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Lecture/Key Summary Notes

by: sun543

Lecture/Key Summary Notes Bio 110

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Covers most between Exam 1 to Exam 2
Fundamentals of Biology I
Professor Athena Anderson
Class Notes
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This 10 page Class Notes was uploaded by sun543 on Thursday September 22, 2016. The Class Notes belongs to Bio 110 at Purdue University taught by Professor Athena Anderson in Fall 2016. Since its upload, it has received 4 views.


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Date Created: 09/22/16
1: Thermodynamics & Kinetics energy= capacity to cause change potential: location or structure kinetic: relative motion thermal: k e in atoms and molecules chemical: p e in chemical reaction (bonds) 1st law: energy can be transformed or transferred, but never created or destroyed 2nd law: every energy transfer increases entropy (disorder), for process to occur spontaneously, it must increase entropy organisms create “order from chaos” (decreasing entropy) ex: building polymers from monomers overall, organisms do more to increase entropy of universe ex: releasing heat, molecules after eating free energy= energy available to do work (G) in living systems, we look at the change in free energy (delta G) from the initial to final states of  a reaction delta G= G(final)­G(initial) exergonic: spontaneous, chemical mixture loses free energy TO universe (delta G = ­) endergonic: not spontaneous, chemical mixture gains free energy FROM  universe (delta G = +) focus on starting and ending points for thermodynamic calculations ignore everything in between most reactions in biological systems are NOT spontaneous  ADP + pi energy input required | ATP ATP synthesis is endergonic  ATP hydrolysis is exergonic & spontaneous thermodynamics: coupled reactions hydrolysis of ATP is exergonic ATP+H2O ­> ADP+Pi delta G=­7.3 kcal/mol this energy is not wasted, but captured use this delta G to drive endergonic reaction rate of reactions exergonic reactions are spontaneous  thermodynamics says NOTHING about rate of reactions kinetics TELLS us about rate of reactions most spontaneous reactions are too slow to support life cellular reactions get help from: ENZYMES activation energy initial energy barrier before new bonding occurs, existing chemical bonds must be broken is difference between starting free energy & maximum free energy enzyme catalysts (of biological reactions) speeds up reaction without being consumed & lowers activation energy 2: Photosynthesis methods of obtaining energy autotrophs: make own energy (self feeding) heterotrophs: eat other organisms for energy (other feeding) energy transfer in living systems (simple food web) plants eaten by herbivores herbivores eaten by carnivores carnivores’ energy added to soil by decomposers plants use energy in soil to grow repeat light+CO2+H2O ­> O2+sugar light reactions: harvest light dark reactions: make glucose (aka calvin cycle, LIGHT INDEPENDENT reactions) photosynthesis captures light energy & converts to chemical energy light is electromagnetic energy / particle / wave wavelength: measurement of energy (SMALLER=MORE ENERGY) pigments REFLECT the color we see, absorb all others  (ex: chlorophyll absorbs all but green/yellow) light reactions: occur in sunlight  takes place in thylakoid membrane capture/use light as energy source oxidize (remove e­) H2O produce ATP & NADPH for dark reactions produce O2 as byproduct  photosystems (PS) are pigments embedded in a cluster of membrane proteins beginning and end of light reactions antenna complex: pigment molecules that absorb light energy & feed it to reaction center reaction center: protein chlorophyll complex that passes high energy e­ out of the PS light reaction steps:  ( KNOW THE MODEL AND NAMES OF MOLECULES) photons excite antenna pigments chlorophyll molecules transfer e­ to e­ acceptor e­ removed from H2O, added to chlorophyll, O2 released (oxygen waste of L.R.) e­ transport chain through cytochrome complex, ATP produced (generated) chlorophyll molecules transfer e­ to e­ acceptor NADP+ + H+ ­> NADPH, in NADP+ reductase molecule dark reactions/calvin cycle/light independent reaction: happens in stroma uses ATP and NADPH from light reactions uses CO2 from air NADP+ & ADP are byproducts produces glucose dark reaction steps: C from CO2 added to RuBp the 6­C molecule splits into 2 phosphoglycerate (PGA) molecules PGAs reduced to glyceraldehyde 3­phosphate (G3P) using ATP/NADPH from L.R. 2 G3Ps combine to form glucose other G3Ps make more RuBP 3: Photosynthesis (continued) three types: C3 (most plants) C4 (grasses) CAM (cacti & succulents)  C3 most energy efficient method good for moderate light & water stomata closed on hot, dry days photosynthesis reduced because CO2 limited photorespiration is a problem photorespiration occurs when CO2 is low & O2 builds up rubisco usually joins CO2 with RuBp, but adds O2 instead products splits and 2­C compound exists chloroplast, breaks down in cell, releases CO2 toxic molecule formed (phosphoglycolate) uses ATP & no sugar produced “evolutionary baggage” from time with less O2 and more CO2 C4 loses less water than C3 adaptive in hot, dry conditions stomata partially closed on hot, dry days photosynthesis not reduced as much due to phosphoenolpryuvate (PEP) carboxylase’s  high affinity for CO2 less photorespiration mesophyll cells & bundle sheath cells evolved 45 times, used by 19 plant families CAM crassulacean acid metabolism named for family crassulaceae  most water efficient for most arid conditions stomata closed in day & opened at night CO2 stored in organic acids at night CO2 added to dark reactions during day CAM “idling” recycles CO2, closed system, not sustainable 4: Cellular Respiration  (KNOW ALL CYCLE ORDER) catabolic pathways: metabolic pathways that release stored energy by breaking down complex molecules organic compounds have potential energy b/c of arrangement of e­’s in bond b/w atoms enzymes usually bond breakers some energy released can be used for work, the rest is lost as heat two types: aerobic respiration anaerobic respiration (fermentation) oxidation reduction / redox reactions: (leo ger) respiration is series of redox reactions one molecule loses e­, being oxidized (interaction w/ oxygen) other molecule gains e­, being reduced sometimes oxidation is change in degree of sharing e­’s, not complete transfer occurs when atom goes from being bonded with many atoms to a few atoms/^e­neg breakdown of glucose in presence of O2 is a redox reaction, where glucose=oxidized C6H12O6+6O2 ­> 6CO2+6H2O+energy oxygen is one of the strongest oxidizers because of its high electronegativity e­ usually travel with proton=hydrogen atom hydrogen atoms usually passed to electron carrier before arriving at destination NAD+ is common e­ carrier b/c it switches easily b/w oxidized (NAD+) ­> reduced (NADH) NAD+ + 2H ­> NADH + H+ (ex: NAD+/empty taxi & NADH loaded taxi) three pathways: glycolysis (cytoplasm) pyruvate oxidation & citric acid cycle (mitochondria) eukaryotes or prokaryotes(cytoplasm) euk prok  oxidative phosphorylation and e­ transport chains (mitochondrial cristae/cell membrane) ATP synthesis: substrate level phosphorylation (uses organic phosphate and enzymes) starts with organic molecule that has a phosphate group(PO4) transfers phosphate to ADP, making ATP oxidative phosphorylation (uses inorganic phosphate(Pi) & chemiosmosis mechanism  with ATP synthase transfers free(inorganic) phosphate(Pi) to ADP to make ATP requires proton pump, usually as part of e­ transport chain relies on chemiosmosis glycolysis: (same in bacteria, archaea, eukarya) glucose gets energy from ATP, splits into w G3P molecules G3Ps donate e­ then H+ joins to it, then NADH formed G3Ps also donate energy to make ATPs (2/G3P) atoms rearranged to form pyruvate (1/G3P) pyruvate oxidation: pyruvate enters mitochondria CO2 removed NADH formed from NAD+ coenzyme a+acetyl group = acetyl CoA acetyl­CoA goes to citric acid cycle citric acid cycle: citrate synthase uses water to split acetyl CoA, CoA leaves acetyl group joined to oxaloacetate, forms citrate water removed from citrate, aconitase arranges atoms to form cis­aconitate aconitase adds water to cis­aconitate, arranges atoms to form isocitrate CO2 removed from isocitrate, then e­’s removed to form NADH & H+ isocitrate dehydrogenase, rearranges atoms to form alpha ketoglutarate succinyl CoA synthetase removes CoA, joins GDP to Pi forms GTP, then arranges atoms to form succinate *some cases, GTP used to form ATP succinate dehydrogenase removes e­’s to form FADH2 and H+ then rearranges atoms to form fumarate FAD+=flavin adenine dinucleotide, similar to NAD+, but can hold more e­’s fumerase adds water to fumarate to produce malate malate dehydrogenase removes e’s to form NADH and H+ then rearranges atoms to form oxaloacetate ***cycle can now start again) 5: Cellular Respiration (continued) FADH & NADH are electron carriers citric acid cycle=molecules carrying electrons oxidative phosphorylation: e­ transport chain and chemiosmosis together lead to ATP synthesis during cellular r. ADP+Pi ­> ATP *know the complexes (5) 1: NADH dehydrogenase 2: succinate dehydrogenase 3: ubiquinol cytochrome c oxidoreductase 4: cytochrome c oxidase 5: ATP synthase electron transport chain: multiprotein complexes numbered I­ IV relay e’s and transport H+ steps: NADH deposits e­’s from glycolysis/citric acid cycle into complex I energy in e­’s allows it to push a H+ to other side of membrane then e­’s are passed on to ubiquinol (Q) FADH2 deposits e­’s into complex II passes the e­’s to Q (gets e­’s from complex I & II) Q transfers e­‘s to complex III , provides energy for pumping out H+ complex III passes e­’s to cytochrome c, which then deposits them to complex IV & complex IV pushes out H+ oxygen accepts e­’s (complex IV), joins with H+ to make H2O  H+ that were pushed are used in chemiosmosis to make ATP chemiosmosis: energy stored in form of H+ gradient across a membrane drives synthesis of ATP ATP synthesis:  (KNOW THE PARTS) rotor spins when H+ flows past down concentration gradient rod/stalk spins w/ rotor, activating knob stator holds knob in place knob is stationery, joins ADP to Pi to make ATP energy yield in aerobic respiration: 26­38 ATP’s/glucose molecule, depending on e­ carrier making energy without oxygen: anaerobic respiration considered cellular respiration b/c e­ transport chain is used difference is that oxygen is not final e­ acceptor fermentation (2 types) creates energy without formal respiration b/c no e­ transport chain is used lactic acid fermentation NADH donates e­’s to pyruvate, then converted to lactate performed by mammals, some bacteria sore muscles, yogurt, sauerkraut, kimchi 2 ATPs alcohol fermentation (KNOW CYCLE) pyruvate converted to acetaldehyde (by removal of CO2) NADH donates e­’s, ethanol formed performed by some fungi, bacteria beer, ethanol fuel, rising bread 2 ATPs evolution & glycolysis evolved very early in history of living things evidence of idea all living things make ATP via glycolysis glycolysis would have allowed prokaryotes to make ATP (even w/ little O2) located in cytoplasm, not using complex membrane bound organelles 6: Genes gene:  sequence of nucleotides that codes for the production of a specific molecule two stages: transcription translation transcription:  to write down/record DNA code is written into mRNA directionality from orientation of backbone molecules transcription steps: promotor sequence in DNA strand tells RMA polymerase where to start transcribing RNA polymerase binds to promotor DNA molecule is uncoiled and separated RNA poly. adds complimentary RNA nucleotides from 5’ to 3’ ends of template strand RNA strand is elongated as RNA poly. moves along DNA template strand translation: ribosomes composed of small and large subunits, which have different functions translation steps: mRNA leaves nucleus (after transcription) & finds a ribosome series of 3 nucleotides on mRNA form codon (complimentary to anticodon on tRNA) each codon corresponds to amino acid, sometimes more than 1 a.a. for same a.a. (one codon NEVER codes more than one amino acid) mRNA is moved in ribosome by small subunit, tRNAs ­> codon (beg w start codon, AUG) large subunit joins amino acids into polypeptide, which “grows” translation stops when arrive at stop codon (UAA,UAG,UGA), then protein released 7: Population Ecology & Biogeography ecology:  study of organisms and their interactions with living things & non­living things biogeography: study of distributions of species in space & time ecological levels of organization: individual (one animal) population (all of that animal in area) community (ALL species in area) ecosystem (ALL species & non­living things in area) biome (major life zone) biosphere (whole planet) sunlight intensity on surface depends on tilt of planet: equator hit directly, HIGH heat & light per unit area poles hit indirectly, LOW heat & light per unit area hadley cells: intense energy striking equator starts air circulation & precipitation patterns warm, wet air rises from equator, releases moisture, creating wet climate dry air falls( 30 deg N and S), absorbing moisture from land, creating dry climate temperature climates 30­60 degrees polar climates >60 degrees seasonality: tilt of planet causes variation in high and temperature bodies of water: carries warm/cold currents, moderate temps because water temperature changes slower  than land temp mountains: moisture dumped on one side, leaves dry conditions on other side (rain shadow) terrestrial biomes: tropical forest near equator avg temp 77­84 little seasonal temperature variation 59’’­157’’ annual rainfall (constant) high biodiversity savana near equator avg temp 75­84 higher seasonal temperature variation 12’’­20’’ annual rainfall, pronounced dry season characterized by scattered trees, large grazing mammals temperate grassland mid­latitudes, continental interiors temp seasonal; winter 14, summer 86 12’’­39’’ annual rainfall, low winter, high summer grasses are dominant plants (1’’­6.5’ tall) characterized by large grazing mammals desert near 30 N & S (continental interiors) temperature varies; <­22 in cold deserts, >122 in hot deserts annual rainfall <12’’ cacti & succulents are dominant plants low overall biodiversity temperate broadleaf forest mostly in mid­latitudes in northern hemisphere, smaller areas in southern  hemisphere temperature seasonal; 32 in winter, 95 in summer annual rainfall 28”­79” deciduous trees dominant (oak, hickory, maple) many mammals hibernate in winter tundra near poles temperature range <­22 in winter, <50 in summer annual precipitation 8”­49” mosses, small grasses dominate migratory species characteristic (birds & caribou) 8: Population Ecology & Biogeography (continued)  limits to geographic distribution: factors include ecological interactions and evolutionary interactions dispersal movement of individuals away from center of origin/high population density biotic factors interactions with other living things (predators, lack of prey/food, competition) *DESERT BIOME IN A RAIN SHADOW abiotic factors interactions with climate, landscape, water, soil, sunlight population ecology: study of how biotic & abiotic factors affect density, dispersion, & size of populations density: number of individuals/unit area/volume (birth, death, immigration, & emigration) dispersion: pattern of spacing individuals within population (behavior, physiology, enviro) either uniform or randomly survivorship curve: graphical representation of demography type 1: high death rate late in life (large mammals) less frequently reproduce, few large offsprings type 2: death rate even throughout life (lizards, annuals) type 3: high death rate early in life (insects, marine invertebrates) frequently reproduce, many small offsprings per capita birth rate: number of offspring produced by average member of population in given unit of time r=b­m r>0 = GROWING population r<0 = SHRINKING population r=0 = rates EQUAL exponential population growth: unlimited food access (J curve) logistical population growth:  carrying capacity (S curve) carrying capacity (K):  maximum population size environment can support life history: organism’s traits that affect its schedule of reproduction age at first reproduction/maturity how often organism reproduces how many offspring produced/reproductive episode frequency of reproduction number of offspring investment in parental care r­selection: when species that live in low population density tend to maximize reproductive success  by producing many small offspring with little parental investment k­selection: when species that live in high population density tend to live near the carrying capacity  of the environment (K), they produce fewer large offspring with high parental  investment 9:  density­independent: birth/death rates that are not affected by population density density­dependent: birth/death rates that are affected by population density 


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