AP Biology

This course can help prepare students who wish to continue their scientific education after high school, as well as students who wish to prepare for the SAT exam. The level of aptitude in this subject will assist students wishing to excel on the SAT and in college courses.

According to the College Board’s website, AP Biology courses are designed to be the equivalent of a college introductory course, usually taken during a biology major’s first year of college. Students who choose to take AP Biology may be allowed to skip over introductory biology courses and enroll in courses in which biology is a prerequisite. Because universities grant college credit for this course, they require that the textbooks, labs, and coursework used by AP courses be equivalent to those used in actual college courses.

This course is offered to highly motivated students who wish to pursue their interests in the biological sciences. Enrollment requirements for the AP Biology course depend on policies established by each high school offering the course, but AP Biology is usually preceded by a less rigorous entry level Biology course, and sometimes by Chemistry as well. While some schools may have selective acceptance into the course, determined by academic record in prerequisite courses, other schools adhere to a policy of open enrollment, encouraging its undertaking by students that demonstrate capability for the course, though they may have performed unsatisfactorily in previous science courses.

Topics covered by this course include, Anatomy & Physiology, Biochemistry, Biodiversity, Botany, The Cell, Developmental Biology, Ecology, Genetics, Molecular Biology, Origin of life, Population Biology, and Evolution.

Students taking AP Biology should first complete an introductory course in Biology, usually lasting one school year. An introductory course will prepare students to study higher levels of science and familiarize them with the scientific process. Students should also have experience with basic mathematical functions in order to complete experiments.

AP Biology is a serious course with a number course goals. According to the College Board’s website, by the time students take their AP Biology exam (or the SAT exam) they should:

  • Develop a conceptual framework of Biology as a science.  Students should focus more on concepts and discoveries rather than simply memorizing terms and technical details and routinely repeating information on exams. Students should be able to appreciate science as a coherent body of information and seek to apply it both inside and outside of the classroom.
  • Gain an appreciation of the scientific process, its history, and its present day applications. Students should also be able to understand the importance of the scientific process while experimenting and be able to explain how they’ve used the scientific process in their own experiments both in writing and through the written word.
  • Develop a deeper understanding of different biological process, particularly as they apply to living beings and life cycles.
  • Use study notes and other study techniques in conjunction with various AP Biology textbooks.

The College Board also recently released a requirement for the AP Biology exam, underlining what portion of the test should be dedicated to what field of study. Accordingly, the following goals for the test were released:

  • 25% of the test should be dedicated to Molecules and Cells.
  • 25% of the test should be dedicated to Heredity and Evolution.
  • 50% of the test should be dedicated to Organisms and Populations.

Students studying for both the AP Biology exam as well as the SAT should keep these parameters in mind. These basic goals may determine how much time is spent covering these different areas of study over the course of the school year as well as how much time is allotted to complete each section of the AP Biology test.

Students interested in taking AP Biology or any other Advanced Placement course should keep in mind that taking college level courses in high school requires a commitment of time and energy.  Students that commit themselves to their classes and treat them as college level courses will see a definite pay off in their grades as well as their confidence.

Students wishing to get into prestigious, well-respected colleges or universities should definitely consider taking Advanced Placement courses. These courses look excellent on high school transcripts and can give students an invaluable look at college courses before they even enroll in them. Students also have the opportunity to earn college credit before graduating, which can save valuable time and money once college begins. The more students work to prepare themselves for the high-pressure college atmosphere before beginning their college education, the more enjoyable and successful their college career will be in the end. So, for student wishing to get a jump start on their college education and their careers after college, the AP course program is the perfect choice! 

Here you will find AP Biology outlines and slides. We are working to add more AP Biology resources such as vocabulary terms, unit notes, topic notes, study questions, practice quizzes and glossary terms. 

Subject X2: 

Biology Labs

Below you will find supplemental biology study materials:

Subject X2: 

Lab Safety, Metric System

safety rules  

  • no eating, drinking, or smoking in the laboratory
  • broken glass must be disposed in the glass disposal box (to be only used for broken glass)
  • inform instructor immediately if anyone is cut or injured
  • mercury from broken thermometers should only be cleaned up by the instructor w/ a mercury cleaning kit
  • be careful w/ glassware, never try to force glass pipettes into the pump
  • wear close toed shoes
  • know where to find emergency equipment
  • report anything that appears hazardous to the instructor
  • don't bring children to the lab

prefixes of metric system  

  • Giga (G) - 109
  • Mega (M) - 106
  • Kilo (k) - 103
  • Deci (d) - 10-1
  • Centi (c) - 10-2
  • Milli (m) - 10-3
  • Micro (µa) - 10-6
  • Nano (n) - 10-9
  • Pico (p) - 10-12
  • Femto (f) - 10-15
Subject X2: 


Parts of Light Microscope (aka compound microscope)  

  • Oculars - lens that you look through
  • Body Tube - metal casing through which light passes to the oculars
  • Arm - where you should hold the microscope when holding it
  • Coarse focus adjustment - should only be used w/ 4x or 10x objectives
  • Fine focus adjustment - used w/ powerful magnifications
  • Nosepiece - holds the objectives
  • Objectives - lenses mounted on the nosepiece
  • Stage - where the specimen is placed
  • Condenser - allows light onto the specimen
  • Iris diaphragm - ring that can be opened/closed to allow light in
  • Condenser Adjustment - used to manipulate the iris diaphragm
  • Lamp - light source
  • Base - bottom of the microscope

Preparing a wet mount  

  • place drop of water on clean microscopic slide
  • place coverslip on at 45 degree angle
  • slowly cover the drop so that no air bubbles remain

Focusing the microscope  

  • use lowest power objective first
  • use coarse adjustment
  • change to higher objectives
  • only use fine adjustive w/ high objectives
  • parafocal - stays in focus after changing objectives
  • parcaentered - stays centered after changing objectives
  • field of view - area that you can see through the microscope
  • wet mount - glass slide containing specimen, usually in water

Finding total magnification and field of view  

  • total magnification = objective's magnification x ocular magnification
  • diameter under low power x low magnification = diameter under high power x high magnification
  • area = pi x radius2

Dissecting Microscope (aka stereoscopic microscope)  

  • more working distance than light microscope
  • light from either top or bottom
  • only 1 objective
Subject X2: 


cytology - study of cellular structure/function  

  • uses light microscopy, electron microscopy, cell chemistry

prokaryotes - no nucleus or organelles  

  • organelles - structures of macromolecules w/ special functions
  • cytoplasm - liquid inside the plasma membrane
  • cell wall - surrounds the membrane, covered by a gelatinous capsule
  • appendages - flagella/pili; used for mov't and attachment
  • ribosomes - used for protein synthesis
  • mesosomes - internal extensions of membrane
  • chromatin bodies - DNA concentrations

Cyanobacteria - largest prokaryotes  

  • aka blue-green algae
  • thylakoids - green pigments for chloroplasts
  • mucilaginous sheath - surrounds cyanobacteria

eukaryotes - contain nuclei and organelles  

  • chloroplasts - where photosynthesis takes place; chlorophyll pigment gives it its green color
  • mitochondria - where aerobic respiration takes place; folds inward to form critae (where respiration enzymes are located)
  • protoplast - collective name for all material/organelles within the membrane

plant cells  

  • cellulose - carboyhydrate material in plant cell walls
  • central vacuole - contains mostly water, held together by cauolar membrane; takes up 90% of cell
  • nucleolus - dense, dark spot in the nucleus
  • cytoplasmic streaming (cyclosis) - mov't of chloroplasts due to cytoplasm
  • primary cell wall - outer part of cell wall
  • middle lamella - substance holding adjacent cell walls together
  • plasmodesmata - cytoplasmic strands penetrating the cell walls; links the protoplasms of adjacent cells

plastids - organelles where food is made  

  • mitochondria/chloroplasts are examples
  • amyloplasts - plastids that store starch; stains darkly w/ iodine

animal cells  

  • epithelial cells - from inner surface of mouth
  • have mitochondria in place of chloroplasts

protists - kingdom of eukaryotic, single-celled organisms  

  • amoeba - irregularly shaped protist
    • move w/ amoeboid mov't, using pseudopodia (temporary cell protrusions)
    • surrounds food particles to digest
    • contractile vacuole - gathers, expels water/waste
  • paramecium
    • gullet - where food enters
    • micro/macronucleus
    • cilia - hair-like appendages, used for mov't
Subject X2: 

Biologically Important Molecules

organic compounds - macromolecules made of subunits in living organisms  

  • carbohydrates, proteins, lipids, nucleic acids
  • dehydration synthesis - water molecule removed to bond 2 subunits
  • hydrolysis - exothermic reaction where water is added to break bonds between subunits
  • different structures and arrangments give compounds different characteristics

controlled experiments - has controls used for comparison  

  • unknown solution - may or may not contain the substance that is being tested for
  • positive control - contains the substance that is being tested for; shows what a positive test should look like
  • negative control - doesn't react in the test; shows what a negative result should look like

carbohydrates - molecules made of C, H, and O in ratio 1:2:1  

  • monosaccharides - simple sugars
  • disaccharides - paired monosaccharides
  • polysaccharides - linking together 3 or more monosaccharides
  • reducing sugars - monosaccharides that have free adlehyde (-CHO) or ketone (-C=O) groups that reduce weak oxidizing agents
  • Benedict's test - identifies reducing sugars that can reduce the cupric ions in Benedict's reagent into cuprous oxide
  • iodine test - iodine-potassium iodide reacts w/ coiled molecules of starch to become bluish black; doesn't react w/ other carbohydrates as much

proteins - made of amino acids  

  • each amino acid has amino group, carboxyl group, and variable side chain
  • peptide bond - forms between amino group and carboxyl group of 2 amino acids
  • Biuret test - peptide bonds of proteins produce a violet color when in contact w/ the copper II found in Biuret reagent; individual amino acids do not react

lipids - nonpolar molecules w/ many C-H bonds  

  • dissolve in nonpolar solvents
  • fats (triglycerides) - made of glycerol and 3 fatty acids
  • tests based on lipid's ability to change color w/ fat-soluble dyes (ex. Sudan IV)
  • grease-spot test - lipids produce translucent grease-marks on unglazed paper

nucleic acids - made of nucleotide subunits  

  • either DNA or RNA (differences in sugar structure and organic bases)
  • Dische diphenylamine test - makes deoxyribose into another molecule that bonds w/ diphenylamine to make a blue color
Subject X2: 

Diffusion, Osmosis

Brownian movement - random mov't of molecules in biological systems

  • occurs due to collisions between molecules
  • molecules' mov't can't directly be seen, but mov't after collisions can be seen

diffusion - directional mov't of molecules down a gradient

  • from areas of high concentration, heat, pressure to areas of low concentration, heat, pressure
  • rate determined by steepness of gradient and characteristics of the molecules
  • temperature/pressure usually constant in most biological systems
  • selective (differentiable) permeability - ability of cell membranes to decide what moleules can pass through it; selects based on size, charge, solubility
  • polar molecules - positive/negative charged areas
  • nonpolar molecules - no local areas of charge
  • small nonpolar molecules pass through the membrane most easily
  • dialysis - separation of dissolved substances by using their unequal diffusions

osmosis - diffusion of water across a differentially permeable membrane

  • follows rules of diffusion, except w/ water
  • hypotonic - solution w/ lower solute concentration than surrounding environment
  • hypertonic - solution w/ higher solute concentration than surrounding environment
  • isotonic - 2 solutions w/ equal solute concentration
  • water moves from hypotonic to hypertonic areas
  • even in isotonic solutions, water still moves, but concentrations stay the same

water potential - effects of concentration/pressure from cell walls

  • increased by high water concentration/pressure
  • decreased by high solute concentration, low pressure
  • water flows from areas of high water potential to areas of low water potential

lysis - destruction of cell by influx of water

  • animal cells lack cell walls, bursts more easily than plant cells
  • hemolysis - lysis of red blood cells
  • crenation - shriveling of cells
  • plasmolysis - shrinking of plant cytoplasm, where cell membrane pulls away from cell wall in plants
Subject X2: 

Cellular Respiration

cellular respiration - oxidation of organic molecules, release of energy

  • C6H12O6 + 6O2 >> 6 CO2 + 6H2O + ATP + heat
  • usually organic molecules taken in, CO2/H2O released as waste
  • adenosine triphosphate (ATP) - used as direct source of energy in cellular metabolism
  • glycolysis - oxidation of glucose to pyruvate
    • some energy stored in ATP
    • occurs w/ or w/o oxygen, but doesn't continue to citric acid cycle w/o oxygen
  • citric acid cycle (tricarboxylic acid cycle or Krebs cycle)
    • oxidizes pyruvate to CO2
    • must use oxygen
    • used by aerobes
    • stores energy in nicotinamide adenine dinucleotide (NAD)
  • electron transport chain - makes proton gradients from energy in NAD
    • makes about 18x as much ATP as glycolysis
    • oxygen - final electron acceptor; chain won't work w/o oxygen
    • measuring O2 consumption/ CO2 production also measures the aerobic respiration rate

anaerobes - live w/o oxygen; may even be poisoned by oxygen

  • use inorganic electron acceptors
  • uses fermentation instead of Krebs cycle to reduce pyruvate
    • makes ethanol in plants/yeast
    • makes lactic acid in animals
  • C6H12O6>> 2C2H5OH (ethanol) + 2CO2 + ATP + heat
  • C6H12O6>> 2CH3CHOHCOOH + ATP + heat
  • produces 18 fewer ATP than aerobic respiration
  • pickling - preserves food, involves anaerobic fermentation of sugars to lactic acid
  • wine making - invovles alcoholic fermentation by yeasts
Subject X2: 


photosynthesis - converts radiant energy to chemical energy

  • 6CO2 + 12H2O >> C6H12O6 + 6O2 + 6H2O
  • dependent on light and chlorophyll
  • oxygen released into environment; sugar used for growth or storage
  • reactant/product water molecules are different
  • chloroplast - organelle for photosynthesis
    • thylakoids - photosynthetic membranes
    • grana - stacks of thylakoids
    • lamellae - holds grana in place
    • stroma - semiliquid in chloroplasts
  • photochemical (light) reactions -
    • splits water to release O2, electrons, protons
    • almost at instantaneous speed
    • light-dependent
  • biochemical (dark) reactions (Calvin cycle) -
    • converts CO2 to sugar
    • fast, but slower than photochemical reaction
    • light-independent

paper chromatography - separates dissolved compounds

  • pigment - substance that absorbs light
    • primary photosynthetic pigments - chlorphyll a/b
    • accessory pigments - also absorb light; ex. carotene, xanthophyll
  • different mov't of pigments on paper due to solubility and tendencies to stick
  • pigments strongly absorbed move slowly
  • pigments weakly absorbed move faster
  • Rf = distance moved by pigment / distance from pigment origin to solvent front

spectroscope - instrument that separates white light into component colors

  • placing chlorophyll between light/spectroscope blocks out light absorbed by chlorophyll

fluorescence - release of light energy

  • light only produces reactions when absorbed by a molecule
  • chlorophyll appears green because it absorbs all other light wavelengths
  • light excites the electrons, bossting them to a higher energy level
Subject X2: 


enzymes - proteins that control most reactions in cells

  • biocatalysts - speeds up metabolic reactions to biologically useful rates
  • lowers activation energy needed for reaction to start
  • substrate - reacting molecules that binds to the enzyme to make enzyme-substrate complex
    • active site - where substrate attaches to the enzyme
  • provides energy of activation to form the transition state (making substrate more reactive)
  • completes reaction when product formed, enzyme goes back to original shape
  • structure/shape determines enzyme’s function
  • denaturation - structural change to enzyme, can destroy its effectiveness
  • optimal conditions - the environmental conditions under which the enzyme works the best
  • phosphate-carrying molecules like ATP turn enzymes on/off through phosphorylation

effect of temperature on enzyme activity

  • heat usually increases rate of most chemical reactions (puts energy into the system)
  • extreme temperatures may denature enzymes

catechol oxidase - plant enzyme converting catechol to benzoquinone

  • benzoquinone responsible for brown color in bruised fruit
  • catechol >> catechol oxidase >> benzoquinone
  • no reaction if either catechol oxidase or catechol missing
  • low temperatures >> slower reaction
  • moderately high temperatures (about 40° C) >> fast reaction
  • extremely high temperatures (about 80° C) >> denatured enzyme, no reaction

effect of pH on enzyme activity

  • H+ and OH- groups from acids/bases react w/ side groups of enzyme molecules
  • lower pH >> more H+ ions
  • higher pH >> more OH- ions
  • can change enzyme shape enough to change active site

catalase - enzyme in plants/animals, speeds up hydrogen peroxide breakdown

  • 2 H2O2>> catalase >> 2 H2O + O2
  • no reaction if either catalase or hydrogen peroxide missing
  • works best in neutral pH
  • adding acid/base/buffer can change the pH

effect of inhibitors on enzyme activity  

  • competitive inhibition - inhibitors that compete for the same active site as a substrate
    • makes enzyme unavailable for substrate
  • can also bond to allosteric site and shut off enzyme
Subject X2: 


cell cycle - all the activities in a cell

  • begins w/ formation of new cell, ends w/ cell replication
  • mitosis - replication/division of nucleus in a eukaryotic cell
    • rarely occurs in bone/neuron cells
  • cytokinesis - division of cell/cytoplasm
    • doesn't take place in multinucleated cells like striated muscle fibers, algal filaments
  • interphase - G1, S, G2 phases
    • G1 phase - majority of cellular activity
    • S phase - DNA replicated, produces identical pairs of chromatids attached at the centromere
    • G2 phase - structures for mitosis made

mitosis - separates genetic material, makes nucleus for each set of DNA

  • prophase - mitotic spindle forms between centrioles
    • kinetochore fibers attach to kinetochore protein disk on centromere
    • aster - microtubules radiating from the centriole to brace it
  • metaphase - chromosomes align in cell's center
  • anaphase - sister chromatids separate
  • telophase - mitotic apparatus disassembles

mitosis in animal cells - asters form w/ centrioles at the center

  • cleavage furrow - forms during cytokinesis, pinches cell in 2
  • embryos offer most examples of mitosis

mitosis in plant cells - no asters, centrioles

  • meristems - areas of rapid cell division at root tips
  • cell plate - separation that forms perpendicular to axis of spindle apparatus, grows out to periphery
Subject X2: 


meiosis - aka "reduction division"

  • makes haploid daughter nuclei
  • diploid - chromosomes coming in pairs (normal in eukaryotic nuclei)
  • homologous chromosomes - chromosomes in a pair
    • loci - sites for a gene, same in both homologous chromosomes
  • haploid - only 1 chromosome in each pair found (normal in gametes)
  • 2 rounds of chromosomal separation, 1 round of DNA replication
  • synapsis - pairing of homologous chromosomes
    • alleles - homologous segments of genetic material, gets exchanged when chromosomes paired up
    • crossing-over - creates new genetic combination
    • no gain/loss of genetic material
  • meiosis I - homologous chromosomes split
  • meiosis II - chromatids split

gametogenesis - formation of gametes

  • gamete - reproductive cells w/ haploid nuclei
  • spermatogenesis - formation of sperm
    • occurs in testes (made of seminiferous tubules)
    • spermatogonia - diploid cells in tubules that constantly divide mitotically
    • primary spermatocytes - cells that move toward lumen and start meiosis
    • secondary spermatocytes - produced by meiosis I of primary spermatocyte, has haploid set of double-stranded chromosomes
    • spermatids - produced by meiosis II of secondary spermatocytes, matures into sperm cells
  • oogenesis - formation of egg
    • occurs in ovaries of females
    • oocyte - cells in ovary that produces female gametes
    • eggs not produced continually, only during early fetal development
    • primary oocytes - about 2 million initially created, start meiosis I but stop in prophase I
    • follicular cells - surround oocytes to form follicules
    • hormones stimulate growth of 1 or 2 follicles per month after puberty
    • ovulation - release of oocyte from ovary, after oocyte completes meiosis I to produce secondary oocyte and polar body (eventually disintegrates)
    • Graafian follicle - mature follicle containing secondary oocyte
    • meiosis II (only after sperm penetrates egg) creates polar body and haploid egg cell ready for fertilization (nuclei fusion)
    • corpus luteum - formed by remaining follicle cells, prepares the uterus for fertilized egg w/ hormones

plant gametogenesis - plants have alternation of generations between haploid/diploid  

  • meiosis occurs in anthers/ovary of flowers
  • anther creates spores (pollen) that eventually produce male gametes
  • ovary creates spores (ovule) that eventually produce female gametes
Subject X2: 


Mendelian genetics - particulate (instead of blending) theory of inheritance

  • inherited characters determined by genes
  • genes occur in pairs (from maternal/paternal homologous chromosomes)
  • Law of Segregation - only 1 chromosome from each pair found in gametes
  • Law of Independent Assortment - genes on different chromosomes distributed randomly into gametes
  • gene - unit of heredity on chromosomes
  • allele - alternate states of genes, contributed from parents
  • dominant alleles - masks expression of other alleles (designated by capital letter)
  • recessive alleles - expression masked by dominant alleles (designated by lower-case letter)
  • genotype - all alleles present in the cell
  • phenotype - physical appearance of a trait
  • homozygous - when paired alleles are identical
  • heterozygous - when paired alleles are different

types of inheritance

  • simple dominance - certain allele completely dominant over another
  • incomplete dominance - heterozygous genotype results in mixed characteristic
    • red/white flowers create pink flowers when cross-bred
  • lethal inheritance - inherits gene that kills offspring
    • albino seedlings cannot photosynthesize, eventually die
  • codominance - evident in blood types
    • 4 blood types - A, B, AB, O; determined by antigens (proteins) on surface of cells
    • A blood - has A antigens, antibodies against B blood cells
    • B blood - has B antigens, antibodies against A blood cells
    • AB blood - has A/B antigens, no antibodies
    • O blood - has antibodies against A/B blood, no antigens

human traits - many determined by just single gene

  • widow's peak - pointed hairline dominant over straight hairline
  • bent little finger - little finger bends toward 4th finger (dominant)
  • albinism - lack pigment in skin (recessive)
  • pigmented iris - pigments (dominant) hides blue/gray color of iris back layer
  • attached earlobes - free earlobes dominant over attached earlobes
  • hitchhiker's thumb - last joint of thumb bends back over 60 degrees (recessive)
  • interlacing fingers - crossing left thumb over right dominant over crossing right over left
  • PTC tasting - ability to taste bitterness dominant over inability
  • mid-digital hair - hair on middle segment of fingers (dominant)

human diseases -

  • cystic fibrosis - chronic bronchial obstruction, growth reduction
  • galactosemia - can't metabolize galactose in human milk (autosomal recessive)
  • phenylketonuria (PKU) - inability to metabolize phenylalanine, leads to mental retardation
  • Huntington's disease - uncontrollable, involuntary muscle movements
  • occurs late in life, often gets passed on to offspring
  • juvenile retinoblastoma - cancer of retina

transposons - fragments of DNA that can move in chromosome

  • useful in genetic engineering
  • can insert foreign DNA into chromosome
Subject X2: 


evolution - genetic change in populations  

  • mutation - changes in genetic message of cell
  • fitness - organism’s tendency to produce more offspring
    • individuals w/ better genes more able to survive, pass down genes
  • natural selection - environmental conditions determine the characteristics of a population
  • major force that guides formation of new species, genetic change
  • frequency - proportion of individuals w/ a certain trait relative to total number of individuals

Hardy-Weinberg principle - used to calculate/predict allelic frequencies

  • based on data for 1 or 2 frequencies
  • p = frequency of dominant allele
  • q = frequency of recessive allele
  • p + q = 1
  • p2 + 2 pq + q2 = 1
  • assumptions - large population, random mating, no mutations, no migration, no selection pressure

selection pressures - factors that affect organisms, lead to selective reproduction 

  • selection - differential reproduction of phenotypes
    • certain phenotypes passed down more often than others
    • positive selection - genotypes for adaptive traits increase in frequency
    • negative selection - genotypes for nonadaptive traits decrease in frequency
  • can totally eliminate a certain trait from the entire population
Subject X2: 


properties of life - fundamental qualities of all living organisms

  • cellular organization
  • sensitivity
  • growth/metabolism
  • reproduction/heredity
  • regulation/homeostasis

taxonomy - science of classification/nomenclature for living things

  • 3 purposes
    • identifies known species
    • names/classifies new species
    • shows evolutionary relationships between species
  • organisms grouped according to phylogeny and binomial names

phylogenetic systems - evolutionary tree diagrams showing the lineage of each organism

  • shows how organisms are related through course of evolution
  • branching = divergence of species
  • upper branches = recently evolved/diverged species
  • lower branches = older, more primitive species
  • breaks animals up into 3 domains (Archaea, Bacteria, Eukarya)
  • domain >> kingdom >> phylum >> class >> order >> family >> genus >> species

binomial nomenclature - based on work of Carolus Linnaeus

  • genus - group of closely related organisms
  • species - type of organism
  • names in Latin
  • capitalize genus name, don’t capitalize species name
  • underline name when handwritten, italicize when typed
Subject X2: 

Porifera, Cnidaria

Porifera - “to bear pores”

  • level of organization - multicellular w/ specialization, but no tissues
  • body symmetry - asymmetrical
  • alimentary structures - no extracellular digestion, only phagocytosis
    • filter feeds
  • reproduction - both sexual/asexual
    • asexual reproduction - budding, gemmule release
    • sexual reproduction - amoebocytes become gametes
  • spicules - crystalline skeletal structures in sponge wall
  • spongocoel - central cavity in sponge
  • porocytes - forms the pores in sponge
  • choanocytes - flagellated cells that draw water through the pores
  • not plants due to lack of photosynthesis
  • Grantia - simplest sponges
    • sessile, filter-feeding
  • Spongia - more complex arrangement of chambers than Grantia

Cnidaria - “stinging cells”

  • level of organization - diploblastic (2 cell layers), tissues but no organs
  • body symmetry - radial symmetry
  • alimentary structures - 1-hole sac plan (same hole used as mouth/anus)
    • digestion in gastrovascular cavity
  • cnidocytes w/ nematocysts to sting prey
  • polymorphism - ability to change body shape
    • polyp - mostly stationary
    • medusa - free-swimming
  • Class Hydrozoa - dominant polyp stage
    • Portuguese man-of-war (Physalia)
  • Class Scyphozoa - dominant medusa stage
    • “true jellyfish”
  • Class Anthozoa - no medusa stage, usually in colonies
    • corals - makes skeleton of calcium carbonate
    • Metridium - commone anemone, has tentacles sticking out like hair
  • reproduction - both sexual/asexual
    • asexual reproduction - budding, fragmentation
    • sexual reproduction - medusa release sperm and eggs that become planula larva, which attaches to substrate to become polyp
Subject X2: 

Platyhelminthes, Nematoda

Platyhelminthes - triploblastic (ectoderm, endoderm, mesoderm)

  • level of organization - organs, no organ systems
  • body symmetry - bilateral
  • alimentary structures - 1-hole sac gut, no digestive cavity
  • acoelomate - lacking body cavity (no fluid-filled space involving mesoderm)
  • Class Turbellaria - flatworms, aka “Planaria”
    • mostly found in freshwater
    • eyespots - light-sensitive pigmented cups
    • simple nervous system
    • pharynx in middle of body leads to branched gastrovascular cavity
    • extracellular/intracellular digestion in gastrovascular cavity
    • hermaphroditic but not self fertilizing
    • asexual reproduction through regeneration
  • Class Tremetoda - parasitic flukes
    • can live inside/outside of hosts
    • no epidermis, covered in epicuticle
    • attaches to host w/ suckers, nutrients absorbed directly
    • mostly hermaphroditic, can self-fertilize, but some dioecious (separate male/female)
  • Class Cestoda - tapeworms
    • mostly endoparasites (living inside host)
    • attaches to host w/ scolex
    • proglottid - segmented units, each is hermaphroditic; ones farthest away from scolex are largest, carry eggs
    • no epidermis, covered in epicuticle
    • nutrients absorbed directly (no digestive enzymes/cavity)
    • regeneration possible only if scolex still attached to host
    • tapeworms can self-fertilize

Nematoda - pseudocoelomates (have body cavity between mesoderm/endoderm)

  • level of organization - organ systems
  • body symmetry - bilateral
  • alimentary structures - 2-hole sac gut
  • holds internal organs
  • triploblastic
  • no flagella/cilia, covered in cuticle
  • no circulatory system
Subject X2: 

Mollusca, Annelida

Mollusca - soft-bodied 

  • level of organization - organ systems
  • body symmetry - bilateral symmetry
  • alimentary structures - 2-hole tube
  • triploblastic
  • coelomate - contains fluid-filled space surrounded by mesoderm layer to hold organ systems
    • coelom isolated to area around heart in mollusks
    • not the same as digestive/mantle cavities
  • mantle - specialized epidermal cells, can secrete shell
  • visceral mass - organ systems, sensory structures
  • open circulatory systems in all except Cephalopods
  • gas exchange occurs in gills
  • Class Polyplacophora - “many moving plates”
    • uses radula (horny tongue) to scrape food from rocks
    • dorsal shell divided into 8 plates
  • Class Gastropoda - “stomach foot”
    • single, coiled shell produced in snails
    • no shells for slugs/nudibranchs
    • uses radula
  • Class Bivalvia - “two doors/valves”
    • hinged shell for protection
    • sessile filter feeders
    • incurrent/excurrent siphon directs water through clam
  • Class Cephalopoda - “head-foot”
    • shell internalized or lost
    • can alter shape/color for camouflage
    • hardened beak for crushing prey
    • tentacles w/ suckers to ensnare prey
    • most intelligent/advanced of invertebrates

Annelida - “ringed/segmented”

  • level of organization - organ systems
  • body symmetry - bilateral symmetry
  • alimentary structures - 2-hole tube
  • triploblastic, coelomate
  • segmentation - divided into parts separated by septa
    • muscles can elongate/contract for locomotion
    • parts specialized for certain tasks
  • closed circulatory system
  • setae - small bristle-like appendages
  • no gills/lungs, oxygen absorbed through moist body surfaces (cutaneous respiration)
  • mouth >> pharynx >> esophagus >> crop >> gizzard >> intestine
  • can only reproduce through cross-fertilization, even though it’s hermaphroditic
    • sperm exchanged through clitellum
  • Class Polychaeta - “many setae”
    • well defined heads
    • can be venomous
    • active predator/scavenger
  • Class Oligochaeta - “few/small setae”
    • earthworms, redworms, etc
  • Class Hirudinea - leeches
    • secretes hirudin as anticoagulant
    • some live as ectoparasites
Subject X2: 


main characteristics - protostomes, largest animal phylum

  • level of organization - organ systems
  • body symmetry - bilateral
  • alimentary structures - 2-hole tube
  • triploblastic
  • hemocoelomate - has blood cavity (hemocoel)
  • chitin exoskeleton
    • shed/renewed as organisms grow
  • jointed/paired appendages
  • much segmentation
    • tagmosis - fusion of segments into functional units
  • open circulatory system
  • respiratory system w/ spiracles, tracheae, book lungs/gills
  • sexual, dioecious reproduction (sometimes parthenogenic)

subphylum Chelicerata - have chelicerae for stinging, absorption of food

  • pedipalps - used to sense surroundings (sort of like antennae)
  • body segments - cephalothorax, abdomen
  • book gills/lungs, tracheae
  • Class Merostomata - Horseshoe crabs
  • Class Arachnida - spiders, scorpions, ticks, mites

subphylum Crustacea - mandibles for chewing instead of chelicerae

  • biramous - double-branched appendages
  • compound eyes (multiple lenses)
  • gills, book lungs
  • 2 pair of antennae
  • Class Malacostraca - shrimp, crabs, crayfish, krill
  • Class Branchiopoda (water fleas), Copepoda (Copepods)

subphylum Uniramia - uniramous (single branch appendages) 

  • mandibles
  • 1 pair of antennae
  • Class Chilopoda - centipedes
    • carnivores
    • 1 pair of legs per segment
  • Class Diplopoda - millipedes
    • herbivores
    • 2 pairs of legs per segment
  • Class Insecta (Hexapoda) - insects
    • 6 legs
    • head, thorax, abdomen
    • modified mouthparts
Subject X2: 

Echinodermata, Chordata

deuterostomes vs protostomes

  • protostomes - Annelida, Mollusca, Arthropoda
    • spiral cell division
    • mesoderm forms near blastospore
    • blastospore >> mouth
    • determinate embryonic development - cell fate fixed early on
  • deuterostomes - Echinodermata, Hemichordata, Chordata
    • radial cell division
    • mesoderm forms opposite blastospore
    • blastospore >> anus
    • indeterminate embryonic development - cell fate fixed later in development

phylum Echinodermata - “spiny-skinned”

  • level of organization - organ systems
  • body symmetry - pentamerous (bilateral larvae, radial adults)
  • alimentary structures - 2-hole tube
  • triploblastic
  • endoskeleton - ossicle bones on inside of organism
    • calcified bones, not chitin
  • water vascular system - uses water to move
    • ring canal - surrounds center
    • five radial canals - 1 on each leg
    • madreporite - where water enters
    • ampulla - controls the tube feet that make the organism move
  • papula - simple gills that project out into the water
  • Class Asteroidea - sea stars
  • Class Ophiuroidea - brittle stars, can move w/ legs like cephalopod instead of tube feet

phylum Chordata - “cord”

  • level of organization - organ systems
  • body symmetry - bilateral
  • alimentary structures - 2-hole tube
  • triploblastic
  • has dorsal hollow nerve cord, notochord, pharyngeal slits, postanal tail
  • subphylum Urochordata - tunicates, sea squirts
    • free-swimming larvae have chordate characteristics
    • sessile adults only keep the pharyngeal slits
  • subphylum Cephalochordata - lancelets
  • subphylum Vertebrata - notochord replaced by bone during development
    • contains fish, amphibians, reptiles, birds, mammals
  • Class Agnatha - “w/o jaws”
    • lampreys, hagfishes
    • no jaws, paired appendages
    • cartilaginous skeleton
  • Class Chondrichthyes - “cartilaginous fish”
    • sharks, skates, rays
    • cartilaginous skeleton
    • placoid scales
  • Class Osteichthyes - “bony fish”
    • gar, bass, coelacanth, perch, etc
    • most diverse vertebrate class
    • air/swim bladder
    • operculum - covers the gills
    • fins - caudal (tail), pectoral (sides), dorsal (top), pelvic (bottom), anal (bottom down, in front of caudal)
  • Class Amphibia - “dual life”
    • frogs, toads, salamanders
    • lives on land, but must return to water for fertilization
  • Class Reptilia - “to creep”
    • turtles, snakes, lizards
    • has dry skin w/ scales >> better suited for land
    • has amniotic land egg
  • Class Aves - birds
    • feathers (replaced scales)
    • forelimbs >> wings
  • Class Mammalia - “beast”
    • hair, body fat
    • mammary glands
    • diaphragm to force air into lungs
Subject X2: 

Fetal Pig Dissection

anatomical orientations -

  • anterior - head end
  • posterior - tail/hindmost end
  • dorsal - back
  • ventral - belly/underside
  • medial - middle of body
  • lateral - sides of body
  • distal - away from point of attachment
  • proximal - nearer to point of attachment

digestive system -

  • glottis - opening from larynx into trachea
  • epiglottis - tissue that closes off the glottis when food is swallowed
    • keeps food out of the respiratory tract
  • mouth - where starch digestion begins
  • esophagus - muscular tube that transports food
  • stomach - physical/chemical digestion of proteins
  • liver - produces bile to emulsify fats
    • largest internal organ
  • jaundice - yellow staining of tissues due to blocked excretion of bile
  • gallbladder - stores bile
  • pancreas - secretes digestive enzymes into small intestine
  • small intestine - primary chemical digestion, nutrient absorption
  • cecum - pouch at beginning of large intestine
    • helps w/ cellulose digestion in herbivores
  • large intestine - vitamin production/absorption
    • compacts waste
  • anus - exit for waste products
  • sphincter - ring of circular smooth muscle
    • prevents food from moving back through digestive tract
    • humans lack true sphincters

lymphatic system -

  • thymus - around neck/heart
  • spleen - filters dead blood cells
    • flap to the left of the stomach

urinary system -

  • kidneys - filters blood, excretes nitrogenous waste
  • nephron - functional unit of kidney
  • ureters - passageway for urine from kidney to bladder
  • bladder - stores urine
  • urethra - connects bladder to outside

reproductive system -

  • male reproductive parts
    • testes - gonad where sperm is created
    • epididymis - sperm storage site
    • ductus deferens (vas deferens) - tubes through which sperm travels to penis
    • seminal vesicle - secretes into semen
    • prostrate gland - secretes basic environment into semen
    • bulbourethral glands - secretes lubrication into semen
  • female reproductive parts
    • ovaries - gonad where ova are created
    • fimbria - fingerlike projections that sweep ova into tube
    • oviducts (fallopian tubes) - where egg is fertilized
    • uterus - where fertilized egg implants
    • ectopic pregnancy - fertilized egg implants outside of the uterus
    • urogenital sinus - fusion of vagina, urethra
    • vagina - birth canal

circulatory system -

  • arteries lead away from heart, veins lead toward heart
  • pulmonary circulation - between heart and lungs
  • systemic circulation - between heart and rest of body
  • major arteries -
    • aorta - largest artery in body, carries blood from left ventricle
    • pulmonary artery - only artery to carry deoxygenated blood
    • common carotids - directs blood toward the head, along the trachea
    • subclavians - branches off from aortic arch towards upper body
    • branchiocephalic trunk - branches off from aortic arch, leads to carotids/subclavians
    • celiac artery - leads to stomach/pancreas
    • renal arteries - leads to kidneys
  • major veins -
    • anterior (superior) vena cava - major vein connecting upper body and right atrium
    • posterior (inferior) vena cava - major vein connecting lower body and right atrium
    • internal/external jugulars - returns blood from head
    • branchiocephalic veins - returns blood from upper body
    • renal veins - returns blood from kidneys
  • heart - 4 chambers
    • atria - receives blood from body/lungs
    • ventricles - pumps blood to body/lungs
    • atrioventricular valves - separates atria from ventricles
    • semilunar valves - separates ventricles from outside of heart
    • chordae tendonae - “heartstrings” that keep valve flaps closed >> prevents backflow
Subject X2: 

Plants - Hepaticophyta, Bryophyta

representative plants - split into 3 groups

  • non-vascular plants - liverworts, mosses, hornworts
  • vascular, non-seed plants - ferns, fern allies
  • vascular, seed plants - gymnosperms, angiosperms

non-vascular plants - lack vascular tissue, true roots, stems, leaves

  • rhizoids - root-like structures that anchor the plant
  • antheridia - produces swimming sperm
  • archegonia - produces eggs
  • gametophyte = dominant generation
    • produces gametes through mitosis
  • sporophyte = dependent generation
    • produces spores through meiosis

phylum Hepaticophyta - liverworts

  • earliest known land plants
  • gametophyte
    • thallus - leaf-like structure, flattened and bilaterally symmetrical
  • asexual reproduction through fragmentation or gemmae production
  • sexual reproduction within the archegonia
  • sporophyte not capable of photosynthesis
    • must stay attached to the gametophyte

phylum Bryophyta - mosses

  • gametophyte - radially symmetrical thallus
    • less water-dependent than liverwort
    • only 1-cell thick in most parts
  • asexual reproduction through fragmentation only
  • sexual reproduction similar to that of liverworts
  • sporophyte - capsule extending on top of the moss
    • more prominent than in liverwort

anthocerophyta - hornworts

  • archegonia imbedded in the thallus
  • sporophyte - horn-shaped structure protruding from thallus
Subject X2: 


seedless vascular plants - all very similar to ferns

  • sporophylls clustered to form strobili (cone-like structure)
  • all have microphyll
  • Lycophyta - club mosses
    • micropyll-covered stems (has single vein)
    • includes resurrection ferns
  • Pterophyta - includes ferns, whisk ferns, scouring rush

gymnosperms - most contain seeds within cones

  • heterosporous - microspores produced in male cones, megaspores created in female cones
  • has microscopic gametophytes, completely dependent on sporophyte generation
  • Cycadophyta - Cycades
    • resembles palm trees
    • evergreen, has cones/strobili
    • flagellated sperm
  • Ginkgophyta - only 1 species (Ginkgo tree)
    • dioecious, doesn’t have cones
    • fan-shaped leaves
    • female tree seeds have buyric acid (has stench)
  • Coniferophyta - conifers
    • largest gymnosperm phylum
    • microsporophyll - male cone, located near bottom of tree
    • megasporophyll - female cone, located at top of tree, bigger than male cone
    • resin duct - used for protection, storage, wound-healing
    • stoma - gas exchange
    • epidermis - for gas exchange, protection, prevents desiccation
    • chlorenchyma - photosynthetic cells
    • endodermis - regulates transport in/out of vascular cylinder
  • Gnetophyta - most similar to angiosperms
Subject X2: 


characteristics of angiosperms - most successful/diverse plant phylum

  • all have seeds in fruits
  • dominant sporophyte, microscopic gametophyte
  • divided into monocots/dicots
  • dicots - less advanced than monocots
    • stem vascular bundles in ring
    • root vascular bundle in x-shape
    • taproot
    • netted veins in leaves
    • 2 cotyledons
  • monocots - fibrous root in place of taproot
    • stem vascular bundle scattered
    • root vascular bundles in ring
    • parallel veins in leaves
    • single cotyledon

pollination/fertilization -

  • pollen lands in sticky stigma
  • tube nuclear creates pollen tube into ovary
  • double fertilization creates zygote and endosperm
  • embryo sac - gametophyte portion that holds the egg
  • hilum - where ovule attaches to ovary
  • micropyle - seed opening through which pollen tube grows

flower structure -

  • peduncle - holds up the flower
  • receptacle - at base of flower
  • sepal/calyx - protects emerging bud
  • petal/corolla - attracts pollinators
  • androecium (stamen) - male reproductive structure
    • anther - produces the pollen
    • filament - holds up the anther
  • gynoecium - female reproductive structure
    • stigma - receives pollen
    • style - connects stigma w/ ovary
    • ovary - makes the ovules

fruit structure - ripened ovaries

  • contains seeds (mature ovules)
  • can be dry or fleshy
  • pericarp (exocarp, mesocarp, endocarp) and placental tissues
Subject X2: 

Plant Anatomy

vegetative structures - roots, shoots, leaves

  • roots - anchors plant in soil, absorbs water/minerals, stores carbohydrates
  • shoots - supports plant, transports solutes/water, stores carbohydrates
  • leaves - site for photosynthesis, area of gas exchange/transpiration

roots - 4 regions (root cap, apical meristem, elongation, maturation)

  • amyloplasts - store carbohydrates
  • xylem - transfers water/minerals
  • phloem - transfers food
  • pericycle - produces secondary roots

shoots (stem) - herbaceous in monocots, woody in dicots

  • pith - center of stem used for food storage
  • vascular cambium - responsible for secondary growth
  • node - where leaf attaches to stem
  • internode - space between nodes
  • axillary bud - produces branch/flower
  • terminal bud - contains apical meristem
  • cutin - waxy, waterproof layer around epidermis
  • periderm - minimizes water loss when epidermis ruptures
  • lenticles - for gas exchange

leaves - made of blade and petiole

  • phyllotaxis - arrangement of leaves
  • palisade mesophyll - on top, main area of photosynthesis
  • spongy mesophyll - on bottom, contains most of the stomata
Subject X2: 

Premium Content

  • Name:
    Pakicetus (Greek for "Pakistan whale"); pronounced PACK-ih-SEE-tuss
    Shores of central Asia
    Historical Epoch:
    Early Eocene (50 million years ago)
    Size and Weight:
    About 3 feet long and 50 pounds
    Distinguishing Characteristics:
    Small size; dog-like appearance
    About Pakicetus:

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  • Name:
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    Shores of central Asia
    Historical Epoch:
    Middle Eocene (46-43 million years ago)
    Size and Weight:
    About 8 feet long and a few hundred pounds
    Fish and squids
    Distinguishing Characteristics:
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  • Patrick Sayers
    Period 9
    Conclusion and Discussion Part 1
    1) As exercise occurs, what happens to pulse rate? Exercise causes your heart to work harder to deliver more blood to energy-hungry muscles, which increases your heart rate

  • Doc

    Text automatically extracted from attachment below. Please download attachment to view properly formatted document.---Extracted text from uploads/biology/doc3.docx---

  • Name:
    Dorudon (Greek for "spear-toothed"); pronounced DOOR-ooh-don
    Seashores of North America and northern Africa
    Historical Epoch:
    Late Eocene (41-33 million years ago)
    Size and Weight:
    About 16 feet long and half a ton
    Fish and mollusks
    Distinguishing Characteristics:
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  • Text automatically extracted from attachment below. Please download attachment to view properly formatted document.---Extracted text from uploads/biology/evolution_of_a_great_white_1.docx---

  • Patrick Sayers
    Period 9

  • Name:
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    Historical Epoch:
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    Size and Weight:
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    Fish and crustaceans
    Distinguishing Characteristics:
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    AP Biology-Chapter #6 & 7 Review

    Multiple Choice

    Identify the choice that best completes the statement or answers the question.

    1. All of the following are part of a prokaryotic

    cell except

    a. DNA.

    b. a cell wall.

    c. a plasma membrane.

  • 1

    Name _______________________________ Date _________________ Period _________

    Extraordinary properties of Water ppt Questions

    1. What is the formula for a molecule of water?

    2. Which atom in water attracts more negative electrons?

    3. Water is a ________________ molecule because it has an equal number of

  • 1

    Kingston College Biology CAPE Unit 1

    Proteins Worksheet

    Name: ________________________________ Date: _________________________

    1. Draw a simple amino acid molecule and label each part. [3]

    2. Polypeptide chains are formed by ______________ bonding and is added to the _________________________


    Hormone Gland produced




    hormone (GnRH)

    Hypothalamus stimulates the release of follicle-stimulating hormone (FSH)

    and luteinizing hormone (LH) from the pituitary gland

    Follicle stimulating hormone


Subject X2: 

Topic Notes

These biology notes and outlines will help you study for specific biology topics.

Subject X2: 

01 - Science of Biology

See included biology topics below:

Subject X2: 

Biology Themes

cell theory - all organisms consist of cells (basic units of life)  

  • Robert Hooke - discovered cells
  • Schleiden/Schwann - concluded that all organisms have cells
  • all cells form from other cells
  • foundation for understanding growth/reproduction of all organisms

molecular basis of inheritance - each cell contains detailed plan in its DNA  

  • nucleotides - DNA building blocks, 4 total types; 2 strands in each DNA molecule
  • A can only pair w/ T, C can only pair with G (knowing 1 strand guarantees that you know the other strand in DNA)
  • gene - specific sequences of thousands of nucleotides; could code a protein or RNA
  • proteins/RNA determine what the cell is like
  • genome - entire set of DNA instructions

evolutionary change/diversity - 3 main groups (Bacteria, Archaea, Eukarya)  

  • Archaea group is prokaryote like Bacteria, but more closely related to Eukarya
  • Kingdom Protista - contains all unicellular eukaryotes except yeast, multicellular algae
  • Kingdom Plantae - organisms w/ cellulose cell walls and perform photosynthesis
  • Kingdom Fungi - organisms w/ chitin cell walls and perform absorbtion
  • Kingdom Animalia - organisms that ingest other organisms, lack cell walls

evolutionary conservation/similarity - belief that all organisms descended from a single one  

  • characteristics of that single organism still exist in cells today
  • all eukaryotes have nucleus w/ chromosomes
  • flagellae in animal kingdom all have 9+2 arrangement of microtubules
  • homeodomain protein - found in animal, fungi, plant kingdoms; developed early on and hasn't been replaced by better versions
Subject X2: 

Darwin's Theory of Evolution

Charles Darwin - wrote On the Origin of Species  

  • contemporaries believed that species were unchangeable, structures made due to will of the Divine Creator
  • proposed that natural laws produced change/evolution over time
  • never challenged the existence of a Divine Creator
  • based his ideas on studies in S America and Galápagos Islands
  • didn't publish his results for 16 years until Alfred Russel Wallace submitted similar theory independently
  • The Descent of Man - argues that humans and apes have similar ancestors

Darwin's evidence - from expeditions to the Americas  

  • fossils of extinct armadillos found in the same area where similar armadillos lived
  • 14 species of finches on the Galápagos Islands all had different beaks from eating different food, but otherwise very similar
  • resemblances in plants in close areas, not similar climates

Thomas Malthus - wrote Essay on the Principle of Population  

  • pointed out that human population grew geometrically, but food supply grew arithmetically
  • only death prevents populations from growing out of control
  • his ideas made Darwin realize that only organisms w/ superior attributes survive

natural selection - survival of the fittest; environment only allows the best fit to survive  

  • artificial selection - breeders selecting specific organisms to pass along desired characteristics
  • organisms ill-suited for the environment die out; their attributes don't get passed on

evidence of evolution after Darwin - more support for evolution has come up since his time  

  • fossil record - goes back 2.5 billion years; shows how organisms changed from simple to complex
  • age of the earth - estimated to be 4.5 billion years; people of Darwin's time thought the earth was only a few thousand years old
  • genetics - explains how new variations occur in organisms
  • comparative anatomy - limbs and appendages of different organisms containing the same type of bones
  • homologous bones - have same evolutionary origin, but have different uses
  • analogous bones - have similar structure but different evolutionary origins
  • molecular evidence - more closely related organisms have less differences in DNA
  • molecular clock - constant change that occurs to proteins over time
  • phylogenetic tree - pattern of descent that maps out the history of an organism
Subject X2: 

Organization of Living Things, Nature of Science

Properties of Life  

  • cellular organization - containing 1 or more cells, w/ basic life activities in each cell; cells are separated by a membrane
  • order - many different types of cells, each w/ molecular structures
  • sensitivity - response to a stimulus (change in the environment)
  • growth, development, reproduction - ability to grow/reproduce, pass down hereditary material
  • energy utilization - taking in energy to do work
  • evolutionary adaptation - long-term response to things that affect survival
  • homeostasis - maintaining constant internal conditions

hierarchical organization - each level builds on the level below it in biology  

  • cellular level - atoms >> molecules >> macromolecules >> organelles >> cell
  • organismal level - tissue >> organ >> organ system >> organism
  • population level - population (group of same species living in one place) >> species (group of organisms able to interbreed) >> biological community >> ecosystem

emergent properties - results from how cells interact and work  

  • cannot be determined just be looking at the cells
  • many creatures have the same type of cells, but appear/work differently

deductive reasoning - uses general principles/rules to predict specific results  

  • reasoning used in mathematics/philosophy
  • used to test validity of general ideas

inductive reasoning - uses specific observations to make general principles/rules  

  • leads to generalizations that can be tested
  • modern science uses specific observations to make general models, which are later tested

scientific investigations - all begins w/ series of observations  

  • hypothesis - suggested explanation that accounts for the observations; can be modified or replaced
  • experiment - test of a hypothesis
  • variable - factor possibly affecting the experiment
  • control experiment - test where the variable is left unchanged
  • differences in results between experiments are due to the variable change
  • inconsistent results can lead to the hypothesis being rejected
  • theory - either an explanation for natural phenomenon, or brings together many concepts once thought to be unrelated
  • basic research - done just to expand knowledge
  • applied research - done as part of some industry or job
  • peer review - evaluation of any experiment to see if it's accurate
Subject X2: 

02 - Nature of Molecules

See included biology topics below:

Subject X2: 

Atoms and Chemical Bonds

atom - makes up all matter and all substances in the universe  

  • can be seen indirectly w/ tech such as tunnel microscopy
  • electrons - (-) charge; revolves around the nucleus
  • neutrons - no charge; in the nucleus
  • protons - (+) positive charge; in the nucleus; determines the atom's atomic number
  • mass - amount of substance
  • weight - force gravity exerts on a substance
  • atomic mass - equal the combined mass of neutrons/protons; measured in daltons (6.02*10^23 daltons=1 gram)

isotopes - atoms of an element w/ different numbers of neutrons  

  • elements - same atomic number, same chemical properties
  • radioactive isotope - isotopes that decay due to unstable nuclei; decay is constant
  • half-life - time is takes 1/2 of the atoms to decay; can be used to determine age of biological material
  • released subatomic particles could cause mutations in genes

electrons - determines the charge in each atom  

  • neutral atoms - not net charge, same number of electrons/protons
  • ions - atoms in which the number of electrons is different from the number of protons
  • cation - ion with positive charge
  • anion - ion with negative charge

orbital - area where an electron is most likely to be found  

  • each can't contain over 2 electrons
  • electrons determine the atom's chemical behavior because the nuclei never interact
  • electrons contain potential energy based on their position
  • oxidation - loss of electron
  • reduction - gain of electron
  • energy level - based on an electron's distance from the nucleus; different from orbitals

periodic table - developed by Dmitri Mendeleev  

  • elements' chemical properties repeated themselves in groups of 8
  • valence electrons - electrons on the outermost energy level; basis for the atoms' chemical properties
  • noble gases - elements w/ filled outer levels; are inert and nonreactive
  • halogens - elements w/ 7 electrons in outer levels; extremely reactive
  • octet rule - atoms tend to completely fill their outer levels

chemical bonds - connects atoms in a molecule and molecules in a compound  

  • ionic bonds - forms between atoms of opposite charge; exists between an ion and all oppositely charged ions in the area
  • covalent bonds - forms between 2 specific atoms when electrons are shared; has no net charge or free electrons
  • single bond - 1 electron is shared
  • double bond - 2 electrons are shared
  • triple bond - 3 electrons are shared
  • structural formulas - shows elements in a compound and their bonds
  • molecular formulas - shows only the elements in a compound
  • atoms can form many covalent bonds (ex. carbon)
  • chemical reaction - forming/breaking of chemical bonds
  • reactants - original molecules before the reaction
  • products - resulting molecules after the reaction

factors influencing reactions  

  • higher temperature increases reaction rate
  • temperature must not be so high that it destroys molecules
  • more reactants exposed to each other increases reaction rate
  • catalyst - substance that increases reaction rate; proteins called enzymes act as catalysts in organisms
Subject X2: 


chemistry of water - no organism can survive/reproduce w/o water  

  • carries no net charge or unpaired electrons
  • can form weak chemical associations w/ a fraction of covalent bonds' strength
  • oxygen atom portion has partial negative charge
  • hydrogen atoms portion have partial positive charge
  • polar molecules - has charge separation and partially charged poles
  • hydrogen bonds - very weak bonds that last for a short while between hydrogen atoms
  • cohesion - attraction between water molecules
  • adhesion - attraction between water molecules and other molecules
  • surface tension - causes water to cling together, allowing some insects to walk on it
  • capillary action - water rises in very narrow tubes due to adhesion

heat storage in water - temperature measures how fast the molecules move  

  • specific heat - energy needed to change 1 gram of a substance by 1 degree C
  • heats up more slowly than most compounds, holds heat longer
  • heat of vaporization - energy needed to change 1 gram of liquid into gas
  • 586 calories needed to change 1 gram of water into water vapor; causes cooling on the surface
  • ice is less dense than liquid water because hydrogen atoms space out the molecules

water as a solvent - forms hydrogen bonds to break up ions or polar molecules  

  • hydration shell - formed around molecules to prevent it from associating with other molecules of its kind
  • hydrophobic - nonpolar molecules that don't form hydrogen bonds w/ water
  • hydrophilic - molecules that readily form hydrogen bonds w/ water
  • hydrophobic exclusion - tendency for nonpolar molecules to group together in water

ionization - separationg of H20 into hydrogen ion and hydroxide ion  

  • ph scale - based on the hydrogen ion concentration
  • each ph level is 10 times as much acidic/basic than the surrounding levels
  • acids - increases hydrogen ion concentration; ph values below 7
  • bases - lowers hydrogen ion concentration; ph values above 7
  • buffer - minimalizes pH changes; acts as a resevoir for hydrogen ions
Subject X2: 

03 - Chemical Building Blocks of Life

See included biology topics below:

Subject X2: 


carbohydrates - molecules w/ carbon, hydrogen, oxygen in ratio 1:2:1  

  • empirical formula - (CH2O)n
  • releases energy from C-H bonds when oxidized
  • sugars - most important energy-storage carbohydrate

monosaccharides - simplest of the carbohydrates  

  • can contain as few as 3 carbon, but most contain 6
  • C6H12O6, or (CH2O)6
  • usually forms rings in aqueous environments (but can form chains)
  • glucose - most important energy-storing monosaccaride; has 7 C-H bonds for energy

disaccharide - "double sugar"  

  • 2 monosaccharides joined by a covalent bond
  • play roles in transporting sugars (so that it is less rapidly used for energy during transport)
  • only special enzymes located at where glucose is to be used can break the bonds
  • normal enzymes along the transport route can't break apart disaccharides
  • sucrose - fructose + glucose; used by plants to transport glucose
  • lactose - galactose + glucose
  • maltose - glucose + glucose

polysaccharide - macromolecules made of monosaccharides  

  • insoluble long polymers of monosaccharides formed by dehydration synthesis
  • starch - used to store energy; consists of linked glucose molecules
  • cellulose - used for structural material in plants; consists of linked glucose molecules
  • amylose - simplest starch; all glucose connected in unbranched chains
  • amylopectin - plant starch; branches into amylose segments
  • glycogen - animal version of starch; has more branches than plant starch

sugar isomers - alternative forms of glucose  

  • same empirical formula, but different atomic arrangement
  • fructose - structural isomer of glucose; oxygen attached to internal carbon, not terminal; tastes sweeter than glucose
  • galactose - stereoisomer of glucose; hydroxyl group oriented differently from glucose

structural carbohydrates  

  • alpha form - where glucose bonds w/ the hydroxyl group below the plane of the ring
  • beta form - where the glucose bonds w/ the hydroxyl group above the plane of the ring
  • starch contains alpha-glucose chains
  • cellulose - contains beta-glucose chains; cannot be broken down by starch-degrading enzymes; serves as structural material
  • a few animals use bacteria/protists to break down cellulose
  • chitin - structural material in arthropods/fungi; modified cellulose w/ nitrogen group added to glucose units
Subject X2: 

Carbon and Functional Groups

carbon - component of all biological molecules  

  • molecules w/ carbon can form straight chains, branches, rings
  • hydrocarbons - molecules containing only carbon and hydrogen; energy-rich, makes good fuels (ex. propane gas, gasoline); nonpolar
  • macromolecules - large, complex assemblies of molecules; separated into proteins, nucleic acids, lipids, carbohydrates
  • polymers - long molecules built by linking together smaller chemical subunits
  • dehydration synthesis - takes a -OH group and a H from 2 molecules to create a covalent bond between them, forming water as a byproduct
  • catalysis - positioning and stressing the correct bonds; done by enzymes
  • hydrolysis - adding water to break a covalent bond in a macromolecule

polymer macromolecules  

  • amino acid >> polypeptide >> intermediate filament
  • nucleotide >> DNA strand >> chromosome
  • fatty acid >> fat molecule >> adipose cells w/ fat droplets
  • monosaccharide >> starch >> starch grains in chloroplasts

functional groups - specific atomic groups added to a hydrocarbon core  

Subject X2: 

Nucleic Acids and Lipids

nucleic acids - information storage devices of cells; 2 varieties  

  • can serve as templates to create exact copies of themselves
  • deoxyribonucleic acid (DNA) - the hereditary material
  • ribonucleic acid (RNA) - used to read DNA in order to create proteins; used as a blueprint to create amino acid sequences
  • finally able to be seen w/ scanning-tunneling microscope

nucleotides - subunits of nucleic acids  

  • contains 5-carbon sugar, phosphate group, organic base
  • purine - large, double-ring molecules; adenine, guanine (both in RNA/DNA)
  • pyrimidine - smaller, single-ring molecules; cytosine (in RNA/DNA), thymine (in DNA only), uracil (in RNA only)


  • made of difference combinations of 4 types of nucleotides (adenine, guanine, cytosine, thymine)
  • 2 chains wrap around each other like a staircase (double helix shape)
  • hydrogen bonds hold 2 chains together
  • adenine only complementary to thymine (in DNA), uracil (in RNA)
  • cytosine only complementary to guanine


  • uses ribose sugar instead of deoxyribose (in DNA)
  • has hydroxyl group where a hydrogen is in DNA >> stops double helix from forming
  • uses uracil in place of thymine (has 1 more methyl group than uracil)
  • usually single-stranded (differentiates itself from double-stranded DNA); serves as a transcript of the DNA
  • evolved into DNA to protect the hereditary material from single-strand cleavage
  • "central dogma" of molecular biology - flow of info from DNA to RNA to protein

ATP - adenosine triphosphate (contains adenine, a nucleotide)  

  • energy currency of the cell
  • tinamide adenine dinucleotide (NAD+), flavin adenine dinucleotide (FAD) both carry electrons to make ATP

lipids - insoluble in water  

  • most familiar forms are fats/oils
  • very high proportion of nonpolar carbon-hydrogen bonds
  • can't fold up like proteins
  • spontaneously exposes polar parts and moves nonpolar parts within when placed in aqueous environment

phospholipids - form the core of all biological membranes  

  • glycerol - 3 carbon alcohol; forms the phospholipid's backbone
  • fatty acid - long chains of CH2 groups, ending in a carboxyl; 2 chains
  • phosphate group - attached to an end of the glycerol; usually has an organic molecule attached to it
  • phosphate group serves as the polar "head"; fatty acids serve as the nonpolar "tails"
  • micelle - spherical forms w/ the tails pointed inward
  • phospholipid bilayer - 2 phospholipid layers w/ the tails pointed towards each other; basic framework of biological membranes

fats - do not have a polar end like phospholipids  

  • contains 3 fatty acids
  • aka triglyceride, triacylglycerol
  • fatty acids don't need to be identical
  • energy stored in the C-H bonds of fats
  • clump together in water to form globules since they lack polar ends
  • saturated fats - carbon atoms in fatty acids each bonded to at least 2 hydrogen
  • unsaturated fats - has double bonds between 1+ carbon atoms
  • polyunsaturated fats - has more than 1 double bond; have lot melting points (usually liquid at room temperature)
  • terpene - long-chain lipids usually found in chlorophyll and visual pigment retinal
  • steroid - has 4 carbon rings; can function as hormones
  • prostaglandins - about 20 lipids acting as chemical messengers, with 2 nonpolar tails attached to a five-carbon ring

fats as energy-storing molecules  

  • fats contain about 40 carbon atoms
  • ratio of C-H bonds to carbon atoms in fats is 2x the ratio of carbohydrates
  • animals produce mostly saturated fats
  • plants produce mostly unsaturated fats
  • adding hydrogen can convert an oil into solid fat
  • hydrogenating oils into solids turns unsaturated fats into saturated
  • excess carbohydrates get converted into fats, starch, glycogen
  • plaque - deposits of fatty tissue found on blood vessel lining; broken pieces can cause strokes, block blood flow
Subject X2: 


proteins - have 7 main functions  

  • enzyme catalysis - faciliates/speeds up certain chemical reactions; ex. enzymes
  • defense - recognizes foreign microbes; forms the center of the immune system; ex. immunoglobulins, toxins, antibodies
  • transport - moves certain small molecules/ions; ex. hemoglobin, proton pump
  • support - structural role; ex. fibers, collagen (most abundant protein in vertebrates), keratin, fibrin
  • motion - contracting muscles; ex. actin, myosin
  • regulation - receives/sends information to regulate body functions; ex. hormones
  • storage - holds molecules such as calcium and iron; ex. ferritin

amino acid - 20 different kinds used in specific orders to form proteins  

  • molecule consists of an amino group, carboxyl group, hydrogen atom, and side group (determines the molecule's characteristics) connected to a central carbon atom
  • nonpolar amino acids have CH2 or CH3 as side group
  • polar amino acids have oxygen or hydrogen as side group
  • charged amino acids have acids/bases as side group
  • aromatic amino acids have organic rings w/ alternating single/double bonds as side group
  • special-function amino acids have unique individual characteristics
  • peptide bond - bonds between amino acids; forms between the hydrogen and carboxyl groups
  • polypeptide - protein composed of 1+ long chains

protein structure - shape determines function  

  • shape found through x-ray diffraction
  • internal amino acids are generally nonpolar
  • most polar/charged amino acids are found on the surface
  • 6 levels of structure - primary, secondary, motifs, tertiary, domains, quaternary
  • factors of protein shape - hydrogen bonds between amino acids, disulfide bridges between side chains, ionic bonds, Van der Waals attractions (weak attractions due to electron clouds), hydrophobic exclusion (polar portions gather on the outside, nonpolar portions go towards the interior)

primary protein structure - specific amino acid sequence  

  • determined by nucleotide sequence that codes for the protein
  • any of the 20 different amino acids can appear at any position in a protein
  • side groups play no role in peptide structure, but important in primary structure

secondary protein structure - determined by hydrogen bonds  

  • folds the amino acid chain
  • alpha helix - forms when hydrogen bonds form in a chain
  • beta helix - when parallel chains are linked into a pleated shape

motif - aka "supersecondary structure"  

  • combining parts of the secondary structure into folds and creases
  • beta alpha beta motif - creates a fold
  • Rossmann fold - beta alpha beta alpha beta motif
  • beta barrel - beta helix folded to form a tube
  • alpha turn alpha - used by proteins to bind DNA double helix

tertiary structure - positions the motifs/folds into the interior  

  • final folded shape of the globular protein
  • protein goes into the tertiary form due to hydrophobic exclusion
  • can be unfolded (denatured) and still return to original shape
  • no holes in the protein interior
  • close nonpolar chains are attracted together by van der Waal's forces
  • change in any amino acid can affect how they stay together in a protein

domain - structurally independent functional unit; ex. exons in genes  

  • independent of all other domains
  • if severed from the protein, would still maintain the same shape
  • connected to other domains by single polypeptide chains

quaternary structure - 2+ polypeptide chains connecting to form a functional protein  

  • arrangement of the subunits
  • subunits connect to each other in nonpolar areas
  • altering a single amino acid can affect the entire structure

chaperone protein - helps new proteins fold correctly  

  • w/o, proteins would fail to fold/function correctly
  • over 17 types, mostly heat shock proteins (high heat causes proteins to unfold)
  • gives wrongly folded proteins a chance to fix itself and fold correctly
  • deficiency in this protein may cause various diseases like Cystic Fibrosis or Alzheimer

denaturation - unfolding of proteins  

  • can occur if pH, temperature, or ionic concentration is changed
  • leads to biologically inactive proteins (venoms, made of proteins, stop working in high temperature or in presence of acids/bases)
  • salt-curing/pickling used high concentrations of salt/vinegar to stop the enzymes of microorganisms from working
  • most enzymes can only function well in very specific conditions
  • usually, only smaller proteins can fully refold themselves after being denatured
  • dissociation - different from denaturation; subunits can dissociate and still go back to their quaternary structure
Subject X2: 

04 - Origin/Early History of Life

See included biology topics below:

Subject X2: 

Cell Evolution and Extraterrestrials

bubbles - possible precursors to cells  

  • each cell's interior differs from the exterior
  • molecules w/ hydrophobic regions spontaneoulsy form bubbles in water
  • edges of early oceans exposed to methane, simple organic molecules, and radiation
  • primary abiogenesis - theory developed by Alexander Oparin
    • early cells evolved in conditions very different from current conditions
    • protobionts - early bubblelike structures that separated their contents from the environment
    • idea became popular after the Urey-Miller experiment
  • Lerman's bubble hypothesis - shows how organic molecules became more complex
    • underwater volcanoes release gases in bubbles
    • gases in bubbles react to form simple organic molecules
    • bubbles pop and release contents into the air once they reach the surface
    • UV rays and energy sources make the simple organic molecules form more complex molecules
    • complex molecules fall back into the water and become in enclosed in bubbles
  • other names for bubbles - microspheres, protocells, protobionts, micelles, liposomes, coacervates (depending on what the bubbles contain)
  • coacervates - lipid bubbles that form an outer 2-layer boundary; can grow by adding more lipid molecules from the environment; can divide by pinching in 2 like bacteria
  • microspheres carrying out metabolic reactions survive longer than those w/o protein or lipids inside
  • bubbles better able to use the molecules/energy from the early oceans and produce offspring w/ similar characteristics would live longer
  • protein microspheres - could possibly have a genetic system, do not form in water (able to form on dry land though)
  • discovery of RNA enzymes >> support for idea that RNA molecules (not lipid/protein bubbles) were 1st lifeforms

microfossils - fossilized form of microscopic life  

  • about 1-2 micrometers in diameter
  • single-celled, lacked outer appendages, similar to present-day bacteria
  • prokaryotes - lack nucleus (found in eukaryotes); very simple organic body plan
  • earliest records go back 2.5 billion years
  • 1st eukaryotes appeared 1.5 billion years ago

archaebacteria - "ancient ones"; live in environments similar to that of early earth  

  • simplest organisms
  • methanogens - produce methane, can't live in presence of oxygen (grows anaerobically); have DNA, lipid cell membrane, cell wall, metabolism based on ATP
  • lack of peptidoglycan in their cell walls (found in other prokaryotes)
  • uses strange lipid not found in any other organisms
  • extreme halophiles - "salt lovers"; live in very salty environments, like the Dead Sea
  • extreme thermophiles - "heat lovers"; live near volcanic vents; could be successors of earliest organisms due to ability to live w/ high heat
  • DNA shows that it split from other life 2 billion years ago

bacteria - 2nd major prokaryote group; larger group than archaebacteria  

  • have very strong cell walls
  • account for the majority of prokaryotes living today
  • some can use light as energy (photosynthetic)
  • cyanobacteria - aka blue-green algae; played important role in increasing the amount of oxygen/ozone in the atmosphere

eukaryotes - 1st microfossils different from prokaryotes  

  • all organisms other than prokarotes
  • may go back 2.7 billions years, but fossil evidence only goes back 1.5 billion years
  • have internal membranes and thicker cell walls
  • early forms were as large as 60 micrometers in diameter
  • possess internal structure called the nucleus (possibly evolved from the endoplasmic reticulum that isolated the nucleus)
  • endosymbiotic bacteria - bacteria that live in other cells and perform functions for it
  • theory of endosymbiosis - claims that bacteria living inside larger bacteria eventually evolved into mitochondria, chloroplasts, and other cellular parts
  • developed sexual reproduction, able to frequently recombine genes

multicellularity - promoted diversity  

  • started when eukaryotic cells started living in colonies
  • colonies began working as a single unit
  • allows for specialization, giving specific tasks to certain cells

6 kingoms  

  • Bacteria - prokaryotic organisms w/ peptidoglycan cell wall
  • Archaebacteria - prokaryotes w/o peptidoglycan in cell wall
  • Protista - eukaryotic, unicellular (except for certain types of algae); can be photosynthetic/heterotrophic
  • Fungi - eukaryotic, multicellular (except for yeast), heterotrophic; have chitin cell walls
  • Plantae - eukaryotic, multicellular, photosynthetic
  • Animalia - eukaryotic, multicellular, motile, heterotrophic

extraterrestrial life?  

  • at least 10% of all stars can have planetary systems
  • highly unlikely that earth is the only planet w/ life
  • Mars meteorite - oldest rock known to science (4.5 billion years old); contained small patches similar to microfossils and bacteria (but many times smaller)
  • Europa - Jupiter's moon; most likely known place for extraterrestrial life due to liquid ocean under icy surface
Subject X2: 

Life's Characteristics/Origin

qualities of life - originated in early waters containing cyanide, methane, hydrocarbons, etc  

  • movement - not necessary for life, nor possessed only by the living
  • sensitivity - all living things respond to stimulus, but not all types of stimuli produce responses
  • death - all living things die, but unless you can prove something is alive, then you can't kill it
  • complexity - all living things are complex (but so are some nonliving things); can't define life by itself
  • fundamental properties of life - cellular organization, sensitivity, growth (metabolism), development, reproduction, regulation, homeostasis

heredity - mechanism to improve the organism  

  • genetic system w/ DNA allows for adaptation/evolution over time
  • able to change and keep the new effects of the change
  • viruses, microspheres aren't life because they can't reproduce/change by themselves
  • evolution/heredity - essential to life; definition of life

hypotheses about the origin of life  

  • special creation - oldest hypothesis; divine force placing life on earth
  • panspermia (extraterrestrial origin) - meteors/cosmic dust brought organic molecules to earth; water on Europa, fossils on Mars indicate evidence of extraterrestrial life
  • spontaneous origin - accepted by most scientists; life developed from inanimate objects as molecules became more complex
  • earliest fossils date back 2.5 billion years
  • special creation hypothesis isn't testable

earth's conditions when life appeared  

  • very likely that 1st organisms lived at very high temperatures
  • atmosphere - mostly CO2 and N2, w/ some water vapor, H2S, NH3, CH4
  • reducing atmosphere - availability of hydrogen allows organic molecules to form more easily
  • lack of oxygen allowed amino acids to last longer (normally would react w/ sugar and form CO2 in oxygen environment)
  • atmosphere didn't change until organisms used photosynthesis to give off oxygen
  • some claim that CO2 was locked up in the atmosphere, and lack of oxygen (and consequently ozone) would've allowed the UV rays to kill all early organisms

areas where life first originated - little agreement over where life first formed  

  • ocean's edge - where bubbles form
  • under frozen ocean - similar to ocean on Europa; unlikely that frozen oceans existed on hot, early earth
  • deep in earth's crust - supported by Gunter Wachtershauser; volcanic activity recombined gases into life's building blocks; attempts to reproduce this effect used chemical concentrations far above those found during this time period
  • within clay - surfaces have postive charges to attract organic molecules and exclude water (silicate surface chemistry)
  • deep-sea vents - metal sulfides from vents attracted negatively charged biological molecules; supported by genomics (claim that early prokaryotes are closely related to the archaebacteria living on deep-sea vents)

Miller-Urey experiment - tried to reproduce conditions of early oceans in reducing atmosphere  

  • started the new field of prebiotic chemistry
  • placed an atmosphere rich in hydrogen and devoid of oxygen over liquid water at slightly below 100° C and used sparks to simulate lightning
  • within a week, 15% of the carbon originally in methane formed simple carbon compounds (which later formed more complex molecules, including amino acids)
  • over 30 different carbon compounds could be created

chemical evolution - disagreement over whether RNA originated before or after proteins  

  • RNA supporters
    • RNA required for molecules to form consistently
    • ribozymes - RNA molecules acting as enzymes (replacing role of proteins)
  • protein supporters
    • w/o enzymes, nothing could replicate
    • RNA nucleotides - too complex to form spontaneously
  • Julius Rebek - created synthetic nucleotide-like molecules that can replicate and make "mistakes" (mutations)
  • PNA (protein-nucleic acid)
    • came before RNA
    • basis for early life
    • simple enough to form spontaneously and self-replicate
Subject X2: 

05 - Cell Structure

See included biology topics below:

Subject X2: 

Cell Diversity and Cell Movement

vacuoles - central storage compartment  

  • plants contain central vacuole to store water, sugars, ions, pigments
  • applies pressure to the plasma membrane, increasing surface area-to-volume ratio
  • also found in some types of fungi/protists

cell walls - found in plants, fungi, some protists 

  • protect/support cell
  • chemically/structurally different from prokaryotic cell walls
  • cellulose found in plant/protist cell walls
  • chitin found in fungi cell walls
  • primary walls - plant cell walls laid down when the cell is still growing
  • middle lamella - sticky substance holding adjacent plant cells together
  • secondary walls - deposited inside the primary walls of fully expanded cells

extracellular matrix (ECM) - substitute cell wall used by animals 

  • composed of glycoproteins
  • contains lots of collagen (same protein found in nails/hair)
  • web of collagen, elastin, proteoglycan form a protective layer over the surface
  • fibronectin - attaches the extracellular matrix to the plasma membrane
  • integrins - proteins extending through the plasma membrane, linking the ECM w/ the cytoplasm

intracellular cell mov't - endomembrane system only effective over short distances 

  • 4 components of high speed intracellular mov't
    • vesicle/organelle to be moved
    • motor molecule that moves
    • connector molecule that connects vesicle to the motor molecule
    • microtubules on which the vesicle will ride like a train
  • motor molecules use ATP to drag transport vesicles across the microtubule tracks (ex. dynein, kinesin)

cell mov't - depends on actin filaments, microtubules, or both 

  • can change shape quickly due to actin filaments
  • polymerization/extension of actin filaments force the cell forward
  • myosin motors in the actin filaments pull the cell towards the extended front edge
  • 9 + 2 structure - circle of 9 microtubule pairs that undulates to move the cell
  • basal body - area from which the flagellum's microtubules are derived; located just below the point where the flagellum extends from the cell
  • cilia - short cellular projections organized in rows
Subject X2: 


cells - found in all organisms  

  • genetic material - found in central nucleoid area of prokaryotes or nucleus (surrounded by nuclear envelope) of eukaryotes
  • DNA has the genes that code for the proteins made by the cell
  • cytoplasm - semifluid substance within the cell containing sugars, amino acids, proteins, and organelles (specialized structures in eukaryotes)
  • plasma membrane - phospholipid bilayer separating the cell from its surroundings
    • proteins in membrane determine how cell interacts w/ the environment
    • transport proteins - help molecules/ions move across the membrane
    • receptor proteins - sends messages to the cell when in contact w/ certain molecules
    • markers - identify to the cell as a particular type

cell theory - cell size ranges from 1 micrometer to 5 centimeters  

  • cells couldn't be observed until microscopes invented in 17th century
  • Robert Hooke - 1st to describe cells when he examined cork; named what he saw after the "small rooms" of monks
  • Antonie van Leeuwenhoek - 1st to examine living cells; named them "animalcules"
  • Matthias Schleiden - stated in 1838 that plants were combinations of tiny/independent cells
  • Theodor Schwann - stated in 1839 that all animal tissue were also made of cells
  • 3 principles of the cell theory
    • all organisms contain cells, where metabolic/hereditary functions take place
    • cells are the smallest living things, basic units of life
    • cells are produced only from other pre-existing cells

cell size - usually not large for practical purposes  

  • most protein processes involve diffusion of substances at some point
  • larger cell >> longer time for substances to diffuse from membrane to cell center
  • smaller cells >> more efficient than larger cells
  • surface area-to-volume ratio - volume increases faster than surface area; larger ratio increases efficiency of the cell
  • muscle cells have more than 1 nucleus to allow genetic information to spread around the larger cell
  • neurons are extremely skinny to ensure that cytoplasm remains close to the membrane

visualizing cells - other than egg cells, most cells very hard to see  

  • resolution - min distance 2 points can be apart and still be seen as separate points
  • human eye can only distinguish points over 100 micrometers apart
  • modern microscopes (compound microscopes) use 2 magnifying lenses to make things appear much larger (resolves objects 200 nms apart)
    • dark-field microscope - only light reflected from the specimen is seen
    • bright-field microscope - light transmitted through the specimen; provides very little contrast
    • phase-contrast microscope - bring light waves out of phase, producing contrast/brightness differences
    • differential-interference-contrast microscope - uses 2 light beams traveling close together to produce more contrast than phase-contrast microscopes
    • fluorescense microscope - filters only shows light emitted by stained molecules
    • confocal microscope - laser focused on a point and scanned in 2 directions
  • light beams reflecting off of objects start to overlap when within a few hundred nms
  • transmission electron microscopes - uses electron beams instead of light beams; can resolve objects only 0.2 nms apart
  • scanning electron microscope - analyzes substance by looking at the electrons that bounce off the surface of the substance
  • immunocytochemistry - uses stains/antibodies to make certain substances more easily seen under a light microscope
Subject X2: 

Eukaryotic Structures

nucleus - largest organelle in a eukaryote 

  • 1st descried by Robert Brown in 1831
  • surrounded by cytoplasmic filaments in some cells
  • some cells have multiple nuclei
  • erythrocytes - mammalian red blood cells; lose nuclei as they mature
  • nucleolus - dark region where synthesis of ribosomal RNA takes place

nuclear envelope - 2 phospholipid bilayers surrounding the nucleus 

  • outer membrane continuous w/ the endoplasmic reticulum
  • nuclear pores - shallow depressions scattered over the surface; contain proteins that determine what substances can enter or leave the nucleus
  • 2 types of molecules allowed to pass through nuclear envelope:
    • proteins moving into the nucleus for nuclear structures, catalyze reactions
    • RNA, protein-RNA complexes made in the nucleus

chromosomes - extended into strands called chromatin except when the cell divides 

  • histones - packaging proteins which DNA wraps around
  • nucleosomes - clusters of histones
  • more extended form allows RNA copies to be made from the DNA
  • condenses into tight rods when the cell divides

endomembrane system - divides the cell into compartments 

  • endoplasmic reticulum - largest internal membrane; made of lipid bilayer embedded w/ proteins
    • cisternal space - inner region of ER
    • cytosol - exterior region of ER
    • rough endoplasmic reticulum - surface studded w/ ribosomes; used for protein synthesis
    • proteins made here eventually sent out from the cell
    • signal sequences - special amino acid sequences found on proteins about to be exported
    • proteins go from the cisternal space to the Golgi apparatus to the plasma membrane
    • smooth endoplasmic reticulum - organizes internal activities w/ enzymes
    • abundant in cells that carry out lots of lipid synthesis
    • endocytosis - process where plasma membrane forms vesicles by budding inward; some move in to the cytoplasm and fuse w/ smooth ER
  • Golgi apparatus - named for Camillo Golgi, 19th century Italian physician
    • abundant in glandular cells (manufacture/secrete substances)
    • contains 1 to a few hundred Golgi bodies
    • cis face - front, receiving end; located near the ER
    • trans face - back, discharging end; substances sent into secretory vesicles
    • modifies proteins/lipids traveling through it by adding sugar chains (making glycoproteins/glycolipids)
    • cisternae - stacked membrane folds where newly formed glycoproteins/glycolipids gather; periodically pinches off small vesicles containing the substances
  • lysosomes - digestive vesicles; break down old organelles, recycle component molecules
    • function best in acidic environments
    • keeps a low internal pH by pumping protons inside
    • primary lysosome - does not maintain an acidic internal pH
    • secondary lysosome - forms when primary lysosome fuses w/ food vesicle to activate hydrolytic enzymes
    • phagocytosis - engulfing foreign cells
  • microbodies - enzyme-bearing vesicles
    • found in all eukarytoes
    • glyoxysome - plant microbody containing enzymes that convert fats into carbohydrates
    • peroxisome - contains enzymes that catalyze removal of electons/hydrogen; would short-circuit cell metabolism if oxidative enzymes weren't isolated

ribosomes - where protein synthesis takes place  

  • large RNA-protein complexes outside the nucleus
  • consist of 2 subunits that only join when attached to messenger RNA (mRNA)
  • proteins that function in the cytoplasm are formed by free ribosomes not found in the ER
  • nucleolus - where ribosomes are assembled in the nucleus

mitochondria - bacteria-sized organelles that produce energy 

  • bounded by smooth outer membrane and cristae (inner/folded membrane)
  • matrix - area within the inner membrane
  • intermembrane space - area between inner/outer membranes
  • proteins on the surface of the inner membrane carry out oxidative metabolism
  • contains DNA that codes for proteins needed for oxidative metabolism in mitochondria
  • cannot grow/split by themselves, still need proteins coded by DNA in the nucleus

chloroplasts - where photosynthesis takes place in plants 

  • contain chlorophyll, gives plants their green color
  • have inner/outer membranes like mitochondria
  • grana - stacked membranes lying inside the inner membrane; contain thylakoids (disk-shaped structures on which photosynthetic pigments are located) surrounded by liquid stroma
  • also contain DNA like mitochondria, lacks DNA for self-replication
  • plastid - organelle acting as storage; includes chloroplasts, leucoplasts, amyloplasts; produced only through division of existing plastids
  • amyloplast - leucoplast (simple plastid) that stores starch

endosymbiosis - claims that eukaryotic organelles evolved when 1 prokaryote lived inside another 

  • symbiosis - close relationship between organisms of different relationships that live together
  • mitochondria thought to come from bacteria capable of oxidative metabolism, chloroplasts thought to come from photosynthetic bacteria
  • supported by size, membrane, cristae, DNA, replication procedures of mitochondria/chloroplasts

cytoskeleton - network of protein fibers 

  • support cell shape and keep organelles in fixed locations
  • polymerization - spontaneous assembly of identical protein subunits into long chains
  • actin filaments - long fibers responsible for contraction, crawling, pinching during cell division, formation of cellular extensions
  • many enzymes and ribosomes bind to actin filaments
  • microtubules - hollow tubes consisting of a ring of 13 protein protofilaments
    • extends from nucleation centers (-) at the center of the cell to the periphery (+)
    • move materials within the cell
    • kinesin - protein that moves organelles towards cell periphery (+)
    • dynein - protein that moves organelles towards the nucleation center (-)
    • help move chromosomes to opposite sides of the cell during replication
  • intermediate filaments - most durable part of the cytoskeleton
    • twined together in overlapping arrangement
    • vimentin - most common type; provides cellular structural stability
    • keratin - found in epithelial cells that line organs/body cavities
    • neurofilaments - found in nerve cells
  • centrioles - barral-shaped organelles
    • occur in pairs; each composed of 9 triplets of microtubules
    • centrosome - region surrounding a pair of centrioles in animal cells
    • help assemble microtubules
Subject X2: 

Prokaryotic vs Eukaryotic Cells

prokaryotes - simplest organisms  

  • 2 main groups - archaebacteria, bacteria
  • no distinct interior compartments
  • perform photosynthesis, break down dead organisms, cause diseases

cell wall - surrounds most prokaryotic cells  

  • peptidoglycan - sugar polymers cross-linked by polypeptides; found in bacteria walls
  • protects cell, maintains shape, prevents overdose of water
  • gram-positive bacteria - have thick, single-layered cell wall; turns purple from gram staining
  • gram-negative bacteria - more complex bacteria w/ multilayered cell wall; doesn't turn purple, turns red
  • drugs often destroy bacteria's cell wall to kill it
  • disease-causing bacteria secrete a jellylike capsule of polysaccharides to allow it to cling to different surfaces

flagellum - long threadlike structure used by some prokaryotes to move  

  • protein fibers extending from the bacteria cell
  • could be more than 1 per cell, depending on the species of bacteria
  • rotated like a screw to propel the cell forward
  • uses proton gradient on the membrane to power the flagellum's mov't (process also used by some enzymes that produce ATP in mitochondria/chloroplasts)

prokaryotic interior organization - very simple, no membrane-bounded organelles  

  • no interior support >> prokaryotic cell's strength depends on cell wall
  • membrane performs much of the tasks done by organelles in eukaryotes
  • prokaryote acts as a single unit (no specific task done only at a specific area)

eukaryotes - much more complex than prokaryotes  

  • compartmentalization possible through endomembrane system and organelles
  • vesicles - sacs that store/transport certain materials
  • chromosomes - compact units of DNA
  • cytoskeleton - internal protein support for the cell
  • animals and some protists lack cell walls
  • central vacuole - large sac holding proteins, pigments, waste in plants


Animal Cell


Plant Cell

Subject X2: 

06 - Membranes

See included biology topics below:

Subject X2: 

Bulk/Active Transport

endocytosis - envelops food particles 

  • substances required for growth are sometimes too large to cross the bilayer
  • 3 main types
  • phagocytosis - enveloping particulate, organic matter
  • pinocytosis - enveloping liquid
  • receptor-mediated endocytosis - transfer of specific molecules
    • only food particles that fit attach to the receptor
    • clathrin - protein that coats the inner pit
    • each pit folds inward to form a vesicle
  • low-density lipoprotein - brings cholestrol into the cell to be used in the membranes

exocytosis - reverse of endocytosis 

  • discharges material from vesicles
  • used by plants to send material for cell wall construction through the membrane
  • used by animals to secrete hormones, neurotransmitters, enzymes, etc
  • protists use contractile vacuoles for exocytosis

active transport - moves substance against the concentration gradient 

  • powered by ATP
  • uses selective protein channels like facilitated diffusion
  • makes cells independent from environmental conditions

sodium-potassium pump - moves sodium and potassium ions across the membrane 

  1. 3 sodium ions bind to protein on the cytoplasm side, causing the protein to change shape
  2. protein turns ATP into ADP (adenine diphosphate) and a phosphate
  3. protein changes shape again, moves the 3 sodium to the exterior
  4. 2 potassium ions bond to protein once 3 sodium ions leave
  5. protein changes shape again, releasing phosphate group
  6. protein goes back to original shape, release potassium into the cell, attract new sodium
  • process found in all animal cells

coupled transport - uses energy from 1 molecule's gradient to move another molecule 

  • energy released from a molecule moving w/ its gradient is used to help move another molecule against its gradient
  • sodium moves back into the cell along its gradient to move glucose into the cell against its gradient
  • symport - both molecules moving the same direction through a membrane
  • countertransport - molecules move in opposite directions through a membrane; molecules attach to the protein known as an antiport in these situations
Subject X2: 

Passive Transport

diffusion - mov't of molecules from higher to lower concentration 

  • continues until concentration is uniform
  • allows certain polar molecules to enter through the channels
  • inner, polar lining of channels allow polar molecules to enter
  • each channel is selectively permeable, only allowing certain molecules to pass through
  • ions need transport proteins to move in/out of the cell
  • ion channels - have hydrated interiors so that ions never come in contact w/ nonpolar fatty acids
    • voltage and concentration determine direction of ions
  • carriers - brings substances across the membrane by binding to them at 1 end and releasing them out the other
    • depends on the concentration gradient of the substance being transported
    • performs facilitated diffusion (either specific, passive, or saturated)
    • certain red blood cell proteins transfers different molecules in different directions
    • glucose transporter - adds phosphate group to glucose to keep internal glucose levels low; used by red blood cells to attract more glucose molecules
  • saturation - occurs when all the protein carriers are used up; transport rate can no longer increase

osmosis - both water/solutes move from higher to lower concentrations 

  • aquaporins - specialized channels for water
  • water moves towards area of more concentrated solutes to form hydration shells
  • osmotic concentration - concentration of all solutes in a solution
    • hyperosmotic - solution w/ higher concentration
    • hypoosmotic - solution w/ lower concentration
    • isosmotic - solutions w/ equal concentrations
    • water flows towards hyperosmotic region
  • hydrostatic pressure - pressure of cytoplasm pushing out against the cell membrane; tends to drive water out of the cell
  • osmotic pressure - pressure needed to stop the mov't of water across the membrane; tends to drive water into a cell

maintaining equilibrium - important to have balance between pressures 

  • animals need to keep isosmotic conditions more than plants/fungi due to lack of cell walls
  • extrusion - used by single-celled eukaryotes w/ vacuoles
    • vacuole collects water from the cell, pumps it out by contracting rhythmically
  • isosmotic solutions - some animals use their environment to adjust internal solute concentration
    • ocean organisms' internal conditions match that of seawater
    • blood contains protein albumin to raise solute concentration of liquid blood to match that of the cells
  • turgor pressure - internal hydrostatic pressure
    • makes plants rigid by pressing against the membrane/cell wall
    • maintains shape of plants
Subject X2: 

Phospholipid Bilayer

plasma membrane - skin of lipids w/ embedded proteins covering cells 

  • protein determines what substances can pass through
  • only 2 phospholipids thick

phospholipids - glycerol + 2 fatty acids + phosphorylated alcohol 

  • normal fatty acids aren't soluble, nonpolar all over
  • phosopholipids have polar, organic heads
  • forms bilayer sheets so that nonpolar fatty acid tails never touch the water
  • phospholipid bilayer - forms spontaneously due to water's tendency to form the max number of hydrogen bonds
  • stops any water-soluble substances from passing through
  • certain proteins act as passageways through the membrane

fluidity of bilayer - phospholipids have weak interactions w/ each other  

  • parts of membrane can freely move
  • less fluidity where phospholipid tails align close together
  • some phospholipids don't align well due to double carbon bonds
  • membranes w/ steroid lipids (ex. cholestrol) increase/decrease in fluidity depending on temperature

fluid mosaic model - embedded proteins also have nonpolar parts 

  • nonpolar parts of phospholipids/proteins come in contact w/ each other; polar parts on the surface
  • developed by Singer/Nicolson, disproved the Davson-Danielli model
  • phospholipid bilayer - impermeable, flexible matrix
    • other parts of the membrane are embedded in it
    • nonpolar interior stops polar substances from getting through
  • transmembrane proteins - float on/in the membrane
    • can move around in the membrane freely
  • interior protein network - reinforces the membrane shape
    • spectrin links - proteins that give red blood cells their biconcave shape
    • anchors some important membrane proteins
  • cell surface markers - sugar coating aka glycocalyx
    • used as identity markers
    • microdomain - distinct areas of the membrane
    • plasma membrane not homogeneous
    • lipid raft - heavily enriched w/ cholestrol, saturated fats; more tightly packed than surrounding area

examining cell membranes - must prepare specimens before viewing w/ electron microscopy 

  • epoxy shavings - transparent peelings from a block of tissue embedded in hard matrix
  • microtome - machine w/ very sharp blade
  • freeze-fracturing - tissue is quick frozen w/ liquid nitrogen
    • crack between phospholipid layers form when cracked
    • thin coating of platinum used to creat a cast of the surface

membrane proteins - 6 main groups of proteins let cell interact w/ environment 

  • transporters - allow only certain substances to enter, usually through a channel or on a carrier
  • enzymes - certain reactions use proteins in the membrane
  • cell surface receptors - detects chemical messages
  • cell surface identity markers - ID tag for each cell
  • cell adhesion proteins - glue cells to each other (temporary/permanent bonds)
  • attachments to cytoskeleton - surface proteins linked to cytoskeleton

membrane protein structure - some proteins anchored in the membrane, others move freely 

  • anchored proteins connected to phospholipids by molecules w/ nonpolar region and chemical bonding domains that link to the protein
  • nonpolar helices/beta-pleated sheets of amino acids keep proteins within the membrane, though polar ends stick out
  • single-pass anchors - receptor proteins w/ single-pass anchors
    • binds to specific hormones outside the cell
    • sends messages into the cell, causing changes inside
  • multiple-pass channels/carriers - uses several helices to form a channel
    • only way that water-soluble substances can pass into the cell
  • pores - beta-pleated sheets forming a barrel to allow water and other substances through
Subject X2: 

07 - Cell-Cell Interactions

See included biology topics below:

Subject X2: 

Cell Identity

tissues - highly specialized cell groups found only in multicellular organisms 

  • each tissue cell performs only the functions of that tissue
  • cells gain their identities by controlling the expression of the genes
  • only specific sets of genes are turned on
  • tissue-specific identity markers - mark cell surfaces as a particular type
    • cells of the same tissue type form connections when they recognize each other
  • glycolipids - lipids w/ carbohydrate heads
    • accounts for majority of tissue-specific surface markers
    • responsible for differences between blood types
  • MHC proteins - distinguishes cells of the organism from foreign cells
    • single-pass proteins anchored in the plasma membrane
    • immune system cells destroy cells w/o the correct identity markers

intercellular adhesion - cells usually in physical contact w/ each other at all times 

  • cell junctions - permanent/long-lasting connections between cells
  • tissue functions depend on how the cells connect
  • 3 main types of connections - tight junctions, anchoring junctions, communicating junctions

tight junctions - aka occluding junctions  

  • connect plasma membranes of adjacent cells in a sheet
  • prevent small molecules from leaking between cells
  • digestive tracts only 1 cell thick, but still prevents food from passing through due to tight junctions
  • prevents certain proteins from drifting from 1 side to another
  • food enters the blood stream by going through the transport proteins

anchoring junctions - mechanically attach the cytoskeletons 

  • most common in muscles and skin
  • desmosomes - connect cytoskeletons of adjacent cells
  • hemidesmosomes - connect epithelial cells to basement membrane
  • connections between proteins not tethered to intermediate filaments not as strong as connections between tethered proteins
  • cadherins - mostly single-pass transmembrane glycoproteins
    • forms the link in the anchoring junction
    • can also connect actin filaments of adjacent cells
    • may have a role in determining where migrating cells go during development
  • adherens junctions - connects actin filaments of neighboring cells or to extracellular matrix
    • integrins - proteins that bind to a protein part of extracellular matrix

communicating junctions - direct connections between adjacent cells used for communication 

  • chemical/electrical signals pass directly from 1 cell to another
  • some small molecules/ions can also pass through
  • gap junctions - communicating junctions in animals
    • made up of connexons (complexes of 6 transmembrane proteins arranged in a circle)
    • forms when connexons line up perfectly
    • small enough to prevent large molecules like proteins from passing through
    • holds plasma membranes of adjacent cells about 4 nm apart
    • can open/close in response to environment
  • plasmodesmata - communicating junctions in plants
    • occurs at holes/gaps in the cell wall
    • more complex than gap functions
    • lined w/ plasma membrane
    • contains a central tubule that connects the ER of 2 cells
Subject X2: 


intracellular receptors - protein receptors within the cell 

  • signal molecules are usually lipid-soluble or very small in order to pass through the membrane
  • gene regulating receptors - has binding site for DNA
    • inhibitor protein may prevent DNA from binding
    • either activates or suppresses certain genes after binding to DNA
    • response varies depending on the cell
    • lipid-soluble signal molecules tend to last longer than water-soluble signals
  • regulators as enzymes - catalyzes reactions when activated
    • nitric oxide binds to guanylyl cyclase, catalyzes synthesis of GMP (messenger molecule that relaxes smooth muscle cells)

cell surface receptors - accounts for the majority of a cell's receptors 

  • turns extracellular signals into intracellular ones
  • water-soluble signals can't pass through the membrane, must bind w/ surface receptors
  • chemically gated ion channels - allow ions through
    • opens only when a neurotransmitter binds to it
    • shape/charge of channel determines what type of ion goes through it
  • enzymic receptors - activates an enzyme when binding to a signal molecule
    • protein kinases - enzymes that add phosphate groups to proteins
    • binds to signal molecule outside the school, enzyme activity occurs in the cytoplasm

G-protein linked receptors - uses GTP-binding protein to indirectly act on enzymes/ion channels 

  • starts a diffusible signal within the cell
  • has short duration
  • G-protein changes shape, leaves receptor once signal molecule arrives
  • GTP can start few events, turns into GDP+phosphate very quickly
  • pathway shuts down if signals stop coming in
  • threads back and forth across the membrane 7 times (7-pass transmembrane protein)
  • more of these surface receptors than any other kind
  • may have evolved from sensory receptors of prokaryotes
  • Rodbell/Gilman - received Noble prize for work w/ G-proteins
Subject X2: 

Signaling Between/Through Cells

intercellular communication - lacking in most prokaryotes/protists 

  • uses many different molecules to communicate
  • dissolved gasses like nitric oxide can also be used as signals
  • signal molecules either attached to surface, secreted through plasma membrane, or released by exocytosis
  • receptor proteins - have 3D shapes that fit the shape of a specific signal molecule
    • signal molecule and receptor protein bind, changing the shape of the protein
    • change in protein shape >> response within the cell
    • hard to find, can make up less than 0.01% of a cell's mass
  • immunochemistry - uses antibodies to target/isolate specific molecules/proteins
  • molecular genetics - intentionally creates mutations in genes
    • receptor malfunction is very evident, more easily seen
    • determines relationship between protein structures and cellular functions

types of cell signaling - 4 basic mechanisms for communication between cells 

  • autocrine signaling - cells sending signals to themselves; may reinforce developmental changes
  • direct contact - when cells are actually close enough to touch each other
  • paracrine signaling - released molecules that only influence cells in close vicinity
  • endocrine signaling - uses hormones, which lasts longer in the circulatory system
  • synaptic signaling - used by animals' nervous systems
    • neurotransmitters - don't travel through the circulatory system; released by nerve cells to very close target cells
    • chemical synapse - association of a neuron and its target cell
    • neurotransmitters pass across the synaptic gap, last very briefly

second messengers - substances used to relay message from receptors to inside the cytoplasm 

  • alter the behavior of certain proteins by binding to them, changing their shape
  • cyclic AMP (cAMP) - used by all animal cells
    • produced by adenylyl cyclase when started by G-protein
    • activates the alpha-kinase enzyme, adding phosphates to certain proteins
    • works in muscle cells to make more glucose available
  • calcium ion - serves as 2nd messengers though found in low levels inside the cell
    • levels are much higher outside the cell
    • gated channels controlled by G-proteins allow Ca++ in to start certain activities
    • IP3 made from phospholipids and phospholipase binds to ER to let Ca++ into the cytoplasm
    • binds to calmodulin (148-amino-acid protein w/ 4 binding sites for C++) to activate other proteins

protein kinase cascades - chains of protein messengers used to relay messages to the nucleus 

  • usually starts w/ phosphorylating a stage 1 protein
  • each stage protein activates a large number of proteins in the next stage, and so forth
  • different signals may use some of the same messengers, but ultimately have different targets
  • vision amplification cascade - starts w/ light activating rhodopsin (a G-protein)
    • rhodopsin activates hundreds of transducin (another G-protein)
    • each transducin causes phosphodiesterase enzyme to change thousands of cyclic GMP
    • human rod cells sensitive enough to detect brief flashes of just 5 photons
  • cell division amplification cascade - starts w/ phosphorylating ras (a protein kinase)
    • ras proteins activate series of phosphorylation, leading to division
    • 1/3 of cancers involve a mutation in the ras protein gene, causing unrestrained growth
Subject X2: 

08 - Energy and Metabolism

See included biology topics below:

Subject X2: 

ATP and Biochemical Pathways

adenosine triphosphate (ATP) - main energy currency used in cells 

  • made of ribose, adenine (w/ 2 C-N rings), triphosphate group
  • adenine forms the base, attracting hydrogen ions
  • phosphates joined by unstable bonds, repelling each other
  • energy of repulsion stored in bonds that hold phosphates together
  • transferring a phosphate group transfers energy
  • bonds easily broken, easily turned into adenosine diphosphate (ADP)
  • nearly all endergonic reactions require less energy than provided by cleavage of ATP
  • enzymes catalyzing endergonic reactions have 2 binding sites: 1 for reactant, other for ATP
  • most cells only contain a few seconds' supply of ATP at a time

metabolism - all chemical reactions carried out by an organism  

  • anabolism - reactions that use energy to make/change bonds
  • catabolism - reactions that produce energy when breaking chemical bonds

biochemical pathways - sequence of reactions; organizational metabolic units  

  • product of 1 reaction becomes substrate for next reaction
  • evolved from a need of certain substances (new reactions would start when a certain substance was lacking)
  • wasteful if more compounds than needed were produced
  • feedback inhibition - where final product acts as an inhibitor on the chemical pathway, shutting it off when enough product has been created
Subject X2: 


enzymes - substances that carry out most of the catalysis in living organisms  

  • RNA may also carry out some catalysis
  • substrates - molecules undergoing a reaction
  • temporarily stabilizes an association between substrates, lowering activation energy
  • carbonic anhydrase - increases production of carbonic acid from 200/hr to 600,000/sec
  • active sites - pockets/clefts on the enzyme where substrates bind to form enzyme-substrate complex
  • substrate must fit perfectly in an active site for catalysis to work; proteins adjust shapes into an induced fit between it and the substrate
  • amino acid side groups of enzymes stress/distort certain bonds, weakening them

enzymes that take many forms - some function as parts of cell membranes/organelles

  • multienzyme complex - associations of several enzymes catalyzing different steps in a reaction sequence
    • doesn't require that products of 1 reaction dissociate to move on to the next enzyme
    • no unwanted side reactions
    • all reactions within the complex can be controlled as a unit
  • pyruvate dehydrogenase - controls entry to Krebs cycle
  • fatty acid synthetase - catalyzes synthesis of fatty acids from 2-carbon precursors
  • RNA catalysts - aka ribozymes
    • intramolecular catalysis - catalyze reactions on themselves
    • intermolecular catalysis - act on other molecules; ribozymes don't change
    • adds more support for belief that RNA came before proteins

factors affecting enzyme activity  

  • temperature - increase in heat leads to increase in random molecular mov't
    • higher temperature adds stress to bonds
    • rate increases w/ temperature up until optimum temperature
    • proteins denature above the optimum temperature
  • pH - controls balance between positively/negatively charged amino acids
    • ionic interactions hold enzymes together
    • optimum pH - ranges from 6 to 8
    • ionic interactions dependent on hydrogen ion concentration
  • inhibitor - substance that binds to an enzyme and decreases its activity
    • feedback inhibition - end product of biochemical pathway acts as inhibitor of an earlier reaction on the pathway
    • competitive inhibitor - competes w/ substrates for same active site
    • noncompetitive inhibitor - binds to enzyme in a location other than the active site; changes the enzyme's shape so that the substrate won't fit
    • allosteric inhibitor - substance that binds to an allosteric site (chemical on/off switch) to reduce enzyme activity
  • activators - binds to allosteric sites and increase enzyme activity
  • enzyme cofactor - additional chemical components that assist enzyme function
    • coenzyme - nonprotein organic molecule
    • serves as an electron acceptor and transfers electrons to substrates in another reaction
  • nicotinamide adenine dinucleotide (NAD+) - made of NMP and AMP bonded together
    • AMP acts as core
    • becomes NADH when reduced, can now supply 2 electrons and a proton for other reactions
Subject X2: 


energy - capacity to do work 

  • kinetic energy - energy of motion
  • potential energy - stored energy in objects not actively moving but w/ capacity to do so
  • all energy can be converted into heat
  • thermodynamics - "heat changes"; study of energy
  • kilocalorie - unit of heat
    • equal to 1000 calories
    • 1 calorie needed to raise temperature of 1g water by 1 degree C
    • 0.239 calorie = 1 joule

oxidation-reduction - energy stored as potential energy in covalent bonds 

  • strength of covalent bond measured by amount of energy needed to break it
  • energy in bonds can transfer to new bonds during reactions
  • oxidation - loss of an electron; oxygen (most common electron acceptor) takes the electron away
  • reduction - gain of an electron
  • redox reactions - chemical reactions w/ oxidation/reduction
    • oxidation/reduction must take place together
    • reduced form has higher energy level than oxidized form
    • reducing power - ability of organisms to store energy by transferring electrons
  • energy of electrons depends on how far it's from the nucleus and how strongly the nucleus attracts it
  • atoms release energy when electrons return to original energy level from a higher energy level

laws of thermodynamics - 2 laws that govern all energy changes 

  • 1st Law of Thermodynamics - energy cannot be created/destroyed, only changed
    • total amount of energy in the universe stays the same
    • w/ every energy conversion, some energy escapes into the environment as heat
    • heat - measure of random motion of particles; can only be used to do work w/ a heat gradient
    • energy available for work decreases as more energy converts to heat
  • 2nd Law of Thermodynamics - disorder in the universe increases continuously
    • energy spontaneously converts from more ordered, less stable form to less ordered, more stable form
    • entropy - measure of disorder in a system
    • largest amount of potential energy availabe when universe originally formed
    • every energy exchange increases disorder

free energy - energy available to do work in a system 

  • heat energy makes it easier for atoms to pull apart, increasing disorder
  • chemical bonding decreases disorder
  • Gibbs' free energy = enthalpy (energy in chemical bonds) - temperature(K) * entropy
    • G = H - TS
    • change in G = change in H - T * change in S
  • endergonic - describes reaction needing an input of energy; has a positive change in free energy, where there's more energy in products than in reactants
  • exergonic - describes spontaneous reactions that release excess free energy as heat; has a negative change in free energy

activation energy - extra energy needed to start a chemical reaction 

  • old bonds must first be broken for new bonds to form
  • rate of exergonic reactions depend on amount of activation energy needed
  • catalysis - process that lowers the activation energy needed; cannot make endergonic reactions start spontaneously
Subject X2: 

09 - Cellular Respiration

See included biology topics below:

Subject X2: 

Overview of Respiration

using chemical energy - only autotrophs can use energy of sunlight through photosynthesis 

  • heterotrophs - use autotrophs for food; accounts for 95% of earth's organisms
  • digestion - 1st step of harvesting energy; breaks down large molecules into smaller ones
  • catabolism - harvesting energy from C-H and other chemical bonds

cellular respiration - harvests energy by shifting electrons from 1 molecule to the next 

  • energy from electrons used for ATP, or lost as heat
  • electrons at end of process lose most of their energy, get transferred to final electron acceptor
  • aerobic respiration - where final acceptor is oxygen
  • anaerobic respiration - where final acceptor is nonorganic molecule other than oxygen
  • fermentation - where final acceptor is organic molecule
  • C6H12O6 + 6O2 >> 6CO2 + 6H2O
  • -720 kilocalorie change per mole in free energy

ATP synthase - enzyme that creates most of ATP 

  • uses energy in gradient of protons produced by pumping protons across the membrane
  • energy used for reactions come from catabolism or light striking chlorophyll
  • spins due to mov't of protons
  • mechanical energy from spin used to attach 3rd phosphate to ADP

glucose catabolism - ATP from catabolism forms in 2 ways 

  • substrate-level phosphorylation - additional phosphate directly transferred
    • glycolysis - glucose chemical bonds shifted to provide energy for ATP
  • aerobic respiration - uses electrons from organic molecules to power ATP synthase
    • electrons donated to oxygen gas in final stage
    • used by eukaryotes, aerobic prokaryotes for majority of ATP
  • organisms combine the 2 processes
  • glycolysis - stage 1
    • 10-reaction biochemical pathway that produces ATP through substrate-level phosphorylation
    • catalyzed by free floating enzymes
    • uses 2 ATP, produces 4 ATP, 4 electrons for NAD+, 2 pyruvate molecules
  • aerobic respiration - stages 2-4
  • pyruvate oxidation - stage 2
    • pyruvate gets converted into CO2 and acetyl-CoA
    • NADH forms for every pyruvate molecule that gets converted
  • Krebs cycle - stage 3
    • aka citric acid cycle or tricarboxylic acid cycle
    • cycle of 9 reactions that produce 2 ATP from substrate-level phosphorylation
    • lots of electrons removed to NADH
  • electron transport chain - stage 4
    • uses electrons from NADH to pump protons across the membrane
    • ATP synthase uses proton gradient to make ATP
  • procedure occurs in prokaryotes and mitochondria of eukaryotes

anaerobic respiration - occurs w/o O; replaced by S, NO3, other inorganic molecules 

  • methanogens - use CO2 as final electron acceptor, reducing it to CH4
  • sulfur bacteria - reduces SO4 to H2S; set the stage for photosynthesis evolution
Subject X2: 


glycolysis - stage 1 

  • 10 reaction sequence converting glucose to 2 3-carbon molecules of pyruvate
  • glucose + 2ADP + 2P + 2NAD+ >> 2 pyruvate + 2ATP + 2NADH + 2H+ + 2H2O
  • can be performed by all organisms (doesn't require oxygen or special organelles)
  • metabolism evolves by adding reactions to each other, so glycolysis was never replaced

priming - 1st half of glycolysis; makes 2 3-carbon glyceraldehyde 3-phosphates from glucose  

  • 5 reactions
  • step A - glucose priming
    • 3 reactions changing glucose into a compound that can be readily cleaved into 3-carbon phosphorylated molecules
    • 2 of the reactions require use of ATP
  • step B - cleavage/rearrangement
    • 2 reactions break up 6-carbon molecule into 2 3-carbon molecules
    • 1st of 2 reactions forms G3P and another molecule that turns into G3P through the 2nd reaction

substrate-level phosphorylation - 2nd half of glycolysis; makes pyruvate from G3P 

  • 5 reactions
  • step C - oxidation
    • 2 electrons, 1 proton transferred from G3P to NAD+ to make NADH
  • step D - ATP generation
    • 4 reactions convert G3P to pyruvate, generating 2 ATP
  • in total, 4 ATP per glucose molecule produced
  • 2 ATP used in beginning, so glycolysis has net ATP gain of 2
  • harvests 24 kcal/mol of glucose, about 3.5% of chemical energy in glucose

regeneration of NADH - only a small amount of NAD+ exists in cells 

  • necessary that the H on NADH be transferred somewhere else
  • aerobic respiration - uses oxygen as electron acceptor (takes the H to become H2O); oxidizes pyruvate to acetyl-CoA
  • fermentation - uses organic molecule (like acetaldehyde) in place of oxygen; reduces all or part of pyruvate
Subject X2: 

Pyruvate Oxidation, Krebs Cycle

pyruvate oxidation - stage 2 

  • occurs in only in mitochondria of eukaryotes
  • 1st forms acetyl-CoA from pyruvate, then oxidizes acetyl-CoA in Krebs cycle
  • single "decarboxylation" reaction that cleaves off one of the carbons on pyruvate (producing acetyl group and CO2)
  • catalyzed in mitochondria by multienzyme complex
  • pyruvate dehydrogenase - enzyme that removes CO2 from pyruvate; has 60 subunits
  • pyruvate + NAD+ + CoA (coenzyme A) >> acetyle-CoA + NADH + CO2
  • acetyl-CoA - produced by a large number of metabolic processes
    • key point for many catabolic processes in eukaryotes
    • used for fatty acid synthesis instead of Krebs cycle when ATP levels are high

Krebs cycle - stage 3 

  • 9 reactions; oxidation of acetyle-CoA
  • takes place in mitochondria matrix
  • combines acetyle-CoA (2-carbon molecule) w/ oxaloacetate (4-carbon molecule) to extract electrons and CO2 to power proton pumps for ATP
  • step A - priming; 3 reactions rearrange chemical groups in acetyl-CoA to prepare the 6-carbon molecule for energy extraction
  • step B - energy extraction; 4/6 reactions oxidize and remove electrons
  • reaction 1 - condensation
    • acetyle-CoA combines w/ oxaloacetate to form citrate
    • irreversible reaction; inhibited when ATP concentration is high
  • reaction 2/3 - isomerization
    • repositions hydroxyl group by taking away H2O and adding it back to a different carbon
    • forms isocitrate from citrate
  • reaction 4 - 1st oxidation
    • oxidized to yield pair of electrons that make NADH from a NAD+
    • decarboxylated to split off a CO2 to form a-ketoglutarate (5-carbon molecule)
  • reaction 5 - 2nd oxidation
    • a-ketoglutarate decarboxylated into succinyl group, which bonds to coenzyme A to form succinyl-CoA
    • CO2 removed
    • oxidized to yield pair of electrons that make NADH from a NAD+
  • reaction 6 - substrate-level phosphorylation
    • bond between succinyl group (4-carbon molecule) and CoA cleaved to phosphorylate GDP into GTP
    • GTP readily converts into ATP
    • succinyl-CoA becomes succinate
  • reaction 7 - 3rd oxidation
    • succinate oxidized into fumarate
    • energy produced not enough for NAD+, so FAD turned into FADH2 instead
    • FAD part of inner mitochondrial membrane, can't diffuse within the organelle
  • reaction 8/9 - oxaloacetate regeneration
    • H2O added to fumarate, making malate
    • malate oxidized to form oxaloacetate and 2 electrons to form NADH from NAD+
  • by end of Krebs cycle, ener
Subject X2: 

Electron Transport Chain

electron extraction - potential energy of electron transferred when it moves  

  • reduction can move electron completely or change degree of sharing in a covalent bond
  • electrons shared equally in C-H bonds because C and H have similar electronegativity
  • when glucose forms CO2 and H2O, oxygen atoms attract electrons away from hydrogen/carbon
    • oxygen more electronegative than hydrogen/carbon
    • energy released when electrons move from a less electronegative atom to a more electronegative atom
    • shift of electrons during oxidative respiration releases energy to create ATP
  • reducing power - NADH can carry energy of electrons donated to it
    • can pass along electrons and reduce other atoms
    • reduces fatty acid precursors to form fats when ATP is plentiful
  • releasing energy in stages is more efficient than releasing it all at once

electron transport chain - stage 4 

  • series of membrane-associated proteins
  • NADH dehydrogenase - 1st protein to receive an electron
  • ubiquinone - carrier that passes electrons to the bc1 complex
  • bc1 complex - protein-cytochrome complex acting as a proton pump
  • cytochrome c - carrier that passes electrons to cytochrome oxidase complex
  • cytochrome oxidase complex - uses 4 electrons to reduce O2 so that it forms 2H2O w/ 4H
  • NADH gives electrons to NADH dehydrogenase, FADH2 gives electrons to ubiquinone
  • energy from electrons transports protons from the mitochondrial matrix into the intermembrane space
  • NADH activates 3 pumps, FADH2 activates 2 pumps

chemiosmosis - process where diffusion force generates energy for ATP 

  • protons transported into the intermembrane space try to go back into matrix due to diffusion
  • protons (ion) can only enter through ATP synthase, which uses proton gradient as an energy source
  • reentry of protons powers the ATP synthase
  • theoretical yield - 36 molecules of ATP formed
    • 4 ATP from glycolysis (though 2 used during the process)
    • 30 ATP from NADH (3 per NADH)
    • 4 ATP from FADH2 (2 per FADH2)
    • -2 ATP (to move NADH produced by glycolysis into the mitochondrian)
  • actual yield - usually lower than 36
    • some protons able to enter matrix w/o using ATP synthase
    • proton gradient not used exclusively for ATP synthesis
    • about 30 ATP actually created
    • aerobic respiration harvests about 32% of energy in glucose

aerobic respiration regulation - ATP stops respiration through feedback inhibition 

  • high concentrations of ADP activates enzymes to stimulate ATP synthesis
  • phosphofructokinase - main control point in glycolysis
    • catalyzes conversion of fructose phosphate to fructose biphosphate
    • 1st non-reversible step in glycolysis
    • stimulated by high levels of ADP and citrate
  • pyruvate decarboxylase - main control point in Krebs cycle
    • inhibited by high levels of NADH
    • citrate synthetase - catalyzes 1st reaction involving conversion of oxaloacetate and acetyl-CoA into citrate
Subject X2: 

Anaerobic Respiration, Metabolism Evolution

cellular respiration of protein - 1st broken down into amino acids 

  • deamination - process that removes the amino group
  • reactions convert remaining carbon chain into parts that take place in glycolysis/Krebs cycle
  • alanine converted to pyruvate
  • glutamate converted into a-ketoglutarate
  • aspartate converted into oxaloacetate

cellular respiration of fat - 1st broken down into fatty acids and glycerol 

  • beta oxidation - process that removes 2-carbon acetyl groups from fatty acids to convert them into acetyl groups
    • takes place in mitochondrial matrix
    • each acetyl group combines w/ coenzyme A to form acetyl-CoA
  • produces 20% more ATP than glucose per 6-carbon molecule
  • contains 2x as much kilocalories per gram

fermentation - process that recycles NAD+ in absence of oxygen 

  • uses organic compound as electron acceptor instead of oxygen

ethanol fermentation - occurs in yeast (single-celled fungi) 

  • pyruvate accepts hydrogen from NADH
  • enzymes remove CO2 from pyruvate through decarboxylation, making acetaldehyde (2-carbon molecule)
  • CO2 released causes bread to rise
  • acetaldehyde + NADH >> ethanol + NAD+
  • ethanol begins to kill yeast at 12% concentration

lactic acid fermentation - uses lactate dehydrogenase to transfer H from NADH to pyruvate  

  • pyruvate + NADH >> lactic acid + NAD+
  • lactate - ionized form of lactic acid
  • interferes w/ muscle function when circulating blood can't remove lactic acid fast enough

evolution of metabolism - changed stage by stage 

  • degradation - breaks down organic molecules abiotically produced
    • started w/ origin of ability to use chemical bond energy
  • glycolysis - initial breakdown of glucose
    • captures a larger amount of chemical bond energy by breaking bonds in steps
    • hasn't changed in over 2 billion years
  • anaerobic photosynthesis - uses light to pump protons from cells
    • still uses chemiosmosis to produce ATP
    • evolved in absence of oxygen
    • dissolved H2S provided hydrogen for procedure
  • oxygen-forming photosynthesis - H2O replaced H2S
    • generates oxygen instead of sulfur
    • all oxygen in atmosphere from oxygen-forming photosynthetic reaction
  • nitrogen fixation - obtaining nitrogen atoms from N2 gas by breaking triple bonds
    • evolved in hydrogen rich atmosphere
    • occurs in oxygen-free environments (oxygen poisons nitrogen-fixation)
  • aerobic respiration - final event in history of metabolic evolution
    • gets energy from electrons in organic molecules
    • uses same proton pumps as photosynthesis
    • 1st evolved among purple nonsulfur bacteria (obtained hydrogen from organic molecules)
    • mitochondria thought to be descendents of nonsulfur bacteria
Subject X2: 

10 - Photosynthesis

See included biology topics below:

Subject X2: 

Overview of Photosynthesis, Light Biophysics

photosynthesis - occurs in bacteria, algae, stems/leaves of plants 

  • Jan Baptista van Helmont - showed that soil didn't add mass to plants; believed that water provided the extra mass
  • Joseph Priestly - found that living vegetation restores oxygen into the air
  • Jan Ingenhousz - found that plants' green leaves (not roots) only restore air in presence of sunlight
  • chloroplasts - organelles that carry out photosynthesis
    • mesophyll - thick layer of cells rich in chloroplasts
    • thylakoids - internal chloroplast membranes
    • grana - stacks of thylakoids
    • stroma - semi-liquid substance that holds enzymes needed to synthesize organic molecules
  • light-dependent reactions - capturing energy from sunlight, using energy to make ATP/NADPH
    • takes place on thylakoid membrane
  • Calvin cycle (light-independent reaction) - carbon fixation
    • synthesizes organic molecules from CO2 in air and energy in ATP/NADPH
    • doesn't need light to work
    • takes place in stroma
  • photosystem - clusters of photosynthetic pigments in thylakoids
    • each pigment can capture photons (energy packets)
    • energy of excited electrons move from chlorophyll molecule to chlorophyll molecule
    • ATP/NADPH generation starts as energy reaches membrane-bound protein

F. F. Blackman - proposed that photosynthesis is comprised of multiple steps 

  • found that first part of photosynthesis required light
  • dark reactions limited by CO2, not directly involved w/ light
  • temperature increased dark reactions up until 35°C, where it would start to denature proteins
  • enzymes involved in dark reactions

C. B. van Niel - discovered roles of light/dark reactions 

  • discovered that O2 produced came from H2O, not CO2
  • NADPH and ATP formed in light reactions are used in Calvin cycle to form simple sugars from CO2
  • carbon fixation - process where reducing power from splitting of water is used to convert CO2 to organic matter
  • high energy electrons form the C-H bonds of new organic molecules
  • lack of CO2 leads to accumulation of ATP

biophysics of light - contains units of energy called photons 

  • photoelectric effect - photons transfer energy to electrons, facilitating passage of electricity
  • short-wavelength light has higher energy than long-wavelength light
  • gamma rays - shortest wavelength, highest energy
  • radio waves - longest wavelength, lowest energy
  • violet - shortest wavelength in visible light
  • red - longest wavelength in visible light
  • UV light - has more energy, shorter wavelength than visible light
    • important source of energy for early life
    • can cause mutations by messing up DNA bonds
  • photon energy either lost as heat or absorbed by electrons when photons strike something
  • absorption spectrum - range/efficiency of photons a substance can absorb

pigments - good absorbers of light  

  • chlorophyll - absorbs violet-blue/red light; reflects green light
  • chlorophyll a - main photosynthetic pigment; only pigment that can directly convert light to chemical energy
  • chlorophyll b - secondary light-absorbing pigment; can absorb wavelengths that chlorophyll alpha can’t
  • carotenoids - absorbs wavelengths not efficiently absorbed by chlorophyll
Subject X2: 

Chlorophyll, Light Reactions

chlorophyll - absorbs photons in a way similar to photoelectric effect


  • porphyrin ring - ring structure w/ alternating single/double bonds w/ Mg atom in middle
    • energy channeled through carbon-bond system
    • side groups on outside of ring change absorption characteristics
  • action spectrum - relative effectiveness of different light wavelengths on photosynthesis
    • T. W. Englemann - found that chlorophyll work best under red/violet light
  • photoefficiency - high absorption efficiency leads to ability to absorb only a narrow bands of light
    • retinal absorbs large range of wavelengths but at low efficiency

carotenoids - made of carbon rings linked to chains w/ alternating single/double bonds  

  • responsible for change in leaf color in fall
  • not very efficient in transferring energy, but absorbs a wide range of energies
  • beta-carotene - typical carotenoid; 2 carbon ring connected by 18-carbon chain
    • halves same as vitamin A
    • oxidation of vitamin A >> creates retinal, pigment used for vertebrate vision

light-reactions - 4 stages


  • primary photoevent - light photon captured by pigment, exciting the electrons in the pigment
  • charge separation - energy transferred to reaction center (special chlorophyll pigment)
    • transfers energetic electron to acceptor molecule, starts electron transport
  • electron transport - electrons go through multiple electron carriers in the membrane
    • pumps induce mov’t of proton across the membrane
    • electron passed to an acceptor in the end
  • chemiosmosis - protons flow down gradient to power ATP synthase

photosystems - light absorbed by clusters of pigments, not single pigments


  • discovered after saturation was reached much faster than expected in experiments
  • contains network of chlorophyll a molecules, accessory pigments, proteins held in protein matrix on photosynthetic membrane
  • antenna complex - captures photons from sunlight
    • web of chlorophyll held together by protein matrix
    • protein matrix holds the chlorophyll in the most efficient shape for absorbing energy
    • energy moves towards reaction center (electrons don’t move)
  • reaction center chlorophyll - transmembrane protein-pigment complex
    • passes energy out of the photosystem so it can be used elsewhere
    • transfers energized electron to primary electron acceptor (quinone)
    • water serves as weak electron donor in plants

bacteria photosystem - 2-stage process w/ just 1 photosystem


  • excited electron combines w/ proton to form hydrogen atom
    • H2S becomes sulfur and protons
    • H2O becomes oxygen and protons
  • electron recycled back to chlorophyll through an electron transport system
    • 1 ATP produced per 3 electrons that move through the path
    • cyclic photophosphorylation - name for electron transfer process
  • only produces energy, no biosynthesis
  • doesn’t have good source of reducing power

plant photosystem - plants use 2 photosystems


  • additional photosystem using different chlorophyll a arrangement added on to bacteria photosystem
  • enhancement effect - where use of 2 different light beams leads to faster rate of photosynthesis
    • due to fact that photosystems have different optimum wavelengths
  • electron moves from H2O to NADPH
  • noncyclic photophosphorylation - name for 2-stage process
    • electrons not recycled
    • 1 NADPH, more than 1 ATP created w/ every 2 electrons from H2O

photosystem II - absorbs shorter wavelength, higher energy photons


  • absorption peak = 680 nanometers
  • reaction center called P680
  • H2O binds to manganese atoms on enzyme bound to reaction center
    • enzyme splits H2O
    • O2 leaves after 4 electrons removed
  • quinone - main electron acceptor for energized electrons leaving photosystem II
    • becomes plastoquinone, strong electron donor after being reduced
    • b6-f complex - proton pump in the thylakoid membrane; pumps a proton into the thylakoid when energetic electron arrives
    • plastocyanin (pC) - copper-containing protein that carries electron to photosystem I
  • ATP produced by ATP synthases like w/ aerobic respiration

photosystem I - older, ancestral photosystem


  • absorption peak = 700 nanometers
  • reaction center called P700
  • receives electrons from plastocyanin
  • incoming electrons have only lost 1/2 of energy, boosted to a very high energy level once photons strike the chlorophyll
  • ferredoxin (Fd) - iron-sulfur protein; acts as main electron acceptor for photosystem I
  • NADP reductase - uses 2 electrons from ferredoxin proteins to make NADPH from NADP+
    • uses up a proton outside the thylakoid in stroma, contributing to proton gradient
  • electrons might get passed back to b6-f complex instead of being used for NADPH (in cyclic photophosphorylation)
Subject X2: 

Calvin Cycle

Calvin cycle - aka C3 photosynthesis 

  • creates organic molecules from CO2
  • uses ATP (from cyclic/noncyclic photophosphorylation) to power endergonic reactions
  • uses reducing power of NADPH to attach H to C atoms
  • carbon fixation - CO2 binds to ribulose 1,5-biphosphate (RuBP)
    • RuBP - 5-carbon sugar made from reassembling bonds of fructose 6-phosphate and glyceraldehyde 3-phosphate
    • forms 2 molecules of 3-phosphoglycerate (PGA)
    • process catalyzed by rubisco (ribulose biphosphate carboxylase/oxygenase)
  • 3 CO2 + 9 ATP + 6 NADPH + water >> glyceraldehydes 3-phosphate + 8 P + 9 ADP + 6 NADP+
  • w/ 3 turns of Calvin cycle, 3 CO2 enters, 3 RuBP regenerated, 1 glyceraldehyde 3-phosphate created
  • uses enzymes that functions best under light
  • glyceraldehydes 3-phosphate - 3-carbon sugar that can be converted to fructose 6-phosphate and glucose 1-phosphate in cytoplasm w/ reversed glycolysis reactions
  • glucose 1-phosphates combined into insoluble polymer as starch when there’s high levels of glyceraldehydes 3-phosphate

energy cycle - metabolisms of chloroplasts/mitochondria are related 

  • photosynthesis uses products of respiration as starting substrates
  • respiration uses products of photosynthesis as starting substrates
  • Calvin cycle uses part of glycolytic pathway, in reverse, to make glucose
  • enzymes used in both processes similar or the same

photorespiration - releases CO2 by attaching O2 to RuBP, reversing Calvin cycle 

  • rubisco can oxidize RuBP, undoing the Calvin cycle
  • CO2/O2 compete for same active site on rubisco enzyme
  • at 25°C, rate of carboxylation 4x that of oxidation (20% of fixed carbon lost)
  • higher temperature >> stomata close to conserve H2O >> CO2 can’t go in >> favors photorespiration
  • 25-50% of photosynthetically fixed carbon lost through photorespiration

C4 photosynthesis - phosphoenolpyruvate (PEP) carboxylated to make 4-carbon compound  

  • uses PEP carboxylase enzyme (attracts CO2 more than rubisco)
  • no oxidation activity in 4-carbon compound >> no photorespiration
  • minimalizes photorespiration when 4-carbon compound decarboxylates to contribute CO2 into the system

C4 pathway - used by plants in much warmer environments 

  • C4 photosynthesis conducted in mesophyll, Calvin cycle conducted in bundle-sheath cells
  • phosphoenolpyruvate (3-carbon) carboxylated to form oxaloacetate (4-carbon)
  • oxaloacetate turned into malate in C4 plants
  • malate decarboxylated into pyruvate in bundle-sheath cells, releasing CO2
  • bundle-sheath cells retain CO2 for Calvin cycle
  • pyruvate goes back to mesophyll, where it turns back to phosphoenolpyruvate
  • requires 30 ATP (C3 photosynthesis needs 18), but more advantageous in hot climate

crassulacean acid metabolism ( CAM) - used by succulent (water-storing) plants 

  • stomata close during the day, open at night (reverse of what happens in most plants)
  • makes organic compounds at night, decarboxylates them to have high CO2 levels during the day
  • uses both C4/C3 pathways in the same cells (C4 plants use C4/C3 pathways in different cells)
Subject X2: 

11 - Cell Division

See included biology topics below:

Subject X2: 

Prokaryotic Cell Division, Chromosomes

prokaryotic cell division - division by binary fission  

  • genome made of single, circular DNA found in nucleoid area
  • replication of DNA begins at specific site and goes bidirectionally around to specific site of termination
  • cell elongates, DNA gets attached to the membrane
  • septum - new membrane growing near the midpoint during division
    • composed of FtsZ protein ring
  • eukaryotic cells developed mitosis to deal w/ larger, nucleus-enclosed genomes

mitosis - occurs differently in different organisms 

  • protists - 2 ways
    • microtubules (w/ tubulin) pass through nucleus membrane tunnels and sets up axis for division (nucleus remains intact)
    • microtubule spindle forms between centrioles at opposite sides; kinetochore microtubules pull chromosomes to each pole (nucleus remains intact)
  • yeasts - spindle microtubule forms inside nucleus between poles
    • single kinetochore microtubule attaches to chromosomes, pulls them to each end
  • animals - spindle microtubule forms between centrioles outside the nucleus
    • nucleus envelope breaks down
    • kinetochore microtubules attach chromosomes to poles

chromosome - found in cells of all eukaryotes; 40% DNA, 60% protein  

  • most eukaryotes have 10-50 chromosomes (humans have 46, 23 pairs)
  • monosomy - condition where organism lacks a chromosome; won’t survive embryonic development
  • trisomy - extra copy of a chromosome; fatal unless extra copy of very small chromosome (genetic defects still take place)
  • chromatin - DNA/protein complex
    • heterochromatin - chromatin domains not expressed
    • euchromatin - chromatin domains expressed
  • DNA coiled to allow it to fit in smaller space
  • nucleosome - 200 nucleotides coiled around 8 histones
    • solenoid - coils of a string of nucleosomes wrapped together; radially loops around protein scaffold during mitosis
  • histones (positively charged) attract negatively charged phosphate groups in DNA

karyotype - specific chromosome array (different between organisms) 

  • haploid (n) - # of chromosomes needed to define an organism
  • diploid (2n) - 2x haploid number; # of chromosomes in humans, some other species
  • centromere - condensed area found on all eukaryotic chromosomes
  • 2 sister chromatids share common centromere after replication
  • chromosomes counted by # of centromeres
Subject X2: 

Cell Cycle

cell cycle - 5 phases 

  • G1 – primary growth phase of cell
    • includes major part of a cell’s life for most organisms
  • S - phase where genome is replicated
  • G2 - 2nd growth phase; preparations made for separation of genomes
    • organelles replicate, chromosomes condense, microtubules assemble
  • interphase - collective name for G1, S, G2 phases
  • M (mitosis) - phase where microtubules pull sister chromatids apart
    • divided into prophase, metaphase, anaphase, telophase
  • C (cytokinesis) - cytoplasm divides, forms 2 daughter cells
    • actin acts as drawstring to pinch animal cells in 2
    • plate forms between dividing cells w/ cell walls
  • embryonic cells have shortest cell cycles
  • G0 phase - resting state before DNA replication
    • most cells in body are in this state at any given time
    • neurons/muscle cells never leave this phase after maturing

interphase - prepares for mitosis 

  • major portion of growth during G1 phase
  • chromosome creates 2 sister chromatids attached at centromere during S phase
  • kinetochore - protein disk bound to specific DNA sequence at centromere
  • proteins made, organelles produced during G1/G2 phases
  • DNA only replicates during S phase
  • condensation - DNA coils together w/ help of motor proteins
  • centrioles - microtubule-organizing centers that form during G2
  • tubulin - protein that makes up microtubules


  • prophase - forming mitotic apparatus
    • begins when condensed chromosomes become visible to light microscope
    • ribosomal RNA synthesis stops when area of chromosome that codes for rRNA condenses
    • centrioles move towards poles as spindle fibers form between them; spindle apparatus made of microtubules form
    • nuclear envelope breaks down, gets absorbed by endoplasmic reticulum during spindle formation
    • aster - radial arrangement of microtubules on centrioles towards membrane; braces centrioles against membrane; no asters in plant cells
    • microtubules must link sister chromatids to opposite sides or they won’t separate later
  • metaphase - centromere alignment
    • chromosomes align in center of the cell in circular array
    • metaphase plate - imaginary plane perpendicular to axis of chromosome circle
  • anaphase - shortest phase
    • centromeres split in 2, freeing sister chromatids
    • separase - enzyme that cleaves the cohesin protein holding the chromatids together
    • anaphase-promoting complex (APC) - makes centromeres divide at the same time
    • poles move apart, centromeres move towards poles
    • microtubules shortens as tubulin subunits are removed (microtubules don’t contract)
  • telophase - nuclei reforms
    • spindle disassembles
    • microtubules broken down into tubulin that can be used for cytoskeleton of daughter cells
    • nucleus forms around sister chromatids

cytokinesis - phase where cell actually divides 

  • relocation of organelles takes place in S/G2 phase
  • cleaves cell into equal halves
  • animal cytokinesis - uses constricting actin filament belt
    • actin filaments slide by each other, forms cleavage furrow, eventually slices into cell’s center
  • plant cytokinesis - creates cell plates between daughter cells
    • middle lamella - space between daughter cells, filled w/ pectins
  • fungi/protist cytokinesis - nucleus doesn’t dissolve during mitosis
    • nucleus divides after mitosis completes
  • nothing determines how organelles get distributed
Subject X2: 

Checkpoints, Cancer

checkpoint - specific points where cell cycle can be put on hold 

  • 2 irreversible points - replication of genetic material, sister chromatid separation
  • kinase - adds phosphate
  • phosphatase - takes away phosphate
  • phosphorylation/dephosphorylation >> activate/deactivate proteins >> drives cell cycle
  • cyclin - proteins displaying characteristic patterns of synthesis/degradation like the cell cycle
  • cyclin-dependent kinase (Cdk) - enzyme that controls passage through the checkpoints
  • multicellular organisms respond to more external signals and use more Cdk’s than unicellular organisms

G1/S checkpoint - main point where the cell decides whether or not to divide 

  • links cell division to cell growth
  • aka “restriction point” (R point) in animals
  • aka “start” in yeasts
  • decision to replicate genome >> decision to replicate
  • internal signals - nutritional cell state, cell size
  • external signals - factors that promote cell growth/division

G2/M checkpoint - point where cell commits to mitosis 

  • can halt if DNA not replicated correctly
  • M-phase-promoting factor (MPF) - Cdk that works at this checkpoint; sensitive to substances that disrupt DNA
  • removal of inhibitor phosphates acts as signal (damaged DNA >> inhibitory phosphorylation of MPF)

spindle checkpoint – makes sure that all chromosomes attached to spindle for anaphase 

  • checks to see if all chromosomes are aligned on metaphase plate
  • anaphase-promoting complex – transmits signal that removes inhibitors of protease (which destroys the cohesion that holds chromatids together)

growth factors – regulatory signals that stimulate cell division 

  • triggers intracellular signaling systems
  • platelet-derived growth factor (PDGF) – promotes fibroblast growth
  • overrides cellular controls that normally stop cell division
  • most cells need combination of different growth factors to totally promote cell division

cancer – uncontrolled cell growth 

  • occurs when cell can’t control division
  • p53 – gene controlling G1 checkpoint
    • tells cell to kill itself (apoptosis) if DNA damage can’t be repared
    • prevents development of mutated cells
    • mutation in gene allows cancer cells to continue dividing
  • oncogenes – genes that can cause cells to be cancerous
  • proto-oncogenes – normal cellular genes; becomes oncogenes when mutated
    • can cause growth receptors to continually stay on, even w/o growth factor
    • can mutate proteins involved in signal cascades between receptor and Cdk
  • tumor-suppressor genes – normally inhibits the cell cycle, recessive to proto-oncogenes
  • retinoblastoma susceptibility gene (Rb) – only needs a single mutated copy to lead to cancer
    • single cancerous cell in retina >> retinoblastoma forms
    • Rb protein – aka “pocket protein,” has binding pockets for other proteins
Subject X2: 

12 - Meiosis

See included biology topics below:

Subject X2: 

Meiosis Overview

fertilization - aka syngamy; fuses gametes to form a new cell 

  • gametes - eggs, sperm
  • somatic cells - nonreproductive cells
    • has twice as many chromosomes as gametes
    • never form gametes
  • zygote - formed by 2 gametes fusing together
  • meiosis produces cells w/ 1/2 the normal number of chromosomes
  • sexual reproduction - uses meiosis/fertilization to give chromosomes from 2 parents to offspring
    • 23 maternal homologues from mother, 23 paternal homologues from father in humans
    • life cycles of organisms w/ sexual reproduction alternate between diploid/haploid periods
  • germ-line cells - will eventually produce gametes
    • undergoes meiosis, not mitosis

synapsis - close association of chromosomes during prophase I of meiosis 

  • synaptonemal complex - homologues paired closely along a protein lattice between them
  • pairs of homologues come together during metaphase I
  • homologues, not sister chromatids, go towards opposite poles during anaphase I
  • meiosis I - aka “reduction division”
  • crossing over - genetic recombination
    • homologues can exchange chromosomal information
    • chiasmata - sites of crossing over, maintained until anaphase I
  • continued association of chromosome pairs until anaphase is needed to ensure accurate separation

2 divisions - genetic material only replicated once 

  • produces cells w/ 1/2 the number of chromosomes
  • meiosis II - like mitosis, but without chromosome duplication
Subject X2: 

Steps of Meiosis

prophase I - DNA coils and becomes visible under light microscopes 

  • sister chromatid cohesion - pairing of homologous pairs side by side
    • guided by heterochromatin sequences
    • homologues attach to nuclear envelope at specific sites
  • recombination nodules - has enzymes for breaking/joining homologous chromatids
  • crossing over between sister chromatids is suppressed
  • only about 2-3 crossovers per chromosome per meiosis
  • sister chromatids held together at centromeres, homologous chromosomal pairs held together where crossing over took place
  • chiasma - X-shaped structure where crossover took place
    • ensures that the microtubule spindle only attaches to 1 side of centromere
    • indicates that crossing over has taken place

metaphase I - nuclear envelope dissolves 

  • microtubules form spindle like in mitosis
  • terminal chiasmata - state of chiasmata where they reach the ends of the chromosomes
  • kinetochores only connect to centromeres on 1 side
  • chromosome pairs line up on metaphase plate randomly

anaphase I - microtubules begin to shorten 

  • chiasmata gets broken, homologues get pulled apart
  • sister chromatids aren’t split up
  • independent assortment - poles can have mixes of maternal/paternal homologues

telophase I - chromosomes located in clusters at each pole 

  • nuclear membrane reforms around chromosomes, each w/ 2 sister chromatids
  • sister chromatids no longer identical due to crossing over

meiosis II - occurs after a brief interphase after meiosis I 

  • prophase II - nuclear membrane breaks down, microtubule spindle forms
  • metaphase II - spindle fibers bind to both sides of centromeres
  • anaphase II - sister chromatids split, go to opposite poles
  • telophase II - nuclear envelope re-forms
  • meiosis I/II result in 4 distinct cells w/ haploid chromosomal set
Subject X2: 

Origin of Sex

asexual reproduction - creates genetically identical offspring

  • all chromosomes from a single parent
  • animal asexual reproduction involves budding off of a mass of cells
  • parthenogenesis - development of an adult from an unfertilized egg
    • common form of reproduction in arthropods
    • diploid female bees, haploid male bees
  • more advantageous than sexual reproduction (recombination does more harm than good in evolution)

sexual reproduction - multiple theories on its origin 

  • no other process makes diversity more quickly, speeds up evolution
  • asexually reproducing organisms tend to live in isolated, demanding habitats where natural selection doesn’t favor change
  • sexually reproducing organisms tend to favor versatility, best supported by genetic recombination

DNA repair hypothesis - diploid cells can repair chromosome damage  

  • protists only use sexual reproduction in times of stress
  • synaptonemal complex may have evolved as a way to fix double-stranded DNA damage
  • undamaged homologous chromosome used as template to fix damaged DNA

contagion hypothesis - mobile genetic elements infected eukaryotes  

  • elements w/ genes for fusion w/ uninfected cells and synapsis can quickly copy itself onto homologous chromosomes
  • idiomorph - genes in homologous positions on chromosomes but are so different that they can’t be of homologous origin
  • explains the mating type “alleles” in fungi

red queen hypothesis - saves recessive alleles useful in the future  

  • keeping alleles allow organism to keep up w/ changing environment
  • sexual species can’t get completely rid of recessive traits in heterozygotes

Muller’s ratchet - can keep mutation level down 

  • asexual populations can’t get rid of mutations
  • sexual populations get rid of mutations through natural selection
Subject X2: 

13 - Patterns of Inheritance

See included biology topics below:

Subject X2: 

Mendel's Experiment

heredity theories before Mendel

  • classical assumption 1 (constancy of species) - heredity occurs within species
    • possible to get weird combinations by cross-breeding different species
    • soon obvious that extreme cross-breeding not possible
    • species maintained w/o much change since creation
  • classical assumption 2 (direct transmission of traits)
    • gonos - “seed;” reproductive material transmitted from parents to offspring
    • information about each body part of offspring came from same body part in parent
  • Charles Darwin - believed that “gemmules” (microscopic granules) passed down to offspring to guide development
  • traits from parents blend and mix in the offspring
  • hybridizations - carried out by Josef Koelreuter on tobacco plants
    • hybrids had different appearances than parents
    • offspring of hybrids either resembled hybrids or grandparents
    • proved the classical assumptions wrong
    • traits/characters segregated among a certain population
  • T. A. Knight - did breeding experiments w/ white/purple plants
    • found that purple/white plants produced purple offspring
    • offspring of purple offspring were both purple/white
  • early scientists didn’t record numbers or specific observations >> science advanced slowly

Mendel’s garden pea - same plant studied by Knight and others 

  • hybrid peas created by breeders consistently in the past, ensuring segregation of traits
  • large variety of peas available
  • many easily identifiable traits
  • small/easy to grow, short generations
  • able to self-fertilize or cross-fertilize

Mendel’s procedure - studied comparable, specific differences 

  • pure-breeding - produced plants that only produce plants w/ the same characteristics
    • pea plants allowed to self-fertilize over and over
    • ensured that certain pea plants would only pass down certain characteristics
  • cross-bred pea varieties w/ different traits
  • hybrids produced by plants w/ different traits allowed to cross-breed many times
  • make quantitative observations (not done by any preceding scientist)

Mendel’s results - analyzed 7 traits each w/ 2 obvious differences  

  • F1 generation (first filial generation)
    • hybrid offspring of purple/white flowered plants
    • all plants had purple flowers, the dominant trait
    • no white flowers (recessive trait)
  • F2 generation (second filial generation)
    • recessive trait reappeared in 1/4 of offspring
    • dominant trait appeared in 3/4 of offspring
  • 3:1 ratio of dominant to recessive (Mendelian ratio) actually a 1:2:1 ratio of pure-breeding dominant to non-pure-breeding dominant to pure-breeding recessive
  • no traits ever blended/mixed, each trait inherited all together
  • recessive traits latent (present but not expressed) in F1 generation
Subject X2: 

Mendelian Principles

Mendel’s model of heredity - 5 main assumptions 

  • parents don’t transmit traits directly to offspring
    • information about traits (factors) get passed down
    • factors encode how an individual expresses those traits
  • 2 factors for each trait
    • factors carried on chromosomes
    • gametes (haploid) each carry a factor for each trait
    • random chance determines which factor goes into each gamete
  • not all copies of factors are the same
    • alleles - alternative forms of a trait
    • homozygous - having the same 2 alleles for a certain trait
    • heterozygous - having different alleles for a certain trait
    • gene - factors that determine traits
    • locus - location of a gene on a chromosome
  • alleles don’t influence/change each other
    • alleles stay the same, don’t blend w/ others
  • an allele doesn’t guarantee that the trait will be expressed
    • genotype - all the alleles that the individual contains
    • phenotype - physical appearance/expression of those alleles

Punnet square - invented by Reginald Crundall Punnett 

  • can predict the possibilities of mixed alleles
  • shows a 3:1 phenotypic ratio and 1:2:1 genotypic ratio when hybrids bred
  • testcross - procedure used to see if plant is heterozygous or homozygous
    • plant crossed w/ homozygous recessive plant
    • only homozygous dominant plant will guarantee that all offspring will have dominant trait

Mendel’s laws of heredity - 2 main laws 

  • 1st law of heredity (segregation)
    • alleles for a trait separate and remain distinct
    • chromosomes align/split during meiosis
  • 2nd law of heredity (independent assortment)
    • alleles don’t affect alleles for another trait
    • chromosomes align in homologous pairs during meiosis
    • dihybrids - heterozygous for 2 genes

problems w/ analyzing inheritance - scientists had problems getting same ratios as Mendel 

  • continuous variation - range of small differences for a trait affected by multiple genes
    • polygeny - many genes affect 1 trait
    • not all phenotypes result from only 1 gene
    • quantitative traits - shows range of small differences
  • pleiotropic effects - allele w/ more than 1 effect
    • single gene affects multiple traits
    • difficult to predict (side effects often unknown)
  • incomplete dominance - not all alleles are totally dominant/recessive
    • allele pairs produce heterozygous phenotype either representative of both alleles or of an intermediate
    • codominance - representative of both parents
  • environmental effects - alleles affected by the environment
    • some alleles heat-sensitive, code for traits that are more sensitive to temperature/light
  • epistasis - 1 gene interfering w/ expression of another gene
    • occurs when genes act sequentially, one after the other
    • if enzyme defective early on in biochemical pathway, impossible to see if later steps work properly
Subject X2: 

Human Genetics

gene disorders - mostly very rare, recessive  

  • mutations - source of all new alleles
  • Tay-Sachs disease - causes lysosomes to burst
    • frequency of disease can vary w/ different populations and different histories
    • highest chance in Jewish populations
  • natural selection can’t always get rid of all gene disorders
  • Huntington disease - disorder caused by dominant gene
    • clinical symptoms don’t appear until middle age
    • those w/ disease have time to reproduce
    • natural selection doesn’t get rid of it
  • Hemophilia - inability to form blood clots; cuts won’t stop bleading
  • pedigree - graphical representation trait passed down many generations
    • uses history of the family to predict future phenotypes
  • sickle-cell anemia - defect in hemoglobin carrier
    • alters shape of red blood cells
    • due to change in a single amino acid
    • those heterozygous for this disease have more resistance to malaria
  • cystic fibrosis - mucus clogs lungs, liver, pancreas
    • due to failure of chloride ion transport protein

blood groups - 4 different phenotypes 

  • codominant traits show effects of both alleles
  • 3 alleles - IB (adds galactose), IA(adds galactosamine), i (doesn’t add sugar
  • type A blood - IAIA homozygotes or IAi heterozygotes
  • type B blood - IBIB homozygotes or IBi heterozygotes
  • type AB blood - IAIB heterozygotes, universal acceptor
  • type O blood - ii homozygotes, universal donor
  • Rh blood group - cell surface markers on human red blood cells
    • Rh-negative people don’t have receptors
    • Rh-positive blood clump when immune system of Rh-negative people attack it

gene therapy - replacing defective genes w/ functional ones 

  • cells w/ damaged genes fixed/replaced w/ working copies of the gene, then put into the body
  • hard to reintroduce the fixed gene back into the body
    • using adenovirus (causes colds) activates the immune system, killing the vector
    • DNA inserted at a random location into the chromosome
  • adeno-associated virus (AAV) - doesn’t cause a strong immune response, can still carry genes
    • less likely than adenovirus to produce cancer mutations
Subject X2: 

Genes on Chromosomes

chromosomal theory of inheritance - similar chromosomes pair w/ each other during meiosis 

  • segregation/independent assortment shown by meiosis I
  • number of traits for each organism always more than number of chromosomes
  • Thomas Hunt Morgan - performed experiments w/ red/white eyed flies
    • found evidence of sex-linked inheritance
    • proved that genes for traits are found on chromosomes
  • males - X/Y chromosomes
  • females - X/X chromosomes
  • sex-linked trait - found on the X chromosome

genetic recombination - crossing over mixed up genes further 

  • physical exchange of chromosomal arms
  • crossing over can occur anywhere along the chromosome
  • more likely that crossing over occurs between chromosomes that are far apart
  • genetic map - measures distance between genes in terms of recombination frequency
    • centimorgan - map unit, distance within which a crossover is expected to happen in 1% of gametes
  • three-point cross - involves 3 linked genes (genes so close that they don’t assort independently)
    • wild type - most common allele of a gene, designated by "+"

human genetic map - uses pedigrees and statistics 

  • LOD (log of odds ratio) - ratio of probability that 2 genes are linked to probability that they aren’t linked
  • anonymous markers - genetic markers that can be detected easily but doesn’t cause a phenotype
    • allows for chromosomes to be mapped
  • polymorphisms - differences between individuals in populations

human chromosomes - 46 chromosomes, 23 pairs; divided into 7 groups 

  • autosomes - 22 of 23 pairs, perfectly matched in males and females
  • sex chromosomes - similar in females, dissimilar in males
  • SRY gene - on Y chromosome, plays important role in male sexual development
    • environmental factors can cause changes in sex of adult fishes/reptiles
  • Barr body - inactive X chromosome in females (deactivated after sex is determined)
  • gap conversion - copies over DNA sequence from other chromosome
    • DNA sections that don’t match are completely discarded
    • Y chromosome consists of palindromes, able to fix itself w/o another DNA sequence (reason why males aren’t extinct)

chromosome number - can cause abnormalities and diseases 

  • nondisjunction - failure of sister chromatids to separate correctly
  • aneuploidy - loss/gain of a chromosome
  • monosomics - humans who lost 1 copy of an autosome, don’t survive development
  • trisomics - humans w/ extra copy of autosome, most don’t survive
    • possible to survive w/ 3 copies of chromosome 13, 15, 18, 21, or 22
  • Down Syndrome - trisomy 21, occurs in 1/750 children
    • translocation - process that adds a small part of chromosome 21
    • cancer more common in people w/ Down Syndrome
    • possible link to cancer/Alzheimer’s on chromosome 21
    • chances of giving birth to a child w/ Down Syndrome increases as the mother gets older (eggs have more time to mutate)
  • Klinefelter syndrome - XXY zygote
    • sterile male w/ many female body characteristics
  • Turner syndrome - XO zygote (O means absence of a chromosome)
    • sterile female w/ webbed neck and sex organs that never mature
  • Jacob syndrome - XYY zygote
    • fertile males w/ normal appearances
    • chances for disease 20x higher in mental/penal institutions

genetic counseling - determining if parents are at risk of producing children w/ defects 

  • checks the genetic state of early embryos
  • pedigree analysis - makes it possible to estimate the probability of someone being a carrier from some disease
  • amniocentesis - amniotic fluid withdrawn from uterus during 4th month of pregnancy
    • cells then grown in cultures in the lab
    • ultrasound used to determine position of needle/fetus so that the fetus won’t be harmed
  • chorionic villi sampling - cells removed from chorion (membrane part of placenta)
    • can be used in 8th week of pregnancy
    • faster than amniocentesis
  • karyotype analysis - checks for aneuploidy
  • lack of normal enzyme activity >> disorder present
Subject X2: 

14 - DNA: Genetic Material

See included biology topics below:

Subject X2: 

Discovery of Genetic Material

Hammerling experiment - determined where cells kept hereditary material

  • used Acetabularia cells, found that hereditary material in foot area
  • transplanted different parts of A. mediterranea and A. crenulata
  • parts eventually developed according to the hereditary material in foot area (intermediate head formed at first due to remaining RNA left in stalk)

transplantation experiments - added support that nucleus contained hereditary material 

  • Thomas King/Robert Briggs - transplanted nuclei from frog cells
    • cells wouldn’t develop w/o nucleus
    • showed that nuclei contained the information needed to direct development
  • F. C. Steward - mixed fragments of carrot tissue w/ liquid growth medium
    • showed that single cells can form entire, mature plants
    • totipotent - containing full set of hereditary instructions

Griffith experiment - discovered transformation  

  • found that S. pneumoniae bacteria could only infect w/ polysaccharide coating
  • dead bacteria w/ polysaccharide coating mixed w/ live bacteria w/o polysaccharide coating to form live bacteria w/ polysaccharide coating
  • transformation - transfer of genetic material from one cell to another

Avery experiments - found the “transforming principle” from Griffith ’s experiments 

  • removed nearly all of the protein in S. pneumoniae, but transformation still occurred
  • purified mixture contained elements close to that of DNA, had same density
  • taking out lipids/proteins didn’t stop transformation
  • DNA-digesting enzyme DNase stopped all transformations
  • showed that DNA provided hereditary material for bacteria

Hershey-Chase experiment - studied bacteriophages, viruses that infect bacteria 

  • viruses - contain DNA or RNA surrounded by protein coat
    • causes cells to produce so many viruses that it bursts (lyses)
  • used radioactive isotopes to track DNA and protein coat
  • showed that DNA caused changes in cells, not protein
Subject X2: 

DNA Structure

nucleic acid - first discovered by Friedrich Miescher 

  • P. A. Levene - determined nucleic acids’ basic structure (5-carbon sugar, phosphate group, nitrogenous base)
    • believed that 4 types of nucleotides available in equal amounts, repeated
  • purine - adenine or guanine
  • pyrimidine - thymine (replaced by uracil in RNA) or cytosine
  • nucleotide - DNA unit, each consists of 5-carbon sugar, phosphate group, base
    • phosphate/hydroxide groups allow nucleotides to attach in long chains
    • phosphodiester bond - holds nucleotides together
  • Erwin Chargaff - showed that DNA didn’t just repeat itself
    • amount of adenine always equals amount of thymine
    • amount of cytosine always equals amount of guanine

3D shape of DNA - shaped like staircase wrapping around a common axis 

  • Rosalind Franklin - used X-ray diffraction to analyze DNA
    • bombarded DNA w/ X-ray beam, diffraction shows shape of molecule
    • used DNA fibers to analyze shape
    • thought that DNA could have helix shape
  • James Watson/Francis Crick - used Franklin ’s results before she published them
    • found that DNA made up of 2 chains of nucleotides, forming a double helix
  • complementarity - sets of hydrogen bonds link together base pairs
    • adenine forms 2 hydrogen bonds w/ thymine
    • guanine forms 3 hydrogen bonds w/ cytosine
    • knowing the sequence of 1 strand gives the sequence of the other strand
  • antiparallel configuration - 2 strands of DNA oriented in different directions
  • collective energy from all the base pairs together makes DNA strand very stable
Subject X2: 

DNA Replication

Meselson-Stahl experiment - supported Watson/Crick’s theories on DNA replication 

  • DNA replication theories
    • semiconservative replication - each strand of DNA duplex used when forming new DNA
    • conservative replication - original DNA duplex remains intact, new DNA has only new molecules
    • dispersive replication - original DNA gets scattered in new DNA, which contains new/old molecules on each strand
  • bacteria w/ heavier nitrogen (15N) isotope in DNA grown and then transferred to bacteria w/ lighter nitrogen isotope (14N)
  • centrifuge used to determine density of DNA after replication
  • results showed that DNA replicates in a semiconservative way

replication process - must be fast/accurate 

  • starts at origin, goes bidirectionally towards the terminus
  • replicon - functional unit containing chromosome and origin
  • polymerase - enzyme that synthesizes nucleic acids
    • 3 main ones: pol I, pol II, pol III
    • DNA pol II used mainly for DNA repair
    • DNA pol III - made up of alpha subunit (main catalytic part) and beta subunit (forms ring around template, acting as sliding clamp)
    • primer - short stretch of DNA/RNA nucleotides hydrogen-bonded to the complementary strand
    • cannot start synthesis of DNA w/o primer
  • endonucleases - cuts DNA internally
  • exonucleases - chews away at end of DNA; helps proofread
    • used by DNA pol I to remove the primers after replication
  • leading strand - can be replicated as 1 continuous strand, uses 1 primer
  • lagging strand - replicated only in short stretches (Okazaki fragments), uses multiple primers
  • DNA primase - synthesizes short RNA primer
    • RNA polymerases don’t need primers to start
  • DNA helicase - enzyme that unwinds/opens the DNA strands
  • DNA gyrase - form of topoisomerase that takes away the torsional strain (coiling up of strands)
  • single-strand binding protein (ssb) - covers the hydrophobic single, unwound DNA strands
  • DNA ligase - creates phosphodiester bond to join the Okazaki fragments
  • replication fork - site where DNA strands open and replication occurs
  • replisome - replication organelle, assembly of proteins
    • primosome - made up of primase/helicase and other proteins
    • 2 DNA pol III, 1 for each strand
  • both pol III move in the same direction, but 1 of the strands looped

stages of replication -

  • initiation - occurs at the origin (OriC)
    • initiator protein recognizes specific sites within the OriC
    • opens up helix at A-T rich region (very few triple bonds)
    • primosome assembled onto strands
    • 2 replication forks form as replication goes bidirectionally
  • elongation - takes up most of the time during replication
    • pol III add new nucleotides to the template strand
    • more complicated process on lagging strand than on leading strand
  • termination - termination site located opposite the origin on circular chromosome
    • DNA gyrase keeps new DNA molecules from intertwining

eukaryotic DNA replication - main difference in amount of DNA reproduced  

  • uses multiple origins for replication
  • more origins/replicons formed when divisions need to be rapid
  • PCNA (proliferating cell nuclear antigen) - replaces beta subunit in eukaryotes
Subject X2: 

Gene Structure

Archibald Garrod - noted prevalence of diseases in certain families 

  • alkaptonuria - lack of enzyme leads to formation of alkapton (homogentisic acid) in urine
  • believed that inherited diseases may be due to enzyme deficiencies

Beadle/Tatum - found that genes specify enzymes  

  • deliberately created mutations in chromosomes
  • used X-rays to damage DNA in some yeast spores
  • placed yeast in minimum medium (only contained sugar, ammonia, salts, water, vitamins)
    • those that couldn’t make growth compounds would die
    • material added to minimum medium to see what the yeast cells w/ damaged DNA lacked
  • found that every enzyme had a different chromosomal site
  • one-gene/one-enzyme hypothesis - genes produce effects by encoding for enzymes (aka one-gene/one-polypeptide hypothesis)

Frederick Sanger - found complete amino acid sequence for insulin 

  • 1st sequence to be determined for a protein
  • showed that all proteins were just strings of amino acids in a certain order

Vernon Ingram - found molecular basis for sickle cell anemia 

  • found that change from glutamic acid to valine in the protein caused sickle cell anemia
  • gene - sequence of nucleotides that determines the amino acid sequence of a protein
  • some genes used to make special RNA forms
Subject X2: 

15 - How Genes Work

See included biology topics below:

Subject X2: 

Central Dogma, Genetic Code

using RNA for protein

  • ribosomes - RNA-protein complexes that make polypeptides
    • has 2 subunits
    • RNA acts as main catalytic unit, ribosomal proteins has structural role
    • protein synthesis occurs at P, A, and E sites
  • ribosomal RNA (rRNA) - type of RNA in ribosomes
    • provides the site where polypeptides get assembled
  • transfer RNA (tRNA) - transports/positions amino acids
  • messenger RNA (mRNA) - long RNA strands transcribed from DNA
  • reads genetic messages in DNA and produces the proteins that the DNA asks for

central dogma - aka gene expression; info passes DNA > RNA > proteins 

  • transcription - transfer of info from DNA to RNA
    • produces mRNA
    • starts when RNA polymerase binds to promoter binding site
    • creates complementary transcript (uracil in place of thymine)
  • translation - transfer of info from RNA to protein
    • directs sequence of amino acids
    • each group of 3 nucleotides codes for an amino acid
    • rRNA reads the mRNA to make the polypeptide chain

genetic code - consists of codons (blocks of information) 

  • same in almost all organisms
    • supports belief that all organisms have the same root
    • mitochondria/chloroplasts read code differently
  • each codon corresponds to a specific amino acid
  • 3-nucleotide sequence in each codon (triplet code)
  • reading frame - part of genetic code being read by mRNA
  • removing a single nucleotide or 2 would mess everything up
  • triplet binding assay - developed by Nirenberg/Leder to see which radioactive amino acid the triplet binded to; tested all 64 possible combinations
  • mRNA can be transferred from 1 organism to another and still work
Subject X2: 


transcription in prokaryotes

  • RNA polymerase - has 5 subunits
    • 2 a subunits bind regulatory proteins
    • b' subunit binds DNA template
    • b subunit binds RNA nucleotide subunits
    • s subunit starts synthesis, recognizes promoter
    • template strand (antisense strand) - strand of DNA that’s copied
    • coding strand (sense strand) - strand of DNA not copied, identical to RNA
  • promoter - sites where transcription starts
    • short sequence not transcribed by polymerase
    • -35 sequence - TTGACA, 35 nucleotides from where transcription starts
    • -10 sequence - TATAAT, 10 nucleotides from where transcription starts
  • initiation - binding of RNA polymerase to promoter
    • s subunit detects promoter (w/o unwinding DNA), attaches polymerase there
    • polymerase begins to unwind DNA helix (section about 17 base-pairs long)
  • elongation - uses ATP or GTP to add ribonucleotides
    • transcription bubble - area containing RNA polymerase, DNA, growing RNA
    • DNA rewinds after leaving bubble
    • RNA polymerase can’t proofread, makes more errors than replication
  • termination - “stop” sequences cause phosphodiester bonds to stop forming
    • RNA-DNA dissociates
    • RNA polymerase releases DNA
    • DNA rewinds
    • GC hairpin - causes polymerase to pause, eventually let go of DNA

transcription in eukaryotes

  • multiple RNA polymerases - 3 different ones used
    • RNA polymerase I - transcribes rRNA, recognizes promoters
    • RNA polymerase II - transcribes mRNA, small nuclear RNA
    • RNA polymerase III - transcribes tRNA, small RNA
  • promoters - different 1 for each polymerase
    • specific for each species
    • pol II promoters - most complex out of the 3
    • TATA box - resembles -10 sequence; found in “core promoters”
    • pol III promoters - internal to gene itself
  • initiation - more complex than prokaryotic initiation
    • initiation complex - forms at promoter/pol II by general transcription factors
  • posttranscriptional modifications - mRNA packaged differently
    • 5’ cap - GTP added to 5’ phosphate group, protects mRNA from degradation
    • 3’ poly-A tail - adenine residues added by poly-A polymerase to end of mRNA, stabilizes mRNA
Subject X2: 


translation - begins when mRNA binds to rRNA 

  • tRNA w/ complementary 3-nucleotide sequence (anticodon)
  • 45 different tRNA molecules (some tRNA recognize more than 1 codon)
  • activating enzymes - pairs 3-nucleotide sequences w/ amino acids
    • aminoacyl-tRNA synthetase - 1 exists for each of 20 common proteins, attaches tRNA to amino acids
    • corresponds to an amino acid and 1-6 different anticodons
  • nonsense codons - UAA, UAG, UGA
    • has no complementary anticodon
    • used as “stop signals
  • methionine - AUG, “start” signal
  • initiation - begins w/ initiation complex formation
    • initiation factors - proteins that position tRNAfMet(in prokaryotes) or methionine (in eukaryotes) at P site, where peptide bonds form
    • A (aminoacyl) site - where successive amino-acid-bearing tRNA will bind
    • E (exit) site - where empty tRNA exit ribosome
    • positioning of mRNA determines reading frame
    • leader sequence - marks beginning of each mRNA
    • prokaryotes include several genes on a single mRNA (polycistronic mRNA)
    • eukaryotes include 1 gene per mRNA (monocistronic mRNA)
  • elongation - elongation factor proteins bind tRNA to mRNA at A site
    • ribosome catalyzes reaction that removes amino acid from tRNA and creates peptide bond w/ next amino acid
  • translocation - ribosome moves amino acids out, through E site
  • termination - nonsense codons recognized by release factors (proteins that release polypeptides from ribosome)
Subject X2: 

Gene Splicing

introns - intervening sequences found in eukaryotic DNA 

  • noncoding DNA that doesn’t show up in mRNA or proteins
  • exons - coding sequences

RNA splicing - cuts apart primary transcript to make final mRNA 

  • occurs in nucleus, before mRNA goes into cytoplasm
  • snRNPs - recognizes intron/exon junctions
  • spliceosome - large complex of snRNPs
    • removes introns by twisting them in lariat shape
  • exon-shuffling - theory that intron-exon arrangements represent shuffling of functional units over time

alternative splicing - splicing primary transcript into many mRNAs 

  • includes different sets of exons
  • experienced by 35-59% of human genes
  • makes 120,000 different mRNAs possible in human cells
  • proteomics - study of proteins

differences between prokaryotic/eukaryotic gene expression 

  • eukaryotic genes have introns, prokaryotic genes don’t
  • prokaryotic mRNA contain transcripts for many genes, eukaryotic mRNA only contain transcript for 1 gene
  • prokaryotes can start translation before transcription is done (no nucleus)
  • 5’ cap and 3’ poly-A tail added to genes by eukaryotes
  • 5’ cap starts translation in eukaryotes, AUG codon starts translation in prokaryotes
  • eukaryotes have larger ribosomes
Subject X2: 

16 - Gene Technology

See included biology topics below:

Subject X2: 

Manipulating DNA

DNA manipulation - uses enzymes (imitates what cells can do) 

  • restriction endonuclease - able to cleave DNA at specific places
    • restriction sites - where nucleases cleave DNA
    • methylation - stops nucleases from cleaving DNA
    • Type I - makes simple cuts on both DNA strands
    • Type II - makes staggered cuts where sequences same on both sides (dyad symmetry)
  • ligase - makes phosphodiester bonds to connect hydroxyl/phosphate groups
    • also joins Okazaki fragments on lagging strands
    • creates recombinant molecules from fragments created by nucleases

vector systems - used to carry recombinant DNA molecule into a cell 

  • not required by the cell, but can be selected w/ addition of marker
  • plasmids - small extrachromosomal DNA
    • must have origin of replication, selectable marker (usually for antibiotic resistance)
    • markers - used to see which cell took in the new DNA
    • multiple cloning site (MCS) - region in plasmid where DNA is inserted
    • inactivation of gene signals plasmid’s acceptance of new DNA
  • phages - viruses that infect bacterial cells
    • larger than plasmids, can insert more DNA
    • needs other live cells to replicate
    • linear DNA (can’t infect unless new DNA gets inserted)
  • chimera - totally new genome, nonexistent in nature
  • yeast artificial chromosome (YAC) - able to introduce larger DNA pieces than plasmids

DNA library - collection of all DNA fragments representing all an organism’s DNA 

  • genomic library - simplest type of DNA library
    • randomly fragmented genome
    • hydrodynamic shear forces - passes DNA through syringe
  • cDNA libraries - set of all expressed genes
    • reverse transcriptase - retrovirus that makes DNA from mRNA
Subject X2: 

Stages of Genetic Engineering

DNA cleavage (stage 1) - restriction endonuclease cleaves DNA into fragments 

  • produces large number of different fragments
  • different endonucleases >> different fragments
  • gel electrophoresis - procedure that separates fragments based on size

recombinant DNA production (stage 2) - DNA fragments inserted into vectors 

  • vectors cleaved w/ same restriction endonuclease as DNA

cloning (stage 3) - more recombinant DNA created 

  • vectors introduced into reproducing cells
  • each reproduced cell contains recombinant DNA

screening (stage 4) - most challenging part of any genetics experiment 

  • 4-I - preliminary screening of clones
    • gets rid of cells w/o any vectors, vectors w/o original DNA
    • uses vector w/ gene for antibiotic resistance
    • based on presence/absence of a certain phenotype
  • 4-II - finding gene of interest
    • hybridization - uses complementary nucleic acid (probe) to find particular fragment
    • solution added to denature DNA, allowing radioactive probe to attach

polymerase chain reaction (PCR) - uses DNA polymerase to mass produce gene sequences 

  • denaturation (step 1) - excess of primer mixed w/ DNA fragment
    • DNA strand heated to 98° C >> strands dissociate
  • annealing of primers (step 2) - DNA solution allowed to cool to 60 C
    • DNA strands reassociate w/ excess of primer instead of other complete complementary strand
    • leaves large parts of DNA single-stranded
  • primer extension (step 3) - uses Taq polymerase (heat-stable DNA polymerase) to copy rest of fragment
    • supply of all 4 nucleotides added to solution
    • creates double the amount of DNA as before (separate strands both replicated)
  • cycle repeated to double amount of DNA each time
  • can create large amount of DNA for study from just a tiny amount of DNA

southern blotting - identifies DNA w/ radioactivity 

  • DNA fragmented by endonucleases, spread apart by gel electrophoresis
  • DNA strands denatured by basic gel solution, transferred to nitrocellulose sheet
  • probe w/ single-stranded DNA complementary to gene of interest poured over sheet, will bind to particular sequence

restriction fragment length polymorphism (RFLP) 

  • identifies particular individual w/ specific gene marker
  • mutations, sequence repetitions, transposons alters length of DNA fragments created by endonucleases
  • pattern of bands produced by gel electrophoresis different for each person
  • DNA fingerprinting - 2 individuals rarely produced identical RFLP analyses
    • used in criminal investigations by forensic teams
    • autoradiographs - parallel bars on X-ray film used for comparison
Subject X2: 

Applying Genetic Engineering

medical applications 

  • pharmaceuticals - uses bacterial cells to mass produce certain proteins cheaply
    • recombinant genes introduced into bacterial cells
    • used to produce insulin, interferon, growth hormones, erythropoietin
    • atrial peptides - small proteins to treat high blood pressure
    • tissue plasminogen activator - human protein that causes blood clots to dissolve
    • hard/expensive to purify proteins produced by bacterial cells
  • genetic therapy - started in 1990 in attempt to fix genetic defects
    • replaces defective gene w/ working copy
  • piggyback vaccine - aka subunit vaccines, used against viruses
    • uses DNA of benign vaccinia virus to make vaccines, stimulate immune system
    • DNA vaccine - depends on killer T cells instead of antibodies to stop viruses

agricultural applications 

  • limited number of possible vectors for plants
  • Ti (tumor-inducing) plasmids - infects broadleaf plants
    • doesn’t infect cereal plants (corn, rice, wheat)
  • “Flavr Savr” - has genes that inhibit ethylene production, delaying over-ripening
  • nitrogen fixation - converts nitrogen gas to ammonia
    • plants use ammonia to make amino acids
    • nifgenes - found in symbiotic root-colonizing bacteria
    • soil runs out of nitrogen w/o addition of fertilizers
    • problems w/ protecting nitrogenase from oxygen
  • herbicide resistance - herbicides used to kill weeds, but can also kill plants
    • glyphosphate - active ingredient that inhibits EPSP synthetase
    • new engineered plants have 20x normal amount of EPSP synthetase, can work even in presence of glyphosphate
  • insect resistance - removes need to use so many insecticides
    • uses genes for proteins harmful to insects but harmless to other organisms
    • transgenic plants - plants w/ altered genes, protected from insects that normally feed on them
  • golden rice ” - used to solve problem of lack of iron in diets
    • ferritin gene from beans added to increase iron content
    • gene added to destroy phytate (inhibits iron absorption)
    • gene for sulfur-rich protein added from wild rice (sulfur needed for iron absorption)
    • ordinary rice lacks certain enzymes to finish provitamin A creation
  • gene technology replacing natural/artificial selection as means for breeding

risk/regulation - tampering w/ genetics >> possible bad long-term side effects 

  • gene modifications make crop easier to grow, improves food itself
  • screening for allergy problems done w/ genetically altered foods
  • pests become resistant to pesticides faster than to genetically altered defenses
  • debates over whether consumers should/need to know about genetically modified foods
Subject X2: 

17 - Genomes

See included biology topics below:

Subject X2: 

Mapping, Sequencing

genome maps - linkage maps showing relative location of genes 

  • 1st map made in 1911 when 5 genes of Drosophila mapped
  • distances measured in centimorgans (cM)
  • genetic maps - distances between genes found by recombination frequencies
  • physical maps - diagrams showing relative landmarks within sequences
    • landmark - specific DNA sequences, where restriction enzymes cut DNA
    • contig - contiguous segment of genome made from pieces cut by restriction enzymes
  • sequenced-tagged sites (STS) - 100-500 base-pair sequence of a clone
    • physical map can be made by overlapping STSs
    • useful when 2 different groups working on certain nonsequenced DNA

sequencing - automated sequencing required for the very large genomes 

  • automated sequencers - provides accurate sequences for up to 500 base-pairs
    • errors still possible, 5-10 copies used
    • DNA prepared w/ fluorescent nucleotides, unlabeled nucleotides
    • fluorescent nucleotides lack hydroxyl groups, halt replication
    • DNA separated by size (1st base in sequence found in shortest band, last base in sequence found in longest band)
  • artificial chromosome - used to clone larger DNA pieces
    • contained replication origin (to replicate independently of genome) and centromere sequences (for stability)
    • bacterial artificial chromosomes (BAC) - used for large-scale sequencing, accepts DNA inserts 100-200kb long
  • clone-by-clone sequencing - physical mapping followed by sequencing
    • cuts DNA fragments which are each cloned into smaller fragments
  • shotgun sequencing - sequencing all the clone fragments all at once, uses computer to put together overlaps
    • assembles consensus sequence from multiple copies of sequenced regions
    • doesn’t use extra info about genome

human genome project - 3.2 gigabase nucleotide sequence in humans 

  • number of genes doesn’t indicate complexity of organism (rice has more genes than humans)
  • physical map finished on June 26, 2000
Subject X2: 

Stages of Genetic Engineering

DNA cleavage (stage 1) - restriction endonuclease cleaves DNA into fragments 

  • produces large number of different fragments
  • different endonucleases >> different fragments
  • gel electrophoresis - procedure that separates fragments based on size

recombinant DNA production (stage 2) - DNA fragments inserted into vectors 

  • vectors cleaved w/ same restriction endonuclease as DNA

cloning (stage 3) - more recombinant DNA created 

  • vectors introduced into reproducing cells
  • each reproduced cell contains recombinant DNA

screening (stage 4) - most challenging part of any genetics experiment 

  • 4-I - preliminary screening of clones
    • gets rid of cells w/o any vectors, vectors w/o original DNA
    • uses vector w/ gene for antibiotic resistance
    • based on presence/absence of a certain phenotype
  • 4-II - finding gene of interest
    • hybridization - uses complementary nucleic acid (probe) to find particular fragment
    • solution added to denature DNA, allowing radioactive probe to attach

polymerase chain reaction (PCR) - uses DNA polymerase to mass produce gene sequences 

  • denaturation (step 1) - excess of primer mixed w/ DNA fragment
    • DNA strand heated to 98° C >> strands dissociate
  • annealing of primers (step 2) - DNA solution allowed to cool to 60 C
    • DNA strands reassociate w/ excess of primer instead of other complete complementary strand
    • leaves large parts of DNA single-stranded
  • primer extension (step 3) - uses Taq polymerase (heat-stable DNA polymerase) to copy rest of fragment
    • supply of all 4 nucleotides added to solution
    • creates double the amount of DNA as before (separate strands both replicated)
  • cycle repeated to double amount of DNA each time
  • can create large amount of DNA for study from just a tiny amount of DNA

southern blotting - identifies DNA w/ radioactivity 

  • DNA fragmented by endonucleases, spread apart by gel electrophoresis
  • DNA strands denatured by basic gel solution, transferred to nitrocellulose sheet
  • probe w/ single-stranded DNA complementary to gene of interest poured over sheet, will bind to particular sequence

restriction fragment length polymorphism (RFLP) 

  • identifies particular individual w/ specific gene marker
  • mutations, sequence repetitions, transposons alters length of DNA fragments created by endonucleases
  • pattern of bands produced by gel electrophoresis different for each person
  • DNA fingerprinting - 2 individuals rarely produced identical RFLP analyses
    • used in criminal investigations by forensic teams
    • autoradiographs - parallel bars on X-ray film used for comparison
Subject X2: 

Applying Genetic Engineering

medical applications 

  • pharmaceuticals - uses bacterial cells to mass produce certain proteins cheaply
    • recombinant genes introduced into bacterial cells
    • used to produce insulin, interferon, growth hormones, erythropoietin
    • atrial peptides - small proteins to treat high blood pressure
    • tissue plasminogen activator - human protein that causes blood clots to dissolve
    • hard/expensive to purify proteins produced by bacterial cells
  • genetic therapy - started in 1990 in attempt to fix genetic defects
    • replaces defective gene w/ working copy
  • piggyback vaccine - aka subunit vaccines, used against viruses
    • uses DNA of benign vaccinia virus to make vaccines, stimulate immune system
    • DNA vaccine - depends on killer T cells instead of antibodies to stop viruses

agricultural applications 

  • limited number of possible vectors for plants
  • Ti (tumor-inducing) plasmids - infects broadleaf plants
    • doesn’t infect cereal plants (corn, rice, wheat)
  • “Flavr Savr” - has genes that inhibit ethylene production, delaying over-ripening
  • nitrogen fixation - converts nitrogen gas to ammonia
    • plants use ammonia to make amino acids
    • nifgenes - found in symbiotic root-colonizing bacteria
    • soil runs out of nitrogen w/o addition of fertilizers
    • problems w/ protecting nitrogenase from oxygen
  • herbicide resistance - herbicides used to kill weeds, but can also kill plants
    • glyphosphate - active ingredient that inhibits EPSP synthetase
    • new engineered plants have 20x normal amount of EPSP synthetase, can work even in presence of glyphosphate
  • insect resistance - removes need to use so many insecticides
    • uses genes for proteins harmful to insects but harmless to other organisms
    • transgenic plants - plants w/ altered genes, protected from insects that normally feed on them
  • golden rice ” - used to solve problem of lack of iron in diets
    • ferritin gene from beans added to increase iron content
    • gene added to destroy phytate (inhibits iron absorption)
    • gene for sulfur-rich protein added from wild rice (sulfur needed for iron absorption)
    • ordinary rice lacks certain enzymes to finish provitamin A creation
  • gene technology replacing natural/artificial selection as means for breeding

risk/regulation - tampering w/ genetics >> possible bad long-term side effects 

  • gene modifications make crop easier to grow, improves food itself
  • screening for allergy problems done w/ genetically altered foods
  • pests become resistant to pesticides faster than to genetically altered defenses
  • debates over whether consumers should/need to know about genetically modified foods
Subject X2: 

18 - Control of Gene Expression

See included biology topics below:

Subject X2: 

Transcriptional Control, DNA Motifs

overview of transcriptional control - important for adaptation, development, homeostasis 

  • regulating promoter access - controls start of transcription
    • binding proteins to regulatory sequence blocks/catalyzes binding of RNA polymerase
    • promoter (nucleotide sequence) tells polymerase where to start transcribing
  • transcriptional control in prokaryotes - prokaryotes grow/divide as quickly as possible
    • adjusts cell’s activities to immediate environment
    • reversible changes, lets cell adjust enzymes levels up/down
  • transcriptional control in eukaryotes - eukaryotes protected from changes in immediate environment
    • regulates body as a whole, not just individual cells
    • controls growth/development
    • enzymes for a particular developmental change stops working after the change takes place
  • posttranscriptional control - changes mRNA produced by transcription

DNA-binding motifs - proteins have special structure to bind to DNA on major groove 

  • major groove - contains hydrogen atoms, hydrogen bond donors/acceptors, hydrophobic methyl groups
  • helix-turn-helix - most common motif
    • made up of 2 alpha-helical segments connected by nonhelical segment
    • recognition helix - fits into major groove of DNA molecule
    • more protein-DNA-binding sites increases strength of bond between them
  • homeodomain motif - helix-turn-helix motfi in center
  • zinc finger motif - uses zinc to coordinate binding to DNA
    • more zinc fingers in cluster >> stronger link between protein/DNA
  • leucine zipper motif - 2 different protein subunits make a single binding site
    • Y-shape, allows for greater flexibility in gene control
Subject X2: 

Prokaryotic/Eukaryotic Gene Regulation

prokaryotic gene regulation - prokaryotes react according to environmental changes 

  • regulatory molecules can increase/decrease initiation rate
  • induction >> prevent negative regulator from binding >> produces proteins
  • repression >> makes negative regulator bind >> stops protein production
  • operons - multiple genes part of a single gene expression unit
    • all part of same mRNA >> controlled by same promoter
    • genes for same biochemical pathway organized this way
  • repressors - proteins that bind to regulatory sites on DNA >> prevent start of transcription
  • trp operon - repressed in presence of tryptophan, induced in absence of tryptophan
    • tryptophan repressor can’t bind to DNA unless it binds to 2 tryptophan molecules first
  • lac operon - makes enzymes when lactose available
    • lack of lactose >> lack of allolactose (metabolite of lactose) >> repressor allowed to bind to DNA >> stops production of enzymes for lactose
  • activators - binds DNA to stimulate transcription initiation
  • catabolite activator protein (CAP) - activator protein stimulating transcription for operons coding for sugar catabolism
    • binding controlled by cAMP (inversely related to glucose level)
    • little glucose >> lots of cAMP >> CAP able to bind to DNA >> stops catabolic operons
  • switches combined when 1 used for more than 1 reaction

eukaryotic gene regulation - much more complex than in prokaryotes 

  • DNA arranged in chromatin >> makes protein-DNA interactions difficult
  • transcription/translation occurs in 2 places
  • basal transcription factors - used for making transcription apparatus, getting RNA pol II to promoter
    • TFIID - contains TATA-binding protein for promoter
    • transcription-associated factors (TAF) - additional accessory factors
    • initiation complex - contains all factors and polymerase, needs other specific factors to work faster than basal level
  • specific transcription factors - increases rate of transcription
    • aka activators
    • has domain that interacts w/ transcription apparatus
  • enhancers - binding sites for specific transcription factors
    • can act over large distances by bending DNA strand
  • coactivator/mediator - binds transcription factor to another part of transcription apparatus
Subject X2: 

Chromatin, Posttranscription

effect of chromatin structure on gene expression - DNA organized around histones into nucleosomes 

  • DNA methylation - blocks accidental transcription of genes that are turned off
    • vertebrates have protein that binds to methylated base pairs, prevents transcription from starting
    • ensures that genes stay turned off when turned off
  • coactivators add acetyl groups to amino acids in chromatin >> makes DNA accessible to transcription factors
  • remove high order chromatin structure >> faster transcription

eukaryotic posttranscriptional control - uses regulatory proteins, small RNA 

  • small RNAs - interacts directly w/ main gene transcripts to regulate gene expression
    • 21-28 nucleotides long
    • RNA interface - inhibition of genes by RNA
    • double-stranded RNA forms when 2 ends complementary to each other loop
    • dicer - enzyme that makes small RNAs
    • microRNAs (miRNA) - binds directly to mRNA, prevents translation
    • small interfering RNAs (siRNA) - degrades mRNA before they get translated
  • epigenetic change - change in gene expression passed down in generations
    • not caused by changes in DNA sequence
    • due to changes in DNA packaging
  • changing how strands twist >> changes which genes are more easily accessible for expression
  • primary transcript - initial mRNA molecule copied by RNA polymerase
    • includes introns/exons
    • spliceosomes (made of snRNPs) cut out the introns
    • alternative splicing >> creates different proteins from same gene
  • RNA editing - produces altered mRNA not coded for the genome, usually through deamination
  • nuclear membrane makes sure that only completely processed transcripts reach the cytoplasm
  • translation factors - controls how mRNA gets translated by ribosomes
    • translation repressor protein - binds to beginning of transcript >> mRNA can’t attach to ribosomes
  • transcripts for regulatory proteins, growth factors less stable than other mRNA, more easily degraded by other enzymes
Subject X2: 

19 - Cellular Mechanisms of Development

See included biology topics below:

Subject X2: 

Types of Development

overview of development - control of gene expression >> specialization 

  • fungi development - only reproductive cells are specialized
    • higher fungi - basidiomycetes/ascomycetes, produce pheromones that influence other cells
    • usually just long cell filaments not completely separated from each other
    • mostly a growth process, not specialization
  • plant development - variety of specialized cells organized into tissues/organs
    • environment determines exact array of tissues
  • animal development
    • environment doesn’t affect animals as much as plants

vertebrate development - cells divide rapidly, forms shape, organs 

  • cleavage - initial period of cell division
    • zygote divides >> blastomeres (small cells) >> ball of cells made
    • no increase in size for embryo
    • animal pole - end of zygote where blastomeres go on to form external tissues
    • vegetal pole - end of zygote where blastomeres go on to form internal tissues
    • point where sperm enters egg = future belly
    • gene transcription begins after about 12 divisions
  • formation of the blastula - creates hollow ball of cells called blastula
    • aka blastocyst in mammals
    • tight junctions join outer blastomeres
    • Na+ pumped into space between cells to draw water into center of blastula
  • gastrulation - creates main axis of vertebrate body
    • lamellipodia used by cells to crawl over other cells
    • converts blastula into symmetrical embryo w/ central gut
    • has 3 germ layers (endoderm, mesoderm, ectoderm)
    • endoderm - forms tube of gut, will form most internal organs
    • ectoderm - cells on outside, will form skin/nervous system
    • mesoderm - will form notochord, bones, blood vessels, muscle
  • neurulation - ectodermal cells thicken, contract actin filaments to make neural tube
    • neural tube - will form brain, spinal chord
  • cell migration - cells move to form distant tissues
    • neural crest - cells that pinch off from neural tube to form sense organs
    • somites - cells move from central muscle blocks, form skeletal muscles
    • receptor proteins change cytoskeleton of cells to stop them from moving after they arrive at the correct locations
  • organogenesis/growth - basic body plan already laid out
    • tissues develop into organs
    • embryo grows to be 100x larger

insect development - produces 2 types of bodies 

  • larva - tubular eating machine, forms flying sex machine through metamorphosis
  • maternal genes - development begins before fertilization, w/ egg construction
    • specialized nurse cells move own mRNA into particular locations in egg
    • zygotic genes don’t determine first part of development
  • syncytial blastoderm - contains about 6000 nuclei
    • formed by 12 nuclear divisions w/o cytokinesis
    • membranes form between nuclei, forming larva (tubular body)
  • larval instars - total of 3 stages (instars) occur over about 4 days
    • exoskeleton prevents growth, must be shed so growth can occur
  • imaginal discs - cells that play no role in larva life, but forms important parts of adult fly’s body
  • metamorphosis - larva >> pupa after last larva stage
    • larval cells break down to release nutrients that fuel growth of imaginal discs
    • imaginal discs associate to form body of adult fly

plant development - plant cells cannot move due to cellulose walls 

  • meristems - self-renewing cells that grow outward
  • body made from types of modules (leaves, roots, branch nodes, flowers) dependent on environment
  • early cell division - off-center division, makes smaller cell w/ dense cytoplasm (future embryo)
    • suspensor - links embryo to nutrients of seed
    • cells near suspensor form roots
    • cells away from suspensor form shoots
  • tissue formation - 3 basic tissues form w/o cell mov’t
    • epidermal cells - outermost cells
    • ground tissue cells - interior cells, will form food/water storage
    • vascular tissue - cells at core of embryo
  • seed formation - flowering plant embryo makes 1-2 coyledons (seed leaves)
    • development pauses, embryo surrounded by nutritive tissue
    • forms seed (resistant to drought, unfavorable conditions)
    • disperses embryo to distant areas
  • germination - occurs in response to environmental changes
    • embryo starts development again to extend roots downward, shoots upward
  • meristematic development - apical meristems form cells needed for leaves/flowers
  • morphogenesis - microtubules direct cellulose deposition, orientation of fibers, direction of growth

nematode development - made up of about 959 somatic cells, 1 mm long 

  • entire genome mapped out as series of overlapping fragments
  • transparency allows viewing of cell mov’t during development
Subject X2: 

Cell Movement During Development

cell mov’t - changing patterns of cell adhesion  

  • cadherins - used in cell-to-cell interactions
    • transmembrane proteins that mediate Ca++ binding
    • cells w/ similar cadherins tend to go together
    • cells w/ most cadherins in interior, cells w/ least cadherins on outside
  • integrins - used in cell-to-substrate interactions (involving interactions w/ extracellular matrix)
    • used when most of tissue made up of spaces between cells (ECM)
    • connects cytoskeleton to the ECM
    • can change cytoskeleton growth, way cell secretes materials

induction - cell changes due to interactions w/ another cell 

  • mosaic development - in Drosophila, where determinants (developmental signals) guide cells on different development paths
  • regulative development - in mammals where cell-cell interactions determine development
  • proteins used as intercellular signals
  • organizers - groups of cells that produce signals for position to other cells
    • tells other cells of distance to organizer
    • morphogen - signal molecule for determining relative position

determination - cell’s commitment to a certain developmental path 

  • early cells totipotent, all capable expressing of their genes
  • chimera - organism w/ cells from different genetic lines
  • differentiation occurs at the end of developmental path, not the same thing as determination
  • positional labels - shows cell’s location in embryo, influences how body develops
  • cloning of Dolly the sheep on July 5, 1996 from fully-differentiated sheep shows that determination can be reversed

pattern formation - unfolding process that lays down the basic body plan 

  • currently only fully understood for Drosophila
  • sets up anterior/posterior, dorsal/ventral axis
  • bicoid protein gradient - determines anterior/posterior axis w/ aid of dynein (protein oskar also plays role for posterior determination)
  • accumulation of certain mRNA on 1 side of cell determines dorsal/ventral axis
  • polarity found by interactions between follicle cells and oocyte (egg)
  • gap genes - map out the subdivision of the embryo
    • hunchback mRNA - develops the thorax, cannot by blocked by nanos protein only in the anterior end
  • pair-rule genes - alters every other body segment when mutated
    • hairy - gene that divides embryo into 7 bands of proteins
  • segment polarity genes - subdivides the zones created by hairy

homeotic genes - gives identity to embryonic segments created in pattern formation 

  • bithorax complex - cluster of genes in 3rd chromosome in Drosophila that affect body parts of thoracic/abdominal segments
  • antennapedia complex - cluster of genes that affect body parts of anterior end
  • homeobox - sequence of 180 nucleotides that codes for the homeodomain (DNA-binding protein)
    • distinguishes portions of genome used for pattern formation
  • Hox genes - genes that contain homeoboxes
    • 4 copies in vertebrates
Subject X2: 

Cell Death

programmed cell death - cells between fingers/toes die

  • 1/2 of neurons created never make connections, eventually die
  • required for proper development
  • necrosis - cells that die due to injury, releases contents into extracellular fluid
  • apoptosis - cell programmed to die shrink/shrivel, remains taken up by other cells
  • bax proteins starts apoptosis by binding to permeable pores of mitochondria
  • bcl-2 prevents cell death by preventing damange from free radicals (highly reactive atomic fragments)
  • antioxidants - proteins, other molecules that destroy free radicals

aging theories - puberty is safest time to live 

  • accumulated mutation hypothesis - oldest general theory about aging
    • accumulation of mutations >> lethal death
    • OH group tends to be added to guanine base as cells age
    • effects of radiation-induced mutations after Hiroshima/Nagasaki bombings show no correlation between aging and mutations
  • telomere depletion hypothesis - older cells have shorter telomeres
    • telomere - repeated TTAGGG sequence
    • portion of telomere cap lost w/ each replication
    • cancer cells avoid telomeric shortening
    • adding to telomeric caps increased number of times cells could perform DNA replication
  • wear-and-tear hypothesis - cells wear out, get damaged through age
    • damage over time limits cell’s ability to work properly
    • free radicals - atomic fragments containing an unpaired electron, produced by oxidative metabolism, can damage cells
    • glycation - process that causes glucose to link to proteins, reducing flexibility
  • gene clock hypothesis - people over 100 years of age more likely to have mutated C150T mitochondrial DNA
    • Werner’s syndrome - causes premature aging, found on chromosome 8, affects helicase enzyme in DNA repair
  • current aging theories - still no true mechanism for counting
    • connection found between aging, signaling from insulin-like receptors
Subject X2: 

20 - Nervous System

See included biology topics below:

Subject X2: 

Central Nervous System

evolution of vertebrate brain - sponges are only multicellular animals w/o nerves 

  • cnidarians - have simplest nervous systems (nerve net)
    • no control/association
  • flatworms - simplest animals w/ association in nervous system
    • bigger mass of nervous tissue (beginnings of brain) >> complex control
  • interneurons/tracts added to brain as it evolved (interneurons - complex, high-level neurons found in brain/spinal cord)
  • hindbrain (rhombencephalon) - extension of spinal cord
    • coordinates motor reflexes
    • cerebellum (“little cerebrum”) - controls balance, body position
    • pons - controls automatic functions, links cerebellum/medulla oblongata w/ other parts of brain
    • medulla oblongata - contains respiration, circulation
  • midbrain (mesencephalon) - consists of mostly optic lobes that receive/process visual information
    • controls eye/ear reflex
  • forebrain (prosencephalon) - processes most of sensory information
    • diencephalons - thalamus, hypothalamus
    • thalamus - relays info between spinal cord and cerebrum
    • hypothalamus - controls emotions, pituitary gland
    • cerebrum (telencephalon) - dominant part of mammalian brain
  • ascending tracts - carry sensory info to brain
  • descending tracts - carry impulses from brain to motor neurons

human forebrain - divided into 2 hemispheres connected by corpus callosum 

  • each hemisphere receives info from opposite side
  • cerebral cortex - layer of gray matter on outer surface of cerebrum
    • contains 10% of all neurons in brain
    • folded/wrinkled to increase surface area
    • primary motor cortex - right in front of central sulcus (crease), controls mov’t
    • primary somatosensory cortex - right behind central sulcus, receives info from sensory neurons of skin/muscles
    • auditory cortex - in temporal lobe
    • visual cortex - in occipital lobe
    • association cortex - used for higher mental activities
  • basal ganglia - collections of cell bodies, dentrites that produce gray matter islands
    • receives info from ascending tracts, motor commands from cerebrum/cortex
    • sends info to spinal cord to control mov’t
    • damaged ganglia >> Parkinson's
  • thalamus - main area of senses (especially pain)
    • receives visual, auditory, somatosensory info
    • relays info to occipital (visual), temporal (auditory), parietal (somatosensory) lobes
  • hypothalamus - controls instinct
    • regulates body temperature, hunger, thirst, emotion
    • controls pituitary gland (regulates other endocrine glands)
  • limbic system - responsible for emotional responses
    • includes hypothalamus, hippocampus (may control memories), amygdala

spinal cord - cable of neurons going from brain through backbone 

  • protected by vertebral column and meninges (membrane layers that also cover the brain)
  • inner zone (gray matter) - consists of interneuron, motor neuron, neuroglia cell bodies
    • unmyelinated cell bodies
  • outer zone (white matter) - consists of sensory axons (in dorsal column) and motor axons (in ventral column)
    • myelinated axons
  • controls reflexes (sudden involuntary muscle mov’t)
    • doesn’t require higher level processing of info
    • only uses a few neurons >> very fast
    • monosynaptic reflex arc - simplest reflex (like knee-jerk reflex), sensory nerve connects directly to motor neuron
    • most reflexes usually involve an interneuron between sensory/motor neurons
  • regeneration - implanted nerve axons can’t penetrate spinal cord tissue
    • factor in spinal cord inhibits nerve growth
    • use of fibroblast growth factor shows limited improvement in neuron regeneration ability
Subject X2: 

Peripheral/Autonomic Nervous Systems

peripheral nervous system - nerves, ganglia

  • nerve - collections of axons (myelinated/unmyelinated)
    • separates into motor/sensory parts at origin
    • dorsal root - sensory axons
    • ventral root - motor axons
  • ganglia - groups of neuron cell bodies outside the central nervous system
    • dorsal root ganglia - contains cell bodies of sensory neurons
    • motor neuron cell bodies found inside spinal cord
  • somatic motor neurons stimulate skeletal muscles to contract
    • for each muscle stimulated to contract, its antagonist must be inhibited by hyperpolarizing the motor neuron

autonomic nervous system - contains sympathetic/parasympathetic areas, medulla oblongata 

  • autonomic neurons control smooth muscles, cardiac muscles, glands
  • medulla oblongata - controls the system
  • 2 neurons used for each pathway (1 has cell body in central nervous system, other has cell body in autonomic ganglion)
  • preganglionic neuron - 1st neuron, releases Ach at synapse
  • postganglionic neuron - releases Ach in parasympathetic division, norepinephrine in sympathetic division
  • sympathetic division - stimulates the adrenal gland to secrete epinephrine
    • prepares the body for fight or flight
    • norepinephrine released at postganglionic neuron synapses
  • parasympathetic division - slows down heart, increases secretions
    • regulates organs by releasing Ach
    • ACh causes G proteins to open up ion channels >> hyperpolarization >> slows down cell

neuroglia - cells that support neurons

  • supplies neurons w/ nutrients, gets rid of waste, provides immunity
  • Schwann cells - produce myelin sheaths in peripheral nervous system
  • oligodendrocytes - produce myelin sheaths in central nervous system
Subject X2: 

Brain Functions

sleep/arousal - reticular formation in brain stem controls consciousness 

  • less stimuli >> less active reticular formation >> easier to sleep
  • sleep = active process, not lack of consciousness
  • electroencephalogram (EEG) - records electrical activity in the brain
    • alpha waves - 8-13 hertz, found in relaxed/awake people
    • beta waves - 13-30 hertz, found in alert people
    • theta/delta waves - found in sleeping people
  • REM sleep - rapid eye mov’t sleep
    • EEG like that of relaxed, awake person
    • difficult to wake up
    • when dreams occur

language/spatial recognition - hemispheres each responsible for different jobs 

  • left hemisphere = dominant language area for 9/10 of right-handed people, 2/3 of left handed people
  • Wernicke’s area - found in parietal lobe between auditory/visual areas
    • controls language comprehension, formation of thoughts
  • Broca’s area - found near motor cortex controlling the face
    • controls motor skills needed for language communication
  • aphasias - language disorder where words lack meaning, due to damage in Wernicke/Broca areas
  • right hemisphere = nondominant hemisphere, good at spatial reasoning and musical ability
    • damaged inferior temporal cortex >> inability to recognize faces

memory/learning - doesn’t take place in any specific part 

  • short-term memory - temporary memory
    • possibly stored electrically as neural excitation
    • can be forgotten w/ electrical shock
  • long-term memory - involves structural changes in neural connections
    • converted from short-term memory by hippocampus/amygdala
  • long-term potentiation (LTP) - frequently used neurons become more sensitive after each transmission

Alzheimer disease - condition where memory/thought processes become dysfunctional 

  • nerve cells either killed from outside in or inside out
  • beta-amyloid peptides - external proteins that could plaque and fill in brain when mutated
  • tau protein - internal protein that normally maintain transport microtubules
    • could cause tangles when mutated
Subject X2: 

Neurons, Drugs

membrane potential - difference in charge across the membrane 

  • cytoplasm = negative, extracellular matrix = positive
  • fixed anions - negatively charged molecules too large to diffuse out of the cell
  • leak channels and sodium-potassium pump keep positively charged ions out of the cell
  • equilibrium potential - point where electrical/chemical forces balance out for a certain ion

graded potentials - small changes in membrane potentials 

  • casued by activation of gated ion channels (can open in response to stimuli like hormones)
  • chemical (ligand) gated channel - open when chemicals bind to them
    • channels open >> change in membrane permeability >> different ions can get in/out
  • depolarization >> membrane potential becomes less negative
  • hyperpolarization >> membrane potential becomes more negative
  • summation - ability of graded potentials to combine
  • threshold - amount of depolarization needed to create action potential

action potential - nerve impulse once voltage-gated ion channels open 

  • voltage-gated ion channel - opens/closes depending on membrane potential
  • Na+ gates open first, before K+ gates
  • Na+ enters cell (depolarization) >> K+ exits cell (repolarization) >> possible undershoot if K+ channels stay open (hyperpolarization)
  • cannot combine w/ other action potentials
  • either occurs completely or none at all
  • can depolarize another area of the membrane, starting a chain of action potentials
  • saltatory connection - action potentials jumping from node to node in myelinated axons
    • speeds up nervous transmissions
  • myelinated + larger axon diamter >> fast action potential transmission

synapse - intercellular junction between dendrites and soma 

  • electrical synapse - uses direct cytoplasmic connections
    • usually found in invertebrate systems
  • chemical synapse - accounts for majority of synapses
    • synaptic cleft - narrow space that separates 2 cells
    • synaptic vesicles - contains neurotransmitters
    • action potential at end of axon >> Ca++ channels open >> depolarization >> vesicles bind to membrane >> neurotransmitters released through exocytosis, bind to receptor proteins on other cell
  • neurotransmitters recycled into cell by transporters, but most go back to cell body before being used again by vesicles
  • excitatory postsynaptic potential (EPSP) - depolarization
  • inhibitory postsynaptic potential (IPSP) - hyperpolarization
  • synaptic integration - EPSP’s and IPSP’s working together to bring about overall effect on cell


  • dopamine - used to control body mov’ts
    • deficiency causes Parkinson’s disease
    • excess causes schizophrenia
  • norepinephrine - adds on to the effect of epinephrine, secreted by adrenal gland
  • serotonin - regulates sleep/emotion
    • deficiency can cause depression
    • drug LSD blocks serotonin receptors >> depression
  • substance P - neuropetide that responds to pain stimuli
    • pain won’t be felt w/o it
  • nitric oxide - 1st gas discovered to act as regulatory molecule
    • cannot be stored (diffuses through membranes)
    • causes smooth muscles to relax

drugs - decreases the sensitivity of receptors, mimics the effects of neurotransmitters 

  • habituation - receptors lost ability to respond if exposed to constant stimulus for long time
    • number of receptor proteins decrease
  • blocks transporters >> excess of neurotransmitters in synapse cleft >> # of receptors decrease due to over-stimulation >> addiction
  • body adjusts to conditions when drug is present >> withdrawal symptoms occur when drug no longer used
  • agonist - acts like the neurotransmitter
  • antagonist - blocks the receptor for a neurotransmitter
Subject X2: 

21 - Sensory Systems

See included biology topics below:

Subject X2: 

Sensory Receptors

sensory information - gets to central nervous system through 4 steps 

  • 4-step process
    • stimulation - activates sensory neuron
    • transduction - stimulus transformed into graded potentials
    • transmission - action potential lead to central nervous system
    • interpretation - brain analyzes/perceives senses from electrochemical messages
  • 3 types of stimuli
    • mechanical forces - stimulate mechanoreceptors
    • chemicals - stimulate chemoreceptors
    • electromagnetic/thermal energy - stimulate photoreceptors
  • free nerve endings - simplest sensory receptors, respond to mov’t of sensory neuron membrane, temperature change, chemicals in extracellular fluid
  • exteroceptors - receptors receiving info from external environment
    • most developed in water for vertebrates
  • interoceptors - receptors receiving info from within body
    • usually more simple than exteroceptors
  • stimuli >> stimulus-gated ion channels open >> depolarization (receptor potential) >> info sent to brain

cutaneous receptors - skin receptors, respond to stimuli at border between external/internal 

  • thermocreceptors - sensitive to changes in temperature
    • cold receptors - found right below epidermis
    • warm receptors - found deeper in dermis
  • nociceptors - sensitive to pain
    • pain = stimulus causing damage to tissue
    • overstimulated sensory receptors can also produce pain
  • mechanoreceptors - sensitive to forces applied to membrane
    • phasic receptors - intermittently activated, hair follicle receptors, Meissner’s corpuscles
    • tonic receptors - always activated, Ruffini corpuscles, touch dome endings (Merkel cells)
    • Pacinian corpuscles - monitor onset/removal of pressure

proprioceptors - muscle spindles giving info about position/mov’t of body parts 

  • activated when muscle is stretched
  • not found in bony fishes
  • inhibits somatic motor neurons when muscle contracts too strongly

baroreceptors - monitor tension/stretch in blood vessel walls 

  • measures blood pressure at carotid sinus (supplies blood to brain) and aortic arch (part of aorta very close to heart)
  • low blood pressure >> less impulses from baroreceptors >> central nervous system stimulates sympathetic division to increase heart rate

chemoreceptors - chemicals/ligands lead to depolarization 

  • used in smell/taste
  • taste buds - collections of epithelial cells connected to neurons
    • most sensitive chemoreceptors in vertebrates
    • insects taste w/ their feet
    • papillae - raised areas in tongue/oral cavity where taste buds are found
    • sour/salty tastes act w/ ion channels
    • sweet/bitter tastes act w/ G proteins
  • smell - receptors found in upper part of nasal passages
    • air particles must become extracellular fluid before activating the neurons
    • humans can tell apart many times more smells than tastes
  • peripheral/central chemoreceptors - detect pH changes in blood and cerebrospinal fluid
Subject X2: 

Body Position, Hearing

sensing body position

  • lateral line system - helps fish sense objects from vibrations around them
    • mov’t in environment causes stereocilia (hair) on cupula membrane to move >> action potential >> messages sent to brain
    • bending of hair can have excitatory/inhibitive effects, depending on direction of bend
  • statocyst - allows invertebrates to move themselves in respect to gravity
    • cilia embedded in calcium carbonate
    • cilia bends when position changes
  • vestibular apparatus - saccule, utricle, semicircular canals used to determine position in vertebrates
    • similar to mechanism used in lateral line system
    • hair found in otolith membrane
    • utricle more sensitive to horizontal mov’t, saccule more sensitive to vertical mov’t
    • semicircular canals - gives sense of angular acceleration

ear - actually works better in water than air 

  • outer ear - air vibrations travel through ear canal to eardrum (tympanic membrane)
  • middle ear - contains 3 ossicles (small bones): malleus (hammer), incus (anvil), stapes (stirrup)
    • connected to throat by Eustachian tube to equalize air pressure
  • inner ear - contains cochlea (contains cochlear duct)
    • vestibular/tympanic canal located on top/bottom of cochlear duct
    • all 3 chambers filled w/ fluid (vibrations >> fluid pressure waves)
    • organ of Corti - contains basilar membrane, hair cells, tectorial membrane
    • stimulation of hair cells >> action potential >> impulses interpreted as sound
    • different fiber lengths in basilar membrane >> different pitch
  • sonar - direction of sound easily determined due to location of 2 ears
    • distance of sound hard to determine due to environment
    • echolocation - emitting sounds and using the time it takes for the sound to come back in order to determine location
Subject X2: 


eye - begins w/ capture of light energy by photoreceptors 

  • eyespot - predecessor to the eye
    • cluster of photoreceptors
    • sensitive to light, but cannot form images
  • sclera - white of the eye, made of connective tissue
  • light enters eye through transparent cornea
  • iris - colored portion of eye
    • can decrease size of pupil (opening)
  • lens focuses image onto the retina on the back of the eye
  • light has to pass layer of bipolar cells and ganglion to reach rods/cones
  • rods - photoreceptor for black/white vision
    • rhodopsin - photopigment in rods
  • cones - photoreceptor for color vision
    • found mostly in fovea (central region of retina)
    • photopsin - photopigment in cones
    • 3 different cones >> 3 color sensitivities (blue, green, red)
  • dark >> photoreceptors release neurotransmitter that inhibits bipolar neurons >> less action potential goes to brain
  • occipital lobe of brain interprets messages from the eye
    • blind spot - where nerves come out of the eye, leading to the brain
  • myopic (near-sighted) - image focused in front of fovea
  • hyperopic (far-sighted) - image focused behind fovea
  • color blindness - sex-linked trait
    • due to lack of certain type of cones
    • trichromats - people w/ normal color vision
  • binocular vision - ability to see 3D images and sense depth
    • due to 2 eyes viewing object from different angles
    • less binocular vision >> larger overall field of view

other sensory experiences - other parts of electromagnetic spectrum used to sense environment 

  • heat - wavelengths longer than visible light
    • poor environmental stimulus in water
    • pit viper - only vertebrate known to sense infrared radiation
  • electricity - good environmental stimulus in water
    • all aquatic animals general electrical currents from muscle mov’t
  • magnetism - eels, sharks, bees, birds navigate according to earth’s magnetic lines
    • used in migration
Subject X2: 

22 - Endocrine System

See included biology topics below:

Subject X2: 


hormone - regulatory chemical secreted by endocrine gland 

  • only target cell can respond to hormone (but blood carries hormone throughout the body)
  • neurotransmitter - only diffuse a short distance, but may be chemically similar to hormones
    • effects the postsynaptic neuron
    • neurohormone - chemicals secreted from neurons into blood
    • some molecules work as both neurotransmitters and hormones
  • targets ligand-gated receptors on target cells
    • messages sometimes relayed through 2nd messenger, magnified through enzyme cascade
  • paracrine regulation - using chemicals as local regulators in an organ
  • pheromone - chemical released into the environment
    • used as communication between animals

types of hormones

  • polypeptides - chains of amino acids (never more than 100)
    • insulin, ADH
  • glycoproteins - polypeptides (w/ over 100 amino acids) attached to carbohydrate
    • FSH, LH
  • amines - derived from tyrosine/tryptophan amino acids
    • catecholamines - secreted by adrenal medulla, includes adrenaline/noradrenaline
    • melatonin, thyroid hormone
  • steroids - lipids derived form cholesterol
    • sex steroids - secreted by testes, ovaries, placenta, adrenal cortex
    • corticosteroids - secreted only by adrenal gland
  • lilophilic hormones - fat soluble, includes steroids/thyroxine
  • lilophobic hormones - water soluble, all other hormones
  • most releases of hormones controlled by the brain

hormones that enter cells - lipophilic hormones easily enter cells (can pass plasma membrane) 

  • either finds receptor in cytoplasm or inside nucleus (either way, eventually reaches nucleus)
  • hormone response elements - DNA segments binding to hormones

hormones that do not enter cells - lipophobic hormones can’t pass plasma membrane 

  • have to bind to receptors
  • 2nd messenger needed within the cell to get the reactions started
Subject X2: 

Pituitary Gland

paracrine regulation - acts on local area 

  • cytokines - regulate other immune system cells
  • growth factors - promotes growth/cell division
    • neurotrophins - paracrine regulators of nervous system
  • prostaglandins - 20-carbon-long fatty acid w/ carbon ring
    • released from phospholipids in membrane
    • promotes inflammation (pain/fever)
    • regulates gamete transport/labor
    • inhibits gastric secretions
    • cause constrictions/dilations of blood vessels
  • nonsteroidal anti-inflammatory drugs (NSAIDs) - drugs that inhibit production of prostaglandins
    • aspirin - most commonly used form
    • can also inhibit enzyme that maintains walls of digestive tract

posterior pituitary gland - fibrous part of pituitary gland, derived from brain 

  • directly controlled by hypothalamus through the supraopticohypophyseal tract
  • consists of axons (cell bodies in hypothalamus)
  • antidiuretic hormone (ADH) - aka vasopressin
    • stimulates water retention in kidneys
    • frequent urination occurs if kidneys don’t retain water
    • alcohol suppresses ADH >> more urination to rid body of toxins
  • oxytocin - stimulates uterus contractions and mammary glands (milk-letdown reflex) in women
    • responds to sucking on nipples
    • regulates orgasm/arousal in men/women
  • neuroendocrine reflex - involves both the neural/endocrine systems

anterior pituitary gland - glandular part of pituitary gland, not derived from brain 

  • controlled by hormones secreted by hypothalamus
  • releases mostly growth hormones (aka tropic hormones, tropins)
  • gonadotropin - hormone that stimulates other reproductive hormones
    • includes FSH, LH
    • positive feedback controls amount of reproductive hormones in females >> cyclic level
    • negative feedback controls amount of reproductive hormones in males >> constant level
  • growth hormone (GH, somatotropin) - stimulates muscle/bone growth
    • targets all tissues, bones in particular
    • can’t increase height once cartilage becomes bone
    • too much >> gigantism, acromegaly (bone deformity)
  • adrenocorticotropic hormone (ACTH, corticotrophin) - stimulates adrenal cortex
    • responds to chronic stress, excess exercise
    • cortisol from adrenal cortex can suppress immune system
    • produces corticosteroid hormones >> regulates glucose metabolism
  • thyroid-stimulating hormone (TSH, thyrotropin) - stimulates thyroid to make thyroxine
    • affects oxidative respiration, thermal regulation
    • underdeveloped thyroid glands >> cretinism (undergrowth, mental retardation)
  • luteinizing hormone (LH) - used for ovulation, production of testosterone
    • develops the corpus luteum (makes estrogen/progesterone)
  • follicle-stimulating hormone (FSH) - used for development of ovarian follicles and sperm
  • prolactin (PRL) - stimulates mammary glands to produce milk
    • also controls electrolyte balance
  • melanocyte-stimulating hormone (MSH) - stimulates melanin (dark skin pigment) production
    • released by middle pituitary
Subject X2: 

Other Endocrine Glands

thyroid gland - found right below Adam’s apple in the neck 

  • promotes growth/brain development
  • responsible for metamorphosis in amphibians
  • calcitonin - lowers blood calcium level
  • also releases triiodothyronine (T3) and thyroxine (T4)

parathyroid glands - 4 small glands attached to the thyroid gland 

  • stimulates release of calcium from bones
  • parathyroid hormone (PTH) - 1 of 2 hormones humans can’t live w/o
    • released in response to falling calcium levels
  • osteoclasts (bone cells) stimulated to release calcium
  • kidneys stimulated to reabsorb calcium in urine by vitamin D

adrenal glands - found above kidneys, contains adrenal medulla (inside), adrenal cortex (outside) 

  • adrenal medulla - receives neural info from sympathetic division
    • secretes epinephrine/norepinephrine
    • produces fight or flight response due to sympathetic nerves
  • adrenal cortex - produces steroids (called corticosteroids)
    • maintains glucose levels, stimulates gluconeogenesis
    • glucocorticoids - breaks down muscle proteins into amino acids, amino acids into glucose
    • aldosterone - 1 of 2 hormones humans can’t live w/o, stimulates kidneys to reabsorb Na+ and secrete K+

pancreas - located next to stomach, connected to duodenum 

  • secretes bicarbonate and enzymes into small intestine
  • islets of Langerhans - secretes insulin in beta cells, glucagon in alpha cells
  • type I diabetes - lacking insulin-secreting cells, but have insulin injections
  • type II diabetes - cells have reduced sensitivity to insulin
    • can only be helped by diet
  • insulin stimulates absorption of glucose
  • glucagon stimulates hydrolysis of glycogen >> antagonistic to insulin

other endocrine glands

  • molting/metamorphosis used for growth since exoskeletons don’t expand
    • brain hormone secreted >> ecdysone produced in thorax >> molting
    • juvenile hormone used up >> metamorphosis no longer inhibited
  • sex steroids - estrogen/progesterone in females, testosterone in males
    • androgens - determines male sex characteristics, overcomes the default female setting in mammals
    • estrogen - determines female sex characteristics, overcomes the default male setting in birds
  • pineal gland - aka “third eye”, secretes melatonin to regulate amount of sleep
    • maintains sleep, seasonal changes during migration, hibernation, mating
  • thymus - produces T cell lymphocytes
    • found in front of chest

endocrine-disrupting chemicals - low concentrations of target cells in blood 

  • small change in concentration >> big changes in effect on organ
  • agonist - chemical that mimic hormone
    • can bind to receptor proteins
  • antagonist - doesn’t mimic hormone, but stops hormones from binding
Subject X2: 

23 - Sex/Reproduction

See included biology topics below:

Subject X2: 

Fertilization, Birth Control

reproduction - sexual/asexual 

  • sexual reproduction - used by most animals
    • union of gametes (sperm/ova) >> zygote
  • asexual reproduction - used by protests, cnidarians, tunicates, and others
    • produces genetically identical cells through mitosis
    • fission - organism divides into 2 identical organisms
    • budding - part of body separates, becomes new organism
  • parthenogenesis - form of asexual reproduction in arthropods
    • females produce offspring from unfertilized eggs
  • hermaphroditism - organism has both testes/ovaries
    • able to fertilize itself
    • sequential hermaphroditism - ability to change sex
  • sex determination - environment or DNA determines sex
    • all mammals will develop into females w/o the SRY gene

fertilization - evolved in the water 

  • external fertilization - sperm/ova unite outside of the organisms
    • must be synchronized or else gametes disperse
  • internal fertilization - evolved due to drying on land
    • male gametes introduced into female reproductive tract
    • oviparity - fertilized eggs placed outside mother to develop
    • ovoviviparity - fertilized eggs stay within mother, but get nutrition from egg yolk
    • viviparity - young develop inside mother, receive nutrition from mother’s blood
  • estrus - period of sexual receptivity in females
    • occurs around time of ovulation

birth control - aka contraception 

  • abstinence - not having sex
  • condoms - most common form of birth control
  • douche - washing out vagina immediately after sex to kill the sperm
  • oral contraceptives - birth control pills
    • blocks ovulation through negative feedback
  • inserting irregularly shaped object >> embryo can’t implant onto the wall
    • major discomfort for women using it
  • “morning after pill” - contains extreme dose of estrogen
    • used as emergency contraception
  • sterilization - vasectomy in males, removing part of fallopian tubes in females

sexual response cycle - excitement, plateau, orgasm, resolution  

  • excitement - sexual arousal
  • plateau - blood goes to reproductive organs
  • orgasm - peak of sexual response
  • resolution - return to pre-sexual stimulation level
  • Viagra - preserves cGMP levels >> maintains erection
    • still requires sexual thoughts to stimulate erection >> not an aphrodisiac
Subject X2: 

Male Reproductive System

male reproductive system - sperm produced in seminiferous tubules 

  • Leydig cells - secretes testosterone to form penis/scrotum
  • scrotum - maintains temperature of 34 C for sperm development
  • spermatogonia (germ cells) - become sperm through meiosis
    • never runs out (undergoes mitosis before 1 goes through meiosis to become sperm)
    • about 100-200 million sperm created each day
  • primary spermatocyte - diploid cell that begins meiosis, produces 4 spermatids each
    • secondary spermatocyte - homologous pairs are split
    • spermatids - chromatids are split
  • Sertoli cells - nurse developing sperm, convert spermatids to spermatozoa by taking extra cytoplasm
  • spermatozoa (sperm) - simple cell consisting of head, body, tail
    • acrosome - vesicle on the head that has enzymes to help sperm penetrate egg

male accessory organs - sperm cannot move immediately after they’re made 

  • epididymus - holds sperm for at least 18 hours while they develop ability to move
  • vas deferens - tube passing into abdominal cavity
    • enters prostate gland at bladder base
    • prostrate gland - provides 30% of semen
  • seminal vesicles - produces fructose fluid (60% of semen’s volume)
  • urethra - carries sperm out through penis tip
    • bulbourethral glands - secrete fluid that lines the urethra for lubrication
  • blood vessels in corpora cavernosa/corpus spongiosum dilate >> erection
    • ejaculation - semen ejecting from the penis
    • sperm only counts as 1% of semen
Subject X2: 

Female Reproductive System

female reproductive system - ovaries develop more slowly than testes 

  • clitoris/labia majora made from same embryonic structures as penis/scrotum in males
  • granulosa cells secrete estrogen to start menstrual cycle and development of female secondary sexual characteristics at puberty
  • progesterone - hormone that maintains the accessory sex organs (fallopian tubes, uterus, vagina)

female accessory organs

  • fallopian tubes (uterine tubes, oviducts) - transport ova from ovaries to uterus
  • cervix - neck of the uterus, leads to vagina
  • endometrium - lining of uterus, shed during menstruation

menstrual/estrous cycles - females born w/ 1 million follicles (each w/ ovum) 

  • primary oocytes - ova halts in prophase I
  • menstrual cycle - lasts about a month, follicular/luteal phase separated by ovulation
  • follicular phase - follicles stimulated to grow
    • 1 matures to become Graafian follicle
    • primary oocyte creates secondary oocyte and polar body
    • secondary oocyte halts in metaphase II, won’t continue until fertilization
  • proliferative phase - from end of menstruation to beginning of ovulation
  • ovulation - follicle releases the oocyte
    • oocyte disintegrates within a day if not fertilized
    • usually fertilized in upper 1/3 of fallopian tube
    • takes 5-6 days for zygote to reach uterus and implant itself
  • secretory phase - from ovulation to beginning of menstruation
  • luteal phase - develops the Graafian follicle into corpus luteum
    • produces estrogen/progesterone to stop development of follicles
    • secretory phase - endometrium becomes enriched w/ glycogen deposits
    • menstrual phase - disappearance of corpus luteum >> abrupt decline in estrogen/progesterone >> endometrieum sheds, along w/ bleeding
    • fertilized embryo would otherwise secretes hCG to maintain the luteum
  • decrease in progesterone/estrogen >> PMS (not possible during pregnancy)
  • human chorionic gonadotropic hormone (hCG) - released once ovum implants into uterus
    • used for pregnancy detection
    • stimulates development of placenta
Subject X2: 

24 - Circulatory/Respiratory Systems

See included biology topics below:

Subject X2: 

Parts of Circulatory System

types of circulatory systems - open/closed 

  • open circulatory system - found in mollusks, arthropods
    • no difference between circulating/extracellular fluid
    • hemolymph - collective name for the fluid
  • closed circulatory system - circulating fluid (blood) always in vessels
    • found in all vertebrates

circulatory system functions - transportation, regulation, protection 

  • interstitial fluid - plasma fluid that leaks out of capillaries
    • some return to capillaries, some enter lymph vessels
  • transportation - substances needed for cellular metabolism carried by circulatory system
    • erythrocytes carry the hemoglobin which carry oxygen for respiration
    • absorbed nutrients sent to cells throughout body
    • metabolic wastes carried out of body
  • regulation - hormones carried in blood to distant organs
    • endotherms - warm-blooded vertebrates
    • cold temperature >> vessels constrict >> warm blood goes to deeper vessels
    • warm temperature >> vessels dilate >> warmth of blood lost through radiation
    • countercurrent heat exchange - vessel w/ warm blood passes by vessel w/ cold blood
  • protection - prevents injury from foreign microbes/toxins
    • blood clotting >> prevents blood loss when vessels get damaged
    • leukocytes (white blood cells) provide immunity against certain microbes

blood - made up of fluid plasma, different types of blood cells 

  • plasma - extracellular matrix w/ solutes
    • contains metabolites (used by cells), ions (mainly Na, Cl), proteins (mostly albumin)
    • globulins - carry lipids, steroid hormones
    • fibrinogen - needed for blood clotting
    • serum - plasma w/o fibrinogen
  • erythrocytes (red blood cells) - carry oxygen through hemoglobin
    • hematocrit - fraction of blood volume occupied by red blood cells (45% in humans)
    • develops from stem cells (unspecialized cells)
    • in mammals only, nuclei disappear
  • leukocytes (white blood cells) - 1% of blood cells
    • able to go outside of capillaries into interstitial fluid
    • defends body against microbes
  • platelets - help blood clot
    • formed from cytoplasm of megakaryocytes
    • reinforced w/ fibrin when blood vessel breaks

blood vessels - high pressure in arteries >> low pressure in veins 

  • arteries - carry blood away from the heart
    • arterioles - smallest branches of arteries
    • aorta - largest artery coming from heart
  • veins - returns blood to the heart
    • venules - smallest branches of veins
    • venous pump - skeletal muscles around veins contract >> squeezes veins
    • venous valves - makes sure blood only moves in 1 direction
  • capillaries - thinnest/most numerous blood vessels, connects arterioles w/ venules
    • lack elastin fibers, smooth muscle layers, and connective tissue layers found in arteries/veins
    • blood can filter in/out
    • every cell within 100 micrometers of capillary
  • vasoconstriction >> increases resistance, decreases flow
  • vasodilation >> decreases resistance, increases flow
  • precapillary sphincters - rings of smooth muscle around arterioles, regulates blood flow through capillaries
  • lymphatic system - interstitial fluid brings oxygen/nutrients to tissue cells
    • blood pressure >> filter out of capillaries near arterioles
    • oncotic pressure (osmosis due to plasma proteins) >> filter in to capillaries near venules
    • lymph - fluid in the system
    • returns excess blood in open circulatory system to closed
    • drains into veins on sides of neck
    • germinal centers - found in lymph nodes/organs, lymphocytes (type of white blood cell) created/activated
Subject X2: 

Parts of Respiratory System

breathing structures

  • visceral pleural membrane - covers outside of each lung
  • parietal pleural membrane - covers inner wall of thoracic cavity
  • pleural cavity - space between parietal/visceral membranes
    • filled w/ fluid, makes the 2 membranes stick together
  • diaphragm - along w/ external intercostals muscles, changes thoracic volume to breathe
    • contract >> expands rib cage to inhale
    • relax >> unforced exhalation
  • tidal volume - amount of air moved w/ each breath
    • anatomical dead space - areas where no exchange of air takes place
  • vital capacity - maximum amount of air that is exhaled
    • reduced in emphysema, due to damaged alveoli
  • hypoventilating >> not enough breathing to maintain normal blood gas
  • hyperventilating >> too much breathing

breathing regulation - controlled by respiratory control center in medulla oblongata 

  • automatic control of skeletal muscles in diaphragm and external intercostals muscles
    • can be overridden voluntarily
  • oxygen, carbon dioxide concentrations change pH >> central/peripheral chemoreceptors in brain
    • peripheral chemoreceptors - control immediate breathing changes
    • central chemoreceptors - control sustained breathing changes
  • dyspnea - difficulty in breathing
    • due to something blocking the airways
  • apnea - temporary pause in breathing

hemoglobin - protein made up of 4 polypeptides, 4 heme groups 

  • iron atom at center of each heme group, can bind to oxygen
  • hemoglobin w/ oxygen = oxyhemoglobin
    • bright red color
  • hemoglobin releases oxygen >> deoxyhemoglobin
    • dark red color, but changes tissue to blue color
  • hemocyanin - found in invertebrates in place of hemoglobin
    • has copper instead of iron
  • carbon monoxide poisoning - CO displaces O2 >> hypoxia (hemoglobin can’t carry oxygen)
Subject X2: 

Cardiac Cycle

fish heart - replaced simple tubular hearts 

  • tube w/ 4 chambers
    • atrium/sinus venosus - 1st 2 chambers, for collection
    • ventricle/conus arteriosus - last 2 chambers, for pumping
  • order of contraction - sinus venosus >> atrium >> ventricle >> conus arteriosus
  • blood passes through gills after going through heart >> much of pressure from pumping lost

amphibian/reptile heart - has 2 separate circulations due to lungs

  • pulmonary circulation - between heart and lungs
  • systemic circulation - between heart, rest of body
  • allows for pumping fully oxygenated blood
  • separated atriums prevent oxygenated/deoxygenated blood from mixing
  • aorta - major artery of systemic circulation
  • cutaneous respiration - breathing through the skin

mammalian/bird hearts - 4 chambered heart w/ separate atria/ventricles 

  • right atrium receives deoxygenated blood >> right ventricle pumps blood to lungs
  • left atrium receives oxygenated blood >> left ventricle pumps blood to body
  • double circulation - atrium/ventricles contract at same time
  • both ventricles must pump same amount of blood
  • heartbeats start in sinoatrial node (able to depolarize w/o neural activation from brain)

cardiac cycle - 2 separate pumping systems in a single organ 

  • diastole (rest) >> systole (contraction)
  • atrioventricular valves - between atria/ventricles
    • prevents blood backflow
    • tricuspid valve - on right side
    • bicuspid (mitral) valve - on left side
  • semilunar valves - between ventricles and arteries
    • pulmonary valve - on right side
    • aortic valve - on left side
  • coronary arteries - first arteries off the aorta, supplies heart
    • superior vena cava - drains upper body
    • inferior vena cava - drains lower body
  • sphygmomanometer - measures blood pressure
    • pressure must be large enough to push blood through capillaries, but not cause damage to arteries
    • systolic pressure - peak pressure during contraction
    • diastolic pressure - minimum pressure between heartbeats
    • hypertension - condition w/ very strong contractions
  • SA node depolarization >> AV (atrioventricular) depolarization >> bundle of His depolarization >> Purkinje fiber depolarization >> ventricle contraction
    • pace-making cell - fire action potentials on their own periodically
    • fibers blocked >> atria/ventricles don’t beat together
    • electrocardiogram (ECG/EKG) - records the depolarization through the heart
    • P wave = atrial depolarization
    • QRS complex = ventricular depolarization
    • T wave = ventricular repolarization (covers up atrial repolarization)

cardiac output - blood volume pumped by each ventricle per minute 

  • equal to amount of blood that travels through systemic/pulmonary circulations per minute
  • increase heart rate, blood volume, vasoconstriction >> increase blood pressure
    • baroreceptors - sense blood pressure changes
    • antidiuretic hormone (ADH) - aka vasopressin, stimulates kidneys to hold more water
    • aldosterone - maintains Na+, water retention in kidneys
    • atrial natriuretic hormone - secreted by the heart, lowers blood volume/pressure by getting rid of Na+ and water
    • nitric oxide - causes blood vessels to relax/dilate

cardiovascular diseases - leading cause of death in US 

  • arrhythmia - missing a heartbeat
  • fibrillation - desynchronized contraction of cardiac fibers
    • atrial fibrillation - decreases filling of ventricles >> not fatal
    • ventricular fibrillation - decreases amount of blood pumped to body >> could be fatal
  • heart attacks (cardial infarction) - due to lack of blood reaching a part of the heart
    • caused by blood clots
  • angina pectoris “chest pain”, not as severe as a heart attack
  • stroke - blood doesn’t reach the brain properly
    • effects depend on location of stroke in brain
  • atherosclerosis - accumulation of fat, muscle, or cholesterol in arteries
    • reduces blood flow
  • arteriosclerosis - hardening of arteries
    • calcium deposits in artery walls
Subject X2: 

Development of Breathing

oxygen diffusion - way for gases to get across plasma membranes 

  • levels needed for metabolism can’t be obtained by diffusion over 0.5 mm
  • respiratory organs increase surface area and decrease distance over which oxygen must move

gills - tissue that projects out into the water 

  • has no support, would collapse w/o water
  • loses lots of water to evaporation when exposed to air
  • external gills - not enclosed within the body
    • must be constantly moved
    • easily damaged
    • branchial chambers - pumps water past nonmoving gills
  • bony fish gills - found between mouth and opercular cavity
    • most efficient of all respiratory organs
    • operculum (gill cover) - moves to open/close opercular cavity
    • water moves in through mouth, leaves through operculum
    • ram ventilation - forces water over gills through body mov’t, not pumping
    • gill arches - 4 on each side of head, each contains 2 rows of gill filaments and lamellae
    • blood flows opposite to the water mov’t (coutercurrent)

air-breathing - different organs for terrestrial organisms 

  • tracheae - network of air passages in insects
    • oxygen diffuses directly into different cells
    • spiracles - openings of tracheae, close to prevent water loss
  • lung - saturates air w/ water vapor before gas exchange
    • air moves in/out through same passages
  • amphibian respiration - less lung surface area than other vertebrates
    • positive pressure breathing - mouth pumps air into lungs
    • cutaneous respiration also used (sometimes more than normal respiration)
  • reptile respiration - cannot breathe through skin (too dry, tough)
    • negative pressure breathing - rib cages, lungs expand through muscular contraction
  • mammal respiration - higher metabolic rate than reptiles/amphibians
    • alveoli - tiny sacs in lungs, adds to surface area for gas diffusion
    • passage of air - mouth >> pharynx >> larynx (voice box) >> glottis (opening in vocal cords) >> trachea (windpipe) >> bronchi >> bronchioles >> alveoli
    • external respiration - between lungs, capillaries
    • internal respiration - between capillaries, tissues
  • bird respiration - has most efficient respiratory system out of all terrestrial vertebrates
    • parabronchi - air vessels w/ unidirectional flow (like fish)
    • new/old air not mixed together like in other terrestrial animals
    • inspiration - inhaled air goes to posterior air sac, air in lungs goes to anterior air sac
    • expiration - air from anterior air sac exhaled, air from posterior air sac goes to lungs
    • cross-current flow - blood flows perpendicular to air flow, more efficient than mammals
Subject X2: 

25 - Immune System

See included biology topics below:

Subject X2: 

1st and 2nd Lines of Defense

skin - 1st line of defense  

  • 15% of an adult’s total weight
  • oil/sweat glands >> low pH on surface >> many microorganisms killed
  • prevents water loss
  • lyxozyme - enzyme in sweat that digests bacterial cell walls
  • stratum corneum - outer skin layer
    • cells constantly injured, worn, replaced
  • stratum basale - innermost skin layer, produces new skin cells
  • stratum spinosum - broad layer in middle of epidermis
  • dermis - skin layer below epidermis, gives structural support
  • mainly adipose (fat) cells below dermis
  • other surfaces leading to outside - digestive tract, respiratory tract, urogenital tract
    • mucus traps microorganisms in bronchi, cilia sweeps mucus towards glottis to stomach

cellular counterattack - 2nd line of defense 

  • uses nonspecific cellular/chemical devices to defend
  • goes after any infection w/ leukocytes
  • identity of pathogen doesn’t matter
  • lymphatic system = central location for distribution of immune system cells
  • macrophages - “big eaters”
    • ingests microbes through phagocytosis
    • uses oxygen-free radicals to destroy microbes
  • neutrophils - most abundant leukocyte
    • can release chemicals (similar to bleach) to kill all cells in surroundings
  • natural killer cells - destroys cells already infected by the microbe
    • drills hole into plasma membrane

complement system - in vertebrates, contains 20 proteins 

  • proteins encounter bacterial/fungal cell wall >> forms membrane attack complex
  • forms pore on membrane >> cell swells/bursts
  • adds on to the effects of other body defenses
  • interferons - messenger to warn other cells of the infection
    • alpha, beta, gamma
  • prostaglandin - produces clotting to block spread of pathogens

inflammatory response - localized, nonspecific response to infection 

  • infected cells release alarm signals >> blood vessels dilate >> increase blood flow >> area = red/warm
  • neutrophils, then macrophages arrive to kill microbes
    • pus = mixture of dead pathogens, tissue, neutrophils
  • temperature response - macrophages release interleukin-1 >> hypothalamus raises body temperature
    • fever >> stimulates phagocytosis, iron production
    • very high fever could start to denature enzymes
Subject X2: 

3rd Line of Defense

immune response - 3rd line of defense 

  • vaccination - infecting harmless virus in order to improve resistance
  • antigen - molecule provoking a specific immune response
    • usually foreign to body
    • antigenic determinant site - parts of antigen that stimulates an immune response
  • antibodies - response to antigens
    • created by B cells (made/mature in bone marrow)
    • secreted into body fluid >> humoral immunity
    • T cells (mature in thymus) directly attack the cells >> cell-mediated immunity
  • exposed to pathogen, gaining immunity >> active immunity
  • gaining antibodies from someone else >> passive immunity

starting the immune response - MHC proteins on cell surface 

  • proteins created y major histocompatibility complex
  • serves as cellular fingerprint >> body can distinguish between its cells + foreign cells >> self-versus-nonself recognition
  • antigen-presenting cells - partially digests microbes, moves their antigens to the surface
    • lets T cells recognize the antigens
  • MHC-I - found on all body cells
  • MHC-II - found only on macrophages, B cells, and CD4+ T cells
  • interleukin-1 - acts as chemical alarm signal between cells

T Cells - produces cell-mediated immune response 

  • protects body from infection, cancer
  • helper T-cell - detects infection, initiates B/T cell responses
  • cytotoxic T-cell - detect/kill infected cells
  • inducer T-cell - helps T-cells mature in thymus
  • suppressor T-cell - terminates immune response after infection
  • cytokines - aka lymphokines
    • regulatory molecules released by antigen-presenting cells
    • interleukin-1 - released by macrophages, stimulates helper T cells promote macrophages
    • interleukin-2 - released by helper T cells, stimulates production of cytotoxic T cells
  • different MHC proteins >> higher chance for transplant rejection by immune system
  • interferons currently used to stimulate immune system to fight cancer

B Cells - marks foreign microbe for destruction 

  • markers activate complement proteins, macrophages, natural killer cells
  • binds to free, unprocessed antibodies
  • trigger antibody production in plasma cells
  • able to create million to billion different antibodies through somatic DNA rearrangement

antibodies - don’t directly destroy the cell 

  • IgM - 1st to be secreted during primary response, causes cells w/ antigens to stick together
  • IgG - secreted in 2ndary response, major form of antibody in blood
  • IgD - serves as receptors on B cell surface
  • IgA - major form of antibody in saliva, milk (external secretions)
  • IgE - promotes release of histamine to attack pathogen, responsible for allergies
  • each consists of 2 light chains, 2 heavy chains

immunological tolerance - acceptance of a body’s own cells 

  • immune system in embryo originally responds to both foreign/self molecules
  • autoimmune disease - when immunological tolerance fails
    • B/T cells recognize their own tissue antigens

clonal selection - creates active immunity 

  • primary immune response - generally weak due to lack of B cells
    • antigen binds to B cell >> cell division >> clones of B cells created
  • 2ndary immune response - much stronger due to increase in recognition
Subject X2: 

Diseases, Uses of Immune System

blood typing - analyzes class of antigens found on red blood cells 

  • must be matched for blood transfusions
  • A blood - A antigens, B antibodies
  • B blood - B antigens, A antibodies
  • AB blood - A and B antigens, no antibodies
  • O blood - no A or B antigens, A and B antibodies
  • different blood types of blood mixed together >> clumping is possible

Rh factor - another group of antigens found on red blood cells 

  • Rh-positive or Rh-negative (mostly Rh-positive)
  • baby can be born anemic if mother creates antibodies against the baby’s blood during birth

monoclonal antibodies - specific for only a single antigenic determinant 

  • antigens may have multiple determinants >> generates polyclonal antibodies when injected into organisms
  • created from hybridoma (fusion of cancer and B cells)

evolution of immune system - started w/ restriction endonucleases to degrade foreign DNA 

  • invertebrates developed self markers to figure out which cells to attack
  • phagocytes - attack microbes, found in all animals
  • lymphocytes - first originated in annelid earthworms
  • lectins = ancestors of antibodies
    • binds to sugar molecules
  • immune system fully evolved by sharks

AIDS - acquired immune deficiency syndrome due to human immunodeficiency virus 

  • destroys CD4+ T cells >> body unable to respond to any foreign antigen
  • HIV-infected cells only die after releasing replicated viruses
  • HIV prevents cells from responding to HIV antigen, blocks transcription of MHC genes
  • die of infection, can’t die of HIV
  • inhibit protease >> inhibit viral assembly, possible treatment

antigen shifting - pathogen mutates frequently >> gets past immune system 

  • 2ndary immune response rarely comes into play
  • malaria - caused by Plasmodium falciparum
    • consumes hemoglobin
    • prevents blood cells from going to the spleen for repair
  • DNA vaccines - uses T cells instead of B cells to defend
    • uses plasmid to mark pathogen

autoimmunity - immune system = source of problem 

  • immune system fails to recognize self antigens
  • leads to organ damage, inflammation
  • stopped w/ corticosteroids, anti-inflammatory drugs

allergy - hypersensitivity to allergens 

  • antihistamine blocks histamine receptor >> inhibits inflammatory response
  • immediate hypersensitivity - B cell response, symptoms within seconds/minutes
    • IgE antibodies created instead of IgG
    • IgE do not circulate in blood, attaches to tissue cells >> makes cells secrete histamine
    • anaphylactic shock - uncontrolled blood pressure drop
  • delayed hypersensitivity - T cell response, symptoms within 48 hours
    • contact dermatitis - caused by poison ivy, oak, sumac
Subject X2: 

26 - Renal System, Digestive System

See included biology topics below:

Subject X2: 


need for homeostasis - constancy of internal environment 

  • controlled through negative feedback loop
  • sensors - measure conditions of internal environment
  • integrating center - contains set point (proper conditions)
  • change occurs >> effectors told to increase/decrease activity
    • effectors - muscles/glands
  • body temperature - set around 37 C
    • hypothalamus detects temperature changes
    • high temperature >> sweating, dilation of blood vessels
    • low temperature >> shivering, constriction of blood vessels
    • ectothermic (cold-blooded) animals use behavior, environment to control internal conditions
  • glucose levels - controlled by islets of Langerhans
    • insulin secreted >> stimulates reuptake of blood glucose in tissues
  • antagonistic effectors - push-pull relationship
    • sets of effectors used to better control homeostasis
  • positive feedback loops - drives condition further from set point
    • don’t help maintain homeostasis
    • used in blood clotting, uterus contractions

osmolality - total moles of solute per kilogram of water 

  • osmotic pressure - measures tendency of a solution to take in water (force placed on semi-permeable membrane)
  • isotonic >> no net mov’t of water
  • osmoconformers - animals w/ same osmolality in body fluids as surrounding seawater
  • osmoregulators - animals w/ different osmolality from environment
    • must maintain constant blood osmolality
    • freshwater vertebrates = hypertonic to surrounds, tend to gain water
    • terrestrial vertebrates have more water than environment, tend to lose water
  • urinary systems evolved to help retain water

osmoregulatory organs - water sometimes removed along w/ metabolic waste 

  • protonephridia - tubules in flatworms, leads to pores on outside
    • doesn’t lead to outside/inside
  • nephridia - tubules leading to outside/inside of earthworm
  • Malphigian tubules - excretory organs in insects
  • reabsorption - transport out of tubule, into surrounding body fluids
  • vertebrate kidneys filter through pressure
  • urea - form in which nitrogenous waste is removed in mammals
    • water soluble
    • uric acid (not as water soluble) >> can precipitate out, forms gout in humans, guano in
Subject X2: 

Parts of Renal System

kidney - urine produced from blood coming through renal artery  

  • ureter - carries urine to urinary bladder
  • split into renal pelvis, renal cortex, renal medulla
  • nephron - cells responsible for the filtration, reabsorption, secretion, excretion
    • glomerulus - where blood gets filtered
    • Bowman’s capsule - surrounds glomerulus like a balloon
    • proximal convoluted tubule - extends into medulla, loops back to cortex; water gets reabsorbed
    • loop of Henle - only found in mammals/birds >> ability to concentrate urine
    • things not filtered go to efferent arteriole >> peritubular capillaries
  • reabsorption/secretion - water, dissolved solutes must return to blood or else animal urinates to death
    • solid molecules reabsorbed through active transport, cotransport
    • substances get secreted by moving from blood capillaries to filtrate
  • excretion - gets rid of harmful substances

transport in nephron - osmotic gradient needed for reabsorption 

  • proximal convoluted tubule - active transport of Na+ and Cl- >> reabsorption
    • most of water reabsorbed through wall of collecting duct
    • leaves behind hypertonic urine
  • loop of Henle - creates the hypertonic renal medulla that draws water out from nephrons
    • water permeates through descending limb
    • water stays through ascending limb, NaCl leaves
  • antidiuretic hormone (ADH) - aka vasopressin
    • produced by hypothalamus, secreted by posterior pituitary gland
    • more ADH >> less water in urine
    • less ADH >> more water in urine
  • aldosterone - maintains the Na+ levels (reabsorption), consequently water levels
    • opposed by atrial natriuretic hormone (promotes excretion of salt/water)
Subject X2: 

Types of Digestion

types of digestive systems - herbivores, carnivores, omnivores 

  • sponges, unicellular organisms digest intracellularly
  • other organisms digest extracellularly, inside digestive cavity
  • gastrovascular cavity - found in cnidarians, flatworms
    • only 1 opening, no specialization
  • specialization starts w/ development of digestive tract (separate mouth/anus)
  • chemical digestion - hydrolysis reactions break down macromolecules in the food

vertebrate digestive system - has gastrointestinal tract + other digestive organs 

  • mouth >> pharynx >> esophagus >> stomach >> small intestine (absorbs nutrients in food) >> large intestine
    • in mammals, urogenital and fecal matter separated in large intestine
    • in nonmammals, waste products go into cloaca cavity
  • herbivores need longer intestines to digest plants properly (cellulose hard to break down)
    • ruminants - animals containing stomachs w/ separate chambers
    • cecum - pouch found at beginning of large intestine in some organisms for digesting cellulose
  • accessory digestive organs
    • liver - produces bile >> emulsifies fat
    • gallbladder - stores/concentrates bile
    • pancreas - produces digestive enzymes, bicarbonate buffer in pancreatic suit
  • tubular gastrointestinal tract
    • mucosa - innermost layer, circular orientation
    • lumen - inside of tract
    • submucosa - outside of mucosa, linear orientation
    • serosa - covers outside of tract
    • plexus - region where nerves concentrated

ruminant digestion - uses 4-chamber stomach 

  • rumen - 1st chamber, contains smaller reticulum
    • protists/bacteria convert cellulose into simpler compounds
    • rumination - regurgitating food to rechew after entering rumen
  • reswallowed food goes through reticulum to omasum to abomasum
  • food mixed w/ gastric juice within abomasums

cecum digestion - used by rodents, horses, deer, lagomorphs (rabbits/hares) 

  • digestion of cellulose in cecum
  • regurgitation not possible >> rodents/lagomorphs eat feces to digest a 2nd time (caprophagy)
Subject X2: 

Parts of Digestive System

mouth/teeth - for chewing (mastication) 

  • sharp teeth in carnivores for cutting
  • flat teeth in herbivores for grinding
  • both types in omnivore
  • saliva - mucous solution
    • makes food easier to swallow
    • contains amylase >> breaks down starch into disaccharide
  • epiglottis prevents food from entering respiratory tract

esophagus - 1/3 skeletal muscle, 2/3 smooth muscle 

  • peristalsis - rhythmic waves of muscle contraction
  • cardiac sphincter - ring of smooth muscle preventing food in stomach from coming back into esophagus

stomach - sac part of digestive tract 

  • can expand due to folds on interior
  • extra layer of smooth muscle for churning food, mixing w/ gastric juice
    • parietal cells - secrete hydrochloric acid, intrinsic factor (for red blood cells)
    • chief cells - secrete pepsinogen (weak protease)
  • only proteins digested in stomach
  • kills most of bacteria w/ acid, survivors go on to live in large intestine
  • ulcer - acid eating hole through stomach wall
  • pyloric sphincter - leads to small intestine

small intestine - limited capacity >> digestion takes time 

  • duodenum - 1st 25 cm of small intestine
    • receives chyme from stomach, digestive enzymes from pancreas, bile from liver
    • digests larger food molecules
  • villi - fingerlike projections w/ microvilli on plasma membrane
    • greatly increases surface area >> better absorption
    • brush border enzymes in epithelial membrane
  • nutrients go into capillaries, to hepatic portal vein

pancreas - secretes fluid to duodenum through pancreatic duct 

  • exocrine gland
  • sends enzymes that are activated by brush border enzymes in intestine
  • islets of Langerhans - produces insulin, glucagon for glucose level in blood

liver/gallbladder - largest internal organ 

  • bile - contains bile pigments, bile salts
    • bile pigments from destruction of red blood cells
    • jaundice - when bile pigments can’t leave liver
    • bile salts - break down fat droplets in duodenum
    • gallstone - formed by hardened cholesterol, blocks bile duct
  • 1st organ to receive digestion products

large intestine (colon) - connects to small intestine at cecum, appendix 

  • no digestion, only limited absorption
  • no villi in inner surface
  • purpose = concentrate waste material
    • waste gets compacted/stored
  • feces - waste material, exit through rectum to anus
  • undigested fiber >> bacterial fermentation produces more gas
Subject X2: 

Digestion Regulation

regulation of digestive tract - controlled by nervous/endocrine systems 

  • nervous system stimulates salivary/gastric secretions in response to food
  • food in stomach >> gastrin secreted >> pepsinogen, HCl secreted (cycle controlled by negative feedback)
  • chymes goes into duodenum >> inhibits stomach contractions >> no additional chyme enters small intestine
  • enterogastrones - duodenal hormones in blood that controls stomach, gastric inhibition
  • liver regulatory functions - can modify absorbed substances from digestive tract before they get to other part of body
    • removes toxins, poisons from body
    • produces most of proteins in blood plasma
    • edema - when concentration of plasma proteins drops too low
  • regulation of blood glucose concentration - neurons get energy from glucose in blood plasma
    • insulin - stimulates conversion of glucose to glycogen
    • blood glucose level decrease >> liver secretes glycogen, gets broken down by glucagon through glycogenolysis to make glucose
    • gluconeogenesis - makes glucose from other molecules

energy expenditure - eat food >> provides energy source, raw materials 

  • basal metabolic rate (BMR) - minimum rate of energy use
  • obesity - having so much fat that it’s unhealthy
  • regulation of food intake - adipose tissue secretes satiety factor to decrease appetite
    • obesity due to lack of sensitivity to protein created by satiety factor?
  • anorexia nervosa - people starve themselves
  • bulimia - people gorge themselves, then vomit everything
  • essential nutrients - cannot be made by animal, but necessary for health
    • vitamins - organic substances needed in humans (humans can not longer made vitamin C)
    • not enough vitamin C >> scurvy
    • 9 essential amino acids for humans
    • essential minerals - calcium, phosphorus, inorganic substances
Subject X2: 

27 - Protists, Fungi

See included biology topics below:

Subject X2: 


protists - probably developed due to endosymbiosis 

  • most diverse kingdom in Eukarya domain
  • symbiotic/aerobic bacteria >> mitochondria
    • most similar to nonsulfur purple bacteria
    • proteins for respiration embedded within folds of membrane
  • symbiotic/photosynthetic bacteria >> chloroplasts
    • 3 different classes of chloroplasts (red, green, algae) >> separate paths of evolution
  • mitochondria/chloroplasts both have their own circular DNA
    • replicates through splitting
    • similar size/membrane structure as prokaryotes
  • evolution of mitosis/cytokinesis not shown in any way
  • about 60 protists don’t have definite places on the phylogeny tree

general protist characteristics - non-fungi, non-plant, non-animal eukaryotes 

  • unicellular/multicellular, some form colonies
  • cell surface - ranges from simple plasma membrane to extracellular material deposits
  • locomotor organelles - provides mov’t
    • mainly through flagella (single or cilia) or pseudopodial (false foot) mov’t
    • lobopodia - large pseudopods used by amoeba
    • filopodia - thin, branching pseudopods
    • axopodia - supported by microtubules to move through extension/retraction
  • cyst formation - dormant forms of cells w/ resistant outer coverings
    • cell metabolism shuts down
  • nutrition - only chemoautotrophic nutrition not used (only found in prokaryotes)
    • phototrophs - photosynthetic
    • phagotrophs - ingests visible food particles
    • osmotrophs - ingests food in soluble form
  • reproduction - usually asexual
    • sexual reproduction during times of stress
    • binary fission - cell splits in 2
    • budding - fission where new cell is much smaller than parent
    • schizogony - multiple fission
Subject X2: 

Protist Groups

Euglenozoa - euglenoids, kinetoplastids 

  • Euglenoids - 1 of earliest organisms w/ mitochondria
    • 1/3 have chloroplasts, are autotrophic; rest are heterotrophic
    • can become heterotrophic when left in the dark
    • pellicle - flexible structure made up protein strips that change the organism’s shape
    • reproduction through mitotic cell division (nuclear envelop stays intact)
    • stigma - light-sensitive organ that helps Euglenoids move
  • Kinetoplastids - has single mitochondrion in each cell
    • mini/maxi circles of DNA in each mitochondrion
    • trypanosomes - causes African sleeping sickness, East Coast fever, Chagas disease, leishmaniasis
    • able to change antigens on glycoprotein coat to fool antibodies
    • don’t infect the flies that carry them

Alveolata - dinoflagellates, apicomplexes, ciliates 

  • alveoli - space below plasma membrane
  • Dinoflagellates - photosynthetic, w/ 2 flagella
    • spins as it moves
    • cellulose-like material forms plates that surround the cell
    • has chlorophyll a, c, and carotenoids
    • responsible for the “red tides”
    • DNA not combined w/ histone proteins
  • Apicomplexes - spore-forming parasites on animals
    • microaerophils - cells that grow best in low-oxygen, high-carbon dioxide areas
    • Plasmodium - responsible for malaria, best-known apicomplex
    • Gregarines - attaches to intestines of arthropods, annelids, mollusks
  • Ciliates - has large number of cilia
    • heterotrophic, w/ cilia in rows or spirals around the cell
    • 2 nuclei - macronuclei needed for physiological functions, micronuclei needed for sexual reproduction
    • some ciliates die after a number of generations w/o sexual reproduction
    • digestive pathway - gullet >> food vacuole >> cytoproct (pore in the pellicle) >> contractile vacuoles empty waste into the outside
    • conjugation - sexual process where 2 ciliates exchange DNA through cytoplasmic bridge

Stramenopila/Rhodophyta - grouped together 

  • Stramenopila - includes brown algae, diatoms, oomycetes
    • brown algae - alternation of generations; most conspicuous of seaweeds
    • diatoms - photosynthetic, w/ double silica shells; moves w/ vibrating fibrils in raphes
    • oomycetes - parasites or saprobes (feeds on dead organic matter); has 2 unequal flagella on spores
    • responsible for the potato famine in Ireland
  • Rhodophyta - red algae
    • no flagella, centrioles
    • uses alternation of generations
    • related to green algae through chloroplast DNA, but not host DNA

Chlorophyta - green algae, ancestors of plants 

  • Streptophyta >> land plants
  • chloroplasts have a/b chlorophylls and carotenoids (like plants)
  • Chlamydomonas - most primitive green algae
    • 2 flagella for mov’t
    • eyespot w/ 100,000 rhodopsin molecules used to direct mov’t
    • mostly haploid
  • Chlorella - nonmotile, cannot form flagella
  • Volvox - forms colonies in a hollow sphere shape

Choanoflagellida - common ancestor of all animals 

  • has single flagellum surrounded by funnel collar
  • feeds on bacteria through water straining
  • has surface receptor involving phosphorylation just like sponges

protists that are hard to categorize - amoebas, foraminifera, slime molds 

  • Amoebas - uses pseudopods for mov’t
    • cytoplasmic streaming - use of cytoplasm extensions to move, eat
    • can move in any direction
    • Actinopoda - aka radiolarians, secretes silica exoskeletons
  • Foraminifera - heterotrophic marine protists, like tiny snails
    • tests - pore-studded shells
    • podia - cytoplasmic projections used for mov’t/eating
    • used as geological markers, indicators of oil
  • slime molds - has at least 3 different lineages
    • plasmodium - nonwalled, multinucleate cytoplasmic mass
    • divides into lots of small mounds when lacking food
    • sporangium - produces the spores
Subject X2: 

General Fungi Characteristics

fungi - studied by mycologists 

  • divided into chytrids, zygomycetes, basidiomycetes, asomycetes
  • more closely related to animals than plants
  • heterotrophs that live on their food (secretes digestive enzymes)
    • hydrolytic enzymes - breaks down food, lets hyphae grow into food
  • multicellular fungi consist of hyphae (long/slender filaments)
  • dikaryon stage - in sexually reproducing fungi
    • 2 haploid cells coexist in a single cell for a short period of time
  • chitin in cell walls
  • mitosis takes place within nucleus (envelope doesn’t dissolve), like protists

fungus structure - made up of hyphae 

  • hyphae - made up of cell chains divided by septa (cross-walls)
    • technically still considered a single cell
    • cytoplasm flows freely through filament >> easy for growth
    • only grows in length
    • haustoria - penetrates land, stays outside
  • mycelium - mass of hyphae
  • hyphae rapidly expands >> reproductive structures form quickly
  • spindle apparatus forms within nucleus
    • no centrioles used

fungi reproduction - cells can hold more than 1 nucleus 

  • monokaryotic - 1 nucleus
  • dikaryotic - 2 haploid nuclei (exists independently of each other)
  • heterokaryotic - hyphae w/ nuclei from distinct individuals
  • homokaryotic - hyphae w/ genetically similar nuclei
  • can produce sexual/asexual spores
  • hyphae fuse in sexual reproduction
  • reproductive structures closed off from rest of fugae by septa w/ blocked pores
  • small spore size >> ability to be suspended in air >> rapid spread of disease

fungi metabolism - absorbs food through external digestion 

  • unicellular fungi have greatest SA-to-volume ratio among fungi >> max absorption area
  • can digest lignin/cellulose from plant cell walls, nematodes
  • used to make fermented goods (soy sauce, miso, wine, cheeses)
  • yeast - unicellular fungi
    • breaks down glucose to ethanol, carbon dioxide
  • able to break down any compound w/ carbon in presence of water
  • bioremediation - using organisms to degrade toxins, clean the environment
Subject X2: 

Fungi Groups

major fungi groups - Chytridiomycota, Zygomycota, Basidiomycota, Asomycota 

  • Chytridiomycota - aquatic fungi w/ flagella
    • proves that fungi/animals first originated from water
  • Zygomycota - includes bread molds, Glomales (helps terrestrial plants)
    • no septa until they form sporangia/gametangia
    • zygosporangium - area where haploid nuclei fuse, has a thick coat to help fungus survive in bad conditions
  • Basidiomycota - includes mushrooms, toadstools, rusts, smuts
    • basidium - club-shaped reproductive structure
    • meiosis occurs immediately after diploid cell forms
    • primary mycelium - made of monokaryotic hyphae
    • secondary mycelium - made of dikaryotic hyphae
    • basidiocarps - mushroom tops, consists of only secondary mycelium
  • Ascomycota - contains 75% of known fungi
    • bread yeasts, truffles, common molds
    • ascus - saclike reproductive structure
    • meiosis occurs immediately after diploid cell forms
    • 8 haploid ascospores form from diploid cell
    • ascus can burst >> spreads spores out very far
    • asexual reproduction in conidia

lichens - symbiosis between fungus and photosynthetic organism 

  • photosynthetic organism found between the filaments in the fungus
  • fungus sometimes feeds off photosynthetic host (but usually mutualism)
  • fungus penetrates cell wall, not cell membrane
  • able to survive in harshest environments
  • pollution decrease >> lichen increase

Mycorrhizae - symbiosis between fungus and plant roots 

  • fungus helps plants absorb nutrients from the soil
  • plants supply fungus w/ carbon
  • arbuscular mycorrhizae - hyphae penetrate outer cells of plant root
    • forms coils, swelling
    • formed w/ earliest terrestrial plants
    • epiparasite - non-photosynthetic plant that feeds off of mycorrhizae
  • ectomycorrhizae - hyphae surrounds root, doesn’t penetrate
    • less common than arbuscular mycorrhizae
    • found w/ forest trees, orchids

endophytes - fungi that live inside plants 

  • parasitism or commensalisms
  • could produce toxins to protect plant from herbivores

parasitic fungi - difficult to treat due to close relationship w/ animals 

  • Candida - causes oral/vaginal infections
  • chytridiomycosis - parasitic symbiosis between fungus and frogs
  • Fusarium - produces vomitoxin on spoiled foods >> brain damage
  • aflatoxins - carcinogenic compound produced by fungus growing on corn, peanuts, cotton seed
Subject X2: 

28 - Evolution of Plants

See included biology topics below:

Subject X2: 

Nonvascular Plants

plants - eukaryotic, multicellular, autotrophic 

  • alternation of generations (heteromorphic) - haploid >> diploid (haplodiplontic)
    • humans have diplontic life cycles (only diploid form = multicellular)
    • sporophyte - diploid, creates spores through meiosis
    • gametophytes - haploid, creates gametes through mitosis
  • adapted to terrestrial environment - cuticle (waxy covering), cork layers, bark prevent drying out
  • gas exchange controlled by guard cells, stomata
  • structural support - no more water to hold up the plant
    • lignin - stiffening substance >> plant stays vertical
    • guarantees maximum surface area for sunlight absorption
  • phloem/xylem transport system evolves to replace intracellular transport
  • 2 major plant groups - nonvascular, vascular
    • nonvascular - 3/12 phyla, no tissue for water/nutrient transport
    • vascular - xylem/phloem transport system

nonvascular plants - “bryophytes,” transition between aquatic algae and land plants 

  • less than 7cm tall
  • no conducting vessels
  • lack true roots, stems, leaves
  • needs water for reproduction
  • Bryophyta - moss
    • anchored by rhizoid
    • 1-cell thick
    • gametophyte - small, leaf-like; archegonia (egg) and antheridia (sperm)
  • Hepaticophyta - leafy/thallose liverworts
    • grows prostrate (horizontal to ground)
    • gametangia - umbrella structure for sexual reproduction
    • gemmae for asexual reproduction
  • Anthrocerophyta - hornworts
    • sporophyte at top, attached to gametophyte
    • sporophyte continues to grow, not just for reproduction
Subject X2: 

Seedless Vascular Plants, Gymnosperms

vascular plants - “tracheophytes” 

  • completely adapted to land
  • structures support body/conducting vessels >> able to grow tall
  • includes seedless vascular plants, gymnosperms, angiosperms

seedless vascular plants

  • Pterophyta - ferns, mostly in tropics
    • can grow up to 24 m
    • sporophyte dominates (unlike nonvascular plants)
    • sori - reproductive structures, on the back of fronds
    • rhizome - underground stem
    • prothallus - haploid, produces gametes
  • Psilophyta - whisk ferns, simplest vascular plants (no roots/leaves)
  • Arthrophyta - Horsetails, under 5 ft tall
    • in wet/marshy places
    • used as pot scrubbers by native Americans
    • stobilus - spore producing body
    • elater - helps spores w/ dispersal
    • bisexual gametophyte - archegonia develops before antheridia >> prevents self-fertilization
  • Lycophyta - club mosses
    • has microphyll (single vein w/o gaps between petiole/stem)

seed - makes it possible for terrestrial life 

  • protects embryo from drought, predator
  • increases dispersal
  • no need for water to reproduce
  • pollination through wind, insects, mammals, birds

gymnosperms - naked seeds, rests in cones 

  • includes oldest/largest trees
    • Bristle Cone Pines > 4000 years old
    • Giant Redwoods > 100 m
  • Coniferophyta - pines, cedars, cypress, redwood
    • needle-like leaves
    • male cones smaller than female cones
    • male cones located below female cones >> can’t self-fertilize
    • takes 2 years for cones to fully form
  • Cycadophyta - tropical/subtropical
    • centrally-located cone
    • similar to pine life cycle
  • Gnetophyta - closest to angiosperms, produces ephedrine
  • Ginkgophyta - only 1 species (Ginkgo)
    • flagellated sperm
    • diecious - 1 sex, male/female trees
    • females stink because of seed (contains butyric/isobutyric acid)
Subject X2: 


angiosperms - 240,000 species 

  • dominant for over 100 million years
  • 3 major advances - flower, broad leaves, fruits
  • flower - male/female gametophytes
    • androecium creates pollen in anther
    • gynoecium creates eggs in ovary
    • pollen makes tube into ovary >> forms embryo >> seed
  • broad leaves - collects more sunlight
    • deciduous trees - leaves drop yearly (goes into dormant period)
  • fruits - seed package >> attracts pollinators
    • digested by animals >> dropped in feces (adds nutrients)
  • monocots - 1 cotyledon (seed leaf)
    • parallel veins in leaves
    • scattered vascular bundles
    • monosculate pollen
    • adventitious roots
    • floral parts in multiples of 3
  • dicots - 2 cotyledons, more woody than monocots
    • netted veins in leaves
    • vascular bundles in rings
    • tricolpate pollen
    • primary/adventitious roots
    • floral parts in multiples of 4, 5
Subject X2: 

29 - Plant Body

See included biology topics below:

Subject X2: 

Meristems, Tissues

meristems - determines how the plant body develops after germination

  • acts like stem cells in animals
  • divides >> 1 meristematic cell, 1 cell able to differentiate
  • apical meristems - elongates roots/shoots
    • located at tips of stems/roots, behind root cap
    • produces primary growth, primary tissues (xylem/phloem)
    • constantly divides >> adds cells to tips of plant body >> size lengthens
    • root cap cells, epicotyl/hypocotyls protect root/shoot meristems
    • primary meristems - protoderm (epidermis), procambium (vascular tissues), ground meristem (ground tissue)
  • lateral meristems - peripheral cylinders of meristematic tissue, increases girth
    • produces secondary growth (sometimes not found in herbaceous, fleshy plants)
    • secondary growth >> treelike plants
    • 2 lateral meristems in woody plants - cork cambium (produces cork in outer bark), vascular cambium (produces secondary vascular tissue, between xylem/phloem)
    • secondary tissues - secondary xylem (main wood component), secondary phloem (near outer surface)

plant body organization - 4 types

  • root system - anchors the plant, penetrates soil to absorb water/nutrients
  • shoot system - stems for positioning leaves (site for photosynthesis)
    • produces flowers, fruits, seeds
    • axillary buds - apical meristems that replaces the main shoot when it gets eaten
  • dermal tissue - epidermis covered by fatty cutin layer in young plants, bark in plants w/ secondary growth
  • ground tissue - consists of mainly parenchyma cells (storage, photosynthesis, secretion)
  • vascular tissue - xylem (transfers water/minerals), phloem (transfers carbohydrates, nutrients)

dermal tissue - epidermal cells, from the protoderm

  • guard cells - cell pairs around a stoma (epidermal opening)
    • contain chloroplasts
    • stomata mostly on lower epidermis >> minimizes water loss
    • forms due to asymmetrical cell division
  • trichomes - hairlike growths from epidermis
    • keeps leaf surfaces cool, reduces evaporation
    • can secrete toxic substances to deter herbivores
  • root hairs - tubular extensions of epidermal cells
    • increases root surface area >> higher absorption efficiency

ground tissue - from ground meristem

  • parenchyma cells - large vacuoles, thin walls
    • most common type of plant cell
    • have only primary walls
    • used to store food/water
    • can remain alive for over 100 years even after fully maturing
    • chlorenchyma - parenchyma cells w/ chloroplasts
    • aerenchyma - loose parenchyma cells, stores O2
  • collenchyma cells - provides mechanical support for plant organs
    • lets plant bend w/o breaking
    • forms continuous cylinders beneath leaf petioles (stalks)
  • sclerenchyma cells - have lignin in secondary cell walls
    • in leaf veins/stems, seed coverings
    • strengthens tissues
    • fibers - long/slender cells grouped in strands
    • sclereids - branched shape

vascular tissue - xylem (inside) / phloem (outside)

  • water mov’t - gravity/atmospheric pressure moves water down
    • capillary action can’t move water more than 1 meter
    • tensile strength - tendency for water molecules to stick together
    • water evaporates at the top >> pulls adjacent molecules up
    • osmotic potential in roots + atmospheric pressure + negative pressure in stomata >> transpiration
  • xylem - main water-conducting plant tissue
    • combination of vessels elements (formed from dead/hollow cylindrical cells) and tracheids (overlapping dead cells)
    • vessels conduct water better than tracheids (favored by natural selection)
    • transpiration - diffusion of water vapor from plant
    • primary xylem - from procambium
    • secondary xylem - from vascular cambium
  • phloem - found near outer part of roots/stems
    • main food-conducting plant tissue (moves food slower than xylem moves water)
    • girdled (removing strips of bark) >> takes away phloem >> plant dies from starvation
    • sieve cells - found in seedless vascular plants, gymnosperms
    • sieve-tube members - found in angiosperms
    • sieve areas - clusters of pores, connects protoplasts in adjoining cells
    • sieve plates - larger sieve areas in sieve-tube members
    • sieve tubes - series of sieve-tube members connected end to end; no nucleus, mitochondria, chloroplasts
    • companion cell - adjacent specialized parenchyma cell associated w/ each sieve-tube member; supplies the sieve tubes w/ nutrients
    • plasmodesmata - cytoplasmic connections between adjacent cells
Subject X2: 


root types - 2 types

  • taproot - enlarged radical root in most dicots
    • smaller lateral roots branch off
    • stores food, reaches for water deep underground
  • fibrous roots - mass of small roots, in most monocots
    • extensive, clings to soil
    • prevents erosion

root structure - split into 4 regions

  • root cap - made of inner columella cells, outer root cap cells
    • columella cells - function in perception of gravity
    • protects tissues behind it as it grows
    • golgi bodies secrete slimy substance to outside >> eases root through soil
    • constantly replaced by new cells
  • zone of cell division - where cells divide ever 12-36 hours
    • daughter cells of apical meristem
    • quiescent center - group of cells at the center of apical meristem, divides slowly
    • inner cell layer >> endodermis, intercellular flow of water
  • zone of elongation - cells from primary meristems elongate >> roots lengthen
    • small vacuoles merge/grow >> occupies 90% of cells’ volume
    • no more size increase beyond zone of elongation
  • zone of maturation - where cells become differentiated
    • root hairs form on each epidermal cell, only stays functional for a few days
    • cortex - made of parenchyma cells, functions as food storage
    • Casparian strips - bands of suberin (fatty substance) that blocks intercellular transport
    • pericycle - cylinder of parenchyma cells interior to the endodermis, becomes lateral roots or vascular cambium
    • primary xylem differentiated as solid core in center of roots
    • primary phloem differentiated as groups of cells
    • secondary tissues added >> primary tissues are replaced

modified roots - usually either taproot (single large root) or fibrous (many smaller roots) 

  • adventitious root - produced from anyplace other than the plant root
  • prop roots - grows from the lower stem to brace plants against the wind
  • aerial roots - extends into the air to prevent water loss
  • pneumatophores - spongy outgrowths formed by plants in swamps
  • contractile roots - roots spiral to pull plant deeper into the soil
  • parasitic roots - found in plants w/o chloroplasts
  • food storage roots - contains extra parenchyma cells
  • water storage roots - found in members of pumpkin family
  • buttress roots - in figs, tropical trees; provides stability at base of trunk
Subject X2: 


stem structure - external/internal 

  • heartwood - inside, nonfunctional part of stem
    • sealed off w/ lignin
    • only for structure
  • sapwood - functional, still acts as transport
  • external form - primordia (bulges) develops into leaves, shoots, flowers
    • phyllotaxy - leaves arranged 137.5 degrees apart (golden mean)
    • node - region where leaf attaches
    • internode - area of stem between 2 nodes
    • sessile leaf - leaf lacking the petiole (stalk)
    • axillary bud at every axil (between petiole/stem)
    • scars - mark where stems branch off
    • lenticels - pores for gas exchange
  • internal form - apical meristem at stem’s tip produces primary meristems
    • protoderm >> epidermis
    • ground meristem >> parenchyma cells (pith in center, cortex away from center)
    • procambium >> primary xylem/phloem
    • trace - strand of xylem/phloem branching off from the main clinder >> enters developing leaf, flower, shoot >> produces gap
    • periderm - cork cambium, cork, phelloderm found between epidermis and collenchyma
    • outer bark - made of cork tissue


modified stems - most grow erect


  • bulbs - swollen underground stems w/ adventitious roots (ex. onion)
  • corms - similar to bulbs but w/ no fleshy leaves
  • rhizomes - horizontal stems growing underground
  • runners/stolons - similar to rhizomes, but grows on the surface
  • tubers - swollen tips of stolons (ex. potatoes)
  • tendrils - twins around supports (ex. climbing plants like grapes)
Subject X2: 


leaf structure - external/internal 

  • external form - initiated by primordial in apical meristems
    • main sites of photosynthesis on land
    • cell enlargement/division >> leaves expand
    • microphyll - leaf w/ 1 vein
    • megaphyll - has several veins, leaves gap in cylinder once it branches off
    • veins - collection of xylem/phloem, parallel in monocots, networked in dicots
    • simple leaves - undivided blades
    • compound leaves - blades divided into leaflets
    • pinnately compound - leaflets arranged in pairs
    • palmately compound - leaflets radiate from a center
    • leaves alternately/oppositely arranged, or in whorls (leaf circle)
  • internal form - transparent epidermis covers each leaf
    • no chloroplasts in epidermal cells
    • mesophyll - tissue between upper/lower epidermis, contains vascular bundles and majority of photosynthesis
    • palisade mesophyll - closer to upper epidermis, contains chlorenchyma
    • spongy mesophyll - closer to lower epidermis, contains many air spaces for gas exchange
  • stomata - surrounded by guard cells, regulates water mov’t/gas exchange
    • K+ controls guard cells
    • water enters osmotically >> guard cells swell >> stomata closes
    • opens in the day, closes at night
Subject X2: 

30 - Plant Reproduction

See included biology topics below:

Subject X2: 

Flower Formation

plant metamorphosis - environment controls how the plant changes

  • phase change - internal development >> competence, ability to reproduce
  • reproductive structures added on to existing structures
  • distinct juvenile, adult phases
  • easier to revert adult into juvenile than to induce phase change

flower production pathways - 3 regulated pathways to flowering

  • light-dependent (photoperiodic) pathway - length of day (amount of daily sunlight) affects flowering
    • daylight shorter than critical length (12 hours) >> flowering in short-day plants (blooms in late summer/fall)
    • daylight longer than critical length >> flowering in long-day plants (crop plants, blooms in spring/summer)
    • day-neutral plants - flower when mature, regardless of day length
    • 2 critical photoperiods >> will not flower if day too long/short
    • facultative-long-or-short-day-plants - flower speed depends on day length
    • cryptochrome/phytochrome detect photoperiods
    • repress gene that represses flowering >> flowering takes place
  • temperature-dependent pathway - cold temperatures >> faster flowering
    • vernalization - shoots/seeds chill >> reproduce
    • gibberellin hormones controls flowering, expression of certain genes
  • autonomous pathway - controlled by basic nutrition
    • 1st pathway to evolve
    • used by day-neutral plants
    • certain shoots determined/committed to flower >> nodes starts the flower
    • inhibitory signals sent from roots
  • ABC model - shows how 3 genes specify floral organs
    • sepals - class A genes
    • petals - class A/B genes
    • stamens - class B/C genes
    • carpels - class C genes
  • formation of gametes - floral parts (modified leaves) transition to meiosis >> gamete-producing gametophytes created

parts of the flower - no direct contact between pollen, ovule

  • pollinators - animals that transfer pollen between plants
  • complete flower - has all 4 whorls (calyx, corolla, androecium, gynoecium)
  • perfect flower - has stamen/carpel (androecium/gynoecium)
  • calyx - outermost whorl
    • contains the sepals (protects the flower in the bud)
  • corolla - collective name for the petals
    • used to attract pollinators
  • androecium - stamens in a flower
    • microsporangia on anthers
    • held up by filaments
  • gynoecium - female flower parts
    • contains single/fused carpel
    • ovules - produced in the ovary, become seeds
    • stigma - receives pollen at top of carpel
    • style - connects stigma to ovary

floral specialization - floral parts either fused or reduced/lost

  • more advanced angiosperm >> less parts in each whorl
  • modifications sometimes due to pollination techniques (wind replaces animals)
  • artificial selection >> flowers less able to adapt
    • corn (maize) wouldn’t be able to survive as easily w/o human aid
  • floral symmetry - different between primitive/advanced flowers
    • primitive >> radial symmetry
    • advanced >> bilateral symmetry

formation of angiosperm gametes - gametophytes completely enclosed by sporophyte

  • male gametophytes = microgametophytes, pollen grains
    • forms in 2 pllen sacs in anther
    • microspore mother cells - found in specialized chambers of sac
    • microspore mother undergoes meiosis >> haploid microspores >> 4 pollen grains after mitosis
  • female gametophytes = megagametophytes, embryo sac
    • forms in ovules
    • megaspore mother cells - found in each ovule
    • megaspore mother cell undergoes meiosis >> haploid megaspores, only 1 survive >> 8 haploid nuclei after mitosis
    • 1 nucleus >> egg, rest arranged in precise locations (2 polar nuclei in middle of sac, 2 in synergids flanking egg, 3 in antipodal cells)
Subject X2: 


pollination - process by which pollen is placed on the stigma

  • can by carried by wind, animals, or flower itself
  • early seed plants pollinated by wind
    • large quantities of pollen shed, blown about
    • must grow close together to work efficiently
    • pollen travels less than 100 meters
  • earliest angiosperms pollinated by insects
  • bees - pollinates the majority of insect-pollinated angiosperms
    • tend to visit blue/yellow flowers
    • locates food first by odor, then by shape/color/texture
    • use nectar as food for adult bees
    • uses pollen as food for developing larvae
    • mostly solitary
  • insect pollinators other than bees
    • butterflies - perch on the landing platforms of phlox flowers
    • target heavily scented flowers (easier to find in the dark)
  • birds - especially hummingbird/sunbird
    • targets flowers w/ lots of nectar (not attractive to insects)
    • attracted by the red color
  • wind-pollinated angiosperms have small/greenish/odorless flowers
    • reduced/missing corolla

self-pollination - mostly in flowers w/ small flowers in temperate regions

  • don’t need pollinators to produce seed >> uses less energy, able to grow where animals are scarce
  • creates more uniform populations
  • outcrossing - necessary for adaptation/evolution
    • dioecious plants - produce only ovules or pollen, cannot self-pollinate
    • monoecious plants - produce both ovules/pollen, must produce gametes at different times to prevent self-pollination (dichogamous plants)
    • self-incompatibility >> locus prevents self-pollination, pollen tube gets blocked

angiosperm double fertilization - creates fertilized egg, endosperm to nourish embryo

  • pollen tube - grows after pollen adheres to stigma
    • pierces the style
    • reaches embryo sac >> nuclei around egg cell disintegrates >> tube tip enters egg
    • tube tip bursts >> 2 sperm cells released (1 fertilizes egg to form zygote, other forms w/ polar nucleus to form triploid endosperm)
  • endosperm completely transferred to cotyledons in dicots (disappears after maturing)
  • seed enclosed in fruit
Subject X2: 

Plant Asexual Reproduction

asexual reproduction - results in genetically identical offspring

  • self-pollination still generates genetic variability
  • found in unchanging environments >> plant less likely to survive if environment suddenly changes
    • most asexual plants found in harsh environments
  • vegetative reproduction - new plants cloned from parts of adults
    • runners - long stems growing along the soil surface, new shoot grows from each 2nd node
    • rhizomes - underground horizontal stems, new shoot can grow from each node
    • suckers - sprouts from roots that can become new plants
    • adventitious plantlets - reproductive leaves
  • apomixes - seeds produced asexually from parent
    • requires seed dispersal

plant tissue culture - cloning plants from tissues w/ growth hormones

  • cell wall removed >> protoplast (plant cell enclosed only by plasma membrane)
  • protoplasts can fuse >> create hybrids (form of genetic engineering)
  • cell wall can regenerate

plant life span - age dependent on species

  • annual plants - grow, flower, form fruits/seeds within a growing season
    • includes most crop plants
    • almost entirely herbaceous (non-woody)
    • starves itself to death after flowering (senescence)
  • biennial plants - 2 year life cycles, only flowers once
    • stores photosynthate underground during 1st year
    • flowering stems produced in 2nd year using energy from underground storages
    • mostly harvested for roots (carrots, beets, cabbage)
  • perennial plants - herbaceous/woody, continues to grow yearly
    • majority of vascular plants
    • trees either deciduous (leaves fall once a year) or evergreen (plants never bare)
  • abscission - process by which leaves/petals are shed
    • gets rid of unproductive parts
    • takes place in abscission zone at base of petiole
    • protective layer filled w/ suberin (fat) on stem side of petiole
    • separation layer develops on leaf side of petiole >> weakened connections between stem/leaf
Subject X2: 

31 - Plant Development

See included biology topics below:

Subject X2: 

Early Plant Formation

root-shoot axis - regulating amount/pattern of cell division >> 3D shape/form

  • cells w/ multiple potentials restricted to meristemic regions
  • apical meristems establish axis in embryogenesis
  • tissue systems organized radially around axis
  • food source for embryo - endosperm in angiosperms, megagametophyte in gymnosperms
  • 1st division of zygote >> smaller cell becomes embryo, larger cell forms suspensor (links embryo to nutrient tissue in seed)
    • cells near suspensor >> root
    • cells at other end >> shoot
  • embryo stops suspensor from developing into another embryo

tissue systems - dermal tissue, ground tissue, vascular tissue

  • dermal tissue - from protoderm, outermost cells of embryo
    • divides w/ cell plate perpendicular to surface
  • ground tissue - functions in food/water storage
  • vascular tissue - from procambium at embryo core
    • functions in water/nutrient transport
  • formation of roots/shoots controlled independently
  • morphogenesis - generation of form, produces the cotyledon(s)
  • seeds need enough nutrients to support sporophyte until it can photosynthesize
    • can’t bury seeds to deep

germination - radicle (1st root) extends through seed coat

  • orients so that roots grow down, shoots grow up
  • starts when seed absorbs water, metabolism resumes
  • most seeds must stratify (spend time in cold conditions) before germinating
    • ensures that seed will not sprout right before cold season
  • amyloplasts - starch-storing plastids, provides metabolic reserves for young plant
  • cotyledon >> scutellum (food source used before endosperm)
  • aleurone - outer layer of endosperm, signaled by gibberellic acid to produce amylase
  • seed very susceptible to disease/drought between germination and young plant stage
Subject X2: 

Seed and Fruit Formation

seed formation - outer cell layers of ovule form seed coat

  • postpones development until more favorable conditions
  • protects young plant when it’s the most vulnerable
  • keeps stored food that keep young plant alive
  • adapted for dispersal
  • seed coat forms >> metabolic activities stop
    • germination can’t start until water/oxygen reaches embryo
  • seeds don’t germinate until appropriate conditions (heat, available nutrients, chemicals, pass through animal intestines, etc)
    • scarification - breaking down seed coat so that first root can emerge

fruit formation - helps angiosperm embryos survive

  • develops from flower ovary
  • different fruit types due to 3 layers (epicarp, mesocarp, endocarp) on ovary wall
    • follicles - split along 1 carpel edge
    • legumes - split along 2 carpel edges
    • samaras - not split, has wing
    • drupes - single seed in hard pit
    • true berries, more than 1 seed, thin skin
    • hesperidia - more than 1 seed, leathery skin
    • aggregate fruits - derived from multiple ovaries
    • multiple fruits - develop from flower cluster
  • fruit dispersal - mostly transferred by animals
    • fruits of maples, elms, ashes have wings >> distributed by wind
    • dandelions have light seeds >> wind distribution
    • coconuts, beach plants distributed by water
Subject X2: 

Plant Chemical Regulation

plant chemical regulation - plant hormones have multiple functions, unlike that of animals 

  • auxin - made in apical meristem
    • if lacking, plant will no longer grow towards light
    • promotes stem, vascular tissue, root growth
    • suppresses lateral bud growth, leaf abscission
    • “agent orange” - derived from auxin to speed up growth, make trees age faster
  • cytokinins - stimulates cell division, differentiation
    • promotes lateral growth
  • gibberellins - synthesized from leaves
    • apical growth, stimulates protein synthesis
  • ethylene - gaseous
    • drops damaged leaves when in contact w/ toxin
    • ripens fruit
  • abscissic acid - controls stomata opening
    • stimulates winter dormancy

tropisms - positive/negative growth toward external stimuli 

  • photoperiodism - response to light
    • lets plant know what time of year it is
    • bright red light >> Pr converts to Pfr phytochrome>> inhibits flower growth
    • far red light (longer wavelength) >> Pfr converts to Pr phytochrome>> no more flower inhibition
  • gravitropism (geotropism) - response to gravity
  • thigmotropism - vines curling around objects
  • etoliated plant - grown in the dark
    • loses chlorophyll >> becomes white
    • acts as fiber optics >> grows longer

parts of early plant

  • coleoptile - in grass, 1st leaf sheath
  • epicotyl - apical end of embryo
  • hypocotyl - between radicle and leaves
  • mesocotyl - embryonic stem axis

dicot germination - hypocotyl emerges in an arch 

  • 2 cotyledons protect plumule (embryonic leaves) as it emerges
  • light >> hypocotyl arch straightens out
  • cotyledons start photosynthesis, later drop off

monocot germination - has sharp primary leaf  

  • coleoptile acts as needle to penetrate ground
Subject X2: 

32 - Evolution

See included biology topics below:

Subject X2: 

Natural Selection

natural selection - mechanism for evolution 

  • individuals w/ better traits tend to produce more surviving offspring
  • Lamarck’s theory - inheritance of acquired characteristics
    • individuals pass on body/behavior changes acquired throughout lives
  • Darwin ’s theory - inheritance of preexisting genetic differences
  • population genetics - study of gene properties in populations

evidence for evolution - proven by modern day evidence

  • correspondence between finch beaks and food supply
    • Peter/Rosemary Grant - studied ground finch, found that frequency of a certain beak size change predictably as food supply differed
  • pollution after 1850 allowed dark colored moths to survive more easily than light-colored ones
    • increase in number of dark colored moths after industrial revolution
    • industrial melanism - darker organisms prevail over lighter ones in industrial areas
  • artificial selection in agriculture - differences due to selection for favorable traits
    • current crops look far different from ancestors
    • corn can no longer survive by itself in the wild
  • fossil record - absolute dating (w/ radioactive decay) has replaced relative dating (w/ rock strata)
    • fossil record (especially for vertebrates) show how they’ve changed/evolved
  • anatomical record - w/o evolution, it’s hard to explain many things in biology
    • homologous structures - structures w/ different functions, derived from same body part
    • imperfect structures - like vertebrate eye, don’t function as efficiently as a result of evolution
    • vestigial structures - have no function, but resembles structures of ancestors
    • analogous structures - due to convergent evolution, has similar functions but derived from different body parts
Subject X2: 

Charles Darwin's Major Points

evidence against Darwin - 7 main objections 

  • evolution still just a theory - still has questions, lacking proof
  • no fossil intermediates - no evidence of transition between organisms
    • increasing fossil evidence says otherwise
  • intelligent design - organs too complex for a random process
    • organs develop as series of slight/tiny improvements
  • evolution violates 2nd law of thermodynamics - things tend towards disorder, not order
    • organisms shouldn’t become more advanced
  • proteins too improbable - 20 proteins, near countless number of arrangements
    • extremely low chance maybe, but still possible when given enough time
    • “give a monkey a typewriter…if given enough time, he will write Shakespeare”
  • natural selection doesn’t imply evolution - production of radically different organisms possible in laboratory now
  • irreducible complexity argument - each part essential to overall process, can’t evolve
    • each part considered to evolve as part of the working system

Darwin ’s major points - variation in all natural populations 

  • most have potential to reproduce at rate that can deplete all natural resources
  • resources limited >> those w/ most advantageous adaptations survive
  • natural selection - “survival of the fittest”
    • produces different reproduction rates
    • not necessarily directly related to death
  • fitness - number of surviving offspring left in the next generation
    • combination of survival, mating success, number of offspring per mating
    • usually involves female fitness (hard to determine father)
    • behavioral ecology - study of how natural selection affects behavior
    • adaptive significance - how behavior increase survival/reproduction

3 tenants of natural selection - number of fertilized eggs isn’t always the number of offspring

  • nonrandom survival - things don’t survive randomly
  • nonrandom mating - purposeful action
  • nonrandom fecundity - a reason to why certain creatures produce more offspring
  • survival strategies
  • altricial - unable to care for itself
  • precocial - born ready/mature
  • reproductive trait - number produced at each reproduction
  • parental care - needed for animal to grow/survive
Subject X2: 

33 - Behavioral Ecology

See included biology topics below:

Subject X2: 


optimal foraging theory - states that natural selection favors those most efficient

  • foragers feed on prey that maximize energy return
  • balance between looking for prey, hiding from predators
  • might have genetic basis rather than learning (due to zebra finch behavior)

territoriality - keeping exclusive use of home range

  • defense against intrusion by others
  • can waste energy, expose oneself to predators
  • balance between costs/benefits of defending territory

habitat - determined by resources, how well organism survives, amount of competition

  • 5 major zones - salt water (70%), terrestrial (29%), freshwater, estuary (where freshwater meets saltwater), endoparisitic
  • streams not connected >> easier for specialization >> more freshwater species than saltwater

Justus Van Liebig - “Law of the Minimum”

  • plants need certain type/amount of nutrients
  • miss an essential part >> die

Victor Shelford - principle of tolerance limits (maximum)

  • too much of something can also inhibit growth
  • growth occurs best under a certain range of conditions
  • factors will vary seasonally, geographically, throughout life
  • placed in area of stress >> some organisms increase fitness
  • generalist - have wide tolerance
  • specialist - have narrow tolerance
  • hormesis - opposite effect in small doses than in high doses
Subject X2: 


reproductive strategies - supposed to maximize reproductive success

  • mate choice - females picks the male w/ best qualities to mate
    • male mate choice less common
    • females pick males w/ best chances of survival (best genes)
    • handicap hypothesis - some females choose males w/ parts that decreases chances of survival on assumption that the male must be strong to survive w/ bad traits
    • sensory exploitation - males have characteristics that females naturally tend to see
  • parental investment - amount of work each sex puts into producing/raising offspring
  • more costly for females during reproduction >> more choosy about who to mate w/
  • sexual selection - either intrasexual or intersexual
    • intrasexual selection - competition between members of same sex
    • sexual dimorphism - differences between the 2 sexes
    • sperm competition - where sperm differs, some faster/larger than others
    • intersexual selection - mate choice

courtship - animals produce signals to communicate w/ potential mates

  • can attack conspecific males (males of same species) to defend nest
  • species-specific signals - only understand within a single species >> reproductive isolation
  • pheromones - chemical signals used as sex attractants
  • level of specificity - relates to the function of the signal

mating strategies - females decide >> males fight to be the most visible

  • monogamy - mating w/ 1 exclusively for a time period
    • for breeding season or life
  • polygamy - mating w/ more than 1
    • polyandry - 1 female w/ more than 1 male
    • polygyny - 1 male w/ more than 1 female
  • promiscuity - no relationships
    • leaves after reproducing
  • altricial - need prolonged/extensive care
  • precocial - requires little care, males more likely to be polygynous
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Fecundity, Selection

fecundity - determined by timing, energy, expense, delayed implantation

  • timing based on biorhythm
    • eggs readiness sometimes linked w/ seasonal changes
  • waits for favorable conditions (kept eggs in stasis)
  • self-preservation more important than reproduction

artificial selection - breeding to get a specific trait

  • natural selection creates organism w/ most favorable characteristics
  • bell curve represents average characteristics
    • disruptive selection - favors an extremes, creates dip in bell curve
    • direction selection - favors a particular extreme
    • stabilizing selection - favors the average
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34 - Community Ecology

See included biology topics below:

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classical limiting factors - abiotic, organisms must conform or regulate themselves

  • temperature - changes biochemical structure/function, influence chemical reaction rate
    • ectotherm (poikilotherm) - cold-blooded w/ slower metabolisms
    • endotherm (homeotherm) - warm-blooded
    • heterotherm - regulators that don’t always regulate themselves
    • Thermal Primacy Paradigm - every organism must deal w/ temperature
  • oxygen - doesn’t follow same patterns as temperature
    • facultative anaerobes - needs oxygen to reproduce, doesn’t need it to survive
  • water - can have too much or too little
    • used to adjust solute content
  • pressure - lighter substances float, heavier ones sink
  • light - needed in some form by most organisms
  • pH - primarily w/ halophiles
    • no organism can handle 0 or 14 pH

responses to environmental change -

  • passive - no response
    • either no point, no need, or response will lead to worse conditions
    • maybe inability to sense the change
  • behavioral - 1st line of defense
    • takes place within seconds/minutes
    • needs sense, ability to move, another place to go to
    • physiological - constrict blood vessels, etc
  • biochemical/physiological - takes hours/days
    • internal change w/ acclimation/acclimatization
    • growing thicker coats of fur during winter
  • adapt/evolve - genetic change passed on
    • involves an entire population
    • “Allen’s Rule” - mammals in cold areas have shorter ears/limbs to reduce surface area across which to lose heat

species interactions - competition for food/space >> displacement of weaker organisms

  • symbiosis - 2 or more kinds of organisms get in a relationship
  • competition - uses limited resources >> harms both organisms
  • neutralism - doesn’t affect anyone’s fitness
  • commensalisms - favors 1 organism, doesn’t do anything for other
  • parasitism - hurts 1 organism, helps other
    • parasites can make hosts more vulnerable to predators >> passes along
    • ectoparasites - feeds on exterior
    • endoparasites - feeds in interior
    • parasitoids - insects that lay eggs in living hosts
  • amensalism - hurts 1 organism, doesn’t do anything for other
  • mutualism - favors both organisms
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population - group of single species living in a certain place

  • size, density, dispersion, demographics
  • population range - area throughout which a population occurs
    • no population occurs in all habitats around the world
    • changes as the environment changes
  • dispersion - how organisms are spaced
    • randomly spaced - when organisms don’t interact much
    • uniformly spaced - due to competition for resources
    • clumped spacing - most common form, due to strong social interaction or important resource in a certain area
    • human effect - humans altering the environment changes dispersion
  • metapopulations - networks of distinct populations that exchange individuals
    • occurs where suitable habitats separated by unsuitable habitats
    • source-sink metapopulations - organisms sent from better areas (source) to bolster worse areas (sink)
  • population growth - will exceed resources if unchecked
    • sex ratio - number of births directly related to number of females
    • generation time - average interval between birth of individual and its offspring
    • cohort - group of individuals of the same age
    • survivorship - percentage of original population that survives to given age
  • biotic potential - rate population will grow if no limits exist
  • sigmoidal growth curve - shows limits of population growth due to carrying capacity
  • density-dependent factors - based on the number of organisms
    • population increases >> mortality increases or birth rates decline (negative feedback)
    • Allee effect - where growth rate actually increases as population increases
    • resources, disease, increased aggression, hormonal changes
  • density-independent factors - natural disasters

r strategy - rapid population growth

  • suited for populations far below carrying capacity
  • small, short-lived growth phase
  • reproduces rapidly w/ large litters

K strategy - low rate of growth

  • suited for populations near carrying capacity
  • takes longer to get to carrying capacity (K)
  • longer generations, smaller litters
  • extended parental care
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community - species found at a certain area

  • individualistic concept - community nothing more than collection of organisms that happen to live in same place
  • holistic concept - community acts as integrated unit (superorganism)
  • ecotones - area where environment suddenly changes

niche - role an organism plays in the ecosystem

  • interspecific competition - when not enough resource for 2 organisms
    • interference competition - fighting over resources
    • exploitative competition - consuming shared resources
  • fundamental niche - entire niche that organism can use
  • realized niche - actual niche that organism occupies
  • competitive exclusion - no 2 organisms can occupy same niche if resources limited
    • species that can use resource more efficiently will prevail
    • can subdivide niche to avoid direct competition
    • grow more similar >> more likely to compete
  • sympatric species - avoid competition by living in different parts of habitat or using different resources
  • character displacement - natural selection makes competing organisms different

coevolution between predator/prey - populations oscillate since predator depends on prey

  • lag and offset oscillations between predator/prey
  • keystone species - presence has much influence on the community
    • ex. beavers

predation - consuming of 1 organism by another

  • kill predator >> increase prey population
  • coevolution >> predator/prey continually develop better offense/defense
  • plant defenses - mostly uses morphological defenses (thorns, spines, hairs)
    • secondary chemical compounds - toxic or disturbs metabolism
  • animal defenses - tries to show predators that they taste bad
    • chemical defenses - used as weapons against predator
    • warning coloration - tells predators that they have toxic chemicals
    • cryptic coloration - blends in w/ surroundings
  • reduces competition
  • indirect effects - 1 organism affecting another indirectly through a 3rd organism
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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

Chapter 1 Exploring Life76 KB
Subject X2: 

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 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 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 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 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

Chapter 6 A Tour of the Cell93 KB
Subject X2: 

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

Subject X2: 

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 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 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

Chapter 33 Invertebrates101 KB
Subject X2: 

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 34 Vertebrates123 KB
    Subject X2: 

    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 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

    Chapter 10 Photosynthesis72.5 KB
    Subject X2: 

    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 sig