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Chapter 8 to 13 for Exam 2

by: Biodoumoye Bokolo

Chapter 8 to 13 for Exam 2 BY 123

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Test Material for Biology Exam 2
Introductory Biology 1
Dr. Raut
Class Notes
Campbell Biology




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This 40 page Class Notes was uploaded by Biodoumoye Bokolo on Thursday July 14, 2016. The Class Notes belongs to BY 123 at University of Alabama at Birmingham taught by Dr. Raut in Summer 2016. Since its upload, it has received 16 views. For similar materials see Introductory Biology 1 in Biology at University of Alabama at Birmingham.


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Date Created: 07/14/16
BIO EXAM 2 MATERIAL CH.8 Metabolism: totality of an organism’s chemical reactions manages the material and energy resources of a cell -stored energy becomes available to do the work Metabolic Pathway: starts with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product biochemical pathways enable cells to release chemical energy from food molecules and use the energy to power life’s processes each step is catalyzed by a specific enzyme catabolic pathways: degradative process; breakdown pathway; CELLULAR RESPIRATION (glucose is broken down in the presence of oxygen to CO 2nd water) -energy that was stored becomes available to do work once broken down -bonds are broken and formedenergy is released and products have lower energy than reactants (-G) -“downhill” anabolic pathway: consumes energy to build more complicated molecules from simpler ones -biosynthetic pathway -“uphill” Bioenergetics: study of how energy flows through living organisms Energy: capacity to do work/cause change ability to rearrange a collection of matter -life depends on this ability to transform energy from one form to another Kinetic energy: energy of motion -heat/thermal energy: KE associated with random movement of atoms/molecules -light energy Potential energy: energy matter possesses because of its location or structure -molecules possess PE because of their electron arrangement between their bonds -Chemical energy: PE available for release in a chemical reaction Thermodynamics Thermodynamics: study of energy transofrmations that occur in a collection of matter system: the matter under study surroundings/universe: everything outside the system isolated system: unable to exchange either energy or matter with its surroundings open system: energy and matter can be transferred between the system and its surroundings -organisms are open systems!! They absorb energy (light/chemical) and release energy (heat) First Law of Thermodynamics: energy can be transferred/transformed, but cannot be created or destroyed ”principle of conservation of energy” Second Law of Thermodynamics: every energy transfer or transformation INCREASES the ENTROPY of the universe during energy transfer/transformation, some energy becomes unavailable to do work; it is partially converted to heat energy (associated with random movement of atoms/molecules) this loss of usable energy makes the universe more DISORDERED/RANDOM=ENTROPY Entropy of the universe appears as increasing amounts of heat and less ordered forms of matter for a process to occur on its own (spontaneously) it must increase the entropy of the universe -spontaneous process: a process that can occur without the input of energy; energetically favorable; increases the entropy of the universe for a process to occur spontaneously, it must INCREASE the ENTROPY of the universe -nonspontaneous: cannot happen without the input of energy; NOT energetically favorable Biological Order and Disorder Although organisms create more ordered structures from more random starting materials, but they also take in organized forms of matter and energy from their surroundings and replace them with less ordered forms an animal obtains starch and protein from the food it eats, then breaks it down, releases CO 2nd water, which are small molecules that have less PE than the food did Energy flows into an ecosystem as light and exits as heat The entropy of a PARTICULAR system (i.e. an organism) may actually DECREASE, as long as the TOTAL entropy of the universe (system + surroundings) INCREASES Free Energy Change, ∆G Gibbs free energy: portion of a system’s energy that is available to do work when temperature and pressure are uniform throughout the system; a measure of a system’s instability/tendency to move to a more stable state H=enthalpy T=absolute temp(K) S=entropy: ∆G=∆H-T∆S -equation can be used to determine whether a process is spontaneous/energetically favorable -∆G must be negative to be spontaneous spontaneous changes can be harnessed to do work ∆G=∆G final - ∆G initial -∆G can be negative only when a process involves a LOSS of free energy during the change from initial to final state state of maximum stability = equilibrium no further net change -as a reaction proceeds toward equilibrium, the free energy of the reactants and products decreases -for a system at equilibrium, G is at its lowest possible value for that system **a process is spontaneous and can perform work only when it is moving toward equilibrium** Exergonic Reaction: proceeds with a net release of free energy and ∆G is negative magnitude of ∆G for an exergonic reaction represents that maximum amount of work the reaction can perform the greater the decrease in ∆G, the more work that can be done products of an exergonic reaction are like the “exhaust” of a process that tapped the free energy stored in bonds -breaking bonds does not release energy, but it’s rather the PE that can be released when new bonds are formed after the original bonds break DRAWING: Endergonic Reaction: absorbs free energy from its surroundings, ∆G is positive, and reactions are nonspontaneous because energy is required to drive the reaction collecting energy is endergonic, then using/releasing it is exergonic DRAWING: Equilibrium & Metabolism Reactions in an isolated system eventually reach equilibrium and can then do no work a cell that has reached equilibrium is dead because metabolism as a whole is NEVER at equilibrium, this is one of the defining features of life!! -there is a constant flow of materials in and out of the cell, which keeps metabolic pathways from ever reaching equilibrium -made possible by using products as reactants for the next step (instead of the products just accumulating), and wastes are expelled from the cell -glucose and oxygen at the top of the hill and CO 2nd water at the downhillas long as we have a constant supply of glucose and oxygen and can expel CO and water as waste, our cells 2 never reach equilibrium ATP powers cellular work by coupling exergonic reactions with endergonic reactions 3 main kinds of work: Chemical work: pushing of endergonic reactions (which don’t occur spontaneously) to synthesize polymers from monomers, etc. Transport work: pumping of substances across membranes against the direction of spontaneous movement Mechanical work: i.e. beating of cilia, contraction of muscle cells, etc. Cells manage their energy resources via energy couplingusing an exergonic process to drive an endergonic one -ATP does this, and acts as the immediate source of energy that powers cellular work ATP (Adenosine Triphosphate): contains 3 phosphate groups, ribose sugar, and nitrogenous base adenine the bonds between the phosphate groups can be broken by hydrolysis, and an inorganic phosphate leaves the ATP (which then becomes ADP, adenosine diphosphate) ATP + H2OADP + Pi (∆G= -13 kcal/mol under cellular conditions) P bonds are not particularly strong, but the reactants (ATP and water) have higher energy compared to the products (ADP and Pi), so the released energy comes from the chemical change to a state of more stable/lower energy -P groups are negatively charged, so they are repelling each other, which makes this region of ATP highly unstable (like a compressed spring) DRAWING: How Hydrolysis of ATP Performs Work -Energy released by the hydrolysis of ATP can be used to drive reactions that are, BY THEMSELVES, endergonic. But if the positive ∆G of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the OVERALL reaction can still be exergonic. If more energy is released than is used up after hydrolysis of ATP, ∆G is still negative a P group is transferred from ATP to another molecule (the reactant) which becomes the phosphorylated intermediate -the phosphorylated intermediate has HIGHER reactivity (less stable) than the original reactant molecule -ATP and Transport Work: Hydrolysis of ATP leads to a change in a protein’s shape (conformational change) and lets it bind to another molecule (carrier proteins) -ATP and Mechanical work: a cycle where ATP binds to a motor protein, the protein changes shape and ATP is hydrolyzed, releasing ADP and Pi. Then another ATP molecule can come and bind and repeat the sequence so the motor protein can take another step Regeneration of ATP ATP is used continuously, and is a renewable resource can be regenerated by adding a Pi group to ADP -∆G required to phosphorylate ADP comes from exergonic breakdown reactions (catabolic reactions) in the cellshuttling Pi and energy is called the ATP Cycle, which is an energy coupling process (exergonic + endergonic): ADP + Pi  ATP + H2O (endergonic); requires input of energy which comes from other catabolic/exergonic pathways in the cell, especially cellular respiration; plants also use light energy to produce ATP Figure 8.11: ATP Cycle DRAWING: How enzymes speed up metabolic reactions by lowering energy barriers A spontaneous reaction doesn’t mean that it will happen quickly it may occur so slowly that it’s imperceptible Enzyme: a macromolecule that acts as a catalyst: a chemical agent that speeds up a reaction WITHOUT being changed/consumed by the reaction usually proteins without enzymatic regulation, chemical “traffic” would build up a lot because chemical reactions would take so much time to occur; like a bunch of airplanes piled up on the runway because the control tower is taking too long to clear them Activation Energy Barrier -Every chemical reaction involves the breaking and reforming of bonds involves contorting the starting molecule into a highly unstable state (transition state) before the reaction can proceed -in order for the molecules to reach this contorted state, they have to absorb energy from their surroundings -when the new bonds of the product are formed, energy is released as heat and the molecules return to stable shapes that are lower in energy than the contorted state -activation energy is the energy required to get these reactants to their contorted state; aka the amount of energy needed to push the reactants to their energy barrier often supplied as thermal energy since heat causes them to move around more often and more forcefully, increasing collisions; also agitates the atoms within the molecule which increases the likelihood of breakage -this doesn’t work for biological cells! Denaturation, etc. -Free energy of the reactant molecules increases until it they reach their transition (unstable, contorted) state and are “activated” and their bonds can be broken atoms then settle into their more stable/less energy state and energy is released to the surroundings formation of new bonds releases more energy than was invested to break the old bonds (for an exergonic reaction) -Activation energy is the barrier that determines the rate of the reaction the reactants need this amount of energy in order for the reaction to proceed, and the faster they reach it, the faster the reaction -so if the activation energy is lowered, reactants can proceed faster because there isn’t as much of a hill to climb; the bar is dropped; this is what enzymes do! -Enzymes catalyze reactions by lowering the Ea barrier they do NOT: change endergonic reactions to exergonic reactions they DO: hasten reactions that would eventually happen anyway they are very specific, and determine which chemical processes will be going on in a cell at any particular moment Enzyme-Substrate Specificity -Substrate: the reactant an enzyme acts on enzyme + substrate= enzyme-substrate complex -enzyme + substrate  enzyme-substrate complex  enzyme + products the reaction catalyzed by each enzyme is very specific -enzymes are proteins with unique 3D shapes, so specificity of an enzyme comes from its shape (which is a result of its AA sequence) -Active site: the only place where a substrate can bind to an enzyme formed by only a few of the enzyme’s AA’s -the rest of the enzyme provides a framework that determines the actual configuration of the active site specificity of an enzyme comes from its compatible fit between its shapeits active site and the substrate -Enzymes “dance” between different shapes in a DYNAMIC equilibrium slight differences in free energy for each enzyme slightly changes shape to more readily accept/bind to the substrate -encourages chemical group/R-group interactions between the substrate and the active site of the enzyme -induced fit: brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction -Substrate is held in place by weak interactions, H-bonds and ionic bonds R-groups of the few AA’s that make up the active site are the ones that catalyze the conversion of substrate to product; once this happens, the product detaches and the enzyme is free to take in another substrate -enzymes are never changed by the reaction, so they emerge in their original form -they function over and over again in catalytic cycles Most metabolic reactions are reversible, so an enzyme can catalyze a reaction in the forward OR reverse direction, depending on which way has a negative ∆G this depends on the relative concentrations of the reactants and products, so the net effect is always in the direction of equilibrium -remember that a process is spontaneous and can perform work only when it is moving toward equilibrium!! Enzymatic Mechanisms for Lowering Ea/Speeding Up a Reaction -When enzymes have more than one substrate/reactantacts like a dating site, bringing together the two reactants together in the orientation necessary to bind -Stretch the substrate molecules toward their transition-state (high instability/energy) form stressing and bending the chemical bonds that need to be broken in the reaction makes it easier for the bonds to break, reduces the activation energy required for it to happen -it’s easier to rip off a slice of pizza if it’s precut -Provides a microenvironment that is more conducive to a certain kind of reaction than the solution itself i.e. if an active site has acidic AA’s, provides a pocket of low pH that can facilitate proton transfer (H+) -Direct participation of the active site in the chemical reaction brief covalent bonding between substrate and side chain of an AA of the enzyme’s active site -The rate at which an enzyme converts the substrate to product is partly a function of the initial concentration of the substrate the more substrate, the more frequently they access the active sites limited by number of enzymes available; enzyme is saturated when all active sites are engaged -reaction rate then is dependent upon the speed at which the enzyme can convert the substrate to product -rate can only be increased if more enzymes are added -Enzyme activity is also affected by general environmental factors and by other chemicals Temperature and pH: each enzyme works better under certain conditions (optimal conditions) that favor the most active shape for the enzyme -rate will increase up to a point with temperature before denaturation occurs (disrupts H bonds, ionic bonds, and other weak interactions that stabilize the enzyme’s active shape) -optimal pH for most enzymes is between 6-8, but is adapted depending on location to maintain its 3D structurepepsin in the stomach is optimal at a pH of 2 (stomach environment) Cofactors: usually inorganic, can bind tightly permanently or bind loosely and reversibly along with the substrate -zinc, magnesium, iron, copper -why vitamins are so important! -coenzymes: an organic cofactor -cofactors and coenzymes perform crucial chemical functions in catalysis Enzyme Inhibitors Certain chemicals selectively inhibit the action of certain enzymes if it binds covalently, usually irreversible usually bind via weak interactions and inhibition is reversible -competitive inhibitors: imitates the substrate and directly competes for the active site; physically blocks substrates from binding -noncompetitive inhibitors: do not directly compete with the substrate to bind at the active site; they bind to ANOTHER part of the enzyme, which causes the enzyme to change shape this makes the active site less effective at catalyzing the conversion of substrate to product antibiotics are inhibitors; penicillin blocks active site of the enzyme that bacteria use to make their cell walls inhibition is not necessarily a bad thing, and can be used to necessarily regulate enzyme activityselective inhibition Enzyme Evolution -If an enzyme is mutated (different AA than normal), the altered enzyme might have a different function/bind to a different substrate; if this new function benefits the organism, then natural selection would tend to favor the mutated form of the gene Regulation of Enzyme Activity Controls Metabolism A cell can regulate its metabolic pathways by controlling when and where its enzymes are active by switching on/off the genes that encode specific enzymes Allosteric Regulation: where a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site; can inhibit OR stimulate an enzyme’s activity -Molecules that naturally regulate enzyme activity in a cell act like noncompetitive inhibitors (but don’t necessarily always inhibit) they change an enzyme’s shape and active site function by binding to the enzyme somewhere other than the active site via noncovalent interactions -Enzymes that are allosterically regulated are made of 2 or more subunits with their own polypeptide chain/active site the entire complex oscillates between two different shapes, one is active and one isn’t the allosteric regulator (inhibitor or activator) binds to a regulatory/allosteric site that is often near where the subunits join -binding of an ACTIVATOR stabilizes the enzyme in the shape that is catalytically active -binding of an INHIBITOR stabilizes the inactive form of the enzyme -a shape change in one subunit is transmitted to all others, so it will affect the active sites of all subunits ATP binds allosterically to catabolic enzymes, and acts as an inhibitor while ADP functions as an activator of the same enzymes -makes sense because catabolism functions in REGENERATING ATP. If ATP lags behind, then ADP accumulates and therefore ACTIVATES the enzymes that speed up catabolism (production of ATP); so if there’s too much ATP, then it will in inhibit the enzymes that make it Cooperativity: when a substrate binds to one active site in a multi- subunit enzyme and triggers a shape change in ALL the subunits, increasing catalytic activity at the other active sites -amplifies the response of enzymes to substrates because one substrate primes an enzyme to act on additional substrate molecules more readily -allosteric because binding to one site affects catalysis in another active site like when one hemoglobin subunit (out of 4) binds to oxygen, the other 3 subunits increase in their affinity for oxygen -How to identify Allosteric Regulators: they exhibit higher specificity for particular enzymes than inhibitors that bind to the active siteregulatory sites are very distinct between enzymes where inhibitors may be able to bind to multiple active sites DRAWING OF INHIBITORS DRAWING OF ALLOSTERIC REGULATION Feedback Inhibition: a metabolic pathway is switched OFF by the INHIBITORY binding of its end product to an enzyme that acts early in the pathway (negative feedback) like how ATP allosterically inhibits an enzyme in an ATP generating pathway 5 step pathway (Figure 8.21) Specific localization of enzymes within the cell Cellular compartments and structures help bring order to metabolic pathways a team of enzymes used for several steps of a metabolic pathway can be assembled into a multi-enzyme complex -this facilitates the sequence of reactions some enzymes/enzyme complexes can have a fixed location within the cell and act as structural components of certain membranes some enzymes are in solution within certain membrane enclosed eukaryotic organelles that have their own internal environment (i.e. mitochondria) MAJOR CLASSES OF ENZYMES: Oxidoreductase: transfers electrons from one substance to another dehydrogenase Transferase: transfers a chemical group Phosphorylase: transfers a phosphate group to a different substance Kinase: transfers a phosphate group from ATP to a different substance Hydrolase: splits a chemical using H O 2 Phosphatase: removes a phosphate Lipase, sucrose Isomerase: converts one isomer into another Mutase: transfers atoms within a molecule Ligase: Bonds two molecules Synthetase: bonds 2 molecules using ATP Lyase: splits a chemical bond in the absence of H2O Decarboxylase: cleaves a molecule to release CO 2 CH.9 -Electron transfer plays a large role in catabolic pathways -Organic compounds have PE as a result of the arrangement of electrons in the bonds between their atoms cells degrade complex organic molecules that have a lot of PE into simpler waste products that have less energy -some of the energy taken out can be used to do work and the rest is released as heat -Fermentation: partial degradation of sugars or other organic fuel that occurs WITHOUT the use of oxygen -Aerobic Respiration: oxygen is consumed as a reactant along with organic fuel; similar to combustion of gasoline in an enginefood is fuel and CO 2water are exhaust Overall process: organic compounds(usually glucose) + Oxygen  CO + Water + 2 Energy (i.e. ATP & heat) -exergonic, spontaneous (no energy input), products are lower in energy than reactants most prevalent and efficient catabolic pathway most eukaryotic and prokaryotic organisms Anaerobic Respiration: similar process but without oxygen -Cellular Respiration: includes aerobic AND anaerobic but usually refers to the former Redox Reaction=Oxidation and Reduction Transfer of electrons during chemical reactions, which releases energy stored in organic molecules and is ultimately used to synthesize ATP OIL RIG: For electrons, “Oxidation Is Losing, Reduction is Gaining” Oxidation: LOSE e- reducing agent (e- donor) is oxidized Reduction: GAIN e- oxidizing agent (e- acceptor) is reduced Oxidation and reduction always go together they don’t always involve complete electron transfer, can just change the degree to which they are sharing in a covalent bond oxygen is one of the most potent of oxidizing agents Energy must be ADDED to pull an electron away from an atom the more EN, the more energy required electrons lose PE when it shifts from a less EN to a more EN, so the energy that is released can be put to work (ETC chain) Oxidation of Glucose: C 6 12+ 6O  62O + 6H 2 + Ene2gy Organic molecules that have lots of H’s are good fuel sources because their bonds are a source of “hilltop” electrons (like Glucose) the oxidation of glucose transfers electrons to a lower energy state, which frees energy for use in ATP synthesis carbohydrates and fats are the main energy-yielding foods because of the abundance of H’s; the only barrier is the E A Energy that is released all at once cannot be harnessed efficiently-like if a gas tank explodes you can’t drive the car very far glucose and other fuels are broken down in a series of steps that are each catalyzed by their own enzyme Each electron travels with a proton (Hydrogen atom) not transferred directly to Oxygen but are oassed to an electron carrier -a coenzyme called NAD+ (derivative of Niacin) acts as an oxidizing agent (and is reduced) in order to carry electronsworks with dehydrogenase enzymes, which transfer electrons from one substance t+ another reduced to NADH + H most versatile electron acceptor Electron Transport Chain (ETC): breaks the fall of electrons into a series of energy releasing steps; consists of a number of molecules (mostly proteins) that are built into the membrane of the mitochondria (plasma membrane of prokaryotic cells) NADH shuttles electrons to the top of the chain, and EN Oxygen pulls them (and Hydrogen nuclei) down to the bottom and ends up forming water 2H + ½ O 2H O 2 this electron transfer is an exergonic reaction; as electrons cascade down the ETC small amounts of energy are released in a series of redox reactions that can be used by the cell Stages of Cellular Respiration 1. Glycolysis: “sugar splitting;” occurs in the cytosol; anaerobic process; breakdown of glucose into 2 pyruvates; energy investment phase: 2 ATP’s are used in steps 1 & 3 -Step 3: Phosphofructokinase: transfers a second P-group to the other end of the sugar; key step for regulation of glycolysiscommits to glycolysis forms Fructose 1,6-bisphosphate which is then split in half into isomers DHAP and Glyceraldehyde 3-phosphate (G3P) which is the substrate required for the next step -these isomers are constantly switching between their 2 forms, so one the original G3P is used up, DHAP will convert back to G3P to maintain equilibrium (LeChatelier’s Principle), and is immediately used up itself -so each G3P ends up being converted to Pyruvate (2 total) energy payoff phase -Step 6: Starting at this step/phase we are working with 2 G3P’s; NAD+ oxidizes EACH G3P and is reduced to NADH (1 per molecule, 2 total) -Step 7 & 9: 1 ATP is produced at steps 7 & 9, 2 total ATP produced PER G3P molecule, and there are 2 G3P molecules so that’s 4 TOTAL ATP since 2 ATP were used in energy investment phase, glycolysis results in NET 2 ATP CREATED -Final step: 2 Pyruvate molecules are formed from the 2 G3P molecules + *Total Products of Glycolysis: Net 2 ATP, 2 pyruvates, 2 NADH + H *substrate phosphorylation: ATP is formed directly by an enzyme that transfers a phosphate group from a substrate molecule to ADP (instead of an inorganic phosphate like in ETC); the substrate molecules are intermediates that are generated during the catabolism of glucose DRAWING: Transition Step: Pyruvate Oxidationoccurs in mitochondrial matrix 2 pyruvates enter mitochondrial via active transport/transport protein 2 pyruvates are converted to 2 Acetyl CoA via a multi-enzyme complex -Carboxyl group is fully oxidized and is removed/given off as a molecule of CO 2 + -Remaining molecule is oxidized by NAD to form 1 NADH per Pyruvate -Finally, Coenzyme A is attached to form Acetyl CoA *Total Products of Pyruvate Oxidation: 2 NADH, 2 CO , and 2 2 Acetyl CoA DRAWING: 2.Citric Acid Cycle/Krebs Cycle: remember that each pyruvate goes through the Krebs Cycle, so this occurs twice! Acetyl CoA (2 C’s) combines with Oxaloacetate (4 C’s) to form Citrate, 6 C’s (hence the Citric Acid cycle) Water is removed and then re-added to form Isocitrate -Isocitrate is oxidized and reduces one NAD to NADH and one CO 2s released -Ketoglutarate is formed (5 C’s), and then releases a second CO 2 and another NAD is reduced to NADH Succinyl CoA is formed (4 C’s) -inorganic phosphate displaces CoA and phosphorylates GDP to GTP donates that phosphate to ADP to form 1 ATP (substrate- level phosphorylation) Succinate is formed, oxidized, and reduces 1 FAD to FADH 2 Fumerate is formed, water is addedforms Malate + Malate is then oxidized and reduces a third NAD to NADH Oxaloacetate (4 C’s) is reformed and ready to be put to use again with the second Acetyl CoA molecule *Total Products of Krebs Cycle: 4 CO , 6 2ADH + H , 2 FADH , 2 2 ATP DRAWING: 3.Electron Transport Chain (ETC): a collection of molecules embedded in the inner membrane (Cristae) of the mitochondria (plasma membrane in prokaryotes); the cristae increase SA to provide more space for thousands of copies of the ETC most components are proteins and form complexes numbered I – IV. -prosthetic groups are non-protein components that are tightly bound to these proteinsthey are essential for the catalytic functions of certain enzymes along the ETC, electron carriers alternate between reduced and oxidized states as they accept and donate electrons electrons removed from glucose/citric acid cycle are transferred from NADH to Complex I contains FMN prosthetic group and FeS protein (electron is passed from FMN to the FeS protein) within Complex I Electrons are then passed from FeS protein to ubiquinone (aka Q or CoQ) -a small hydrophobic molecule; only ETC component that is NOT a protein -individually MOBILE within the membrane remaining electron carriers are cytochromesproteins that have a heme prosthetic group (Fe containing) -ETC has several types of cytochromes that differ in protein type/heme group -last cytochrome in chain is cyt 3 which is very EN & passes electrons to oxygen FADH 2s another source of electrons and adds them to the ETC from within Complex II at a lower energy level than NADH does ETC makes NO ATP DIRECTLY oxidative phosphorylation: energy released at each step of the ETC is used to make ATP from ADP; inorganic phosphate is added to ADP + Major function is also to create H gradientuses exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane from mitochondrial matrix into intermembrane space (H+ can come from oxidized NAD and FADH or other H’s around) 4. Chemiosmosis: energy coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work; energy stored as an H gradient is used to drive the synthesis of ATP; “osmosis” refers to the flow of H ions across a membrane ATP Synthase: protein complex/enzyme that actually makes ATP from ADP and inorganic phosphate -populates the inner membrane of the mitochondria -uses energy of existing H ion gradient (created by ETC) to power ATP synthesis -protons flow into binding sites of the rotor that cause it to spin in a way that catalyzes ATP production from ADP and Pi active transport at certain points along the ETC, electron transfer causes H+ to be taken up from the mitochondrial matrix and is deposited in the intermembrane space (in eukaryotes) -H+ gradient that results is called a proton-motive force: this is the PE energy stored in the form of a proton electrochemical gradient, generated by the pumping of H+ across the membrane plants use chemiosmosis to drive ATP synthesis but uses light energy instead of chemical energy to drive the flow of electrons/creation of H+ gradient DRAWING of ETC+CHEMIOSMOSIS We aren’t sure the exact number of ATP produced because: we don’t know exactly how many H’s we need to drive ATP Synthase NADH is not easily welcomed into the membrane, so it depends on the type of shuttle used to transport electrons (NAD+ or FADH) -FAD: 1.5 ATP -NAD+: 2.5 ATP use of proton-motive force is not always powering JUST ATP Synthase *90% of ATP comes from oxidative-phosphorylation (ETC) *10% ATP comes from substrate-level phosphorylation (Glycolysis, Krebs) Aerobic Respiration & Fermentation -ETC is used in anaerobic respiration but not in fermentation Oxygen is not the final electron acceptor; instead use atoms like S -i.e. sulfate-reducing marine bacteria -Oxidation does not need to involve oxygen, it only refers to a loss of electrons from an electron acceptor -Fermentation harvests chemical energy without using oxygen/ETC essentially an extension of glycolysis that allows continuous generation of ATP by substrate-level phosphorylation + requires a sufficient supply of NAD to accept electrons during glycolysis consists of glycolysis and reactions that regenerate NAD (which can be resued to) -NADH transfers electrons to Pyruvate/pyruvate derivatives, which can then be reused to oxidize sugar by glycolysis alcohol fermentation: pyruvate is converted to ethanol in two steps -Step 1: CO2 is released from Pyruvate and is converted to acetaldehyde -Step 2: Acetaldehyde is reduced by NADH to ethanol this regenerates NAD+ supply needed for continuation of glycolysis -used to make wine, bread DRAWING lactic acid fermentation: pyruvate is reduced DIRECTLY by NADH to form lactate as an end product, with no release of CO2 -used to make cheese, yogurt -also in human muscle cells (when we can’t keep up with oxygen demand) DRAWING: Fermentation vs. Anaerobic Vs. Aerobic Respiration All 3 use glycolysis and form pyruvate with a net production of 2 ATP by substrate-level phosphorylation All3 use NAD as the oxidizing agent that accepts electrons during glycolysis Final electron acceptor differs fermentation: pyruvate/other organic molecule anaerobic: EN atom besides O; uses ETC aerobic: oxygen uses ETC Obligate s: carry out only fermentation or anaerobic respiration cannot survive in the presence of oxygen Facultative Anaerobes: can survive under aerobic or anaerobic conditions (can use either respiration or fermentation) our muscle cells -Under aerobic conditions: pyruvate can be converted to Acetyl CoA and oxidation continues into Krebs cycle -Under anaerobic conditions: lactic acid fermentation occurs: pyruvate is diverted from citric +cid cycle and serves as an electron acceptor to recycle NAD Evolutionary significance: ancient prokaryotes are thought to have used glycolysis long before the presence of oxygen in earth’s atmosphere (hence why glycolysis is an anaerobic process) early prokaryotes may have generated ATP exclusively from glycolysis How Glycolysis and Krebs Cycle connect to other metabolic pathways -Products produced when you breakdown proteins and fats may not be similar to glucose, but can be similar to the intermediates created during glycolysis/Krebs Cycle; so they just start cellular respiration there  “skip” glycolysis DRAWING: -Compounds formed during glycolysis and Krebs cycle can be diverted int anabolic pathways if needed Regulation of Cellular Respiration via Feedback Mechanisms Feedback inhibition: the end product of anabolic/catabolic pathways inhibits the enzyme that catalyzes an early step of the pathway prevents needless diversion of key metabolic intermediates from uses that are more urgent/doesn’t waste energy or material Phosphofructokinase: catalyzes Step 3 of glycolysis; commits substrate irreversibly to glycolysis by controlling this step, the cell can speed up/slow down the entire catabolic process the “pacemaker” of cellular respiration allosteric enzyme with TWO receptor sites -one functions as the actual active site -the other is an allosteric site where the amounts of ADP/AMP or ATP/Citrate can bind to regulate ADP/AMP serve as allosteric activators of PFK; if ATP is being converted to ADP/AMP faster than the cell is regenerating ATP, then ADP/AMP will will bind and speed up glycolysis/citric acid cycle ATP/Citrate are allosteric inhibitors; if too much accumulates in the cell they will bind to inhibit glycolysis/citric acid cycle CH.10 Photosynthesis (PS) : conversion of light energy from the sun to chemical energy that is stored in sugar and other organic molecules Autotrophs: “self-feeders;” they sustain themselves without eating anything derived from other living beings produce organic molecules from CO an2 other inorganic raw materials obtained from the environment almost all plants -specifically photoautotrophs: use light as an energy source Heterotrophs: obtain organic material from other organisms, consumers decomposers: consume the remains of dead organisms by decomposing and feeing on organic litter -most fungi and many prokaryotes completely dependent on photoautotrophs for food and oxygen Light Reactions (LR)solar energy is captured and transformed to chemical energy Calvin Cycle (CC)chemical energy is used to make organic molecules of food All green parts of a plant have chloroplasts, but leaves are major sites of PS in most plants Chloroplasts are found mainly in cells of Mesophyll: tissue in interior of leaf -Mesophyll cells: contain 30-40 chloroplasts  Chloroplasts have a double membrane surrounding its stroma (dense fluid) -suspended in stroma are Thylakoids: sacs that segregate the stroma from the Thylakoid space inside the sacs; stacked in columns called grana Chlorophyll: green pigment that gives leaves color; resides in Thylakoid membranes; absorb light energy that drives the synthesis of organic material Stomata: microscopic pores through which CO enters 2eaf and O exits lea2 Water absorbed by roots is delivered to leaves in veins; leaves also use veins to export sugar to roots and other non-photosynthetic parts of the plant PS Equation: 6 CO 2 12 H O +2Light Energy  C H O + 6 6 12 6 2 *direct product is actually a 3 C sugar that can be used to make glucose *reverse of cellular respiration; CR also occurs in plant cells!! Splitting of Water O 2iven off by plants comes from water and NOT CO2! chloroplast splits water into hydrogen and oxygen as a source of e- from the H atoms, releasing O as a 2yproduct (only the O’s from H O 2 show up in O )2 -all photosynthetic organisms need a source of Hydrogen, but varies from species to species (H S in sulfur bacteria, H O in 2 2 plants, etc.) PS and CR both involve redox reactions PS reverses the flow of e- -water is split and e- are transferred along with H ions from the water to CO2, reducing it to sugar REQUIRES energy [e- increase in PE as they move from a more EN molecule (H O)2to a less EN molecule (sugar)] -energy boost is provided by LIGHT 2 Stages of PS: Intro PS is 2 processes, each with multiple steps 1.Light Reactions (photo part of PS: convert solar energy to chemical energy happens in THYLAKOIDS water is split, providing e- and p+ source and giving off O2as a byproduct Transfer of e- to NADP+ and reduces it to NADPH generate ATP using chemiosmosis to carry out photophosphorylation (addition of a P group to ADP) NO SUGAR 2.Calvin Cycle (synthesis part of PS) happens in STROMA incorporates CO f2om the air into organic molecules already present in the chloroplast -carbon fixation: initial incorporation of carbon into organic compounds reduces fixed carbon to carb by the addition of e- from the LR’s and NADPH also requires ATP (also provided by LR) to convert the CO t2 a carb aka Dark Reactions because CC requires NO LIGHT directly; still occurs during the daytime because that’s when the LR can provide ATP and NADPH Light Reactions Light= electromagnetic energy, it travels in waves Wavelength: distance between crests of electromagnetic waves -the SHORTER the wavelength, the MORE energy of a photon (inversely related) Electromagnetic Spectrum: entire range of radiation Visible Light: 380nm-750nm -drives photosynthesis -white light: mixture of all wavelengths of visible light Light behaves like discreet particles, called photonshave a fixed quantity of energy (inversely related to wavelength) Pigments: substances that absorb visible light different pigments absorb light of different wavelengths -those that absorb disappear, those reflected are what we see -if all wavelengths are absorbed, it appears black Light can perform work in chloroplasts only if it’s absorbed by pigments 3 types of pigments in chloroplasts 1.Cholorophyll a: participates DIRECTLY in light reactions -absorbs violet-blue and red light, so these wavelengths work best for PS -green is least effective because it is reflected; appears blue-green 2.Chlorophyll b: accessory pigment; slight structural difference between chlorophyll a -absorbs slightly different wavelengths of red and blue -appears olive green 3.Carotenoids: accessory pigment; hydrocarbons -absorbs violet and blue-green light, -appears orange/yellow (fall colors) -function as photoprotection: absorb and dissipate excessive light energy that would otherwise damage chlorophyll or interact with oxygen, forming reactive molecules dangerous to the cell -phytochemicals: compounds with antioxidant properties action spectrum: profiles the relative effectiveness of different wavelengths of radiation in driving PS Excitation by Light -When a molecule absorbs a photon of light, one of the molecule’s e- is elevated to a higher energy orbital/excited state excited e- can’t stay there long (unstable), so they drop back down to their gorund state and release their exess energy as heat -in isolation, when the e- don’t have anywhere to go (not absorbed by the e-acceptor in reaction-center complex), as they fall back they release heat AND give off photonsfluorescence -The only photons absorbed are those whose energy is exactly equal to the difference between the ground state and an excited statevaries from one molecule to another so this is why pigments have a unique absorption spectrum Photosystems A photosystem is composed of: Reaction-center complex: organized association of proteins holding a special pair of chlorophyll a molecules Light-harvesting complex: various pigments (include chlorophyll a/b, carotenoids) bound to proteins -number and variety og pigments enable a photosystem to harvest light over a larger surface area and larger portion of the spectrum than any single pigment molecule alone. - “antenna” for the reaction-center complex (for photons) When a pigment molecule absorbs a photon, the energy is transferred from pigment molecule to pigment molecule within the light-harvesting complex until it is passed into the reaction-center complex reaction-center complex contains the pair of chlorophyll a molecules, which accept the energy from the light-harvesting complex -this enables them to boost one of their e- to the primary e- acceptor (capable of accepting the e- and becoming reduced) REDOX REACTION Thylakoid membrane is populated by 2 types of photosystems: 1.Photosystem I (PSI): discovered first; functions second P700 pair of chlorophyll a molecules; absorb this wavelength best -almost identical to those in PSII, but differ in the proteins they are associated with in the thylakoid membrane (affects e- distribution) 2.Photosystem II (PSII): discovered second; functions first P680 pair of chlorophyll a molecules; absorb this wavelength best Linear Electron Flow Occurs during light reactions of PS; takes place in Thylakoid membrane 1. Photon of light strikes pigment molecules in PSII, boosting one of its electrons to a higher energy level; as it falls back to its ground state, an electron in a nearby pigment molecule is simultaneously raised to an excited state; process continues until it reaches the P680 pair of chlorophyll a molecules in PS reaction center complex and excites an electron in the pair to a higher energy state 2. Electron is transferred from excited P680 to primary electron acceptor -P680+ 3. An enzyme catalyzes the splitting of a water molecule into 2 electrons, 2 hydrogen ions, and an oxygen atom; electrons are supplied one by one to the P680+ pair, replacing the one transferred to the primary electron acceptor -P680+ is the strongest biological oxidizing agent known -water provides constant flow of e- to replace those being passed to primary electron acceptor -H+ are released into the thylakoid lumen -Oxygen atom immediate combines with another oxygen atom generated by the splitting of another water forms byproduct O 2 4. Each photo-excited e- passes from primary electron acceptor of PSII to PSI via an electron transport chain -made of up e- carrier plastoquinone (Pq), a cytochrome complex, and protein plastocyanin (Pc) 5. Exergonic fall of e- to a lower energy level provides energy for ATP synthesis -as e- are passed through cytochrome complex, H+ are pumped into the thylakoid lumen, contributing to the proton gradient (used in chemiosmosis) 6. Simultaneously, light energy has been transferred via light- harvesting complexes of PSI pigments to reaction-center complex, exciting the P700 pair and sending one of its e- to the PSI primary electron acceptor -P700+ then accepts e- passed from ETC/PSII 7. Photoexcited e- are passed in a series of redox reactions from primary e- acceptor in PSI down a second ETC through the protein ferredoxin (Fd) -this ETC does NOT produce ATP/proton gradient 8. the enzyme NADP+ reductase catalyzes the transfer of e- from Fd to NADP+ -needs 2 e- to reduce to NADPH (has higher energy level than water, so its e- are more readily available for the reactions of the Calvin cycle) -also removes an H+ form stroma *the light reactions use solar power to generate ATP and NADPH, which provide chemical energy and reducing power to the carbohydrate- synthesizing reactions of the Calvin cycle* DRAWING Cyclic Electron Flow -Alternative pathway that uses PSI but NOT PSII -Short circuit: electrons cycle back from Fd to the Cytochrome complex and from there continue on to P700 chlorophyll a molecules in PSI reaction-center complex NO production of NADPH and NO release of oxygen produces ATP -Found in photosynthetic bacteria (purple sulfur bacteria) also found in photosynthetic species that posses both photosystems -some prokaryotes (cyanobacteria) and eukaryotic photosynthetic species -Beneficial role: may be photoprotective for plants that grow in intense light Chemiosmosis in Mitochondria vs Chloroplasts Chloroplasts and mitochondria both generate ATP by chemiosmosis have an ETC assembled in a membrane that pumps protons across the membrane as electrons are passed through a series of carries that are progressively more EN -transform redox energy to a proton-motive force have ATP synthase complex that couples the diffusion of hydrogen ions own their gradient to the phosphorylation of ADP Cytochromes are similar (iron-containing proteins) Oxidative phosphorylation vs photophosphorylation: OP: e- come from organic molecules; PP: e- come from water Chloroplasts don’t need molecules from food to make STP, use photosystems to capture light energy and use it to drive the electrons from water to ETC -transform light energy into chemical energy in ATP -mitochondria use chemiosmosis to transfer chemical energy from good to ATP Inner membrane of mitochondria pumps protons from matrix to intermembrane space (reservoir of H+ ions) protons diffuse down their gradient from intermembrane space through ATP synthase to the matrix Thylakoid membrane pumps protons from stroma into thylakoid space (reservoir of H+ ions) ATP is synthesized as H+ ions diffuse from thylakoid space back to the stroma through ATP synthase complex -ATP forms in the stroma (along with NADPH), where CC takes place DRAWING: Calvin Cycle (CC) Similar to Krebs cycle in that a starting material is regenerated after molecules enter and leave the cycle CC is anabolic, forming carbs and consuming energy (whereas Krebs is catabolic) Carbon enters as CO a 2eaves in the form of glyceraldehyde 3-phosphate (G3P), a 3 C sugar spends ATP and consumes NADPH as reducing power for adding high energy e- to make 1G3P per 3 cycles -fixes 3 CO 2olecules 3 PHASES: 1.Carbon Fixation: CC incorporates 3 CO mole2ules, one at a time by attaching it to a 5 C sugar Ribulose Bisphosphate (RuBP); the entire cycle must proceed 3 times, once PER CO for2a total of 3 RuBP’s enzyme used is Rubisco (most abundant protein on Earth/in chloroplasts) Product: 6 C intermediate that so unstable that it immediately splits in HALF, forming 2 molecules of 3-phosphoglycerate (3 C molecule) PER CO 26 total) 2.Reduction: each of the six 3-phosphoglycerate molecules is phosphorylated via ATP created from light reactions; spends 6 ATP’s total (2 per pair of 3-phosphoglycerate molecules per each CO ) 2 then reduced via NADPH (6 total), causing them to lose a P group, transforming into G3P -6 total G3P’s: two 3 –phosphoglycerates are phosphorylated and reduced per CO mo2ecule (3 total) we started with 15 C’s worth of carbs (3 molecules of 5 C RuBP; one molecule per CO ) 2ut now have 18 C’s worth (6 molecules of G3P of 3 C’s) so only ONE G3P molecule exits to be used by the plant cell, the rest have to be recycled in order to regenerated the 3 molecules of RuBP 3.Regeneration of the CO acceptor (RuBP): C skeletons of 5 remaining 2 G3P’s are rearranged into 3 molecules of RuBP 3 more ATP molecules are spent doing this *neither light reactions nor CC alone can make sugar from CO ; NO 2ugar is made, but the starting materials emerge from CC* *for net synthesis of one G3P molecule, CC consumes 9 ATP and 6 NADPH* DRAWING: Alternative Mechanisms of Carbon Fixation Dehydration is a problem in many plantsmetabolic adaptations CO required for PS enters via stomata 2 also the avenue of transpiration (evaporation of water) -plants will close stomata, but this leads to lower CO 2 concentration and increased O c2ncentration, which can lead to photorespiration C 3lants: first organic product of carbon fixation is a 3C compound (rice, wheat, soybeans, etc.) on hot dry, days, produce less sugar because of declining levels of CO 2tarves the leaf rubisco binds to O2 instead and produces a 2C compound instead of a 3 C compound -peroxisomes & mitochondria rearrange and split this compound to release CO 2 called photorespiration because it occurs in the light (photo) and consumes O whi2e producing CO (respi2ation) -consumes instead of produces ATP (energetically expensive process) and produces no sugardecreases photosynthetic output -this process is a metablic relic from a time where the atmosphereon Earth had less O and 2ore CO than it2does today C 4lants: forms a 4 C product after carbon fixation; has a unique leaf anatomy; PHYSICAL SEPARATION of PS cycles two distinct types of cells: 1.Mesophyll cells: loosely arranged cells b/t leaf surface and bundle-sheath cells Light reactions take place 2.Bundle-Sheath cells: arranged into tightly packed sheaths around the veins of the leaf CC takes place 1. PEP Carboxylase (only in mesophyll cells), adds CO to PEP,2forming oxaloacetate PEP has higher affinity for CO t2an does rubisco for O , so 2t can fix carbon efficiently when rubisco cannot (hot/dry climate when stomata are partially closed and CO concentration decreases/O concentration 2 2 increases) 2. Mesophyll cells export their 4 C products to bundle-sheath cells 3. Within Bundle Sheath cells, 4 C compound releases CO which is re- 2 assimilated into organic material by rubisco and the CC also regenerates pyruvate (3 C’s) which is transported to Mesophyll cells where ATP is used to convert pyruvate to PEP, allowing the cycle to continue -this ATP is the “price” of concentrating CO ins2de the Bundle Sheath cells (so Bundle Sheath cells carry out cyclic electron flow; also because they don’t have PSII) -Mesophyll cells of a C p4ant pump CO into 2he BS, keeping the CO 2 concentration in the Bundle Sheath cells high enough for rubisco to bind CO 2 rather than oxygen -PEP carboxylase and PEP are like a CO conc2ntration pump that is powered by ATP CAM Plants: succulent (water-storing) plants; open their stomata at night and close them during the day helps conserve water and prevents CO from e2tering leaves take up CO a2 night and incorporate it into organic acidscrassulacean acid metabolism (CAM) -Mesophyll cells store the organic acids theymae during the night in their vacuoles until the morning when the stomata close during the day, light reactions can supply ATP and NADPH for the CC, CO 2s released from the organic acids made the night before to be incorporated into sugar similar to C4plants in that CO i2 incorporated into organic intermediates before it enters the CC -Difference: C pl4nts are separated structurally, CAM plants are temporally separated (happens within same cell but at different TIMES) CHAPTER OVERVIEW: Light reactions capture solar energy and use it to make ATP and transfer electrons from water to NADP+ to form NADPH. CC uses the ATP and NADPH to produce sugar from CO .2The energy that enters the chloroplasts as sunlight becomes stored as chemical energy in organic compounds sugar made supplies the plant with energy and carbon skeletons for the synthesis of all the major organic molecules of plant cells -green cells are the only autotrophic parts of the plant, the rest depends on the organic molecules exported from leaves via veins (sucrose, disaccharide) most plants make more organic material than they need, so they store it as starch PS is the process responsible for presence of oxygen on Earth There’s no other chemical process that can match the output of PS no process more important to the welfare of life on Earth CH.12 -Cell division: reproduction of cells division of one prokaryotic cell reproduces an entire organism, same for a unicellular eukaryote enables a multicellular eukaryote to develop from a single cell functions not only in reproduction, but also in renewal and repair Cell cycle: life of a cell from the time it’s first formed (from a dividing parent cell), until its own division into 2 daughter cells -passing identical genetic material to cellular offspring is a crucial function of cell division -Genome: a cell’s genetic information/endowment of DNA prokaryotes usually have one, eukaryotes usually have a number of DNA molecules -DNA is packaged into chromosomes (named because they take up certain dyes, “chromo”) eukaryotic chromosomes consist of one long, linear DNA molecule associated with many proteins (several hundred to thousands of genesunit of info that specifies traits) -proteins maintain structure of chromosome and help control gene activity -Chromatin: the entire complex of DNA and proteins; building material of chromosomes -Every species has a specific number of chromosomes in their nucleus somatic cells: all body cells except reproductive cells -contain 46 chromosomes in humans gametes: sperm and eggs; contain 23 chromosomes (half as many) -When a cell is dividing (even as it replicates its DNA in preparation for cell division) each chromosome is in the form of a long, thin chromatin fiber chromatin becomes densely packed together -Each duplicated chromosome has 2 sister chromatidsjoined copies of the original chromosome contain identical DNA molecule attached initially via cohesions: protein complexes each have a centromere: region containing specific DNA sequences where chromatid is attached most closely to its sister -mediated by proteins that give a narrow “waist” -part on either side of centromere is called an arm (long and short) once they separate during mitosis, they are considered individual chromosomes Mitosis: division of genetic material in the nucleus usually followed immediately by cytokinesis (division of cytoplasm) -one cell them becomes two, each genetically equivalent to parent cell M-phase, includes mitosis and cytokinesis -usually shortest part of the cell cycle Mitotic Spindle -consists of fibers made from MT’s and associated proteins -MT’s in the cytoskeleton disassemble to supply those for the spindle -Spindle polymerizes by incorporating more tubulin (protein) subunits and depolymerizes by removing them -source is at the centrosome: subcellular region containing the materials needed to organize the MT’scalled “MT organizing center” pair of centrioles at center but not essential for cell division (plant cells divide this way but don’t have centrioles) -centrosome divides into 2 during interphase but move apart during prophase/prometaphase -Aster: radial array of short MT’s that extend from each centrosome -each sister chromatid has a kinetochore: a structure of proteins associated with specific sections of DNA at each centromere face opposite directions where MT’s of spindle attach and pull each sister chromatid towards their respective poles -kinetochore microtubules -like a tug of war, and chromosomes settle midway between the two ends of the cell on the metaphase plate during metaphase -MT’s that do NOT attach to kinetochores have been elongating, and by metaphase are overlapping with each other (from opposite poles) MT’s of the asters also grow and are in contact with the plasma membrane -Anaphase commences suddenly when the cohesions holding the sister chromatids together are cleaved by an enzyme called separase sister chromatids are now each individual chromosomes motor proteins on the kinetochores “walk” the chromosomes along the MT’s -depolymerize their kinetochore ends after the motor proteins have passed  “Pacman” mechanism chromosomes are reeled in by motor proteins at the spindle poles, and the MT’s depolymerize at this end too -Non-kinetochore microtubules are responsible for elongating the whole cell during anaphase those from opposite poles overlap e


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