinant DNA molecule.
      • The plasmid is returned to a bacterial cell, producing a recombinant bacterium, which reproduces to form a clone of identical cells.
      • Every time the bacterium reproduces, the recombinant plasmid is replicated as well.
      • Under suitable conditions, the bacterial clone will make the protein encoded by the foreign gene.
    • The potential uses of cloned genes fall into two general categories.
      • First, the goal may be to produce a protein product.
        • For example, bacteria carrying the gene for human growth hormone can produce large quantities of the hormone.
      • Alternatively, the goal may be to prepare many copies of the gene itself.
        • This may enable scientists to determine the gene’s nucleotide sequence or provide an organism with a new metabolic capability by transferring a gene from another organism.
      • Most protein-coding genes exist in only one copy per genome, so the ability to clone rare DNA fragments is very valuable.

      Restriction enzymes are used to make recombinant DNA.

    • Gene cloning and genetic engineering were made possible by the discovery of restriction enzymes that cut DNA molecules at specific locations.
    • In nature, bacteria use restriction enzymes to cut foreign DNA, to protect themselves against phages or other bacteria.
      • They work by cutting up the foreign DNA, a process called restriction.
    • Most restriction enzymes are very specific, recognizing short DNA nucleotide sequences and cutting at specific points in these sequences.
      • Bacteria protect their own DNA by methylating the sequences recognized by these enzymes.
    • Each restriction enzyme cleaves a specific sequence of bases or restriction site.
      • These are often a symmetrical series of four to eight bases on both strands running in opposite directions.
        • If the restriction site on one strand is 3’-CTTAAG-5’, the complementary strand is 5’-GAATTC-3’.
    • Because the target sequence usually occurs (by chance) many times on a long DNA molecule, an enzyme will make many cuts.
      • Copies of a DNA molecule will always yield the same set of restriction fragments when exposed to a specific enzyme.
    • Restriction enzymes cut covalent sugar-phosphate backbones of both strands, often in a staggered way that creates single-stranded sticky ends.
      • These extensions can form hydrogen-bonded base pairs with complementary single-stranded stretches (sticky ends) on other DNA molecules cut with the same restriction enzyme.
    • These DNA fusions can be made permanent by DNA ligase, which seals the strand by catalyzing the formation of covalent bonds to close up the sugar-phosphate backbone.
    • Restriction enzymes and DNA ligase can be used to make a stable recombinant DNA molecule, with DNA that has been spliced together from two different organisms.

      Eukaryotic genes can be cloned in bacterial plasmids.

    • Recombinant plasmids are produced by splicing restriction fragments from foreign DNA into plasmids.
      • The original plasmid used to produce recombinant DNA is called a cloning vector, defined as a DNA molecule that can carry foreign DNA into a cell and replicate there.
    • Bacterial plasmids are widely used as cloning vectors for several reasons.
      • They can be easily isolated from bacteria, manipulated to form recombinant plasmids by in vitro insertion of foreign DNA, and then reintroduced into bacterial cells.
    • Bacterial cells carrying the recombinant plasmid reproduce rapidly, replicating the inserted foreign DNA.
    • The process of cloning a human gene in a bacterial plasmid can be divided into six steps.
      1. The first step is the isolation of vector and gene-source DNA.
        • The source DNA comes from human tissue cells grown in lab culture.
        • The source of the plasmid is typically E. coli.
        • This plasmid carries two useful genes, ampR, conferring resistance to the antibiotic ampicillin and lacZ, encoding the enzyme ß-galactosidase that catalyzes the hydrolysis of sugar.
        • The plasmid has a single recognition sequence, within the lacZ gene, for the restriction enzyme used.
      2. DNA is inserted into the vector.
        • Both the plasmid and human DNA are digested with the same restriction enzyme. The enzyme cuts the plasmid DNA at its single restriction site within the lacZ gene. It cuts the human DNA at many sites, generating thousands of fragments. One fragment carries the human gene of interest. All the fragments—bacterial and human—have complementary sticky ends.
      3. The human DNA fragments are mixed with the cut plasmids, and base-pairing takes place between complementary sticky ends.
        • DNA ligase is added to permanently join the base-paired fragments.
        • Some of the resulting recombinant plasmids contain human DNA fragments.
      4. The recombinant plasmids are mixed with bacteria that are lacZ?, unable to hydrolyze lactose.
        • This creates a diverse pool of bacteria: some bacteria that have taken up the desired recombinant plasmid DNA, and other bacteria that have taken up other DNA, both recombinant and nonrecombinant.
      5. The transformed bacteria are plated on a solid nutrient medium containing ampicillin and a molecular mimic of lactose called X-gal.
        • Only bacteria that have the ampicillin-resistance (ampR) plasmid will grow.
        • Each reproducing bacterium forms a clone by repeating cell divisions, generating a colony of cells on the agar.
        • The lactose mimic in the medium is used to identify plasmids that carry foreign DNA.
        • Bacteria with plasmids lacking foreign DNA stain blue when ß-galactosidase from the intact lacZ gene hydrolyzes X-gal.
        • Bacteria with plasmids containing foreign DNA inserted into the lacZ gene are white because they lack ß-galactosidase.
      6. Cell clones with the right gene are identified.
    • In the final step, thousands of bacterial colonies with foreign DNA must be sorted through to find those containing the gene of interest.
    • One technique, nucleic acid hybridization, depends on base-pairing between the gene and a complementary sequence, a nucleic acid probe, on another nucleic acid molecule.
      • The sequence of the RNA or DNA probe depends on knowledge of at least part of the sequence of the gene of interest.
      • A radioactive or fluorescent tag is used to label the probe.
      • The probe will hydrogen-bond specifically to complementary single strands of the desired gene.
      • After denaturating (separating) the DNA strands in the bacterium, the probe will bind with its complementary sequence, tagging colonies with the targeted gene.

    Cloned genes are stored in DNA libraries.

    • In the “shotgun” cloning approach described above, a mixture of fragments from the entire genome is included in thousands of different recombinant plasmids.
    • A complete set of recombinant plasmid clones, each carrying copies of a particular segment from the initial genome, forms a genomic library.
      • The library can be saved and used as a source of other genes or for gene mapping.
    • In addition to plasmids, certain bacteriophages are also common cloning vectors for making genomic libraries.
      • Fragments of foreign DNA can be spliced into a phage genome using a restriction enzyme and DNA ligase.
      • An advantage of using phage as vectors is that phage can carry larger DNA inserts than plasmids can.
      • The recombinant phage DNA is packaged in a capsid in vitro and allowed to infect a bacterial cell.
      • Infected bacteria produce new phage particles, each with the foreign DNA.
    • A more limited kind of gene library can be developed by starting with mRNA extracted from cells.
    • The enzyme reverse transcriptase is used to make single-stranded DNA transcripts of the mRNA molecules.
    • The mRNA is enzymatically digested, and a second DNA strand complementary to the first is synthesized by DNA polymerase.
      • This double-stranded DNA, called complementary DNA (cDNA), is modified by the addition of restriction sites at each end.
      • Finally, the cDNA is inserted into vector DNA.
      • A cDNA library represents that part of a cell’s genome that was transcribed in the starting cells.
        • This is an advantage if a researcher wants to study the genes responsible for specialized functions of a particular kind of cell.
        • By making cDNA libraries from cells of the same type at different times in the life of an organism, one can trace changes in the patterns of gene expression.
    • If a researcher wants to clone a gene but is unsure in what cell type it is expressed or unable to obtain that cell type, a genomic library will likely contain the gene.
    • A researcher interested in the regulatory sequences or introns associated with a gene will need to obtain the gene from a genomic library.
      • These sequences are missing from the processed mRNAs used in making a cDNA library.

      Eukaryote genes can be expressed in prokaryotic host cells.

    • A clone can sometimes be screened for a desired gene based on detection of its encoded protein.
    • Inducing a cloned eukaryotic gene to function in a prokaryotic host can be difficult.
      • One way around this is to insert an expression vector, a cloning vector containing a highly active prokaryotic promoter, upstream of the restriction site.
      • The prokaryotic host will then recognize the promoter and proceed to express the foreign gene that has been linked to it.
      • Such expression vectors allow the synthesis of many eukaryotic proteins in prokaryotic cells.
    • The presence of long noncoding introns in eukaryotic genes may prevent correct expression of these genes in prokaryotes, which lack RNA-splicing machinery.
      • This problem can be surmounted by using a cDNA form of the gene inserted in a vector containing a bacterial promoter.
    • Molecular biologists can avoid incompatibility problems by using eukaryotic cells as hosts for cloning and expressing eukaryotic genes.
      • Yeast cells, single-celled fungi, are as easy to grow as bacteria and, unlike most eukaryotes, have plasmids.
    • Scientists have constructed yeast artificial chromosomes (YACs) that combine the essentials of a eukaryotic chromosome (an origin site for replication, a centromere, and two telomeres) with foreign DNA.
      • These chromosome-like vectors behave normally in mitosis and can carry more DNA than a plasmid.
    • Another advantage of eukaryotic hosts is that they are capable of providing the posttranslational modifications that many proteins require.
      • Such modifications may include adding carbohydrates or lipids.
      • For some mammalian proteins, the host must be an animal cell to perform the necessary modifications.
    • Many eukaryotic cells can take up DNA from their surroundings, but inefficiently.
    • Several techniques facilitate entry of foreign DNA into eukaryotic cells.
      • In electroporation, brief electrical pulses create a temporary hole in the plasma membrane through which DNA can enter.
      • Alternatively, scientists can inject DNA into individual cells using microscopically thin needles.
      • Once inside the cell, the DNA is incorporated into the cell’s DNA by natural genetic recombination.

      The polymerase chain reaction (PCR) amplifies DNA in vitro.

    • DNA cloning is the best method for preparing large quantities of a particular gene or other DNA sequence.
    • When the source of DNA is scanty or impure, the polymerase chain reaction (PCR) is quicker and more selective.
    • This technique can quickly amplify any piece of DNA without using cells.
    • The DNA is incubated in a test tube with special DNA polymerase, a supply of nucleotides, and short pieces of single-stranded DNA as a primer.
    • PCR can make billions of copies of a targeted DNA segment in a few hours.
      • This is faster than cloning via recombinant bacteria.
    • In PCR, a three-step cycle—heating, cooling, and replication—brings about a chain reaction that produces an exponentially growing population of identical DNA molecules.
      • The reaction mixture is heated to denature the DNA strands.
      • The mixture is cooled to allow hydrogen-bonding of short, single-stranded DNA primers complementary to sequences on opposite sides at each end of the target sequence.
      • A heat-stable DNA polymerase extends the primers in the 5’ --> 3’ direction.
    • If a standard DNA polymerase were used, the protein would be denatured along with the DNA during the heating step.
    • The key to easy PCR automation was the discovery of an unusual DNA polymerase, isolated from prokaryotes living in hot springs, which can withstand the heat needed to separate the DNA strands at the start of each cycle.
    • PCR is very specific.
    • By their complementarity to sequences bracketing the targeted sequence, the primers determine the DNA sequence that is amplified.
      • PCR can make many copies of a specific gene before cloning in cells, simplifying the task of finding a clone with that gene.
      • PCR is so specific and powerful that only minute amounts of partially degraded DNA need be present in the starting material.
    • Occasional errors during PCR replication impose limits to the number of good copies that can be made when large amounts of a gene are needed.
      • Increasingly, PCR is used to make enough of a specific DNA fragment to clone it merely by inserting it into a vector.
    • Devised in 1985, PCR has had a major impact on biological research and technology.
      • PCR has amplified DNA from a variety of sources:
        • Fragments of ancient DNA from a 40,000-year-old frozen woolly mammoth.
        • DNA from footprints or tiny amounts of blood or semen found at the scenes of violent crimes.
        • DNA from single embryonic cells for rapid prenatal diagnosis of genetic disorders.
        • DNA of viral genes from cells infected with HIV.

    Concept 20.2 Restriction fragment analysis detects DNA differences that affect restriction sites

    • Once we have prepared homogeneous samples of DNA, each containing a large number of identical segments, we can begin to ask some interesting questions about specific genes and their functions.
      • Does a particular gene differ from person to person?
      • Are certain alleles associated with a hereditary disorder?
      • Where in the body and when during development is a gene expressed?
      • What is the location of a gene in the genome?
      • Is expression of a particular gene related to expression of other genes?
      • How has a gene evolved, as revealed by interspecific comparisons?
    • To answer these questions, we need to know the nucleotide sequence of the gene and its counterparts in other individuals and species, as well as its expression pattern.
    • One indirect method of rapidly analyzing and comparing genomes is gel electrophoresis.
      • Gel electrophoresis separates macromolecules—nucleic acids or proteins—on the basis of their rate of movement through a gel in an electrical field.
        • Rate of movement depends on size, electrical charge, and other physical properties of the macromolecules.
    • In restriction fragment analysis, the DNA fragments produced by restriction enzyme digestion of a DNA molecule are sorted by gel electrophoresis.
      • When the mixture of restriction fragments from a particular DNA molecule undergoes electrophoresis, it yields a band pattern characteristic of the starting molecule and the restriction enzyme used.
      • The relatively small DNA molecules of viruses and plasmids can be identified simply by their restriction fragment patterns.
      • The separated fragments can be recovered undamaged from gels, providing pure samples of individual fragments.
    • We can use restriction fragment analysis to compare two different DNA molecules representing, for example, different alleles of a gene.
      • Because the two alleles differ slightly in DNA sequence, they may differ in one or more restriction sites.
      • If they do differ in restriction sites, each will produce different-sized fragments when digested by the same restriction enzyme.
      • In gel electrophoresis, the restriction fragments from the two alleles will produce different band patterns, allowing us to distinguish the two alleles.
    • Restriction fragment analysis is sensitive enough to distinguish between two alleles of a gene that differ by only one base pair in a restriction site.
    • A technique called Southern blotting combines gel electrophoresis with nucleic acid hybridization.
      • Although electrophoresis will yield too many bands to distinguish individually, we can use nucleic acid hybridization with a specific probe to label discrete bands that derive from our gene of interest.
    • The probe is a radioactive single-stranded DNA molecule that is complementary to the gene of interest.
      • Southern blotting reveals not only whether a particular sequence is present in the sample of DNA, but also the size of the restriction fragments that contain the sequence.
    • One of its many applications is to identify heterozygous carriers of mutant alleles associated with genetic disease.
    • In the example below, we compare genomic DNA samples from three individuals: an individual who is homozygous for the normal ß-globin allele, a homozygote for sickle-cell allele, and a heterozygote.
    • We combine several molecular techniques to compare DNA samples from three individuals.
      1. We start by adding the same restriction enzyme to each of the three samples to produce restriction fragments.
      2. We then separate the fragments by gel electrophoresis.
      3. We transfer the DNA fragments from the gel to a sheet of nitrocellulose paper, still separated by size.
        • This also denatures the DNA fragments.
      4. Bathing the sheet in a solution containing a radioactively labeled probe allows the probe to attach by base-pairing to the DNA sequence of interest.
      5. We can visualize bands containing the label with autoradiography.
    • The band pattern for the heterozygous individual will be a combination of the patterns for the two homozygotes.

      Restriction fragment length differences are useful as genetic markers.

    • Restriction fragment analysis can be used to examine differences in noncoding DNA as well.
    • Differences in DNA sequence on homologous chromosomes that produce different restriction fragment patterns are scattered abundantly throughout genomes, including the human genome.
    • A restriction fragment length polymorphism (RFLP or Rif-lip) can serve as a genetic marker for a particular location (locus) in the genome.
    • RFLPs are detected and analyzed by Southern blotting, frequently using the entire genome as the DNA starting material.
      • The probe is complementary to the sequence under consideration.
    • Because RFLP markers are inherited in a Mendelian fashion, they can serve as genetic markers for making linkage maps.
      • The frequency with which two RFPL markers—or an RFLP marker and a certain allele for a gene—are inherited together is a measure of the closeness of the two loci on a chromosome.

    Concept 20.3 Entire genomes can be mapped at the DNA level

    • The field of genomics is based on comparisons among whole sets of genes and their interactions.
    • As early as 1980, Daniel Botstein and his colleagues proposed that the DNA variations reflected in RFLPs could serve as the basis of an extremely detailed map of the entire human genome.
      • Since then, researchers have used such markers in conjunction with the tools and techniques of DNA technology to develop detailed maps of the genomes of a number of species.
    • The most ambitious research project made possible by DNA technology has been the sequencing of the human genome, officially begun as the Human Genome Project in 1990.
      • This effort was largely completed in 2003 when the nucleotide sequence of the vast majority of DNA in the human genome was obtained.
      • An international, publicly funded consortium of researchers at universities and research institutes has taken this project through three stages that provided progressively more detailed views of the human genome: genetic (linkage) mapping, physical mapping, and DNA sequencing.
    • In addition to mapping human DNA, the genomes of other organisms important to biological research are also being mapped.
      • Completed sequences include those of E. coli and other prokaryotes, Saccharomyces cerevisiae (yeast), Drosophila melanogaster (fruit fly), Mus musculus (mouse), and others.
    • These genomes are providing important insights of general biological significance.
    • In mapping a large genome, cytogenetic maps based on karyotyping and fluorescence hybridization provide a starting point for more detailed mapping.
      • The first stage is to construct a linkage map of several thousand markers spaced throughout the chromosomes.
      • The order of the markers and the relative distances between them on such a map are based on recombination frequencies.
      • The markers can be genes or any other identifiable sequences in DNA, such as RFLPs or simple sequence DNA.
    • The human map with 5,000 genetic markers enabled researchers to locate other markers, including genes, by testing for genetic linkage with the known markers.
    • The next step was converting the relative distances to some physical measure, usually the number of nucleotides along the DNA.
    • For whole-genome mapping, a physical map is made by cutting the DNA of each chromosome into identifiable restriction fragments and then determining the original order of the fragments.
      • The key is to make fragments that overlap and then use probes or automated nucleotide sequencing of the ends to find the overlaps.
    • When working with large genomes, researchers carry out several rounds of DNA cutting, cloning, and physical mapping.
      • The first cloning vector is often a yeast artificial chromosome (YAC), which can carry inserted fragments up to a million base pairs long, or a bacterial artificial chromosome (BAC), which can carry inserts of 100,000 to 500,000 base pairs.
      • After the order of these long fragments has been determined, each fragment is cut into pieces that are cloned in plasmids or phages, ordered, and finally sequenced.
    • The complete nucleotide sequence of a genome is the ultimate map.
      • Starting with a pure preparation of many copies of a relatively short DNA fragment, the nucleotide sequence of the fragment can be determined by a sequencing machine.
      • The usual sequencing technique combines DNA labeling, DNA synthesis with special chain-terminating nucleotides, and high-resolution gel electrophoresis.
      • A major thrust of the Human Genome Project has been the development of technology for faster sequencing and more sophisticated computer software for analyzing and assembling the partial sequences.
    • One common method of sequencing DNA, the Sanger or dideoxyribonucleotide chain-termination method, is similar to PCR.
      • Inclusion of special dideoxyribonucleotides in the reaction mix ensures that rather than copying the whole template, fragments of various lengths will be synthesized.
      • These dideoxyribonucleotides, marked radioactively or fluorescently, terminate elongation when they are incorporated randomly into the growing strand because they lack a 3’-OH to attach the next nucleotide.
    • The order of these fragments via gel electrophoresis can be interpreted as the nucleotide sequence.
    • While the public consortium followed a hierarchical, three-stage approach for sequencing an entire genome, J. Craig Venter decided in 1992 to try a whole-genome shotgun approach.
      • This used powerful computers to assemble sequences from random fragments, skipping the first two steps.
    • The worth of his approach was demonstrated in 1995 when he and colleagues reported the complete sequence of a bacterium.
    • His private company, Celera Genomics, finished the sequence of Drosophila melanogaster in 2000.
    • In February 2001, Celera and the public consortium separately announced sequencing more than 90% of the human genome.
    • Sequencing of the human genome is now virtually complete, although some gaps remain to be mapped.
      • Areas with repetitive DNA and certain parts of the chromosomes of multicellular organisms resist detailed mapping by the usual methods.
    • On one level, genome sequences of humans and other organisms are simply lists of nucleotide bases.
      • On another level, analyses of these sequences and comparisons between species are leading to exciting discoveries.

    Concept 20.4 Genome sequences provide clues to important biological questions

    • Genomics, the study of genomes and their interactions, is yielding new insights into fundamental questions about genome organization, the regulation of gene expression, growth and development, and evolution.
    • Rather than inferring genotype from phenotype as classical geneticists did, molecular geneticists can study genes directly.
      • This approach poses the challenge of determining phenotype from genotype.
      • Starting with a long DNA sequence, how does a researcher recognize genes and determine their function?
    • DNA sequences are collected in computer data banks that are available via the Internet to researchers everywhere.
    • Special software scans the sequences for the telltale signs of protein-coding genes, looking for start and stop signals, RNA-splicing sites, and other features.
    • The software also looks for expressed sequence tags (ESTs), sequences similar to those in known genes.
      • From these clues, researchers collect a list of gene candidates.
    • Although genome size increases from prokaryotes to eukaryotes, it does not always correlate with biological complexity among eukaryotes.
      • One flowering plant has a genome 40 times the size of the human genome.
    • An organism may have fewer genes than expected from the size of its genome.
      • The estimated number of human genes is 25,000 or fewer, only about one-and-a-half times the number found in the fruit fly.
      • This is surprising, given the great diversity of cell types in humans.
    • Genes account for only a small fraction of the human genome.
      • Much of the enormous amount of noncoding DNA in the human genome consists of repetitive DNA and unusually long introns.
    • By doing more mixing and matching of modular elements, humans—and vertebrates in general—reach greater complexity than flies or worms.
      • Gene expression is regulated in more subtle and complicated ways in vertebrates than in other organisms.
      • The typical human gene specifies several different polypeptides by using different combinations of exons.
        • Nearly all human genes contain multiple exons, and an estimated 75% of these multiexon genes are alternatively spliced.
        • Along with this is additional polypeptide diversity via posttranslational processing.
        • There are a much greater number of possible interactions between gene products as a result of greater polypeptide diversity.
    • About half of the human genes were already known before the Human Genome Project.
    • To determine what the others are and what they may do, scientists compare the sequences of new gene candidates with those of known genes.
      • In some cases, the sequence of a new gene candidate will be similar in part to that of a known gene, suggesting similar function.
      • In other cases, the new sequences will be similar to a sequence encountered before, but of unknown function.
      • In still other cases, the sequence is entirely unlike anything ever seen before.
        • About 30% of the E. coli genes are new to us.
    • How can scientists determine the function of new genes identified by genome sequencing and comparative analysis?
    • One way to determine their function is to disable the gene and observe the consequences.
      • Using in vitro mutagenesis, specific mutations are introduced into a cloned gene, altering or destroying its function.
      • When the mutated gene is returned to the cell, it may be possible to determine the function of the normal gene by examining the phenotype of the mutant.
      • Researchers may put a mutated gene into cells from the early embryo of an organism to study the role of the gene in development and functioning of the whole organisms.
    • In nonmammalian organisms, a simpler and faster method, RNA interference (RNAi), has been applied to silence the expression of selected genes.
      • This method uses synthetic double-stranded RNA molecules matching the sequences of a particular gene to trigger breakdown of the gene’s mRNA.
      • The RNAi technique has had limited success in mammalian cells but has been valuable in analyzing the functions of genes in nematodes and fruit flies.
      • In one study, RNAi was used to prevent expression of 86% of the genes in early nematode embryos, one gene at a time.
      • Analysis of the phenotypes of the worms that developed from these embryos allowed the researchers to group most of the genes into functional groups.
    • A major goal of genomics is to learn how genes act together to produce a functioning organism.
      • Part of the explanation for how humans get along with so few genes probably lies in the unusual complexity of networks of interactions among genes and their products.
    • As the sequences of entire genomes of several organisms neared completion, some researchers began to investigate which genes are transcribed under different situations.
    • They also looked for groups of genes that are expressed in a coordinated pattern to identify global patterns or networks of expression.
    • The basic strategy in global expression is to isolate mRNAs from particular cells and use the mRNA as a template to build cDNA by reverse transcription.
      • Each cDNA can be compared to other collections of DNA by hybridization.
      • This will reveal which genes are active at different developmental stages, in different tissues, or in tissues in different states of health.
    • Automation has allowed scientists to detect and measure the expression of thousands of genes at one time using DNA microarray assays.
      • Tiny amounts of a large number of single-stranded DNA fragments representing different genes are fixed on a glass slide in a tightly spaced grid (array).
        • The array is called a DNA chip.
      • The fragments, sometimes representing all the genes of an organism, are tested for hybridization with various samples of fluorescently labeled cDNA molecules.
    • Spots where any of the cDNA hybridizes fluoresce with an intensity indicating the relative amount of the mRNA that was in the tissue.
    • Ultimately, information from microarray assays should provide us a grander view: how ensembles of genes interact to form a living organism.
      • DNA microarray assays are being used to compare cancerous versus noncancerous tissues.
        • This may lead to new diagnostic techniques and biochemically targeted treatments, as well as a fuller understanding of cancer.
    • The genomes of about 150 species have been completely or almost completely sequenced by the spring of 2004, with many more in progress.
      • Most of these are prokaryotes, including 20 archaean genomes.
      • Among the 20 eukaryotic species are vertebrates, invertebrates, and plants.
    • Comparisons of genome sequences from different species allow us to determine the evolutionary relationships even between distantly related organisms.
    • The more similar the nucleotide sequences between two species, the more closely related these species are in their evolutionary history.
    • Comparisons of the complete genome sequences of bacteria, archaea, and eukarya support the theory that these are the three fundamental domains of life.
    • Comparative genome studies confirm the relevance of research on simpler organisms to our understanding of human biology.
      • The yeast genome is proving useful in helping us to understand the human genome.
        • Comparisons of noncoding sequences in the human genome to those in the much smaller yeast genome revealed regions with highly conserved sequences that are important regulatory sequences in both species.
        • Several yeast protein-coding genes are so similar to certain human disease genes that researchers have figured out the functions of the disease genes by studying their normal yeast counterparts.
    • The genomes of two closely related species are likely to be similarly organized.
      • Once the sequence and organization of one genome is known, it can greatly accelerate the mapping of a related genome.
        • For example, the mouse genome can be mapped quickly, with the human genome serving as a guide.
    • The small number of gene differences between closely related species makes it easier to correlate phenotypic differences between species with particular genetic differences.
      • One gene that is clearly different in chimps and humans appears to function in speech.
      • Researchers may determine what a human disease gene does by studying its normal counterpart in mice, who share 80% of our genes.
    • The next step after mapping and sequencing genomes is proteomics, the systematic study of full protein sets (proteomes) encoded by genomes.
      • One challenge is the sheer number of proteins in humans and our close relatives because of alternative RNA splicing and posttranslational modifications.
      • Collecting all the proteins produced by an organism will be difficult because a cell’s proteins differ with cell type and its state.
      • Unlike DNA, proteins are extremely varied in structure and chemical and physical properties.
      • Because proteins are the molecules that actually carry out cell activities, we must study them to learn how cells and organisms function.
    • Complete catalogs of genes and proteins will change the discipline of biology dramatically.
      • With such catalogs in hand, researchers are turning their attention to the functional integration of individual components in biological systems.
    • Advances in bioinformatics, the application of computer science and mathematics to genetic and other biological information, will play a crucial role in dealing with the enormous mass of data.
    • These analyses will provide understanding of the spectrum of genetic variation in humans.
      • Because we are all probably descended from a small population living in Africa 150,000 to 200,000 years ago, the amount of DNA variation in humans is small.
      • Most of our diversity is in the form of single nucleotide polymorphisms (SNPs), single base-pair variations.
        • In humans, SNPs occur about once in 1,000 bases, meaning that any two humans are 99.9% identical.
      • The locations of the human SNP sites will provide useful markers for studying human evolution, the differences between human populations, and the migratory routes of human populations throughout history.
      • SNPs and other polymorphisms will be valuable markers for identifying disease genes and genes that influence our susceptibility to diseases, toxins, or drugs.
        • This will change the practice of 21st-century medicine.

    Concept 20.5 The practical applications of DNA technology affect our lives in many ways

      DNA technology is reshaping medicine and the pharmaceutical industry.

    • Modern biotechnology is making enormous contributions both to the diagnosis of diseases and in the development of pharmaceutical products.
      • The identification of genes whose mutations are responsible for genetic diseases may lead to ways to diagnose, treat, or even prevent these conditions.
      • Susceptibility to many “nongenetic” diseases, from arthritis to AIDS, is influenced by a person’s genes.
      • Diseases of all sorts involve changes in gene expression within the affected genes and within the patient’s immune system.
      • DNA technology can identify these changes and lead to the development of targets for prevention or therapy.
    • PCR and labeled nucleic acid probes can track down the pathogens responsible for infectious diseases.
      • For example, PCR can amplify and thus detect HIV DNA in blood and tissue samples, detecting an otherwise elusive infection.
      • RNA cannot be directly amplified by PCR.
      • The RNA genome is first converted to double-stranded cDNA by a technique called RT-PCR, using a probe specific for one of the HIV genes.
    • Medical scientists can use DNA technology to identify individuals with genetic diseases before the onset of symptoms, even before birth.
      • Genetic disorders are diagnosed by using PCR and primers corresponding to cloned disease genes, and then sequencing the amplified product to look for the disease-causing mutation.
        • Cloned disease genes include those for sickle-cell disease, hemophilia, cystic fibrosis, Huntington’s disease, and Duchenne muscular dystrophy.
        • It is even possible to identify symptomless carriers of these diseases.
    • It is possible to detect abnormal allelic forms of genes, even in cases in which the gene has not yet been cloned.
      • The presence of an abnormal allele can be diagnosed with reasonable accuracy if a closely linked RFLP marker has been found.
      • The closeness of the marker to the gene makes crossing over between them unlikely, and the marker and gene will almost always be inherited together.
    • Techniques for gene manipulation hold great potential for treating disease by gene therapy, the alteration of an afflicted individual’s genes.
      • A normal allele is inserted into somatic cells of a tissue affected by a genetic disorder.
      • For gene therapy of somatic cells to be permanent, the cells that receive the normal allele must be ones that multiply throughout the patient’s life.
    • Bone marrow cells, which include the stem cells that give rise to blood and immune system cells, are prime candidates for gene therapy.
      • A normal allele can be inserted by a retroviral vector into bone marrow cells removed from the patient.
      • If the procedure succeeds, the returned modified cells will multiply throughout the patient’s life and express the normal gene, providing missing proteins.
    • This procedure was used in a 2000 trial involving ten young children with SCID (severe combined immunodeficiency disease), a genetic disease in which bone marrow cells do not produce a vital enzyme because of a single defective gene.
      • Nine of the children showed significant improvement after two years.
      • However, two of the children developed leukemia.
        • It was discovered that the retroviral vector used to carry the normal allele into bone marrow cells had inserted near a gene involved in proliferation and development of blood cells, causing leukemia.
        • The trial has been suspended until researchers learn how to control the location of insertion of the retroviral vectors.
    • Gene therapy poses many technical questions.
      • These include regulation of the activity of the transferred gene to produce the appropriate amount of the gene product at the right time and place.
      • In addition, the insertion of the therapeutic gene must not harm other necessary cell functions.
    • Gene therapy raises some difficult ethical and social questions.
      • Some critics suggest that tampering with human genes, even for those with life-threatening diseases, is wrong.
      • They argue that this will lead to the practice of eugenics, a deliberate effort to control the genetic makeup of human populations.
    • The most difficult ethical question is whether we should treat human germ-line cells to correct the defect in future generations.
      • In laboratory mice, transferring foreign genes into egg cells is now a routine procedure.
      • Once technical problems relating to similar genetic engineering in humans are solved, we will have to face the question of whether it is advisable, under any circumstances, to alter the genomes of human germ lines or embryos.
      • Should we interfere with evolution in this way?
    • From a biological perspective, the elimination of unwanted alleles from the gene pool could backfire.
      • Genetic variation is a necessary ingredient for the survival of a species as environmental conditions change with time.
      • Genes that are damaging under some conditions could be advantageous under other conditions, as in the example of the sickle-cell allele.
    • DNA technology has been used to create many useful pharmaceuticals, mostly proteins.
    • By transferring the gene for a protein into a host that is easily grown in culture, one can produce large quantities of normally rare proteins.
      • By including highly active promoters (and other control elements) into vector DNA, the host cell can be induced to make large amounts of the product of a gene.
      • In addition, host cells can be engineered to secrete a protein, simplifying the task of purification.
    • One of the first practical applications of gene splicing was the production of mammalian hormones and other mammalian regulatory proteins in bacteria.
      • These include human insulin, human growth factor (HGF), and tissue plasminogen activator.
      • Human insulin, produced by bacteria, is superior for the control of diabetes to the older treatment of pig or cattle insulin.
      • Human growth hormone benefits children with hypopituitarism, a form of dwarfism.
      • Tissue plasminogen activator (TPA) helps dissolve blood clots and reduce the risk of future heart attacks.
        • Like many such drugs, it is expensive.
    • New pharmaceutical products are responsible for novel ways of fighting diseases that do not respond to traditional drug treatments.
      • One approach is to use genetically engineered proteins that either block or mimic surface receptors on cell membranes.
      • For example, one experimental drug mimics a receptor protein that HIV bonds to when entering white blood cells. HIV binds to the drug instead and fails to enter the blood cells.
    • DNA technology can also be used to produce vaccines, which stimulate the immune system to defend against specific pathogens.
      • A vaccine is a harmless variant or derivative of a pathogen that stimulates the immune system.
      • Traditional vaccines are either killed microbes or attenuated microbes that do not cause disease.
      • Both are similar enough to the active pathogen to trigger an immune response.
    • Recombinant DNA techniques can generate large amounts of a specific protein molecule normally found on the pathogen’s surface.
      • If this protein triggers an immune response against the intact pathogen, then it can be used as a vaccine.
      • Alternatively, genetic engineering can modify the genome of the pathogen to attenuate it.
        • These attenuated microbes are often more effective than a protein vaccine because they usually trigger a greater response by the immune system.
        • Pathogens attenuated by gene-splicing techniques may be safer than the natural mutants traditionally used.

      DNA technology offers forensic, environmental, and agricultural applications.

    • In violent crimes, blood, semen, or traces of other tissues may be left at the scene or on the clothes or other possessions of the victim or assailant.
    • If enough tissue is available, forensic laboratories can determine blood type or tissue type by using antibodies for specific cell surface proteins.
      • However, these tests require relatively large amounts of fresh tissue.
      • Also, this approach can only exclude a suspect.
    • DNA testing can identify the guilty individual with a much higher degree of certainty, because the DNA sequence of every person is unique (except for identical twins).
      • RFPL analysis by Southern blotting can detect similarities and differences in DNA samples and requires only a tiny amount of blood or other tissue.
      • Radioactive probes mark electrophoresis bands that contain certain RFLP markers.
      • As few as five markers from an individual can be used to create a DNA fingerprint.
      • The probability that two people who are not identical twins have the same DNA fingerprint is very small.
    • DNA fingerprints can be used forensically to present evidence to juries in murder trials.
      • An autoradiograph of RFLP bands of samples from a murder victim, the defendant, and the defendant’s clothes may be consistent with the conclusion that the blood on the clothes is from the victim, not the defendant.
    • The forensic use of DNA fingerprinting extends beyond violent crimes.
      • For instance, DNA fingerprinting can be used to settle conclusively questions of paternity.
      • DNA fingerprinting recently provided strong evidence that Thomas Jefferson fathered at lease one of the children of his slave Sally Hemings.
      • These techniques can also be used to identify the remains of individuals killed in natural or man-made disasters.
    • Variations in the lengths of repeated base sequences are increasingly used as markers in DNA fingerprinting.
      • Such polymorphic genetic loci have repeating units of only a few base pairs and are highly variable from person to person.
      • Individuals may vary in the numbers of simple tandem repeats (STRs) at a locus.
      • Restriction fragments with STRs vary in size among individuals because of differences in STR lengths.
      • PCR is often used to amplify selectively particular STRs or other markers before electrophoresis, especially if the DNA is poor or in minute quantities.
    • The DNA fingerprint of an individual would be truly unique if it were feasible to perform restriction fragment analysis on the entire genome.
      • In practice, forensic DNA tests focus on only about five tiny regions of the genome.
      • The probability that two people will have identical DNA fingerprints in these highly variable regions is typically between one in 100,000 and one in a billion.
      • The exact figure depends on the number of markers and the frequency of those markers in the population.
      • Despite problems that might arise from insufficient statistical data, human error, or flawed evidence, DNA fingerprinting is now accepted as compelling evidence.
    • Increasingly, genetic engineering is being applied to environmental work.
    • Scientists are engineering the metabolism of microorganisms to help cope with some environmental problems.
      • For example, genetically engineered microbes that can extract heavy metals from their environments and incorporate the metals into recoverable compounds may become important both in mining materials and cleaning up highly toxic mining wastes.
      • In addition to the normal microbes that participate in sewage treatment, new microbes that can degrade other harmful compounds are being engineered.
      • Bacterial strains have been developed that can degrade some of the chemicals released during oil spills.
    • For many years, scientists have been using DNA technology to improve agricultural productivity.
      • DNA technology is now routinely used to make vaccines and growth hormones for farm animals.
    • Transgenic organisms are made by introducing genes from one species into the genome of another organism.
      • An egg cell is removed from a female animal and fertilized in vitro.
      • Meanwhile, the desired gene is obtained from another organism and cloned.
      • The cloned DNA is injected directly into the nuclei of the fertilized egg.
      • Some of the cells integrate the transgene into their genomes and express the foreign gene.
      • The engineered embryos are surgically implanted in a surrogate mother.
    • Transgenic animals may be created to exploit the attributes of new genes (for example, genes for faster growth or larger muscles).
    • Other transgenic organisms are pharmaceutical “factories”—producers of large amounts of otherwise rare substances for medical use.
      • Transgenic farm mammals may secrete the gene product of interest in their milk.
      • Researchers have engineered transgenic chickens that express large quantities of the transgene’s product in their eggs.
    • The human proteins produced by farm animals may or may not be structurally identical to natural human proteins.
      • Therefore, they have to be tested very carefully to ensure that they will not cause allergic reactions or other adverse effects in patients receiving them.
      • In addition, the health and welfare of transgenic farm animals are important issues, as they often suffer from lower fertility or increased susceptibility to disease.
    • Agricultural scientists have engineered a number of crop plants with genes for desirable traits.
      • These include delayed ripening and resistance to spoilage and disease.
      • Because a single transgenic plant cell can be grown in culture to generate an adult plant, plants are easier to engineer than most animals.
    • The Ti plasmid, from the soil bacterium Agrobacterium tumefaciens, is often used to introduce new genes into plant cells.
      • The Ti plasmid normally integrates a segment of its DNA into its host plant and induces tumors.
    • Foreign genes can be inserted into the Ti plasmid (a version that does not cause disease) using recombinant DNA techniques.
      • The recombinant plasmid can be put back into Agrobacterium, which then infects plant cells, or introduced directly into plant cells.
    • Genetic engineering is quickly replacing traditional plant-breeding programs, especially for useful traits determined by one or a few genes, like herbicide or pest resistance.
      • Use of genetically modified crops has reduced the need for chemical insecticides.
    • Scientists are using gene transfer to improve the nutritional value of crop plants.
      • For example, a transgenic rice plant has been developed that produces yellow grains containing beta-carotene, which our bodies use to make vitamin A.
        • Large numbers of young people in southeast Asia are deficient in vitamin A, leading to vision impairment and increased disease rates.
    • DNA technology has led to new alliances between the pharmaceutical industry and agriculture.
      • Plants can be engineered to produce human proteins for medical use and viral proteins for use as vaccines.
      • Several such “pharm” products are in clinical trials, including vaccines for hepatitis B and an antibody that blocks the bacteria that cause tooth decay.
      • The advantage of pharm plants is that large amounts of proteins might be made more economically by plants than by cultured cells.

      DNA technology raises important safety and ethical questions.

    • The power of DNA technology has led to worries about potential dangers.
      • Early concerns focused on the possibility that recombinant DNA technology might create hazardous new pathogens.
    • In response, scientists developed a set of guidelines that have become formal government regulations in the United States and some other countries.
      • Strict laboratory procedures are designed to protect researchers from infection by engineered microbes and to prevent their accidental release.
      • Some strains of microorganisms used in recombinant DNA experiments are genetically crippled to ensure that they cannot survive outside the laboratory.
      • Finally, certain obviously dangerous experiments have been banned.
    • Today, most public concern centers on genetically modified (GM) organisms used in agriculture.
      • GM organisms have acquired one or more genes (perhaps from another species) by artificial means.
      • Salmon have been genetically modified by addition of a more active salmon growth hormone gene.
      • However, the majority of GM organisms in our food supply are not animals but crop plants.
    • In 1999, the European Union suspended the introduction of new GM crops pending new legislation.
      • Early in 2000, negotiators from 130 countries, including the United States, agreed on a Biosafety Protocol that requires exporters to identify GM organisms present in bulk food shipments.
    • Advocates of a cautious approach fear that GM crops might somehow be hazardous to human health or cause ecological harm.
      • In particular, transgenic plants might pass their new genes to close relatives in nearby wild areas through pollen transfer.
      • Transference of genes for resistance to herbicides, diseases, or insect pests may lead to the development of wild “superweeds” that would be difficult to control.
    • To date there is little good data either for or against any special health or environmental risks posed by genetically modified crops.
    • Today, governments and regulatory agencies are grappling with how to facilitate the use of biotechnology in agriculture, industry, and medicine while ensuring that new products and procedures are safe.
      • In the United States, all projects are evaluated for potential risks by various regulatory agencies, including the Food and Drug Administration, Environmental Protection Agency, the National Institutes of Health, and the Department of Agriculture.
      • These agencies are under increasing pressures from some consumer groups.
    • As with all new technologies, developments in DNA technology have ethical overtones.
      • Who should have the right to examine someone else’s genes?
      • How should that information be used?
      • Should a person’s genome be a factor in suitability for a job or eligibility for life insurance?
    • The power of DNA technology and genetic engineering demands that we proceed with humility and caution.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 20-21

    Subject: 
    Subject X2: 

    Chapter 21 - The Genetic Basis of Development

    Chapter 21 The Genetic Basis of Development
    Lecture Outline

    Overview: From Single Cell to Multicellular Organism

    • The application of genetic analysis and DNA technology to the study of development has brought about a revolution in our understanding of how a complex multicellular organism develops from a single cell.
      • In 1995, Swiss researchers identified a gene that functions as a master switch to trigger the development of the eye in Drosophila.
        • A similar gene triggers eye development in mammals.
      • Developmental biologists are discovering remarkable similarities in the mechanisms that shape diverse organisms.
    • While geneticists were advancing from Mendel’s laws to an understanding of the molecular basis of inheritance, developmental biologists were focusing on embryology.
      • Embryology is the study of the stages of development leading from fertilized egg to fully formed organism.
    • In recent years, the concepts and tools of molecular genetics have reached a point where a real synthesis of genetics and developmental biology has been possible.
    • When the primary research goal is to understand broad biological principles, the organism chosen for study is called a model organism.
      • Researchers select model organisms that are representative of a larger group, suitable for the questions under investigation, and easy to grow in the lab.
    • For study of the connections between genes and development, suitable model organisms have short generation times and small genomes that are suitable for genetic analysis.
      • Model organisms used in developmental genetics include the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, the mouse Mus musculus, the zebra fish Danio rerio, and the plant Arabidopsis thaliana.
    • The fruit fly Drosophila melanogaster was first chosen as a model organism by geneticist T. H. Morgan and intensively studied by generations of geneticists after him.
      • The fruit fly is small and easily grown in the laboratory.
      • It has a generation time of only two weeks and produces many offspring.
      • Embryos develop outside the mother’s body.
      • There are vast amounts of information on its genes and other aspects of its biology.
      • However, because first rounds of mitosis occur without cytokinesis, parts of its development are superficially quite different from that of other organisms.
      • Sequencing of the Drosophila genome was completed in 2000.
        • It has 180 × 106 base pairs (180 Mb) and contains about 13,700 genes.
    • The nematode Caenorhabditis elegans normally lives in the soil but is easily grown in petri dishes.
      • Only a millimeter long, it has a simple, transparent body with only a few cell types and grows from zygote to mature adult in only three and a half days.
      • Its genome has been sequenced. It is 97 Mb long and contains an estimated 19,000 genes.
      • Because individuals are hermaphrodites, it is easy to detect recessive mutations.
        • Self-fertilization of heterozygotes produces some homozygous recessive offspring with mutant phenotypes.
      • Every adult C. elegans has exactly 959 somatic cells.
        • These arise from the zygote in virtually the same way for every individual.
        • By following all cell divisions with a microscope, biologists have constructed the organism’s complete cell lineage, showing the ancestry of every cell in the adult body.
    • The mouse Mus musculus has a long history as a mammalian model of development.
      • Much is known about its biology.
      • The mouse genome is about 2,600 Mb long with about 25,000 genes, about the same as the human genome.
      • Researchers are adept at manipulating mouse genes to make transgenic mice and mice in which particular genes are “knocked out” by mutation.
      • Mice are complex animals with a genome as large as ours.
        • Their embryos develop in the mother’s uterus, hidden from view.
    • A second vertebrate model, the zebra fish Danio rerio, has some unique advantages.
      • These small fish (2–4 cm long) are easy to breed in the laboratory in large numbers.
      • The transparent embryos develop outside the mother’s body.
      • Although generation time is two to four months, the early stages of development proceed quickly.
        • By 24 hours after fertilization, most tissues and early versions of the organs have formed.
        • After two days, the fish hatches out of the egg case.
        • The zebra fish genome is estimated to be 1,700 Mb, and is still being mapped and sequenced.
    • For studying the molecular genetics of plant development, researchers are focusing on a small weed, Arabidopsis thaliana (a member of the mustard family).
      • One plant can grow and produce thousands of progeny after eight to ten weeks.
      • A hermaphrodite, each flower makes eggs and sperm.
      • For gene manipulation research, scientists can induce cultured cells to take up foreign DNA (genetic transformation).
      • Its relatively small genome, about 118 Mb, contains an estimated 25,500 genes.
    • In the development of most multicellular organisms, a single-celled zygote gives rise to cells of many different types.
      • Each type has a different structure and corresponding function.
    • Cells of similar types are organized into tissues, tissues into organs, organs into organ systems, and organ systems into the whole organism.
    • Thus, the process of embryonic development must give rise not only to cells of different types, but also to higher-level structures arranged in a particular way in three dimensions.

    Concept 21.1 Embryonic development involves cell division, cell differentiation, and morphogenesis

    • An organism arises from a fertilized egg cell as the result of three interrelated processes: cell division, cell differentiation, and morphogenesis.
    • Through a succession of mitotic cell divisions, the zygote gives rise to a large number of cells.
      • Cell division alone would produce only a great ball of identical cells.
    • During development, cells become specialized in structure and function, undergoing cell differentiation.
    • Different kinds of cells are organized into tissues and organs.
    • The physical processes that give an organism its shape constitute morphogenesis, the “creation of form.”
    • The processes of cell division, differentiation, and morphogenesis overlap during development.
    • Early events of morphogenesis lay out the basic body plan very early in embryonic development.
      • These include establishing the head of an animal embryo or the roots of a plant embryo.
      • Later morphogenetic events establish relative locations within smaller regions of the embryo, such as the digits on a vertebrate limb.
    • The overall schemes of morphogenesis in animals and plants are very different.
      • In animals, but not in plants, movements of cells and tissues are necessary to transform the embryo into the characteristic 3-D form of the organism.
      • In plants, morphogenesis and growth in overall size are not limited to embryonic and juvenile periods but occur throughout the life of the plant.
    • Apical meristems, perpetually embryonic regions in the tips of shoots and roots, are responsible for the plant’s continual growth and formation of new organs, such as leaves and roots.
    • In animals, ongoing development in adults is restricted to the generation of cells, such as blood cells, that must be continually replenished.

    Concept 21.2 Different cell types result from differential gene expression in cells with the same DNA

    • During differentiation and morphogenesis, embryonic cells behave and function in ways different from one another, even though all of them have arisen from the same zygote.
    • The differences between cells in a multicellular organism come almost entirely from differences in gene expression, not differences in the cell’s genomes.
    • These differences arise during development, as regulatory mechanisms turn specific genes off and on.

      Different types of cells in an organism have the same DNA.

    • Much evidence supports the conclusion that nearly all the cells of an organism have genomic equivalence—that is, they all have the same genes.
    • An important question that emerges is whether genes are irreversibly inactivated during differentiation.
    • One experimental approach to the question of genomic equivalence is to try to generate a whole organism from differentiated cells of a single type.
      • In many plants, whole new organisms can develop from differentiated somatic cells.
      • During the 1950s, F. C. Steward and his students found that differentiated root cells removed from the root could grow into normal adult plants when placed in a medium culture.
    • These cloning experiments produced genetically identical individuals, popularly called clones.
    • The fact that a mature plant cell can dedifferentiate (reverse its function) and give rise to all the different kinds of specialized cells of a new plant shows that differentiation does not necessarily involve irreversible changes in the DNA.
    • In plants, at least, cells can remain totipotent.
      • They retain the zygote’s potential to form all parts of the mature organism.
    • Plant cloning is now used extensively in agriculture.
    • Differentiated cells from animals often fail to divide in culture, much less develop into a new organism.
    • Animal researchers have approached the genomic equivalence question by replacing the nucleus of an unfertilized egg or zygote with the nucleus of a differentiated cell.
      • The pioneering experiments in nuclear transplantation were carried out by Robert Briggs and Thomas King in the 1950s and extended later by John Gordon in the 1980s.
      • They destroyed or removed the nucleus of a frog egg and transplanted a nucleus from an embryonic or tadpole cell from the same species into an enucleated egg.
    • The ability of the transplanted nucleus to support normal development is inversely related to the donor’s age.
      • Transplanted nuclei from relatively undifferentiated cells from an early embryo lead to the development of most eggs into tadpoles.
      • Transplanted nuclei from fully differentiated intestinal cells lead to fewer than 2% of the cells developing into normal tadpoles.
        • Most of the embryos failed to make it through even the earliest stages of development.
    • Developmental biologists agree on several conclusions about these results.
      • First, nuclei do change in some ways as cells differentiate.
        • While the DNA sequences do not change, histones may be modified or DNA may be methylated.
      • In frogs and most other animals, nuclear “potency” tends to be restricted more and more as embryonic development and cell differentiation progress.
        • However, chromatin changes are sometimes reversible, and the nuclei of most differentiated animal cells probably have all the genes required for making an entire organism.
    • The ability to clone mammals using nuclei or cells from early embryos has long been possible.
    • In 1997, Scottish researchers announced the birth of Dolly, a lamb cloned from an adult sheep by nuclear transplantation from a differentiated mammary cell.
    • The mammary cells were fused with sheep egg cells whose nuclei had been removed.
      • The resulting cells divided to form early embryos, which were implanted into surrogate mothers.
    • One of several hundred implanted embryos completed normal development.
    • In 2003, Dolly developed a lung disease usually seen in much older sheep and was euthanized.
      • Dolly’s premature death as well as her arthritis led to speculation that her cells were older than those of a normal sheep, possibly reflecting incomplete reprogramming of the original transplanted nucleus.
    • Since 1997, cloning has been demonstrated in numerous mammals, including mice, cats, cows, horses, and pigs.
    • The possibility of cloning humans raises unprecedented ethical issues.
      • In most cases, the goal is to produce new individuals.
      • This is known as reproductive cloning.
    • These experiments have led to some interesting results.
      • Cloned animals in the same species do not look or behave identically.
      • Clearly, environmental influences and random phenomena can play a significant role during development.
    • The successful cloning of various mammals raised interest in human cloning.
      • In early 2004, South Korean researchers reported success in the first step of reproductive cloning of humans.
      • Nuclei from differentiated human cells were transplanted into unfertilized enucleated eggs.
        • The eggs divided, and some embryos reached the blastocyst stage before development was halted.
    • In most nuclear transplantation studies, only a small percentage of cloned embryos develop normally to birth.
      • Like Dolly, many cloned animals have various defects, such as obesity, pneumonia, liver failure, and premature death.
    • In the nuclei of fully differentiated cells, a small subset of genes is turned on and the expression of the rest is repressed.
      • This regulation is often the result of epigenetic changes in chromatin, such as the acetylation of histones or the methylation of DNA.
      • Many of these changes must be reversed in the nucleus of the donor animal in order for genes to be expressed or repressed appropriately for early stages of development.
      • Researchers have found that the DNA in embryonic cells from cloned embryos, like that of differentiated cells, often has more methyl groups than does the DNA in equivalent cells from uncloned embryos of the same species.
      • Because DNA methylation helps regulate gene expression, methylated DNA of donor nuclei may interfere with the pattern of gene expression necessary for normal embryonic development.
    • Another hot research area involves stem cells.
      • A stem cell is a relatively unspecialized cell that can reproduce itself and, under appropriate conditions, differentiate into specialized cell types.
    • In addition to contributing to the study of differentiation, stem cell research has enormous potential in medicine.
      • The ultimate goal is to supply cells for the repair of damaged or diseased organs.
      • For example, providing insulin-producing pancreatic cells to diabetics or certain brain cells to individuals with Parkinson’s disease could cure these diseases.
    • Many early animal embryos contain totipotent stem cells, which can give rise to differentiated cells of any type.
      • In culture, these embryonic stem cells reproduce indefinitely and can differentiate into various specialized cells.
    • The adult body has various kinds of stem cells, which replace nonreproducing specialized cells.
      • Adult stem cells are said to be pluripotent, able to give rise to many, but not all, cell types.
        • For example, stem cells in the bone marrow give rise to all the different kinds of blood cells.
      • The adult brain contains stem cells that continue to produce certain kinds of nerve cells.
      • Although adult animals have only tiny numbers of stem cells, scientists are learning to identify, isolate, and culture these cells from various tissues.
        • Under some culture conditions, with the addition of specific growth factors, cultured adult stem cells can differentiate into multiple types of specialized cells.
      • Stem cells from early embryos are somewhat easier to culture than those from adults and can produce differentiated cells of any type.
        • Embryonic stem cells are currently obtained from embryos donated by parents undergoing fertility treatments, or from long-term cell cultures originally established with cells isolated from donated embryos.
        • Because the cells are derived from human embryos, their use raises ethical and political issues.
        • With the recent cloning of human embryos to the blastocyst stage, scientists might be able to use these clones as the source of embryonic stem cells in the future.
        • When the major aim of cloning is to produce embryonic stem cells to treat disease, the process is called therapeutic cloning.
          • Opinions vary about the morality of therapeutic cloning.

      Different cell types make different proteins, usually as a result of transcriptional regulation.

    • During embryonic development, cells become visibly different in structure and function as they differentiate.
    • The earliest changes that set a cell on a path to specialization show up only at the molecular level.
    • Molecular changes in the embryo drive the process, termed determination, which leads up to observable differentiation of a cell.
      • At the end of this process, an embryonic cell is irreversibly committed to its final fate.
      • If a determined cell is experimentally placed in another location in the embryo, it will differentiate as if it were in its original position.
    • The outcome of determination—cell differentiation—is caused by the expression of genes that encode tissue-specific proteins.
      • These give a cell its characteristic structure and function.
      • Differentiation begins with the appearance of mRNA and is finally observable in the microscope as changes in cellular structure.
    • In most cases, the pattern of gene expression in a differentiated cell is controlled at the level of transcription.
    • Cells produce the proteins that allow them to carry out their specialized roles in the organism.
      • For example, lens cells, and only lens cells, devote 80% of their capacity for protein synthesis to making just one type of protein, crystallin proteins.
        • These form transparent fibers that allow the lens to transmit and focus light.
      • Similarly, skeletal muscle cells have high concentrations of proteins specific to muscle tissues, such as a muscle-specific version of the contractile protein myosin and the structural protein actin.
        • They also have membrane receptor proteins that detect signals from nerve cells.
    • Muscle cells develop from embryonic precursors that have the potential to develop into a number of alternative cell types, including cartilage cells, fat cells, or multinucleate muscle cells.
      • As the muscle cells differentiate, they become myoblasts and begin to synthesize muscle-specific proteins.
      • They fuse to form mature, elongated, multinucleate skeletal muscle cells.
    • Researchers developed the hypothesis that certain muscle-specific regulatory genes are active in myoblasts, leading to muscle cell determination.
      • To test this, researchers isolated mRNA from cultured myoblasts and used reverse transcriptase to prepare a cDNA library containing all the genes that are expressed in cultured myoblasts.
      • Transplanting these cloned genes into embryonic precursor cells led to the identification of several “master regulatory genes” that, when transcribed and translated, commit the cells to become skeletal muscle.
    • One of these master regulatory genes is called myoD, a transcription factor.
      • myoD encodes MyoD protein, which binds to specific control elements and stimulates the transcription of various genes, including some that encode for other muscle-specific transcription factors.
        • These secondary transcription factors activate the muscle protein genes.
        • MyoD also stimulates expression of the myoD gene itself, perpetuating its effect in maintaining the cell’s differentiated state.
    • MyoD protein is capable of changing fully differentiated nonmuscle cells into muscle cells.
    • However, not all cells will transform.
      • Nontransforming cells may lack a combination of regulatory proteins, in addition to MyoD.

      Transcriptional regulation is directed by maternal molecules in the cytoplasm and signals from other cells.

    • Two sources of information “tell” a cell, such as a myoblast or even the zygote, which genes to express at any given time.
    • One source of information is the cytoplasm of the unfertilized egg cell, which contains RNA and protein molecules encoded by the mother’s DNA.
      • Messenger RNA, proteins, other substances, and organelles are distributed unevenly in the unfertilized egg.
      • This impacts embryonic development in many species.
    • Maternal substances that influence the course of early development are called cytoplasmic determinants.
      • These substances regulate the expression of genes that affect the developmental fate of the cell.
      • After fertilization, the cell nuclei resulting from mitotic division of the zygote are exposed to different cytoplasmic environments.
        • The set of cytoplasmic determinants a particular cell receives helps determine its developmental fate by regulating expression of the cell’s genes during the course of cell differentiation.
    • The other important source of developmental information is the environment around the cell, especially signals impinging on an embryonic cell from other nearby embryonic cells.
      • In animals, these include contact with cell-surface molecules on neighboring cells and the binding of growth factors secreted by neighboring cells.
      • In plants, the cell-cell junctions known as plasmodesmata allow signal molecules to pass from one cell to another.
        • The synthesis of these signals is controlled by the embryo’s own genes.
    • These signal molecules cause induction, triggering observable cellular changes by causing a change in gene expression in the target cell.

    Concept 21.3 Pattern formation in animals and plants results from similar genetic and cellular mechanisms

    • Before morphogenesis can shape an animal or plant, the organism’s body plan must be established.
    • Cytoplasmic determinants and inductive signals contribute to pattern formation, the development of spatial organization in which the tissues and organs of an organism are all in their characteristic places.
      • Pattern formation continues throughout the life of a plant in the apical meristems.
      • In animals, pattern formation is mostly limited to embryos and juveniles.
    • Pattern formation begins in the early embryo, when the major axes of an animal and the root-shoot axis of the plant are established.
      • The molecular cues that control pattern formation, positional information, tell a cell its location relative to the body axes and to neighboring cells.
      • They also determine how the cells and their progeny will respond to future molecular signals.

      Drosophila development is controlled by a cascade of gene activations.

    • Pattern formation has been most extensively studied in Drosophila melanogaster, where genetic approaches have had spectacular success.
      • These studies have established that genes control development and have identified the key roles that specific molecules play in defining position and directing differentiation.
      • Combining anatomical, genetic, and biochemical approaches in the study of Drosophila development, researchers have discovered developmental principles common to many other species, including humans.
    • Fruit flies and other arthropods have a modular construction, an ordered series of segments.
      • These segments make up the three major body parts: the head, thorax (with wings and legs), and abdomen.
      • Like other bilaterally symmetrical animals, Drosophila has an anterior-posterior axis and a dorsal-ventral axis.
        • Cytoplasmic determinants in the unfertilized egg provide positional information for the two developmental axes before fertilization.
      • After fertilization, positional information establishes a specific number of correctly oriented segments and finally triggers the formation of each segment’s characteristic structures.
      • The Drosophila egg cell develops in the female’s ovary, surrounded by ovarian cells called nurse cells and follicle cells that supply the egg cell with nutrients, mRNAs, and other substances needed for development.
    • Development of the fruit fly from egg cell to adult fly occurs in a series of discrete stages.
      1. Mitosis follows fertilization and egg laying.
        • Early mitosis occurs without growth of the cytoplasm and without cytokinesis, producing one big multinucleate cell.
      2. At the tenth nuclear division, the nuclei begin to migrate to the periphery of the embryo.
      3. At division 13, the cytoplasm partitions the 6,000 or so nuclei into separate cells.
        • The basic body plan—including body axes and segment boundaries—has already been determined by this time.
        • A central yolk nourishes the embryo, and the eggshell continues to protect it.
      4. Subsequent events in the embryo create clearly visible segments, which at first look very much alike.
      5. Some cells move to new positions, organs form, and a wormlike larva hatches from the shell.
        • During three larval stages, the larva eats, grows, and molts.
      6. During the third larval stage, the larva transforms into the pupa enclosed in a case.
      7. Metamorphosis, the change from larva to adult fly, occurs in the pupal case, and the fly emerges.
        • Each segment is anatomically distinct, with characteristic appendages.
    • The results of detailed anatomical observations of development in several species and experimental manipulations of embryonic tissues laid the groundwork for understanding the mechanisms of development.
    • In the 1940s, Edward B. Lewis demonstrated that the study of mutants could be used to investigate Drosophila development.
    • He studied bizarre developmental mutations and located the mutations on the fly’s genetic map.
    • This research provided the first concrete evidence that genes somehow direct the developmental process.
    • In the late 1970s, Christiane Nüsslein-Volhard and Eric Weischaus pushed the understanding of early pattern formation to the molecular level.
    • Their goal was to identify all the genes that affect segmentation in Drosophila, but they faced three problems.
      • Because Drosophila has about 13,700 genes, there could be only a few genes affecting segmentation or so many that the pattern would be impossible to discern.
      • Mutations that affect segmentation are likely to be embryonic lethals, leading to death at the embryonic or larval stage.
        • Because flies with embryonic lethal mutations never reproduce, they cannot be bred for study.
      • Because of maternal effects on axis formation in the egg, researchers also need to study maternal genes.
    • Nüsslein-Volhard and Wieschaus focused on recessive mutations that could be propagated in heterozygous flies.
      • After mutating flies, they looked for dead embryos and larvae with abnormal segmentation among the fly’s descendents.
      • Through appropriate crosses, they could identify living heterozygotes carrying embryonic lethal mutations.
      • They hoped that the segmental abnormalities would suggest how the affected genes normally functioned.
    • Nüsslein-Volhard and Wieschaus identified 1,200 genes essential for embryonic development.
      • About 120 of these were essential for pattern formation leading to normal segmentation.
      • After several years, they were able to group the genes by general function, map them, and clone many of them.
    • Their results, combined with Lewis’s early work, created a coherent picture of Drosophila development.
      • In 1995, Nüsslein-Volhard, Wieschaus, and Lewis were awarded the Nobel Prize.

      Gradients of maternal molecules in the early embryo control axis formation.

    • Cytoplasmic determinants establish the axes of the Drosophila body.
      • Substances are produced under the direction of maternal effect genes that are deposited in the unfertilized egg.
        • When a maternal effect gene is mutated, the offspring has an abnormal mutant phenotype.
    • In fruit fly development, maternal effect genes encode proteins or mRNA that are placed in the egg while it is still in the ovary.
      • When the mother has a mutated gene, she makes a defective gene product (or none at all), and her eggs will not develop properly when fertilized.
    • These maternal effect genes are also called egg-polarity genes, because they control the orientation of the egg and consequently the fly.
      • One group of genes sets up the anterior-posterior axis, while a second group establishes the dorsal-ventral axis.
    • One of these, the bicoid gene, affects the front half of the body.
    • An embryo whose mother has a mutant bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends.
      • This suggests that the product of the mother’s bicoid gene is essential for setting up the anterior end of the fly.
      • It also suggests that the gene’s products are concentrated at the future anterior end.
    • This is a specific version of a general gradient hypothesis, in which gradients of morphogens establish an embryo’s axes and other features.
    • Using DNA technology and biochemical methods, researchers were able to clone the bicoid gene and use it as a probe for bicoid mRNA in the egg.
      • As predicted, the bicoid mRNA is concentrated at the extreme anterior end of the egg cell.
    • After the egg is fertilized, bicoid mRNA is transcribed into bicoid protein, which diffuses from the anterior end toward the posterior, resulting in a gradient of proteins in the early embryo.
    • Injections of pure bicoid mRNA into various regions of early embryos results in the formation of anterior structures at the injection sites as the mRNA is translated into protein.
    • The bicoid research is important for three reasons.
      1. It identified a specific protein required for some of the earliest steps in pattern formation.
      2. It increased our understanding of the mother’s role in development of an embryo.
        • As one developmental biologist put it, “Mom tells Junior which way is up.”
      3. It demonstrated a key developmental principle that a gradient of molecules can determine polarity and position in the embryo.
        • Gradients of specific proteins determine the posterior end as well as the anterior and also are responsible for establishing the dorsal-ventral axis.

      A cascade of gene activations sets up the segmentation pattern in Drosophila.

    • The bicoid protein and other morphogens are transcription factors that regulate the activity of some of the embryo’s own genes.
    • Gradients of these morphogens bring about regional differences in the expression of segmentation genes, the genes that direct the actual formation of segments after the embryo’s major axes are defined.
    • In a cascade of gene activations, sequential activation of three sets of segmentation genes provides the positional information for increasingly fine details of the body plan.
      • The three sets are called gap genes, pair-rule genes, and segment polarity genes.
    • The products of many segmentation genes are transcription factors that directly activate the next set of genes in the hierarchical scheme of pattern formation.
    • Other segmentation proteins operate more indirectly.
      • Some are components of cell-signaling pathways, including signal molecules used in cell-cell communication and the membrane receptors that recognize them.
    • Working together, the products of egg-polarity genes such as bicoid regulate the regional expression of gap genes, which control the localized expression of pair-rule genes, which in turn activate specific segment polarity genes in different parts of each segment.
    • The boundaries and axes of segments are set by this hierarchy of genes (and their products).

      Homeotic genes direct the identity of body parts.

    • In a normal fly, structures such as antennae, legs, and wings develop on the appropriate segments.
    • The anatomical identity of the segments is controlled by master regulatory genes, the homeotic genes.
    • Discovered by Edward Lewis, these genes specify the types of appendages and other structures that each segment will form.
    • Mutations to homeotic genes produce flies with such strange traits as legs growing from the head in place of antennae.
      • Structures characteristic of a particular part of the animal arise in the wrong place.
    • Like other developmental genes, the homeotic genes encode transcription factors that control the expression of genes responsible for specific anatomical structures.
      • For example, a homeotic protein made in a thoracic segment may activate genes that bring about leg development, while a homeotic protein in a certain head segment activates genes for antennal development.
      • A mutant version of this protein may label a segment as “thoracic” instead of “head,” causing legs to develop in place of antennae.
    • Scientists are now working to identify the genes activated by the homeotic proteins—the genes specifying the proteins that actually build the fly structures.
    • Amazingly, many of the molecules and mechanisms that regulate development in the Drosophila embryo have close counterparts throughout the animal kingdom.

      Neighboring cells instruct other cells to form particular structures: cell signaling and induction in the nematode.

    • The development of a multicellular organism requires close communication among cells.
      • Signals generated by neighboring nurse cells trigger the localization of bicoid mRNA in the egg of the Drosophila.
    • Once the embryo is truly multicellular, cells signal nearby cells to change in a specific way, in a process called induction.
      • Induction brings about cell differentiation through transcriptional regulation of specific genes.
    • The nematode C. elegans has proved to be a very useful model organism for investigating the roles of cell signaling, induction, and programmed cell death in development.
    • Researchers know the entire ancestry of every cell in the body of an adult C. elegans—the organism’s complete cell lineage.
    • As early as the four-cell stage in C. elegans, cell signaling helps direct daughter cells down appropriate pathways.
    • Researchers have combined genetic, biochemical, and embryological approaches to study the development of the vulva, through which the worm lays its eggs.
    • The pathway from fertilized egg to adult nematode involves four larval stages (during which the larvae look much like smaller versions of the adult) during which this structure develops.
      • Already present on the ventral surface of the second-stage larva are six cells from which the vulva will arise.
      • A single cell in the embryonic gonad, the anchor cell, initiates a cascade of signals that establishes the fate of the six vulval precursor cells.
      • If an experimenter destroys the anchor cell with a laser beam, the vulva fails to form and the precursor cells simply become part of the worm’s epidermis.
    • Secreted factors or cell-surface proteins bind to receptors on the recipient cell, initiating intracellular signal transduction pathways.
    • This example illustrates a number of important concepts that apply to development of C. elegans and many other animals.
      • In the developing embryo, sequential inductions drive organ formation.
      • The effect of an inducer can depend on its concentration.
      • Inducers produce their effects via signal transduction pathways similar to those operating in adult cells.
      • The induced cell’s response is often the activation of genes—transcriptional regulation—that, in turn, establishes a pattern of gene activity characteristic of a particular kind of differentiated cell.
    • Lineage analysis of C. elegans highlights another outcome of cell signaling, programmed cell death, or apoptosis.
      • The timely suicide of cells occurs exactly 131 times in the course of C. elegans’s normal development.
      • At precisely the same points in development, signals trigger the activation of a cascade of “suicide” proteins in the cells destined to die.
    • During apoptosis, a cell shrinks and becomes lobed (called “blebbing”), the nucleus condenses, and the DNA is fragmented.
      • Neighboring cells quickly engulf and digest the membrane-bound remains, leaving no trace.
    • Genetic screening of C. elegans has revealed two key apoptosis genes, ced-3 and ced-4 (ced stands for cell death), which encode proteins (Ced-3 and Ced-4) that are essential for apoptosis.
    • In C. elegans, a protein in the outer mitochondrial membrane called Ced-9 (the product of ced-9) is a master regulator of apoptosis.
      • ced-9 acts as a brake in the absence of a signal promoting apoptosis.
    • When the cell receives an external death signal, Ced-9 is inactivated, allowing both Ced-4 and Ced-3 to be active.
      • The apoptosis pathway activates proteases and nucleases to cut up the proteins and DNA of the cell.
    • The main proteases of apoptosis are called caspases.
      • In nematodes, Ced-3 is the chief caspase—the main protease of apoptosis.
    • Apoptosis is regulated not at the level of transcription or translation, but through changes in the activity of proteins that are continually present in the cell.
    • Apoptosis pathways in humans and other mammals are more complicated.
    • Research on mammals has revealed a prominent role for mitochondria in apoptosis.
      • Signals from apoptosis pathways or others somehow cause the outer mitochondrial membrane to leak, releasing proteins that promote apoptosis.
        • Surprisingly, these proteins include cytochrome c, which functions in mitochondrial electron transport in healthy cells but acts as a cell death factor when released from mitochondria.
      • Still controversial is whether mitochondria play a central role in apoptosis or only a subsidiary role.
    • A cell must make a life-or-death “decision” by somehow integrating both the “death” and “life” (growth factor) signals that it receives.
    • A built-in cell suicide mechanism is essential to development in all animals.
      • Similarities between the apoptosis genes in mammals and nematodes, as well as the observation that apoptosis occurs in multicellular fungi and unicellular yeast, indicate that the basic mechanism evolved early in animal evolution.
      • The timely activation of apoptosis proteins in some cells functions during normal development and growth in both embryos and adults.
        • It is part of the normal development of the nervous system, normal operation of the immune system, and normal morphogenesis of human hands and feet.
    • A low level of apoptosis in developing limbs accounts for the webbed feet of ducks.
    • Problems with the cell suicide mechanism may have health consequences, ranging from minor to serious.
      • Failure of normal cell death during morphogenesis of the hands and feet can result in webbed fingers and toes.
      • Researchers are also investigating the possibility that certain degenerative diseases of the nervous system result from inappropriate activation of the apoptosis genes.
      • Others are investigating the possibility that some cancers result from a failure of cell suicide that normally occurs if the cell has suffered irreparable damage, especially DNA damage.
        • Damaged cells normally generate internal signals that trigger apoptosis.

      Plant development depends on cell signaling and transcriptional regulation.

    • The genetic analysis of plant development, using model organisms such as Arabidopsis, has lagged behind that of animal models.
      • Biologists are just beginning to understand the molecular basis of plant development.
    • In general, cell linage is less important for pattern formation in plants than in animals.
      • Many plant cells are totipotent, and their fates depend more on positional information than on cell lineage.
    • Plant development, like that of animals, depends on cell signaling (induction) and transcriptional regulation.
    • The embryonic development of most plants occurs in seeds that are relatively inaccessible to study.
    • However, other important aspects of plant development are observable in plant meristems, particularly the apical meristems at the tips of shoots.
      • These give rise to new organs, such as leaves or the petals of flowers.
    • Environmental signals (such as day length or temperature) trigger signal transduction pathways that convert ordinary shoot meristems to floral meristems.
      • A floral meristem is a “bump” with three cell layers, all of which participate in the formation of a flower with four types of organs: carpels (containing egg cells), petals, stamens (containing sperm-bearing pollen), and sepals (leaflike structures outside the petals).
    • To examine induction of the floral meristem, researchers grafted stems from a mutant tomato plant onto a wild-type plant and then grew new plants from the shoots at the graft sites.
      • Plants homozygous for the mutant allele fasciated (f) produce flowers with an abnormally large number of organs.
    • The new plants were chimeras, organisms with a mixture of genetically different cells.
    • Some of the chimeras produced floral meristems in which the three cell layers did not all come from the same “parent.”
    • The number of organs per flower depends on genes of the L3 (innermost) cell layer.
      • This induces the L2 and L1 layers to form that number of organs.
    • In contrast to genes controlling organ number in flowers, genes controlling organ identity (organ identity genes) determine the types of structure that will grow from a meristem.
    • In Arabidopsis and other plants, organ identity genes are analogous to homeotic genes in animals and are often referred to as plant homeotic genes.
      • Mutations cause plant structures to grow in unusual places, such as carpels in the place of sepals.
    • Researchers have identified and cloned a number of floral identity genes, and they are beginning to determine how they act.
      • In plants with a “homeotic” mutation, specific organs are missing or repeated.
      • Like the homeotic genes of animals, the organ identity genes of plants encode transcription factors that regulate specific target genes by binding to their enhancers in the DNA.

    Concept 21.4 Comparative studies help explain how the evolution of development leads to morphological diversity

    • Biologists in the field of evolutionary developmental biology, or “evo-devo,” compare developmental processes of different multicellular organisms.
      • Their aim is to understand how developmental processes have evolved and how changes in the processes can modify existing organismal features or lead to new ones.
      • Biologists are finding that the genomes of related species with strikingly different forms may have only minor differences in gene sequence or regulation.
    • All homeotic genes of Drosophila include a 180-nucleotide sequence called the homeobox, which specifies a 60-amino-acid homeodomain.
      • An identical, or very similar, sequence of nucleotides (often called Hox genes) is found in many other animals, including humans.
      • The vertebrate genes homologous to the homeotic genes of fruit flies have even kept their chromosomal arrangement.
      • Related sequences have been found in the regulatory genes of plants, yeasts, and even prokaryotes.
    • The homeobox DNA sequence must have evolved very early in the history of life and is sufficiently valuable that it has been conserved virtually unchanged in animals and plants for hundreds of millions of years.
    • Most, but not all, homeobox-containing genes are homeotic genes that are associated with development.
      • For example, in Drosophila, homeoboxes are present not only in the homeotic genes, but also in the egg-polarity gene bicoid, in several segmentation genes, and in the master regulatory gene for eye development.
    • The homeobox-encoded homeodomain is part of a protein that binds to DNA when the protein functions as a transcriptional regulator.
      • However, the shape of the homeodomain allows it to bind to any DNA segment.
      • Other, more variable, domains of the overall protein determine which genes it will regulate.
      • Interaction of these latter domains with still other transcription factors helps a homeodomain-protein recognize specific enhancers in the DNA.
    • Proteins with homeodomains probably regulate development by coordinating the transcription of batteries of developmental genes.
      • In Drosophila, different combinations of homeobox genes are active in different parts of the embryo and at different times, leading to pattern formation.
    • Many other genes involved in development are highly conserved from species to species.
      • These include numerous genes encoding components of signaling pathways.
    • How can the same genes be involved in the development of so many different animals?
      • In some cases, small changes in regulatory sequences of particular genes can lead to major changes in body form.
      • For example, varying expression of the Hox genes along the body axis produce different numbers of leg-bearing segments in insects and crustaceans.
    • Plants also have homeobox-containing genes.
      • However, they do not appear to function as master regulatory switches in plants.
      • Other genes appear to be responsible for pattern formation in plants.

      There are some basic similarities—and many differences—in the development of plants and animals.

    • The last common ancestor of plants and animals was a single-celled microbe living hundreds of millions of years ago, so the processes of development evolved independently in the two lineages.
      • Plants have rigid cell walls that prevent cell movement, while morphogenetic movements are very important in animals.
      • Morphogenesis in plants is dependent on differing planes of cell division and selective cell enlargement.
    • Nevertheless, there are some basic similarities of development.
      • In both plants and animals, development relies on a cascade of transcriptional regulators turning on or off genes in a finely tuned series.
    • The genes that direct these processes are very different in plants and animals.
      • Quite a few of the master regulatory switches in Drosophila are homeobox-containing Hox genes.
      • Those in Arabidopsis belong to the Mads-box family of genes.
    • Although homeobox-containing genes can be found in plants and Mads-box genes can be found in animals, they do not play the same major roles in development in plants and animals.
    • The unity of life is reflected in the similarity of biological mechanisms used to establish body pattern, although the exact genes directing develop may differ.
    • The similarities reflect the common ancestry of life on Earth, while the differences have created the diversity of living organisms.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 21-1

    Subject: 
    Subject X2: 

    Chapter 22 - Descent with Modification: Darwinian View of Life

    Chapter 22 Descent with Modification: Darwinian View of Life
    Lecture Outline

    Overview: Darwin Introduces a Revolutionary Theory

    • On November 24, 1859, Charles Darwin published On the Origin of Species by Means of Natural Selection.
    • Darwin’s book drew a cohesive picture of life by connecting what had once seemed a bewildering array of unrelated facts.
    • Darwin made two major points in The Origin of Species:
      1. Today’s organisms descended from ancestral species that were different from modern species.
      2. Natural selection provided a mechanism for this evolutionary change.
      • The basic idea of natural selection is that a population can change over time if individuals that possess certain heritable traits leave more offspring than other individuals.
      • Natural selection results in evolutionary adaptation, an accumulation of inherited characteristics that increase the ability of an organism to survive and reproduce in its environment.
    • Eventually, a population may accumulate enough change that it constitutes a new species.
    • In modern terms, we can define evolution as a change over time in the genetic composition of a population.
      • Evolution also refers to the gradual appearance of all biological diversity.
    • Evolution is such a fundamental concept that its study is relevant to biology at every level, from molecules to ecosystems.
      • Evolutionary perspectives continue to transform medicine, agriculture, biotechnology, and conservation biology.

    Concept 22.1 The Darwinian revolution challenged traditional views of a young Earth inhabited by unchanging species

      Western culture resisted evolutionary views of life.

    • Darwin’s view of life contrasted with the traditional view of an Earth that was a few thousand years old, populated by life forms that were created at the beginning and had remained fundamentally unchanged.
      • The Origin of Species challenged a worldview that had been long accepted.
    • The Greek philosopher Aristotle (384–322 B.C.E.) opposed any concept of evolution and viewed species as fixed and unchanging.
      • Aristotle believed that all living forms could be arranged on a ladder of increasing complexity (scala naturae) with perfect, permanent species on every rung.
    • The Old Testament account of creation held that species were individually designed by God and, therefore, perfect.
    • In the 1700s, natural theology viewed the adaptations of organisms as evidence that the Creator had designed each species for a purpose.
    • Carolus Linnaeus (1707–1778), a Swedish physician and botanist, founded taxonomy, a system for naming species and classifying species into a hierarchy of increasingly complex categories.
      • Linnaeus developed the binomial system of naming organisms according to genus and species.
      • In contrast to the linear hierarchy of the scala naturae, Linnaeus adopted a nested classification system, grouping similar species into increasingly general categories.
      • For Linnaeus, similarity between species did not imply evolutionary kinship but rather the pattern of their creation.
    • Darwin’s views were influenced by fossils, remains or traces of organisms from the past mineralized in sedimentary rocks.
      • Sedimentary rocks form when mud and sand settle to the bottom of seas, lakes, and marshes.
      • New layers of sediment cover older ones, creating layers of rock called strata.
      • Erosion may later carve through sedimentary rock to expose older strata at the surface.
      • Fossils within layers of sedimentary rock show that a succession of organisms have populated Earth throughout time.
    • Paleontology, the study of fossils, was largely developed by the French anatomist Georges Cuvier (1769–1832).
    • In examining rock strata in the Paris Basin, Cuvier noted that the older the strata, the more dissimilar the fossils from modern life.
      • Cuvier recognized that extinction had been a common occurrence in the history of life.
      • Instead of evolution, Cuvier advocated catastrophism, speculating that boundaries between strata were due to local floods or droughts that destroyed the species then present.
      • He suggested that the denuded areas were later repopulated by species immigrating from unaffected areas.

      Theories of geologic gradualism prepared the path for evolutionary biologists.

    • In contrast to Cuvier’s catastrophism, Scottish geologist James Hutton (1726–1797) proposed a theory of gradualism that held that profound geological changes took place through the cumulative effect of slow but continuous processes identical to those currently operating.
      • Thus, valleys were formed by rivers flowing through rocks and sedimentary rocks were formed from soil particles that eroded from land and were carried by rivers to the sea.
    • Later, geologist Charles Lyell (1797–1875) proposed a theory of uniformitarianism, which held that geological processes had not changed throughout Earth’s history.
    • Hutton’s and Lyell’s observations and theories had a strong influence on Darwin.
      • First, if geologic changes result from slow, continuous processes rather than sudden events, then the Earth must be far older than the 6,000 years estimated by theologians from biblical inference.
      • Second, slow and subtle processes persisting for long periods of time can also act on living organisms, producing substantial change over a long period of time.

      Lamarck placed fossils in an evolutionary context.

    • In 1809, French biologist Jean-Baptiste de Lamarck (1744–1829) published a theory of evolution based on his observations of fossil invertebrates in the collections of the Natural History Museum of Paris.
      • By comparing fossils and current species, Lamarck found what appeared to be several lines of descent.
      • Each was a chronological series of older to younger fossils, leading to a modern species.
    • He explained his observations with two principles: use and disuse of parts and the inheritance of acquired characteristics.
      • Use and disuse was the concept that body parts that are used extensively become larger and stronger, while those that are not used deteriorate.
      • The inheritance of acquired characteristics stated that modifications acquired during the life of an organism could be passed to offspring.
      • A classic example is the long neck of the giraffe. Lamarck reasoned that the long, muscular neck of the modern giraffe evolved over many generations as the ancestors of giraffes reached for leaves on higher branches and passed this characteristic to their offspring.
    • Lamarck thought that evolutionary change was driven by the innate drive of organisms to increasing complexity.
    • Lamarck’s theory was a visionary attempt to explain the fossil record and the current diversity of life with recognition of gradual evolutionary change.
      • However, modern genetics has provided no evidence that acquired characteristics can be inherited.
      • Acquired traits such as a body builder’s bigger biceps do not change the genes transmitted through gametes to offspring.

    Concept 22.2 In The Origin of Species, Darwin proposed that species change through natural selection

    • Charles Darwin (1809–1882) was born in western England.
      • As a boy, he developed a consuming interest in nature.
      • When Darwin was 16, his father sent him to the University of Edinburgh to study medicine.
    • Darwin left Edinburgh without a degree and enrolled at Cambridge University with the intent of becoming a clergyman.
      • At that time, most naturalists and scientists belonged to the clergy and viewed the world in the context of natural theology.
    • Darwin received his B.A. in 1831.
    • After graduation Darwin joined the survey ship HMS Beagle as ship naturalist and conversation companion to Captain Robert FitzRoy.
      • FitzRoy chose Darwin because of his education, and because his age and social class were similar to that of the captain.

      Field research helped Darwin frame his view of life.

    • The primary mission of the five-year voyage of the Beagle was to chart poorly known stretches of the South American coastline.
    • Darwin had the freedom to explore extensively on shore while the crew surveyed the coast.
    • He collected thousands of specimens of the exotic and diverse flora and fauna of South America.
      • Darwin explored the Brazilian jungles, the grasslands of the Argentine pampas, the desolation of Tierra del Fuego near Antarctica, and the heights of the Andes.
    • Darwin noted that the plants and animals of South America were very distinct from those of Europe.
      • Organisms from temperate regions of South America more closely resembled those from the tropics of South America than those from temperate regions of Europe.
      • Further, South American fossils, though different from modern species, more closely resembled modern species from South America than those from Europe.
    • While on the Beagle, Darwin read Lyell’s Principles of Geology.
      • He experienced geological change firsthand when a violent earthquake rocked the coast of Chile, causing the coastline to rise by several feet.
      • He found fossils of ocean organisms high in the Andes and inferred that the rocks containing the fossils had been raised there by a series of similar earthquakes.
      • These observations reinforced Darwin’s acceptance of Lyell’s ideas and led him to doubt the traditional view of a young and static Earth.
    • Darwin’s interest in the geographic distribution of species was further stimulated by the Beagle’s visit to the Galapagos, a group of young volcanic islands 900 km west of the South American coast.
      • Darwin was fascinated by the unusual organisms found there.
      • After his return to England, Darwin noted that while most of the animal species on the Galapagos lived nowhere else, they resembled species living on the South American mainland.
      • He hypothesized that the islands had been colonized by plants and animals from the mainland that had subsequently diversified on the different islands.
    • After his return to Great Britain in 1836, Darwin began to perceive that the origin of new species and adaptation of species to their environment were closely related processes.
      • For example, clear differences in the beaks among the 13 species of finches that Darwin collected in the Galapagos are adaptations to the specific foods available on their home islands.
    • By the early 1840s, Darwin had developed the major features of his theory of natural selection as the mechanism for evolution.
    • In 1844, he wrote a long essay on the origin of species and natural selection, but he was reluctant to publish and continued to compile evidence to support his theory.
    • In June 1858, Alfred Russel Wallace (1823–1913), a young naturalist working in the East Indies, sent Darwin a manuscript containing a theory of natural selection essentially identical to Darwin’s.
    • Later that year, both Wallace’s paper and extracts of Darwin’s essay were presented to the Linnaean Society of London.
    • Darwin quickly finished The Origin of Species and published it the next year.
    • While both Darwin and Wallace developed similar ideas independently, the theory of evolution by natural selection is attributed to Darwin because he developed his ideas earlier and supported the theory much more extensively.
      • The theory of evolution by natural selection was presented in The Origin of Species with immaculate logic and an avalanche of supporting evidence.
    • Within a decade, The Origin of Species had convinced most biologists that biological diversity was the product of evolution.

      The Origin of Species developed two main ideas: that evolution explains life’s unity and diversity and that natural selection is the mechanism of adaptive evolution.

    • Darwin scarcely used the word evolution in The Origin of Species.
      • Instead he used the phrase descent with modification.
        • All organisms are related through descent from a common ancestor that lived in the remote past.
        • Over evolutionary time, the descendents of that common ancestor have accumulated diverse modifications, or adaptations, that allow them to survive and reproduce in specific habitats.
    • Viewed from the perspective of descent with modification, the history of life is like a tree with multiple branches from a common trunk.
      • Closely related species, the twigs on a common branch of the tree, shared the same line of descent until their recent divergence from a common ancestor.
    • Linnaeus recognized that some organisms resemble each other more closely than others, but he did not explain these similarities by evolution.
      • However, his taxonomic scheme fit well with Darwin’s theory.
      • To Darwin, the Linnaean hierarchy reflected the branching history of the tree of life.
        • Organisms at various taxonomic levels are united through descent from common ancestors.
    • How does natural selection work, and how does it explain adaptation?
    • Evolutionary biologist Ernst Mayr has dissected the logic of Darwin’s theory into three inferences based on five observations.
      • Observation #1: All species have such great potential fertility that their population size would increase exponentially if all individuals that are born reproduced successfully.
      • Observation #2: Populations tend to remain stable in size, except for seasonal fluctuations.
      • Observation #3: Environmental resources are limited.
        • Inference #1: Production of more individuals than the environment can support leads to a struggle for existence among the individuals of a population, with only a fraction of the offspring surviving each generation.
      • Observation #4: Individuals of a population vary extensively in their characteristics; no two individuals are exactly alike.
      • Observation #5: Much of this variation is heritable.
        • Inference #2: Survival in the struggle for existence is not random, but depends in part on inherited traits. Those individuals whose inherited traits are best suited for survival and reproduction in their environment are likely to leave more offspring than less fit individuals.
        • Inference #3: This unequal ability of individuals to survive and reproduce will lead to a gradual change in a population, with favorable characteristics accumulating over generations.
    • A 1798 essay on human population by Thomas Malthus heavily influenced Darwin’s views on “overreproduction.”
      • Malthus contended that much human suffering—disease, famine, homelessness, war—was the inescapable consequence of the potential for human populations to increase faster than food supplies and other resources.
    • The capacity to overproduce seems to be a characteristic of all species.
    • Only a tiny fraction of offspring produced complete their development and reproduce successfully to leave offspring of their own.
    • In each generation, environmental factors filter heritable variations, favoring some over others.
      • Differential reproductive success—whereby organisms with traits favored by the environment produce more offspring than do organisms without those traits—results in the favored traits being disproportionately represented in the next generation.
      • This increasing frequency of the favored traits in a population is evolutionary change.
    • Darwin’s views on the role of environmental factors in the screening of heritable variation were heavily influenced by artificial selection.
      • Humans have modified a variety of domesticated plants and animals over many generations by selecting individuals with the desired traits as breeding stock.
      • If artificial selection can achieve so much change in a relatively short period of time, Darwin reasoned, then natural selection should be capable of considerable modification of species over thousands of generations.
    • Darwin’s main ideas can be summarized in three points.
      • Natural selection is differential success in reproduction (unequal ability of individuals to survive and reproduce) that results from individuals that vary in heritable traits and their environment.
      • The product of natural selection is the increasing adaptation of organisms to their environment.
      • If an environment changes over time, or if individuals of a species move to a new environment, natural selection may result in adaptation to the new conditions, sometimes giving rise to a new species in the process.
    • Three important points need to be emphasized about evolution through natural selection.
      1. Although natural selection occurs through interactions between individual organisms and their environment, individuals do not evolve. A population (a group of interbreeding individuals of a single species that share a common geographic area) is the smallest group that can evolve. Evolutionary change is measured as changes in relative proportions of heritable traits in a population over successive generations.
      2. Natural selection can act only on heritable traits, traits that are passed from organisms to their offspring. Characteristics acquired by an organism during its lifetime may enhance its survival and reproductive success, but there is no evidence that such characteristics can be inherited by offspring.
      3. Environmental factors vary from place to place and from time to time. A trait that is favorable in one environment may be useless or even detrimental in another environment.
    • Darwin envisioned the diversity of life as evolving by a gradual accumulation of minute changes through the actions of natural selection operating over vast spans of time.

    Concept 22.3 Darwin’s theory explains a wide range of observations

    • The power of evolution by natural selection as a unifying theory is its versatility as a natural explanation for diverse data from many fields of biology.
    • We will consider two examples of natural selection as a mechanism of evolution in populations.
    • Our first example concerns differential predation and guppy populations.
    • Guppies (Poecilia reticulata) live in the wild in pools in the Aripo River system in Trinidad.
    • John Endler and David Reznick have been studying these small fish for more than a decade.
    • The researchers observed significant differences between populations of guppies that live in different pools in the river system.
      • Populations varied in the average age and size of sexual maturity.
      • These variations were correlated to the type of predator present in each pool.
      • In some pools, the main predator is the small killifish, which eats juvenile guppies.
      • In other pools, the major predator is the large pike-cichlid, which eats adult guppies.
      • Guppies in populations preyed on by pike-cichlids begin reproducing at a younger age and are smaller at maturity than guppies in populations preyed on by killifish.
    • To test whether these differences are due to natural selection, Reznick and Endler introduced guppies from pike-cichlid locations to new pools that contained killifish but no guppies.
      • After eleven years, the transplanted guppies were, on average, 14% heavier at maturity than the nontransplanted populations.
      • Their average age at maturity had also increased.
    • These results support the hypothesis that natural selection caused the changes in the transplanted population.
      • Because pike-cichlids prey mainly on reproductively mature adults, the chance that a guppy will survive to reproduce several times is low.
      • The guppies with the greatest reproductive success in ponds with pike-cichlid predators are those that mature at a young age and small size, enabling them to produce at least one brood before growing to a size preferred by pike-cichlids.
      • In ponds with killifish predators, guppies that survive early predation can grow slowly and produce many broods of young.
    • A second example of ongoing natural selection is the evolution of drug-resistant HIV (human immunodeficiency virus).
    • Researchers have developed numerous drugs to combat HIV, but using these medications selects for viruses resistant to the drugs.
      • A few drug-resistant viruses may be present by chance at the beginning of treatment.
      • The drug-resistant pathogens are more likely to survive treatment and pass on the genes that enable them to resist the drug to their offspring.
      • As a result, the frequency of drug resistance in the viral population rapidly increases.
    • Scientists designed the drug 3TC to interfere with reverse transcriptase, the enzyme that HIV uses to copy its RNA genome into the DNA of the host cell.
      • Because 3TC is similar in shape to the cytosine nucleotide of DNA, HIV’s reverse transcriptase incorporates 3TC into its growing DNA chain instead of cytosine. This error terminates elongation of DNA and thus prevents HIV reproduction.
      • 3TC-resistant varieties of HIV have a form of reverse transcriptase that can discriminate between cytosine and 3TC.
        • These viruses have no advantage in the absence of 3TC. In fact, they replicate more slowly than viruses with normal reverse transcriptase.
        • Once 3TC is added to their environment, it becomes a powerful selective agent, favoring reproduction of resistant individuals.
    • The examples of the guppies and HIV highlight two important points about natural selection.
      • First, natural selection is an editing mechanism, not a creative force. It can only act on existing variation in the population; it cannot create favorable traits.
      • Second, natural selection favors traits that increase fitness in the current, local environment. What is adaptive in one situation is not adaptive in another.
        • For example, guppies that mature at an early age and small size are at an advantage in a pool with pike-cichlids, but at a disadvantage in a pool with killifish.
        • In the absence of 3TC, HIV with the modified form of reverse transcriptase grows more slowly than HIV with normal reverse transcriptase.

      Evidence of evolution pervades biology.

    • In the cases described, natural selection brought about change rapidly enough that it could be observed directly.
    • Darwin’s theory also provides a cohesive explanation for observations in the fields of anatomy, embryology, molecular biology, biogeography, and paleontology.
    • Descent with modification can explain why certain traits in related species have an underlying similarity even if they have very different functions.
    • Similarity in characteristic traits from common ancestry is known as homology.
      • For example, the forelimbs of human, cats, whales, and bats share the same skeletal elements, even though the appendages have very different functions.
      • These forelimbs are homologous structures that represent variations on the ancestral tetrapod forelimb.
    • Homologies that are not obvious in adult organisms may become evident when we look at embryonic development.
      • For example, all vertebrate embryos have structures called pharyngeal pouches in their throat at some stage in their development.
      • These embryonic structures develop into very different, but still homologous, adult structures, such as the gills of fish or the Eustacian tubes that connect the middle ear with the throat in mammals.
    • Some of the most interesting homologous structures are vestigial organs, structures that have marginal, if any, importance to a living organism, but which had important functions in the organism’s ancestors.
      • For example, the skeletons of some snakes and of fossil whales retain vestiges of the pelvis and leg bones of walking ancestors.
    • Comparative anatomy confirms that evolution is a remodeling process, an alteration of existing structures.
      • Because evolution can only modify existing structures and functions, it may produce structures that are less than perfect.
      • For example, the back and knee problems of bipedal humans are an unsurprising outcome of adapting structures originally evolved to support four-legged mammals.
    • Similarities among organisms can also be seen at the molecular level.
      • For example, all species of life have the same basic genetic machinery of RNA and DNA, and the genetic code is essentially universal.
      • The ubiquity of the genetic code provides evidence of a single origin of life.
      • It is likely that the language of the genetic code has been passed along through all the branches of the tree of life ever since its inception in an early life form.
    • Homologies mirror the taxonomic hierarchy of the tree of life.
      • Some homologies, such as the genetic code, are shared by all living things because they arose in the deep ancestral past.
      • Other homologies that evolved more recently are shared only by smaller branches of the tree of life.
        • For example, all tetrapods (amphibians, reptiles, birds, and mammals) share the same five-digit limb structure.
      • Thus homologies are found in a nested pattern, with all life sharing the deepest layer and each smaller group adding new homologies to those they share with the larger group.
      • This hierarchical pattern of homology is exactly what we would expect if life evolved and diversified from a common ancestor.
    • Anatomical resemblances among species are generally reflected in their genes (DNA) and gene products (proteins).
      • If hierarchies of homology reflect evolutionary history, then we should expect to find similar patterns whether we are comparing molecules or bones.
      • Different kinds of homologies will coincide because they have followed the same branching pattern through evolutionary history.
    • The geographical distribution of species—biogeography—first suggested evolution to Darwin.
      • Species tend to be more closely related to other species from the same area than to other species with the same way of life that live in different areas.
        • Consider Australia, home to a unique group of marsupial mammals, which complete their development in an external pouch.
        • Some marsupial mammals superficially resemble eutherian mammals (which complete their development in the uterus) from other continents.
          • For example, the Australian sugar glider and North American flying squirrel are adapted to the same mode of life and look somewhat similar.
          • However, the sugar glider shares more characteristics with other Australian marsupials than with the flying squirrel.
          • The resemblance between the two gliders is an example of convergent evolution.
    • Islands and island archipelagos have provided strong evidence of evolution.
      • Islands generally have many species of plants and animals that are endemic, found nowhere else in the world.
    • As Darwin observed when he reassessed his collections from the Beagle’s voyage, these endemic species are typically more closely related to species living on the nearest mainland (despite different environments) than to species from other island groups.
    • In island chains, or archipelagos, individual islands may have different, but related, species. The first mainland invaders reached one island and then evolved into several new species as they colonized other islands in the archipelago.
      • Several well-investigated examples of this phenomenon include the diversification of finches on the Galapagos Islands and fruit flies (Drosophila) on the Hawaiian Archipelago.
    • The succession of fossil forms is consistent with what is known from other types of evidence about the major branches of descent in the tree of life.
      • For example, considerable evidence suggests that prokaryotes are the ancestors of all life and should precede all eukaryotes in the fossil record. In fact, the oldest known fossils are prokaryotes.
      • Fossil fishes predate all other vertebrates, with amphibians next, followed by reptiles, then mammals and birds.
      • This is consistent with the history of vertebrate descent supported by many other types of evidence.
    • The Darwinian view of life also predicts that evolutionary transitions should leave signs in the fossil record.
    • Paleontologists have discovered fossils of many such transitional forms that link ancient organisms to modern species.
      • For example, fossil evidence documents the origin of birds from one branch of dinosaurs.
      • Recent discoveries include fossilized whales that link these aquatic mammals to their terrestrial ancestors.

      What is theoretical about the Darwinian view of life?

    • Some people dismiss the Darwinian view as “just a theory.”
      • As we have seen, Darwin’s explanation makes sense of large amounts of data.
      • The effects of natural selection can be observed in nature.
    • What is theoretical about evolution?
      • The term theory has a very different meaning in science than in everyday use.
      • The word theory in colloquial use is closer to the concept of a hypothesis in science.
    • In science, a theory is more comprehensive than a hypothesis, accounting for many observations and data and attempting to explain and integrate a great variety of phenomena.
    • A unifying theory does not become widely accepted unless its predictions stand up to thorough and continual testing by experiments and additional observation.
      • That has certainly been the case with the theory of evolution by natural selection.
    • Scientists continue to test this theory.
      • For example, many evolutionary biologists now question whether natural selection is the only mechanism responsible for evolutionary history.
      • Other factors may have played an important role, particularly in the evolution of genes and proteins.
    • By attributing the diversity of life to natural causes, Darwin gave biology a sound scientific basis.
      • As Darwin said, “There is grandeur in this view of life.”

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 22-1

    Subject: 
    Subject X2: 

    Chapter 23 - The Evolution of Populations

    Chapter 23 The Evolution of Populations
    Lecture Outline

    Overview: The Smallest Unit of Evolution

    • One common misconception about evolution is that organisms evolve, in a Darwinian sense, during their lifetimes.
    • Natural selection does act on individuals. Each individual’s combination of inherited traits affects its survival and its reproductive success relative to other individuals in the population.
    • However, the evolutionary impact of natural selection is only apparent in the changes in a population of organisms over time.
    • It is the population, not the individual, that evolves.
    • Consider the example of bent grass (Agrostis tenuis) growing on the tailings of an abandoned mine. These tailings are rich in toxic heavy metals.
    • While many bent grass seeds land on the mine tailings each year, the only plants that germinate, grow, and reproduce are those that possess genes enabling them to tolerate metallic soils.
    • These plants tend to produce metal-tolerant offspring.
    • Individual plants do not evolve to become more metal-tolerant during their lifetimes.

    Concept 23.1 Population genetics provides a foundation for studying evolution

    • Darwin proposed a mechanism for change in species over time.
    • What was missing from Darwin’s explanation was an understanding of inheritance that could explain how chance variations arise in a population while also accounting for the precise transmission of these variations from parents to offspring.
    • The widely accepted hypothesis of the time—that the traits of parents are blended in their offspring—would eliminate the differences in individuals over time.
    • Just a few years after Darwin published On the Origin of Species, Gregor Mendel proposed a model of inheritance that supported Darwin’s theory.
    • Mendel’s particulate hypothesis of inheritance stated that parents pass on discrete heritable units (genes) that retain their identities in offspring.
    • Although Gregor Mendel and Charles Darwin were contemporaries, Darwin never saw Mendel’s paper, and its implications were not understood by the few scientists who did read it at the time.
    • Mendel’s contribution to evolutionary theory was not appreciated until half a century later.

      The modern evolutionary synthesis integrated Darwinian selection and Mendelian inheritance.

    • When Mendel’s research was rediscovered in the early 20th century, many geneticists believed that his laws of inheritance conflicted with Darwin’s theory of natural selection.
    • Darwin emphasized quantitative characters, those that vary along a continuum.
    • These characters are influenced by multiple loci.
    • Mendel and later geneticists investigated discrete “either-or” traits.
    • It was not obvious that there was a genetic basis to quantitative characters.
    • Within a few decades, geneticists determined that quantitative characters are influenced by multiple genetic loci and that the alleles at each locus follow Mendelian laws of inheritance.
    • These discoveries helped reconcile Darwin’s and Mendel’s ideas and led to the birth of population genetics, the study of how populations change genetically over time.
    • A comprehensive theory of evolution, the modern synthesis, took form in the early 1940s.
    • It integrated discoveries and ideas from paleontology, taxonomy, biogeography, and population genetics.
    • The first architects of the modern synthesis included statistician R. A. Fisher, who demonstrated the rules by which Mendelian characters are inherited, and biologist J. B. S. Haldane, who explored the rules of natural selection. Later contributors included geneticists Theodosius Dobzhansky and Sewall Wright, biogeographer and taxonomist Ernst Mayr, paleontologist George Gaylord Simpson, and botanist G. Ledyard Stebbins.
    • The modern synthesis emphasizes:
    • The importance of populations as the units of evolution.
    • The central role of natural selection as the most important mechanism of adaptive evolution.
    • The idea of gradualism to explain how large changes can evolve as an accumulation of small changes over long periods of time.
    • While many evolutionary biologists are now challenging some of the assumptions of the modern synthesis, it has shaped our ideas about how populations evolve.

      A population’s gene pool is defined by its allele frequencies.

    • A population is a localized group of individuals that belong to the same species.
    • One definition of a species is a group of natural populations whose individuals have the potential to interbreed and produce fertile offspring.
    • Populations of a species may be isolated from each other and rarely exchange genetic material.
    • Members of a population are far more likely to breed with members of the same population than with members of other populations.
    • Individuals near the population’s center are, on average, more closely related to one another than to members of other populations.
    • The total aggregate of genes in a population at any one time is called the population’s gene pool.
    • It consists of all alleles at all gene loci in all individuals of a population.
    • If only one allele exists at a particular locus in a population, that allele is said to be fixed in the gene pool, and all individuals will be homozygous for that gene.
    • If there are two or more alleles for a particular locus, then individuals can be either homozygous or heterozygous for that gene.
    • Each allele has a frequency in the population’s gene pool.
    • For example, imagine a population of 500 wildflower plants with two alleles (CR and CW) at a locus that codes for flower pigment.
    • Suppose that in the imaginary population of 500 plants, 20 (4%) are homozygous for the CW allele (CWCW) and have white flowers.
    • Of the remaining plants, 320 (64%) are homozygous for the CR allele (CRCR) and have red flowers.
    • These alleles show incomplete dominance. 160 (32%) of the plants are heterozygous (CRCW) and produce pink flowers.
    • Because these plants are diploid, the population of 500 plants has 1,000 copies of the gene for flower color.
    • The dominant allele (CR) accounts for 800 copies (320 × 2 for CRCR + 160 × 1 for CRCW).
    • The frequency of the CR allele in the gene pool of this population is 800/1,000 = 0.8, or 80%.
    • The CW allele must have a frequency of 1.0 ? 0.8 = 0.2, or 20%.
    • When there are two alleles at a locus, the convention is to use p to represent the frequency of one allele and q to represent the frequency of the other.
    • Thus p, the frequency of the CR allele in this population, is 0.8.
    • The frequency of the CW allele, represented by q, is 0.2.

      The Hardy-Weinberg Theorem describes a nonevolving population.

    • The Hardy-Weinberg theorem describes the gene pool of a nonevolving population.
    • This theorem states that the frequencies of alleles and genotypes in a population’s gene pool will remain constant over generations unless acted upon by agents other than Mendelian segregation and recombination of alleles.
    • The shuffling of alleles by meiosis and random fertilization has no effect on the overall gene pool of a population.
    • In our imaginary wildflower population of 500 plants, 80% (0.8) of the flower color alleles are CR, and 20% (0.2) are CW.
    • How will meiosis and sexual reproduction affect the frequencies of the two alleles in the next generation?
    • We assume that fertilization is completely random and all male-female mating combinations are equally likely.
    • Because each gamete has only one allele for flower color, we expect that a gamete drawn from the gene pool at random has a 0.8 chance of bearing an CR allele and a 0.2 chance of bearing an CW allele.
    • Suppose that the individuals in a population not only donate gametes to the next generation at random, but also mate at random. In other words, all male-female matings are equally likely.
    • The allele frequencies in this population will not change from one generation to the next. Its genotype frequencies, which can be predicted from the allele frequencies, will also remain unchanged.
    • For the flower-color locus, the population’s genetic structure is in a state of Hardy-Weinberg equilibrium.
    • Using the rule of multiplication, we can determine the frequencies of the three possible genotypes in the next generation.
    • The probability of picking two CR alleles (to obtain a CRCR genotype) is 0.8 × 0.8 = 0.64, or 64%.
    • The probability of picking two CW alleles (to obtain a CWCW genotype) is 0.2 × 0.2 = 0.04, or 4%.
    • Heterozygous individuals are either CRCW or CWCR, depending on whether the CR allele arrived via sperm or egg.
    • The probability of being heterozygous (with a CRCW genotype) is 0.8 × 0.2 = 0.16 for CRCW, 0.2 × 0.8 = 0.16 for CWCR, and 0.16 + 0.16 = 0.32, or 32%, for CRCW + CWCR.
    • As you can see, the processes of meiosis and random fertilization have maintained the same allele and genotype frequencies that existed in the previous generation.
    • The Hardy-Weinberg theorem states that the repeated shuffling of a population’s gene pool over generations does not increase the frequency of one allele over another.
    • Theoretically, the allele frequencies in our flower population should remain at 0.8 for CR and 0.2 for CW forever.
    • To generalize the example, in a population with two alleles with frequencies of p and q, the combined frequencies must add to 100%.
    • Therefore p + q = 1.
    • If p + q = 1, then p = 1 ? q and q = 1 ? p.
    • In the wildflower example, p is the frequency of red alleles (CR) and q is the frequency of white alleles (CW).
    • The probability of generating an CRCR offspring is p2 (an application of the rule of multiplication).
    • In our example, p = 0.8 and p2 = 0.64.
    • The probability of generating a CWCW offspring is q2.
    • In our example, q = 0.2 and q2 = 0.04.
    • The probability of generating a CRCW offspring is 2pq.
    • In our example, 2 × 0.8 × 0.2 = 0.32.
    • The genotype frequencies must add up to 1.0:

      p2 + 2pq + q2 = 1.0

    • For the wildflowers, 0.64 + 0.32 + 0.04 = 1.0.
    • This general formula is the Hardy-Weinberg equation.
    • Using this formula, we can calculate frequencies of alleles in a gene pool if we know the frequency of genotypes, or the frequency of genotypes if we know the frequencies of alleles.

      Five conditions must be met for a population to remain in Hardy-Weinberg equilibrium.

    • The Hardy-Weinberg theorem describes a hypothetic population that is not evolving. However, real populations do evolve, and their allele and genotype frequencies do change over time.
    • That is because the five conditions for nonevolving populations are rarely met for long in nature.
    • A population must satisfy five conditions if it is to remain in Hardy-Weinberg equilibrium:
      1. Extremely large population size. In small populations, chance fluctuations in the gene pool can cause genotype frequencies to change over time. These random changes are called genetic drift.
      2. No gene flow. Gene flow, the transfer of alleles due to the migration of individuals or gametes between populations, can change the proportions of alleles.
      3. No mutations. Introduction, loss, or modification of genes will alter the gene pool.
      4. Random mating. If individuals pick mates with certain genotypes, or if inbreeding is common, the mixing of gametes will not be random.
      5. No natural selection. Differential survival or reproductive success among genotypes will alter their frequencies.
    • Evolution usually results when any of these five conditions are not met.
    • Although natural populations are rarely, if ever, in true Hardy-Weinberg equilibrium, the rate of evolutionary change in many populations is so slow that they appear to be close to equilibrium.
    • In such cases, we can use the Hardy-Weinberg equation to estimate genotype and allele frequencies.
    • We can use the theorem to estimate the percentage of the human population that carries the allele for the inherited disease phenylketonuria (PKU).
    • About 1 in 10,000 babies born in the United States is born with PKU, a metabolic condition that results in mental retardation and other problems if left untreated.
    • The disease is caused by a recessive allele.
    • Is the U.S. population in Hardy-Weinberg equilibrium with respect to the PKU gene?
      1. The U.S. population is very large.
      2. Populations outside the United States have PKU allele frequencies similar to those seen in the United States, so gene flow will not alter allele frequencies significantly.
      3. The mutation rate for the PKU gene is very low.
      4. People do not choose their partners based on whether or not they carry the PKU allele, and inbreeding (marriage to close relatives) is rare in the United States.
      5. Selection against PKU only acts against the rare heterozygous recessive individuals.
    • From the epidemiological data, we know that frequency of homozygous recessive individuals (q2 in the Hardy-Weinberg theorem) = 1 in 10,000, or 0.0001.
    • The frequency of the recessive allele (q) is the square root of 0.0001 = 0.01.
    • The frequency of the dominant allele (p) is p = 1 ? q, or 1 ? 0.01 = 0.99.
    • The frequency of carriers (heterozygous individuals) is 2pq = 2 × 0.99 × 0.01 = 0.0198, or about 2%.
    • Thus, about 2% of the U.S. population carries the PKU allele.

    Concept 23.2 Mutation and sexual recombination produce the variation that makes evolution possible

      New genes and new alleles originate only by mutation.

    • A mutation is a change in the nucleotide sequence of an organism’s DNA.
    • Most mutations occur in somatic cells and are lost when the individual dies.
    • Only mutations in cell lines that form gametes can be passed on to offspring, and only a small fraction of these spread through populations and become fixed.
    • A new mutation that is transmitted in a gamete to an offspring can immediately change the gene pool of a population by introducing a new allele.
    • A point mutation is a change of a single base in a gene.
    • Point mutations can have a significant impact on phenotype, as in the case of sickle-cell disease.
    • However, most point mutations are harmless.
    • Much of the DNA in eukaryotic genomes does not code for protein products.
    • However, some noncoding regions of DNA do regulate gene expression.
    • Changes in these regulatory regions of DNA can have profound effects.
    • Because the genetic code is redundant, some point mutations in genes that code for proteins may not alter the protein’s amino acid composition.
    • On rare occasions, a mutant allele may actually make its bearer better suited to the environment, increasing reproductive success.
    • This is more likely when the environment is changing.
    • Some mutations alter gene number or sequence.
    • Chromosomal mutations that delete or rearrange many gene loci at once are almost always harmful.
    • In rare cases, chromosomal rearrangements may be beneficial.
    • For example, the translocation of part of one chromosome to a different chromosome could link genes that act together to positive effect.
    • Gene duplication is an important source of new genetic variation.
    • Small pieces of DNA can be introduced into the genome through the activity of transposons.
    • Such duplicated segments can persist over generations and provide new loci that may eventually take on new functions by mutation and subsequent selection.
    • New genes may also arise when the coding subsections of genes known as exons are shuffled within the genome, within a single locus or between loci.
    • Such beneficial increases in gene number appear to have played a major role in evolution.
    • For example, mammalian ancestors carried a single gene for detecting odors that has been duplicated though various mutational mechanisms.
    • Modern humans have close to 1,000 olfactory receptor genes.
    • 60% of these genes have been inactivated in humans, due to mutations.
    • Mice, who rely more on their sense of smell, have lost only 20% of their olfactory receptor genes.
    • Mutation rates vary from organism to organism.
    • Mutation rates are low in animals and plants, averaging about 1 mutation in every 100,000 genes per generation.
    • In microorganisms and viruses with short generation spans, mutation rates are much higher and can rapidly generate genetic variation.

      Sexual recombination also produces genetic variation.

    • On a generation-to-generation timescale, sexual recombination is far more important than mutation in producing the genetic differences that make adaptation possible.
    • Sexual reproduction rearranges alleles into novel combinations every generation.
    • Bacteria and viruses can also undergo recombination, but they do so less regularly than animals and plants.
    • Bacterial and viral recombination may cross species barriers.

    Concept 23.3 Natural selection, genetic drift, and gene flow can alter a population’s genetic composition

    • Although new mutations can modify allele frequencies, the change from generation to generation is very small.
    • Recombination reshuffles alleles but does not change their frequency.
    • Three major factors alter allele frequencies to bring about evolutionary change: natural selection, genetic drift, and gene flow.

      Natural selection is based on differential reproductive success.

    • Individuals in a population vary in their heritable traits.
    • Those with variations better suited to the environment tend to produce more offspring than those with variations that are less well suited.
    • As a result of selection, alleles are passed on to the next generation in frequencies different from their relative frequencies in the present population.
    • Imagine that in our imaginary wildflower population, white flowers are more visible to herbivorous insects and thus have lower survival. Imagine that red flowers are more visible to pollinators.
    • Such differences in survival and reproductive success would disturb the Hardy-Weinberg equilibrium. The frequency of the CW allele would decline and the frequency of the CR allele would increase.

      Genetic drift results from chance fluctuations in allele frequencies in small populations.

    • Genetic drift occurs when changes in gene frequencies from one generation to another occur because of chance events (sampling errors) that occur in small populations.
    • For example, you would not be too surprised if a thrown coin produced seven heads and three tails in ten tosses, but you would be surprised if you saw 700 heads and 300 tails in 1,000 tosses—you would expect close to 500 of each.
    • The smaller the sample, the greater the chance of deviation from the expected result.
    • In a large population, allele frequencies will not change from generation to generation by chance alone.
    • However, in a small wildflower population with a stable size of only ten plants, genetic drift can completely eliminate some alleles.
    • Genetic drift at small population sizes may occur as a result of two situations: the bottleneck effect or the founder effect.
    • The bottleneck effect occurs when the numbers of individuals in a large population are drastically reduced by a disaster.
    • By chance, some alleles may be overrepresented and others underrepresented among the survivors.
    • Some alleles may be eliminated altogether.
    • Genetic drift will continue to change the gene pool until the population is large enough to eliminate the effect of chance fluctuations.
    • The bottleneck effect is an important concept in conservation biology of endangered species.
    • Populations that have suffered bottleneck incidents have lost genetic variation from the gene pool.
    • This reduces individual variation and may reduce adaptation.
    • For example, in the 1890s, hunters reduced the population of northern elephant seals in California to 20 individuals.
    • Now that it is a protected species, the population has increased to more than 30,000.
    • However, a study of 24 gene loci in a representative sample of seals showed no variation. One allele had been fixed for each gene.
    • Populations of the closely related southern elephant seal, which did not go through a bottleneck, show abundant genetic variation.
    • The founder effect occurs when a new population is started by only a few individuals who do not represent the gene pool of the larger source population.
    • At an extreme, a population could be started by a single pregnant female or single seed with only a tiny fraction of the genetic variation of the source population.
    • Genetic drift would continue from generation to generation until the population grew large enough for sampling errors to be minimal.
    • Founder effects have been demonstrated in human populations that started from a small group of colonists.

      A population may lose or gain alleles by gene flow.

    • Gene flow is genetic exchange due to migration of fertile individuals or gametes between populations.
    • For example, if a nearby wildflower population consisted entirely of white flowers, its pollen (CW alleles only) could be carried into our target population.
    • This would increase the frequency of CW alleles in the target population in the next generation.
    • Gene flow tends to reduce differences between populations.
    • If extensive enough, gene flow can amalgamate neighboring populations into a single population with a common gene pool.
    • Humans today migrate much more freely than in the past, and gene flow has become an important agent of evolutionary change in human populations that were previously isolated.

    Concept 23.4 Natural selection is the primary mechanism of adaptive evolution

    • Of all the factors that can change a gene pool, only natural selection leads to adaptation of an organism to its environment.
    • Natural selection accumulates and maintains favorable genotypes in a population.
    • Most populations have extensive genetic variation.
    • Not all variation is heritable. For example, body builders alter their phenotypes but do not pass on their huge muscles to their children.
    • Only the genetic component of variation can have evolutionary consequences as a result of natural selection.
    • This is because only heritable traits pass from generation to generation.

      Genetic variation occurs within and between populations.

    • Both quantitative and discrete characters contribute to variation within a population.
    • Quantitative characters are those that vary along a continuum within a population.
    • For example, plant height in a wildflower population ranges from short to tall.
    • Quantitative variation is usually due to polygenic inheritance in which the additive effects of two or more genes influence a single phenotypic character.
    • Discrete characters, such as flower color, are usually determined by a single locus with different alleles that produce distinct phenotypes.
    • Phenotypic polymorphism occurs when two or more discrete phenotypes are represented in high enough frequencies to be noticeable in a population.
    • The contrasting forms are called morphs, as in the red-flowered and white-flowered morphs in our wildflower population.
    • Human populations are polymorphic for a variety of physical (e.g., freckles) and biochemical (e.g., blood types) characters.
    • Polymorphism applies only to discrete characters, not quantitative characters.
    • Human height, which varies in a continuum, is not a phenotypic polymorphism.
    • Population geneticists measure genetic variation by determining the amount of heterozygosity at the level of whole genes (gene variability) and at the molecular level of DNA (nucleotide variability).
    • Average heterozygosity measures gene variability, the average percent of gene loci that are heterozygous.
    • In the fruit fly (Drosophila), about 86% of their 13,000 gene loci are homozygous (fixed).
    • About 14% (1,800 genes) are heterozygous.
    • Nucleotide variability measures the mean level of difference in nucleotide sequences (base pair differences) among individuals in a population.
    • In fruit flies, about 1% of the bases differ between two individuals.
    • Two individuals differ, on average, at 1.8 million of the 180 million nucleotides in the fruit fly genome.
    • Why does average heterozygosity tend to be greater than nucleotide diversity?
    • This is because a gene can consist of thousands of bases of DNA. A difference at only one of these bases is sufficient to make two alleles of that gene different and count toward average heterozygosity.
    • Humans have relatively little genetic variation.
    • Nucleotide diversity is only 0.1%.
    • You and your neighbor probably have the same nucleotide at 999 out of every 1,000 nucleotide sites in your DNA.
    • Geographic variation results from differences in phenotypes or genotypes between populations or between subgroups of a single population that inhabit different areas.
    • Natural selection contributes to geographic variation by modifying gene frequencies in response to differences in local environmental factors.
    • Genetic drift can also lead to variation among populations through the cumulative effect of random fluctuations in allele frequencies.
    • Geographic variation can occur on a local scale, within a population, if the environment is patchy or if dispersal of individuals is limited, producing subpopulations. This is termed spatial variation.
    • Geographic variation in the form of graded change in a trait along a geographic axis is called a cline.
    • Clines may represent intergrade zones where individuals from neighboring, genetically different, populations interbreed.
    • Alternatively, clines may reflect the influence of natural selection based on gradation in some environmental variable.
    • For example, the average body size of many North American species of birds and mammals increases gradually with increasing latitude, allowing Northern populations to conserve heat in cold environments by decreasing the ratio of surface area to volume.

      Let’s take a closer look at natural selection.

    • The terms “struggle for existence” and “survival of the fittest” are misleading because they suggest that individuals compete directly in contests.
    • In some animal species, males do compete directly for mates.
    • Reproductive success is generally subtler and depends on factors other than battle for mates.
    • For example, a barnacle may produce more eggs than its neighbors because it is more efficient at filtering food from the water.
    • Wildflowers may be successful because they attract more pollinators.
    • These examples of adaptive advantage are all components of evolutionary fitness.
    • Fitness is defined as the contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals.
    • Population geneticists define relative fitness as the contribution of a genotype to the next generation compared to the contribution of alternative genotypes for the same locus.
    • Consider our wildflower population.
    • Let’s assume that individuals with red flowers produce fewer offspring than those with white or pink flowers, which produce equal numbers of offspring.
    • The relative fitness of the most successful variants is set at 1.0 as a basis for comparison, so the relative fitness of white (CWCW) and pink (CRCW) plants is 1.0.
    • If plants with red flowers (CRCR) produce only 80% as many offspring, their relative fitness is 0.8.
    • Although population geneticists measure the relative fitness of a genotype, it is important to remember that natural selection acts on phenotypes, not genotypes.
    • The whole organism is subjected to natural selection.
    • The relative fitness of an allele depends on the entire genetic and environmental context in which it is expressed.
    • Survival alone does not guarantee reproductive success.
    • Relative fitness is zero for a sterile organism, even if it is robust and long-lived.
    • On the other hand, longevity may increase fitness if long-lived individuals leave more offspring than short-lived individuals.
    • In many species, individuals that mature quickly, become fertile at an early age, and live for a short time have greater relative fitness than individuals that live longer but mature later.

      There are three modes of selection: directional, disruptive, and stabilizing.

    • Natural selection can alter the frequency distribution of heritable traits in three ways, depending on which phenotypes in a population are favored.
    • The three modes of selection are called directional, disruptive, and stabilizing selection.
    • Directional selection is most common during periods of environmental change or when members of a population migrate to a new habitat with different environmental conditions.
    • Directional selection shifts the frequency curve for a phenotypic character in one direction by favoring individuals who deviate from the average.
    • For example, fossil evidence indicates that the average size of black bears in Europe increased during each glacial period, only to decrease again during the warmer interglacial periods.
    • Large bears have a smaller surface-to-volume ratio and are better at conserving body heat during periods of extreme cold.
    • Disruptive selection occurs when environmental conditions favor individuals at both extremes of the phenotypic range over those with intermediate phenotypes.
    • For example, two distinct bill types are present in Cameroon’s black-bellied seedcrackers. Larger-billed birds are more efficient in feeding on hard seeds and smaller-billed birds are more efficient in feeding on soft seeds.
    • Birds with intermediate bills are relatively inefficient at cracking both types of seeds and thus have lower relative fitness.
    • Disruptive selection can be important in the early stages of speciation.
    • Stabilizing selection favors intermediate variants and acts against extreme phenotypes.
    • Stabilizing selection reduces variation and maintains the status quo for a trait.
    • Human birth weight is subject to stabilizing selection.
    • Babies much larger or smaller than 3–4 kg have higher infant mortality than average-sized babies.

      Diploidy and balancing selection preserve genetic variation.

    • The tendency for natural selection to reduce variation is countered by mechanisms that preserve or restore variation, including diploidy and balanced polymorphisms.
    • Diploidy in eukaryotes prevents the elimination of recessive alleles via selection because recessive alleles do not affect the phenotype in heterozygotes.
    • Even recessive alleles that are unfavorable can persist in a population through their propagation by heterozygous individuals.
    • Recessive alleles are only exposed to selection when both parents carry the same recessive allele and combine two recessive alleles in one zygote.
    • This happens only rarely when the frequency of the recessive allele is very low.
    • The rarer the recessive allele, the greater the degree of protection it has from natural selection.
    • Heterozygote protection maintains a huge pool of alleles that may not be suitable under the present conditions but may become beneficial when the environment changes.
    • Natural selection itself preserves variation at some gene loci.
    • Balancing selection occurs when natural selection maintains stable frequencies of two or more phenotypes in a population, a state called balanced polymorphism.
    • One mechanism producing balanced polymorphism is heterozygote advantage.
    • In some situations, individuals who are heterozygous at a particular locus have greater fitness than homozygotes.
    • In these cases, natural selection will maintain multiple alleles at that locus.
    • Heterozygous advantage maintains genetic diversity at the human gene for one chain of hemoglobin.
    • Homozygous recessive individuals suffer from sickle-cell disease.
    • Homozygous dominant individuals are vulnerable to malaria.
    • Heterozygous individuals are resistant to malaria.
    • The frequency of the sickle-cell allele is highest in areas where the malarial parasite is common.
    • In some African tribes, it accounts for 20% of the gene pool, a very high frequency for such a harmful allele.
    • Even at this high frequency, only 4% of the population suffers from sickle-cell disease (q2 = 0.2 × 0.2 = 0.04), while 32% of the population is resistant to malaria (2pq = 2 × 0.8 × 0.2 = 0.32).
    • The aggregate benefit of the sickle-cell allele in the population balances its aggregate harm.
    • A second mechanism promoting balanced polymorphism is frequency-dependent selection.
    • Frequency-dependent selection occurs when the fitness of any one morph declines if it becomes too common in the population.
    • Predators may develop “search images” of the most common forms of prey. A prey morph that becomes too common may become disproportionately vulnerable to predation.
    • Frequency-dependent selection has been observed in a number of predator-prey interactions in the wild.
    • Some genetic variations, neutral variations, have negligible impact on fitness, and thus natural selection does not affect these alleles.
    • For example, the diversity of human fingerprints seems to confer no selective advantage to some individuals over others.
    • Most of the base differences between humans that are found in untranslated parts of the genome appear to confer no selective advantage.
    • Pseudogenes, genes that have become inactivated by mutations, accumulate genetic variations.
    • Over time, some neutral alleles will increase and others will decrease by the chance effects of genetic drift.
    • There is no consensus among biologists on how much genetic variation can be classified as neutral or even if any variation can be considered truly neutral.
    • It is almost impossible to demonstrate that an allele brings no benefit at all to an organism.
    • Also, variant alleles may be neutral in one environment but not in another.
    • Even if only a fraction of the extensive variation in a gene pool significantly affects an organism, there is still an enormous reservoir of raw material for natural selection and adaptive evolution.

      Sexual selection may lead to pronounced secondary differences between the sexes.

    • Charles Darwin was the first scientist to investigate sexual selection, which is natural selection for mating success.
    • Sexual selection results in sexual dimorphism, marked differences between the sexes in secondary sexual characteristics not directly associated with reproduction.
    • Males and females may differ in size, coloration, and ornamentation.
    • In vertebrates, males are usually the larger and showier sex.
    • It is important to distinguish between intrasexual and intersexual selection.
    • Intrasexual selection is direct competition among individuals of one sex (usually males) for mates of the opposite sex.
    • Competition may take the form of direct physical battles between individuals.
    • The stronger individuals gain status.
    • More commonly, ritualized displays discourage lesser competitors and determine dominance.
    • Evidence is growing that intrasexual selection can take place between females as well.
    • Intersexual selection or mate choice occurs when members of one sex (usually females) are choosy in selecting their mates from individuals of the other sex.
    • Because females invest more in eggs and parental care, they are choosier about their mates than males.
    • A female tries to select a mate that will confer a fitness advantage on their mutual offspring.
    • In many cases, the female chooses a male based on his showy appearance or behavior.
    • Some male showiness does not seem to be adaptive except in attracting mates and may put the male at considerable risk.
    • For example, bright plumage may make male birds more visible to predators.
    • Even if these extravagant features have some costs, individuals that possess them will have enhanced fitness if they help an individual gain a mate.
    • Every time a female chooses a mate based on appearance or behavior, she perpetuates the alleles that caused her to make that choice.
    • She also allows a male with that particular phenotype to perpetuate his alleles.
    • How do female preferences for certain male characteristics evolve? Are there fitness benefits to showy traits?
    • Several researchers are testing the hypothesis that females use male sexual advertisements to measure the male’s overall health.
    • Males with serious parasitic infections may have dull, disheveled plumage.
    • These individuals are unlikely to win many females.
    • If a female chooses a showy mate, she may be choosing a healthy one, and her benefit is a greater probability of having healthy offspring.

      Sex is an evolutionary enigma.

    • As a mechanism of rapid population growth, sex is far inferior to asexual reproduction.
    • Consider a population in which half the females reproduce only asexually and half the females reproduce only sexually.
    • Assume that both types of females produce equal numbers of offspring each generation.
    • The asexual condition will increase in frequency, because:
      • All offspring of asexual females will be reproductive daughters.
      • ? Only half of the offspring of sexual females will be daughters; the other half will necessarily be males.
    • Sex is maintained in the vast majority of eukaryotic species, even those that also reproduce asexually.
    • Sex must confer some selective advantage to compensate for the costs of diminished reproductive output.
    • Otherwise, migration of asexual individuals or mutation permitting asexual reproduction would outcompete sexual individuals and the alleles favoring sex.
    • The traditional explanation for the maintenance of sex was that the process of meiosis and fertilization generate genetic variation on which natural selection can act.
    • However, the assumption that sex is maintained in spite of its disadvantages because it produces future adaptation in a variable world is difficult to defend.
    • Natural selection acts in the present, favoring individuals here and now that best fit the current, local environment.
    • Let us instead consider how the genetic variation promoted by sex might be advantageous in the short term, on a generation-to-generation timescale.
    • Genetic variability may be important in resistance to disease.
    • Parasites and pathogens recognize and infect their hosts by attaching to receptor molecules on the host’s cells.
    • There should be an advantage to producing offspring that vary in their resistance to different diseases.
    • One offspring may have cellular markers that make it resistant to virus A, while another is resistant to virus B.
    • This hypothesis predicts that gene loci that code for receptors to which pathogens attack should have many alleles.
    • In humans, there are hundreds of alleles for each of two gene loci that give cell surfaces their molecular fingerprints.
    • At the same time, parasites evolve very rapidly in their ability to use specific host receptors.
    • However, sex provides a mechanism for changing the distribution of alleles and varying them among offspring.
    • This coevolution in which host and parasite must evolve quickly to keep up with each other has been called a “Red Queen race.”

      Natural selection cannot fashion perfect organisms.

    • There are at least four reasons natural selection cannot produce perfection.
      1. Evolution is limited by historical constraints.
        • Evolution does not scrap ancestral features and build new complex structures or behavior from scratch.
        • Evolution co-opts existing features and adapts them to new situations.
        • For example, birds might benefit from having wings plus four legs. However, birds descended from reptiles that had only two pairs of limbs. Co-opting the forelimbs for flight left only two hind limbs for movement on the ground.
      2. Adaptations are often compromises.
        • Each organism must do many different things.
        • Because the flippers of a seal must allow it to walk on land and also swim efficiently, their design is a compromise between these environments.
        • Similarly, human limbs are flexible and allow versatile movements, but are prone to injuries, such as sprains, torn ligaments, and dislocations.
        • Better structural reinforcement would compromise agility.
      3. Chance and natural selection interact.
        • Chance events affect the subsequent evolutionary history of populations.
        • For example, founders of new populations may not necessarily be the individuals best suited to the new environment, but rather those individuals that were carried there by chance.
      4. Selection can only edit existing variations.
        • Natural selection favors only the fittest variations from those phenotypes that are available.
        • New alleles do not arise on demand.
        • Natural selection works by favoring the best variants available.
        • The many imperfections of living organisms are evidence for evolution.

        Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 23-1

    Subject: 
    Subject X2: 

    Chapter 24 - The Origin of Species

    Chapter 24 The Origin of Species
    Lecture Outline

    Overview: That “Mystery of Mysteries”

    • Darwin visited the Galápagos Islands and found them filled with plants and animals that lived nowhere else in the world.
      • He realized that he was observing newly emerged species on these young islands.
    • Speciation—the origin of new species—is at the focal point of evolutionary theory because the appearance of new species is the source of biological diversity.
    • Microevolution is the study of adaptive change in a population.
    • Macroevolution addresses evolutionary changes above the species level.
      • It deals with questions such as the appearance of evolutionary novelties (e.g., feathers and flight in birds) that can be used to define higher taxa.
    • Speciation addresses the question of how new species originate and develop through the subdivision and subsequent divergence of gene pools.
    • The fossil record chronicles two patterns of speciation: anagenesis and cladogenesis.
    • Anagenesis, phyletic evolution, is the accumulation of changes associated with the gradual transformation of one species into another.
    • Cladogenesis, branching evolution, is the budding of one or more new species from a parent species.
      • Only cladogenesis promotes biological diversity by increasing the number of species.

    Concept 24.1 The biological species concept emphasizes reproductive isolation

    • Species is a Latin word meaning “kind” or “appearance.”
      • Traditionally, morphological differences have been used to distinguish species.
      • Today, differences in body function, biochemistry, behavior, and genetic makeup are also used to differentiate species.
    • Are organisms truly divided into the discrete units we called species, or is this classification an arbitrary attempt to impose order on the natural world?
    • In 1942, Ernst Mayr proposed the biological species concept.
      • A species is defined as a population or group of populations whose members have the potential to breed with each other in nature to produce viable, fertile offspring, but who cannot produce viable, fertile offspring with members of other species.
      • A biological species is the largest set of populations in which genetic exchange is possible and that is genetically isolated from other populations.
    • Species are based on interfertility, not physical similarity.
    • For example, eastern and western meadowlarks have similar shapes and coloration, but differences in song help prevent interbreeding between the two species.
    • In contrast, humans have considerable diversity, but we all belong to the same species because of our capacity to interbreed.

      Prezygotic and postzygotic barriers isolate the gene pools of biological species.

    • Because the distinction between biological species depends on reproductive incompatibility, the concept hinges on reproductive isolation, the existence of biological barriers that prevent members of two species from producing viable, fertile hybrids.
    • A single barrier may not block all genetic exchange between species, but a combination of several barriers can effectively isolate a species’ gene pool.
      • Typically, these barriers are intrinsic to the organisms, not due to simple geographic separation.
      • Reproductive isolation prevents populations belonging to different species from interbreeding, even if their ranges overlap.
    • Reproductive barriers can be categorized as prezygotic or postzygotic, depending on whether they function before or after the formation of zygotes.
    • Prezygotic barriers impede mating between species or hinder fertilization of ova if members of different species attempt to mate.
      • These barriers include habitat isolation, behavioral isolation, temporal isolation, mechanical isolation, and gametic isolation.
    • Habitat isolation. Two organisms that use different habitats (even in the same geographic area) are unlikely to encounter each other to even attempt mating.
      • Two species of garter snakes in the genus Thamnophis occur in the same areas. Because one lives mainly in water and the other is primarily terrestrial, they rarely encounter each other.
    • Behavioral isolation. Many species use elaborate courtship behaviors unique to the species to attract mates.
      • In many species, elaborate courtship displays identify potential mates of the correct species and synchronize gonadal maturation.
      • In the blue-footed booby, males perform a high-step dance that calls the female’s attention to the male’s bright blue feet.
    • Temporal isolation. Two species that breed during different times of day, different seasons, or different years cannot mix gametes.
      • The geographic ranges of the western spotted skunk and the eastern spotted skunk overlap. However, they do not interbreed because the former mates in late summer and the latter in late winter.
    • Mechanical isolation. Closely related species may attempt to mate but fail because they are anatomically incompatible and transfer of sperm is not possible.
      • For example, mechanical barriers contribute to the reproductive isolation of flowering plants that are pollinated by insects or other animals.
      • With many insects, the male and female copulatory organs of closely related species do not fit together, preventing sperm transfer.
    • Gametic isolation. The gametes of two species do not form a zygote because of incompatibilities preventing fertilization.
      • In species with internal fertilization, the environment of the female reproductive tract may not be conducive to the survival of sperm from other species.
      • For species with external fertilization, gamete recognition may rely on the presence of specific molecules on the egg’s coat, which adhere only to specific molecules on sperm cells of the same species.
      • A similar molecular recognition mechanism enables a flower to discriminate between pollen of the same species and pollen of a different species.
    • If a sperm from one species does fertilize the ovum of another, postzygotic barriers may prevent the hybrid zygote from developing into a viable, fertile adult.
      • These barriers include reduced hybrid viability, reduced hybrid fertility, and hybrid breakdown.
    • Reduced hybrid viability. Genetic incompatibility between the two species may abort the development of the hybrid at some embryonic stage or produce frail offspring.
      • This is true for the occasional hybrids between frogs in the genus Rana. Most do not complete development, and those that do are frail.
    • Reduced hybrid fertility. Even if the hybrid offspring are vigorous, the hybrids may be infertile, and the hybrid cannot backbreed with either parental species.
      • This infertility may be due to problems in meiosis because of differences in chromosome number or structure.
      • For example, while a mule, the hybrid product of mating between a horse and donkey, is a robust organism, it cannot mate (except very rarely) with either horses or donkeys.
    • Hybrid breakdown. In some cases, first generation hybrids are viable and fertile.
      • However, when they mate with either parent species or with each other, the next generation is feeble or sterile.
      • Strains of cultivated rice have accumulated different mutant recessive alleles at two loci in the course of their divergence from a common ancestor.
      • Hybrids between them are vigorous and fertile, but plants in the next generation that carry too many of these recessive alleles are small and sterile.
      • These strains are in the process of speciating.
    • Reproductive barriers can occur before mating, between mating and fertilization, or after fertilization.

      The biological species concept has some major limitations.

    • While the biological species concept has had an important impact on evolutionary theory, it is limited when applied to species in nature.
      • For example, one cannot test the reproductive isolation of morphologically similar fossils, which are separated into species based on morphology.
      • Even for living species, we often lack information on interbreeding needed to apply the biological species concept.
      • In addition, many species (e.g., bacteria) reproduce entirely asexually and are assigned to species based mainly on structural and biochemical characteristics.
      • Many bacteria transfer genes by conjugation and other processes, but this transfer is different from sexual recombination.

      Evolutionary biologists have proposed several alternative concepts of species.

    • Several alternative species concepts emphasize the processes that unite the members of a species.
    • The ecological species concept defines a species in terms of its ecological niche, the set of environmental resources that a species uses and its role in a biological community.
      • As an example, a species that is a parasite may be defined in part by its adaptations to a specific organism.
      • This concept accommodates asexual and sexual species.
    • The paleontological species concept focuses on morphologically discrete species known only from the fossil record.
      • There is little or no information about the mating capability of fossil species, and the biological species concept is not useful for them.
    • The phylogenetic species concept defines a species as a set of organisms with a unique genetic history.
      • Biologists compare the physical characteristics or molecular sequences of species to those of other organisms to distinguish groups of individuals that are sufficiently different to be considered separate species.
      • Sibling species are species that appear so similar that they cannot be distinguished on morphological grounds.
      • Scientists apply the biological species concept to determine if the phylogenetic distinction is confirmed by reproductive incompatibility.
    • The morphological species concept, the oldest and still most practical, defines a species by a unique set of structural features.
      • The morphological species concept has certain advantages. It can be applied to asexual and sexual species, and it can be useful even without information about the extent of gene flow.
      • However, this definition relies on subjective criteria, and researchers sometimes disagree about which structural features identify a species.
      • In practice, scientists use the morphological species concept to distinguish most species.
    • Each species concept may be useful, depending on the situation and the types of questions we are asking.

    Concept 24.2 Speciation can take place with or without geographic separation

    • Two general modes of speciation are distinguished by the way gene flow among populations is initially interrupted.
    • In allopatric speciation, geographic separation of populations restricts gene flow.
    • In sympatric speciation, speciation occurs in geographically overlapping populations when biological factors, such as chromosomal changes and nonrandom mating, reduce gene flow.

      Allopatric speciation: geographic barriers can lead to the origin of species.

    • Several geological processes can fragment a population into two or more isolated populations.
      • Mountain ranges, glaciers, land bridges, or splintering of lakes may divide one population into isolated groups.
      • Alternatively, some individuals may colonize a new, geographically remote area and become isolated from the parent population.
        • For example, mainland organisms that colonized the Galápagos Islands were isolated from mainland populations.
    • How significant a barrier must be to limit gene exchange depends on the ability of organisms to move about.
      • A geological feature that is only a minor hindrance to one species may be an impassible barrier to another.
      • The valley of the Grand Canyon is a significant barrier for the ground squirrels that have speciated on opposite sides.
      • For birds that can fly across the canyon, it is no barrier.
    • Once geographic separation is established, the separated gene pools may begin to diverge through a number of mechanisms.
      • Mutations arise.
      • Sexual selection favors different traits in the two populations.
      • Different selective pressures in differing environments act on the two populations.
      • Genetic drift alters allele frequencies.
    • A small, isolated population is more likely to have its gene pool changed substantially over a short period of time by genetic drift and natural selection.
      • For example, less than 2 million years ago, small populations of stray plants and animals from the South American mainland colonized the Galápagos Islands and gave rise to the species that now inhabit the islands.
    • However, very few small, isolated populations develop into new species; most simply persist or perish in their new environment.
    • To confirm that allopatric speciation has occurred, it is necessary to determine whether the separated populations have become different enough that they can no longer interbreed and produce fertile offspring when they come back in contact.
      • In some cases, researchers bring together members of separated populations in a laboratory setting.
      • Biologists can also assess allopatric speciation in the wild.
        • For example, females of the Galápagos ground finch Geospiza difficilis respond to the songs of males from the same island but ignore the songs of males of the same species from other islands.

      Sympatric speciation: a new species can originate in the geographic midst of the parent species.

    • In sympatric speciation, new species arise within the range of the parent populations.
      • Here reproductive barriers must evolve between sympatric populations.
      • In plants, sympatric speciation can result from accidents during cell division that result in extra sets of chromosomes, a mutant condition known as polyploidy.
      • In animals, it may result from gene-based shifts in habitat or mate preference.
    • An individual can have more than two sets of chromosomes.
      • An autopolyploid mutant is an individual that has more than two chromosome sets, all derived from a single species.
      • For example, a failure of mitosis or meiosis can double a cell’s chromosome number from diploid (2n) to tetraploid (4n).
      • The tetraploid can reproduce with itself (self-pollination) or with other tetraploids.
      • It cannot mate with diploids from the original population, because of abnormal meiosis by the triploid hybrid offspring.
    • A more common mechanism of producing polyploid individuals occurs when allopolyploid offspring are produced by the mating of two different species.
      • While the hybrids are usually sterile, they may be quite vigorous and propagate asexually.
      • In subsequent generations, various mechanisms may transform a sterile hybrid into a fertile polyploid.
      • These polyploid hybrids are fertile with each other but cannot breed with either parent species.
      • They thus represent a new biological species.
    • The origin of polyploid plant species is common and rapid enough that scientists have documented several such speciations in historical times.
      • For example, two new species of plants called goatsbeard (Tragopodon) appeared in Idaho and Washington in the early 1900s.
      • They are the results of allopolyploidy events between pairs of introduced European Tragopodon species.
    • Many plants important for agriculture are polyploid.
      • For example, wheat is an allohexaploid, with six sets of chromosomes from three different species.
      • Oats, cotton, potatoes, and tobacco are polyploid.
      • Plant geneticists now use chemicals that induce meiotic and mitotic errors to create new polyploid plants with special qualities.
        • One example is an artificial hybrid combining the high yield of wheat with the hardiness and disease resistance of rye.
    • While polyploid speciation does occur in animals, other mechanisms also contribute to sympatric speciation in animals.
      • Reproductive isolation can result when genetic factors cause individuals to exploit resources not used by the parent.
      • One example is the North American maggot fly, Rhagoletis pomonella.
        • The fly’s original habitat was native hawthorn trees.
        • About 200 years ago, some populations colonized newly introduced apple trees.
        • Because apples mature more quickly than hawthorn fruit, the apple-feeding flies have been selected for more rapid development and now show temporal isolation from the hawthorn-feeding maggot flies.
        • Speciation is underway.
    • Sympatric speciation is one mechanism that has been proposed for the explosive adaptive radiation of cichlid fishes in Lake Victoria, Africa.
      • This vast, shallow lake has filled and dried up repeatedly due to climate changes.
      • The current lake is only 12,000 years old but is home to 600 species of cichlid fishes.
        • The species are so genetically similar that many have likely arisen since the lake last filled.
      • While these species are clearly specialized for exploiting different food resources and other resources, nonrandom mating in which females select males based on a certain appearance has probably contributed, too.
    • Individuals of two closely related sympatric cichlid species will not mate under normal light because females have specific color preferences and males differ in color.
      • However, under light conditions that de-emphasize color differences, females will mate with males of the other species and produce viable, fertile offspring.
      • It seems likely that the ancestral population was polymorphic for color and that divergence began with the appearance of two ecological niches that divided the fish into subpopulations.
      • Genetic drift resulted in chance differences in the genetic makeup of the subpopulations, with different male colors and female preferences.
      • Sexual selection reinforced the color differences.
      • The lack of postzygotic barriers in this case suggests that speciation occurred relatively recently.
      • As pollution clouds the waters of Lake Victoria, it becomes more difficult for female cichlids to see differences in male color.
      • The gene pools of these two closely related species may blend again.
    • We will summarize the differences between sympatric and allopatric speciation.
    • In allopatric speciation, a new species forms while geographically isolated from its parent population.
      • As the isolated population accumulates genetic differences due to natural selection and genetic drift, reproductive isolation from the ancestral species may arise as a by-product of the genetic change.
      • Such reproductive barriers prevent breeding with the parent even if the populations reestablish contact.
    • Sympatric speciation requires the emergence of some reproductive barrier that isolates a subset of the population without geographic separation from the parent population.
      • In plants, the most common mechanism is hybridization between species or errors in cell division that lead to polyploid individuals.
      • In animals, sympatric speciation may occur when a subset of the population is reproductively isolated by a switch in food source or by sexual selection in a polymorphic population.
    • The evolution of many diversely adapted species from a common ancestor when new environmental opportunities arise is called adaptive radiation.
    • Adaptive radiation occurs when a few organisms make their way into new areas or when extinction opens up ecological niches for the survivors.
      • A major adaptive radiation of mammals followed the extinction of the dinosaurs 65 million years ago.
    • The Hawaiian archipelago is a showcase of adaptive radiation.
      • Located 3,500 km from the nearest continent, the volcanic islands were formed “naked” and gradually populated by stray organisms that arrived by wind or ocean currents.
      • The islands are physically diverse, with a range of altitudes and rainfall.
      • Multiple invasions and allopatric and sympatric speciation events have ignited an explosion of adaptive radiation of novel species.

      Researchers study the genetics of speciation.

    • Researchers have made great strides in understanding the role of genes in particular speciation events.
    • Douglas Schemske and his colleagues at Michigan State University examined two species of Mimulus.
      • The two species are pollinated by bees and hummingbirds respectively, keeping their gene pools separate through prezygotic isolation.
      • The species show no postzygotic isolation and can be mated readily in the greenhouse to produce hybrids with flowers that vary in color and shape.
      • Researchers observed which pollinators visit which flowers and then investigated the genetic differences between plants.
      • Two gene loci have been identified that are largely responsible for pollinator choice.
      • One locus influences flower color; the other affects the amount of nectar flowers produce.
      • By determining attractiveness of the flowers to different pollinators, allelic diversity at these loci has led to speciation.

      The tempo of speciation is important.

    • In the fossil record, many species appear as new forms rather suddenly (in geologic terms), persist essentially unchanged, and then disappear from the fossil record.
    • Darwin noted this when he remarked that species appeared to undergo modifications during relatively short periods of their total existence and then remained essentially unchanged.
    • Paleontologists Niles Eldredge and Stephen Jay Gould coined the term punctuated equilibrium to describe these periods of apparent stasis punctuated by sudden change.
    • Some scientists suggest that these patterns require an explanation outside the Darwinian model of descent with modification.
      • However, this is not necessarily the case.
    • Suppose that a species survived for 5 million years, but most of its morphological alterations occurred in the first 50,000 years of its existence—just 1% of its total lifetime.
      • Because time periods this short often cannot be distinguished in fossil strata, the species would seem to have appeared suddenly and then lingered with little or no change before becoming extinct.
      • Even though the emergence of this species actually took tens of thousands of years, this period of change left no fossil record.
    • Stasis can also be explained.
      • All species continue to adapt after they arise, but often by changes that do not leave a fossil record, such as small biochemical modifications.
    • Paleontologists base hypotheses of descent almost entirely on external morphology.
      • During periods of apparent equilibrium, changes in behavior, internal anatomy, and physiology may not leave a fossil record.
    • If the environment changes, the stasis will be broken by punctuations that leave visible traces in the fossil record.

    Concept 24.3 Macroevolutionary changes can accumulate through many speciation events

    • Speciation is at the boundary between microevolution and macroevolution.
      • Microevolution is a change over generations in a population’s allele frequencies, mainly by genetic drift and natural selection.
      • Speciation occurs when a population’s genetic divergence from its ancestral population results in reproductive isolation.
      • While the changes after any speciation event may be subtle, the cumulative change over millions of speciation episodes must account for macroevolution, the scale of changes seen in the fossil record.

      Most evolutionary novelties are modified versions of older structures.

    • The Darwinian concept of descent with modification can account for the major morphological transformations of macroevolution.
    • It may be difficult to believe that a complex organ like the human eye could be the product of gradual evolution, rather than a finished design created specially for humans.
    • However, the key is to remember is that a very simple eye can be very useful to an animal.
    • The simplest eyes are just clusters of photoreceptors, light-sensitive pigmented cells.
    • These simple eyes appear to have had a single evolutionary origin.
      • They are now found in a variety of animals, including limpets.
    • These simple eyes have no lenses and cannot focus an image, but they do allow the animal to distinguish light from dark.
      • Limpets cling tightly to their rocks when a shadow falls on them, reducing their risk of predation.
    • Complex eyes have evolved several times independently in the animal kingdom.
      • Examples of various levels of complexity, from clusters of photoreceptors to camera-like eyes, can be seen in molluscs.
      • The most complex types did not evolve in one quantum leap, but by incremental adaptation of organs that benefited their owners at each stage.
    • Evolutionary novelties can also arise by gradual refinement of existing structures for new functions.
      • Structures that evolve in one context, but become co-opted for another function, are exaptations.
    • It is important to recognize that natural selection can only improve a structure in the context of its current utility, not in anticipation of the future.
    • An example of an exaptation is the changing function of lightweight, honeycombed bones of birds.
      • The fossil record indicates that light bones predated flight.
      • Therefore, they must have had some function on the ground, perhaps as a light frame for agile, bipedal dinosaurs.
      • Once flight became an advantage, natural selection would have remodeled the skeleton to better fit their additional function.
      • The wing-like forelimbs and feathers that increased the surface area of these forelimbs were co-opted for flight after functioning in some other capacity, such as courtship, thermoregulation, or camouflage.

      Genes that control development play a major role in evolution.

    • “Evo-devo” is a field of interdisciplinary research that examines how slight genetic divergences can become magnified into major morphological differences between species.
    • A particular focus is on genes that program development by controlling the rate, timing, and spatial pattern of changes in form as an organism develops from a zygote to an adult.
    • Heterochrony, an evolutionary change in the rate or timing of developmental events, has led to many striking evolutionary transformations.
    • Allometric growth tracks how proportions of structures change due to different growth rates during development.
    • Change relative rates of growth even slightly, and you can change the adult form substantially.
      • Different allometric patterns contribute to the contrast of adult skull shapes between humans and chimpanzees, which both developed from fairly similar fetal skulls.
    • Heterochrony appears to be responsible for differences in the feet of tree-dwelling versus ground-dwelling salamanders.
      • The feet of the tree-dwellers are adapted for climbing vertically, with shorter digits and more webbing.
      • This modification may have evolved due to mutations in the alleles that control the timing of foot development.
      • Stunted feet may have resulted if regulatory genes switched off foot growth early.
      • In this way, a relatively small genetic change can be amplified into substantial morphological change.
    • Another form of heterochrony is concerned with the relative timing of reproductive development and somatic development.
    • If the rate of reproductive development accelerates compared to somatic development, then a sexually mature stage can retain juvenile structures—a process called paedomorphosis.
      • Some species of salamander have the typical external gills and flattened tail of an aquatic juvenile, but have functioning gonads.
    • Macroevolution can also result from changes in genes that control the placement and spatial organization of body parts.
      • For example, genes called homeotic genes determine such basic features as where a pair of wings and a pair of legs will develop on a bird or how a plant’s flower parts are arranged.
    • The products of one class of homeotic genes, the Hox genes, provide positional information in an animal embryo.
      • This information prompts cells to develop into structures appropriate for a particular location.
    • One major transition in the evolution of vertebrates is the development of the walking legs of tetrapods from the fins of fishes.
      • A fish fin that lacks external skeletal support evolved into a tetrapod limb that extends skeletal supports (digits) to the tip of the limb.
      • This may be the result of changes in the positional information provided by Hox genes during limb development, determining how far digits and other bones should extend from the limb.

      Evolution is not goal oriented.

    • The fossil record shows apparent evolutionary trends.
      • For example, the evolution of the modern horse can be interpreted to have been a steady series of changes from a small, browsing ancestor (Hyracotherium) with four toes to modern horses (Equus) with only one toe per foot and teeth modified for grazing on grasses.
    • It is possible to arrange a succession of animals intermediate between Hyracotherium and modern horses to show trends toward increased size, reduced number of toes, and modifications of teeth for grazing.
    • If we look at all fossil horses, the illusion of coherent, progressive evolution leading directly to modern horses vanishes.
      • Equus is the only surviving twig of an evolutionary bush that included several adaptive radiations among both grazers and browsers.
    • Differences among species in survival can also produce a macroevolutionary trend.
    • The species selection model developed by Steven Stanley considers species as analogous to individuals.
      • Speciation is their birth, extinction is their death, and new species are their offspring.
    • In this model, Stanley suggests that just as individual organisms undergo natural selection, species undergo species selection.
    • The species that endure the longest and generate the greatest number of new species determine the direction of major evolutionary trends.
    • The species selection model suggests that “differential speciation success” plays a role in macroevolution similar to the role of differential reproductive success in microevolution.
    • To the extent that speciation rates and species longevity reflect success, the analogy to natural selection is even stronger.
      • However, qualities unrelated to the overall success of organisms in specific environments may be equally important in species selection.
      • As an example, the ability of a species to disperse to new locations may contribute to its giving rise to a large number of “daughter species.”
    • The appearance of an evolutionary trend does not imply some intrinsic drive toward a preordained state of being.
      • Evolution is a response to interactions between organisms and their current environments, leading to changes in evolutionary trends as conditions change.

      Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 24-1

    Subject: 
    Subject X2: 

    Chapter 25 - Phylogeny and Systematics

    Chapter 25 Phylogeny and Systematics
    Lecture Outline

    Overview: Investigating the Tree of Life

    • Evolutionary biology is about both process and history.
      • The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species.
      • A major goal of evolutionary biology is to reconstruct the history of life on earth.
    • In this chapter, we will consider how scientists trace phylogeny, the evolutionary history of a group of organisms.
    • To reconstruct phylogeny, scientists use systematics, an analytical approach to understanding the diversity and relationships of living and extinct organisms.
      • Evidence used to reconstruct phylogenies can be obtained from the fossil record and from morphological and biochemical similarities between organisms.
      • In recent decades, systematists have gained a powerful new tool in molecular systematics, which uses comparisons of nucleotide sequences in DNA and RNA to help identify evolutionary relationships between individual genes or even entire genomes.
    • Scientists are working to construct a universal tree of life, which will be refined as the database of DNA and RNA sequences grows.

    Concept 25.1 Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence

      Sedimentary rocks are the richest source of fossils.

    • Fossils are the preserved remnants or impressions left by organisms that lived in the past.
    • In essence, they are the historical documents of biology.
    • Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and swamps, where the minerals settle to the bottom along with the remains of organisms.
      • As deposits pile up, they compress older sediments below them into layers called strata.
      • The fossil record is the ordered array in which fossils appear within sedimentary rock strata.
        • These rocks record the passing of geological time.
      • Fossils can be used to construct phylogenies only if we can determine their ages.
      • The fossil record is a substantial, but incomplete, chronicle of evolutionary change.
      • The majority of living things were not captured as fossils upon their death.
        • Of those that formed fossils, later geological processes destroyed many.
        • Only a fraction of existing fossils have been discovered.
      • The fossil record is biased in favor of species that existed for a long time, were abundant and widespread, and had hard shells or skeletons that fossilized readily.

      Morphological and molecular similarities may provide clues to phylogeny.

    • Similarities due to shared ancestry are called homologies.
    • Organisms that share similar morphologies or DNA sequences are likely to be more closely related than organisms without such similarities.
    • Morphological divergence between closely related species can be small or great.
      • Morphological diversity may be controlled by relatively few genetic differences.
    • Similarity due to convergent evolution is called analogy.
      • When two organisms from different evolutionary lineages experience similar environmental pressures, natural selection may result in convergent evolution.
        • Similar analogous adaptations may evolve in such organisms.
      • Analogies are not due to shared ancestry.
    • Distinguishing homology from analogy is critical in the reconstruction of phylogeny.
      • For example, both birds and bats have adaptations that allow them to fly.
      • However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb that to a bird’s wing.
      • Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors.
      • Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing.
    • Analogous structures that have evolved independently are also called homoplasies.
    • In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently.
      • For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones.
      • The two skulls match almost perfectly, bone for bone.
      • It is highly unlikely that such complex structures have separate origins.
      • More likely, the genes involved in the development of both skulls were inherited from a common ancestor.
    • The same argument applies to comparing genes, which are sequences of nucleotides.
    • Systematists compare long stretches of DNA and even entire genomes to assess relationships between species.
      • If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous.
    • It may be difficult to carry out molecular comparisons of nucleic acids.
      • The first step is to align nucleic acid sequences from the two species being studied.
      • In closely related species, sequences may differ at only one or a few sites.
      • Distantly related species may have many differences or sequences of different length.
        • Over evolutionary time, insertions and deletions accumulate, altering the lengths of the gene sequences.
    • Deletions or insertions may shift the remaining sequences, making it difficult to recognize closely matching nucleotide sequences.
      • To deal with this, systematists use computer programs to analyze comparable DNA sequences of differing lengths and align them appropriately.
    • The fact that molecules have diverged between species does not tell us how long ago their common ancestor lived.
      • Molecular divergences between lineages with reasonably complete fossil records can serve as a molecular yardstick to measure the appropriate time span of various degrees of divergence.
    • As with morphological characters, it is necessary to distinguish homology from analogy to determine the usefulness of molecular similarities for reconstruction of phylogenies.
      • Closely similar sequences are most likely homologies.
      • In distantly related organisms, identical bases in otherwise different sequences may simply be coincidental matches or molecular homoplasies.
    • Scientists have developed mathematical tools that can distinguish “distant” homologies from coincidental matches in extremely divergent sequences.
      • For example, such molecular analysis has provided evidence that humans share a distant common ancestor with bacteria.
    • Scientists have sequenced more than 20 billion bases worth of nucleic acid data from thousands of species.

    Concept 25.2 Phylogenetic systematics connects classification with evolutionary history

    • In 1748, Carolus Linnaeus published Systema naturae, his classification of all plants and animals known at the time.
    • Taxonomy is an ordered division of organisms into categories based on similarities and differences.
    • Linneaus’s classification was not based on evolutionary relationships but simply on resemblances between organisms.
      • Despite this, many features of his system remain useful in phylogenetic systematics.

      Taxonomy employs a hierarchical system of classification.

    • The Linnaean system, first formally proposed by Linnaeus in Systema naturae in the 18th century, has two main characteristics.
      1. Each species has a two-part name.
      2. Species are organized hierarchically into broader and broader groups of organisms.
    • Under the binomial system, each species is assigned a two-part Latinized name, a binomial.
      • The first part, the genus, is the closest group to which a species belongs.
      • The second part, the specific epithet, refers to one species within each genus.
      • The first letter of the genus is capitalized and both names are italicized and Latinized.
      • For example, Linnaeus assigned to humans the optimistic scientific name Homo sapiens, which means “wise man.”
    • A hierarchical classification groups species into increasingly broad taxonomic categories.
    • Species that appear to be closely related are grouped into the same genus.
      • For example, the leopard, Panthera pardus, belongs to a genus that includes the African lion (Panthera leo) and the tiger (Panthera tigris).
    • Genera are grouped into progressively broader categories: family, order, class, phylum, kingdom, and domain.
    • Each taxonomic level is more comprehensive than the previous one.
      • As an example, all species of cats are mammals, but not all mammals are cats.
    • The named taxonomic unit at any level is called a taxon.
      • Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all of the many orders of mammals.
    • Higher classification levels are not defined by some measurable characteristic, such as the reproductive isolation that separates biological species.
    • As a result, the larger categories are not comparable between lineages.
      • An order of snails does not necessarily exhibit the same degree of morphological or genetic diversity as an order of mammals.

      Classification and phylogeny are linked.

    • Systematists explore phylogeny by examining various characteristics in living and fossil organisms.
    • They construct branching diagrams called phylogenetic trees to depict their hypotheses about evolutionary relationships.
    • The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups.
    • Methods for tracing phylogeny began with Darwin, who realized the evolutionary implications of Linnaean hierarchy.
    • Darwin introduced phylogenetic systematics in On the Origin of Species when he wrote: “Our classifications will come to be, as far as they can be so made, genealogies.”

    Concept 25.3 Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters

    • Patterns of shared characteristics can be depicted in a diagram called a cladogram.
    • If shared characteristics are homologous and, thus, explained by common ancestry, then the cladogram forms the basis of a phylogenetic tree.
      • A clade is defined as a group of species that includes an ancestral species and all its descendents.
    • The study of resemblances among clades is called cladistics.
      • Each branch, or clade, can be nested within larger clades.
    • A valid clade is monophyletic, consisting of an ancestral species and all its descendents.
      • When we lack information about some members of a clade, the result is a paraphyletic grouping that consists of some, but not all, of the descendents.
      • The result may also be several polyphyletic groupings that lack a common ancestor.
      • Such situations call for further reconstruction to uncover species that tie these groupings together into monophyletic clades.
    • Determining which similarities between species are relevant to grouping the species in a clade is a challenge.
    • It is especially important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy.
    • Systematists must also sort through homologous features, or characters, to separate shared derived characters from shared primitive characters.
      • A “character” refers to any feature that a particular taxon possesses.
      • A shared derived character is unique to a particular clade.
      • A shared primitive character is found not only in the clade being analyzed, but also in older clades.
    • For example, the presence of hair is a good character to distinguish the clade of mammals from other tetrapods.
      • It is a shared derived character that uniquely identifies mammals.
    • However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals.
      • Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates.
    • Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.
      • The status of a character shared derived versus shared primitive may depend on the level at which the analysis is being performed.
    • A key step in cladistic analysis is outgroup comparison, which is used to differentiate shared primitive characters from shared derived ones.
    • To do this, we need to identify an outgroup, a species or group of species that is closely related to the species that we are studying, but known to be less closely related than any members of the study group are to each other.
    • To study the relationships among an ingroup of five vertebrates (a leopard, a turtle, a salamander, a tuna, and a lamprey) on a cladogram, an animal called the lancelet is a good choice.
      • The lancelet is a small member of the Phylum Chordata that lacks a backbone.
    • The species making up the ingroup display a mixture of shared primitive and shared derived characters.
    • In an outgroup analysis, the assumption is that any homologies shared by the ingroup and outgroup are primitive characters that were present in the common ancestor of both groups.
    • Homologies present in some or all of the ingroup taxa are assumed to have evolved after the divergence of the ingroup and outgroup taxa.
    • In our example, a notochord, present in lancelets and in the embryos of the ingroup, is a shared primitive character and, thus, not useful for sorting out relationships between members of the ingroup.
      • The presence of a vertebral column, shared by all members of the ingroup but not the outgroup, is a useful character for the whole ingroup.
      • The presence of jaws, absent in lampreys and present in the other ingroup taxa, helps to identify the earliest branch in the vertebrate cladogram.
    • Analyzing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.
    • A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.
      • However, this chronology does not indicate the time of origin of the species that we are comparing, only the groups to which they belong.
      • For example, a particular species in an old group may have evolved more recently than a second species that belongs to a newer group.
    • A cladogram is not a phylogenetic tree.
      • To convert it to a phylogenetic tree, we need more information from sources such as the fossil record, which can indicate when and in which groups the characters first appeared.
    • Any chronology represented by the branching pattern of a phylogenetic tree is relative (earlier versus later) rather than absolute (so many millions of years ago).
    • Some kinds of tree diagrams can be used to provide more specific information about timing.
    • In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in a lineage.
    • Even though the branches in a phylogram may have different lengths, all the different lineages that descend from a common ancestor have survived for the same number of years.
      • Humans and bacteria had a common ancestor that lived more than 3 billion years ago.
      • This ancestor was a single-celled prokaryote and was more like a modern bacterium than like a human.
      • Even though bacteria have apparently changed little in structure since that common ancestor, there have nonetheless been 3 billion years of evolution in both the bacterial and eukaryotic lineages.
    • These equal amounts of chronological time are represented in an ultrameric tree.
    • In an ultrameric tree, the branching pattern is the same as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal lengths.
    • Ultrameric trees do not contain the information about different evolutionary rates that can be found in phylograms.
      • However, they draw on data from the fossil record to place certain branch points in the context of geological time.

      The principles of maximum parsimony and maximum likelihood help systematists reconstruct phylogeny.

    • As available data about DNA sequences increase, it becomes more difficult to draw the phylogenetic tree that best describes evolutionary history.
      • If you are analyzing data for 50 species, there are 3 × 1076 different ways to form a tree.
    • According to the principle of maximum parsimony, we look for the simplest explanation that is consistent with the facts.
      • In the case of a tree based on morphological characters, the most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters.
      • For phylograms based on DNA sequences, the most parsimonious tree requires the fewest base changes in DNA.
    • The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree should reflect the most likely sequence of evolutionary events.
      • Maximum likelihood methods are designed to use as much information as possible.
    • Many computer programs have been developed to search for trees that are parsimonious and likely:
      • “Distance” methods minimize the total of all the percentage differences among all the sequences.
      • More complex “character-state” methods minimize the total number of base changes or search for the most likely pattern of base changes among all the sequences.
    • Although we can never be certain precisely which tree truly reflects phylogeny, if they are based on a large amount of accurate data, the various methods usually yield similar trees.

      Phylogenetic trees are hypotheses.

    • Any phylogenetic tree represents a hypothesis about how the organisms in the tree are related.
      • The best hypothesis is the one that best fits all the available data.
    • A hypothesis may be modified when new evidence compels systematists to revise their trees.
      • Many older phylogenetic hypotheses have been changed or rejected since the introduction of molecular methods for comparing species and tracing phylogeny.
    • Often, in the absence of conflicting information, the most parsimonious tree is also the most likely.
      • Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious.
      • Nature does not always take the simplest course.
      • In some cases, the particular morphological or molecular character we are using to sort taxa actually did evolve multiple times.
    • For example, the most parsimonious assumption would be that the four-chambered heart evolved only once in an ancestor common to birds and mammals but not to lizards, snakes, turtles, and crocodiles.
    • But abundant evidence indicated that birds and mammals evolved from different reptilian ancestors.
      • The hearts of birds and mammals develop differently, supporting the hypothesis that they evolved independently.
      • The most parsimonious tree is not consistent with the above facts, and must be rejected in favor of a less parsimonious tree.
    • The four-chambered hearts of birds and mammals are analogous, not homologous.
    • Occasionally misjudging an analogous similarity in morphology or gene sequence as a shared derived homology is less likely to distort a phylogenetic tree if several derived characters define each clade in the tree.
      • The strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as by fossil evidence.

    Concept 25.4 Much of an organism’s evolutionary history is documented in its genome

    • Molecular systematics is a valuable tool for tracing an o