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• homeodomain protein - found in animal, fungi, plant kingdoms; developed early on and hasn't been replaced by better versions

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

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

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

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

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

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  

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)

DNA  

• 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

RNA  

• 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

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)

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

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

mitosis  

• 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

neurotransmitters - 

• 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

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

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

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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)

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)

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

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

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

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

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

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