Chapter 19- Oxidative Phosphorylation

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Page 1 1. For mitochondria where an uncoupler for oxidative phosphorylation is present, which statement is TRUE? A) The rate of NADH reoxidation will decrease relative to coupled mitochondria. B) The citric acid cycle will be inhibited relative to uncoupled mitochondria. C) The P:O ratio for FADH 2 will increase relative to uncoupled mitochondria. D) The amount of ATP generated from FADH 2 will be less than the amount of ATP generated from NADH. E) None of the statements is true. 2. Which statement regarding oxidative phosphorylation is TRUE? A) The rate of electron transport is independent of the magnitude of the proton electrochemical gradient. B) ATP synthase utilizes oxidized cofactors. C) Proton transfer through the F o subunit of ATP synthase is required in order for ATP synthesis to occur. D) The addition of an uncoupler decreases the rate of re-oxidation of NADH and FADH 2 , therefore decreasing the rate of the citric acid cycle. E) All of the statements are true. 3. The consumption of acetyl-CoA by the citric acid cycle is DECREASED under which condition? A) the concentration of NAD + being high B) the concentration of oxaloacetate being high C) NADH being rapidly re-oxidized via the electron-transport chain D) the mitochondrial ATP synthase being inactive E) the concentration of both NAD + and oxaloacetate being high 4. Which molecule can reduce the proton gradient in mitochondria? A) P i -H + symporter B) ATP synthase C) pyruvate translocase D) All of the answers are correct. E) None of the answers is correct. 5. How many molecules of water are produced by the electron-transport chain during the complete aerobic oxidation of one molecule of pyruvate? A) 3 H 2 O B) 4 H 2 O C) 5 H 2 O D) 8 H 2 O E) 10 H 2 O 0 pinato si de hewn 1H20 NADH X2 action e Toe

Page 2 6. The electron-transport chain and ATP synthase are effectively coupled. Which statement BEST describes how this occurs? A) The electron-transport chain reoxidizes reduced cofactors. B) The electron-transport chain generates an electrochemical gradient that provides energy for the production of ATP. C) ATP synthase utilizes oxidized cofactors. D) Through a series of conformational changes, ATP synthase generates ATP. 7. Which statement is NOT true of electron transport? A) The mobile electron carrier coenzyme A is located in the inner mitochondrial membrane. B) Electrons flow from redox centers with a lower reduction potential to redox centers with a higher reduction potential. C) The electron transport chain oxidizes reduced cofactors. D) Cytochrome C has a higher reduction potential than FADH 2 . E) None of the statements is true. 8. During oxidative phosphorylation, the proton motive force (electrochemical gradient) that is generated by electron transport is used to: A) create a pore in the inner mitochondrial membrane. B) generate the substrates (ADP and P i ) for ATP synthase. C) drive transport processes essential to oxidative phosphorylation. D) reduce NAD + to NADH. E) reduce O 2 to H 2 O. 9. Coenzyme Q is a prosthetic group for which of the following complexes in the electron transport chain? A) Complex I B) Complex II C) Complex III D) All of the answers are correct. E) None of the answers is correct. toe O O O O

Page 3 10. Which statement does NOT describe a difference between the inner and outer mitochondrial membranes? A) The outer mitochondrial membrane contains porins, whereas the inner mitochondrial membrane does not. B) The outer mitochondrial membrane is permeable to large proteins ( M r > 10,000), whereas the inner mitochondrial membrane is not. C) A pH gradient exists across the inner mitochondrial membrane but not the outer mitochondrial membrane. D) The inner mitochondrial membrane contains a smaller percentage of lipid relative to protein compared with the outer mitochondrial membrane. E) The outer mitochondrial membrane has a smaller surface area than the inner mitochondrial membrane. 11. What factor makes the outer mitochondrial membrane permeable to protons? A) proton symports B) proton antiports C) porins D) the presence of proton ionophores E) the presence of negatively charged lipids 12. Which cofactor is MOST commonly involved as a cosubstrate in catabolic reactions where a metabolite is oxidized? A) NAD + B) FAD C) NADPH D) NADH E) coenzyme Q 13. Which statement is FALSE regarding flavoproteins? A) They may contain either FMN or FAD. B) The reduction potential of the flavin will depend on the amino acids in the polypeptide chain. C) They will need at least two substrates in order to function as enzymes. D) They are always integral membrane proteins. E) Most flavoproteins in electron transport have a lower reduction potential than coenzyme Q.

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Page 4 14. Complex III contains which cofactor as a prosthetic group? A) iron-sulfur clusters B) FAD C) FMN D) coenzyme Q E) copper 15. Which characteristic describes heme a but not heme c ? A) noncovalently associated prosthetic group B) contains an isoprenoid structure C) contains an aldehyde substituent on the porphyrin ring D) contains two propionate substituents on the porphyrin ring E) contains a vinyl substituent on the porphyrin ring 16. Which component of the electron-transport chain is NOT an integral membrane protein? A) NADH dehydrogenase B) cytochrome c C) cytochrome oxidase D) ubiquinone:cytochrome c oxidoreductase E) succinate dehydrogenase 17. Which protein associated with electron transport below is NOT a flavoprotein? A) NADH dehydrogenase B) mitochondrial glycerol-3-phosphate dehydrogenase C) cytochrome oxidase D) succinate dehydrogenase E) acyl-CoA dehydrogenase 18. If a drug that specifically prevented the interaction of cytochrome c with other proteins was added to respiring mitochondria in a test tube, what effects would be observed? A) ATP synthesis would immediately stop. B) Oxygen consumption would increase. C) Reduced cofactors (NADH/FADH 2 ) would accumulate. D) Coenzyme Q would become oxidized. E) Proton export from the matrix would increase. E I

Page 5 19. Which statement is FALSE concerning Complex III and the Q cycle? A) Both Q and QH 2 are substrates for Complex III. B) Four protons are released on the P side of the membrane for every two electrons transferred to cytochrome c . C) This protein contains both iron-sulfur clusters and heme as prosthetic groups. D) Two protons from the matrix side are used to generate QH 2 from the semiquinone radical. E) Overall, in each cycle one cytochrome c is reduced for every QH 2 oxidized (net). 20. How many of cytochrome c need to be reoxidized for every oxygen molecule (O 2 ) converted to water? A) one B) two C) three D) four E) eight 21. Which list shows the proteins in the CORRECT order from highest to lowest reduction potential? A) acyl-CoA dehydrogenase  ETF:Q oxidoreductase  ETF B) ETF  ETF:Q oxidoreductase  acyl-CoA dehydrogenase C) ETF:Q oxidoreductase  acyl-CoA dehydrogenase  ETF D) ETF:Q oxidoreductase  ETF  acyl-CoA dehydrogenase E) ETF  acyl-CoA dehydrogenase  ETF:Q oxidoreductase 22. What is the P:O ratio for electrons entering the electron-transport chain that originate from reoxidation of acyl-CoA dehydrogenase? A) greater than the P:O ratio for NADH reoxidation B) approximately the same as the P:O ratio for NADH reoxidation C) less than the P:O ratio for NADH reoxidation but more than the P:O ratio for Complex II reoxidation D) approximately the same as the P:O ratio for Complex II reoxidation E) less than the P:O ratio for Complex II reoxidation 23. Which complex in the electron-transport chain contains copper ions? A) Complex I B) Complex II C) Complex III D) Complex IV E) None of these complexes contains copper ions. 0

Page 6 24. Cytochrome c can be reduced directly by small molecules such as ascorbate (vitamin C). If ascorbate is added to an oxygenated solution containing purified cytochrome c and cytochrome oxidase, what would you predict would occur? A) ATP synthesis would occur. B) Cytochrome c would become reduced and remain reduced. C) Oxygen would be reduced to water. D) Ascorbate would become more reduced. E) No apparent change would be observed. 25. What compound is a product of the reaction involving the superoxide free radical catalyzed by superoxide dismutase? A) water B) hydrogen peroxide C) reduced glutathione D) oxidized glutathione E) NADPH 26. In some organisms, an alternative oxidase will accept electrons from ubiquinol and reduce oxygen to water with no associated proton translocation. What would be a consequence of having this oxidase active? A) decreased rate of NADH reoxidation B) decreased P:O ratio C) decreased rate of oxygen consumption D) inhibition of oxidative pathways like the citric acid cycle E) increased sensitivity to cyanide poisoning 27. During the operation of the malate-aspartate shuttle, what process does NOT occur? A) net movement of reducing potential from the cytosol to the matrix B) transfer of amino groups from glutamate to oxaloacetate in the cytosol C) transport of two different amino acids through an antiport D) simultaneous transport of malate and oxaloacetate through an antiport E) reduction of oxaloacetate to malate in the cytosol 28. Which statement is TRUE regarding the reduction potential of mitochondrial glycerol 3 phosphate dehydrogenase? A) It will be higher than those of both NADH and Complex III. B) It will be lower than those of both NADH and Complex III. C) It will be higher than that of NADH but lower than that of Complex III. D) It will be lower than that of NADH but higher than that of Complex III. E) No conclusion can be drawn regarding its reduction potential.

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Page 7 29. Which statement is FALSE regarding 2,4-dinitrophenol? A) It is a proton carrier ionophore. B) It may be either neutral or negatively charged. C) It is soluble in the lipid core of membranes. D) It requires a specific transporter to enter mitochondria. E) It decreases ATP synthesis will increasing oxygen consumption. 30. What effect will increasing the number of c subunits in ATP synthase have on the P:O ratio? A) It will increase for both NADH and FADH 2 . B) It will increase for NADH and decrease for FADH 2 . C) It will decrease for NADH and increase for FADH 2 . D) It will decrease for both NADH and FADH 2 . E) It will remain unchanged for both NADH and FADH 2 . 31. Which statement is FALSE regarding ATP synthase? A) The active site contains multiple positive charges that interact with the substrates. B) The energy difference between bound substrate and bound product is close to zero. C) As an enzyme, ATP synthase is classified as a hydrolase. D) ATP synthase can be classified as a primary active transporter. E) ADP binds more tightly to the active site than ATP. 32. Which statement is TRUE regarding the gamma (  ) subunit of ATP synthase? A) It contains mostly  -helical regular secondary structure. B) It exists as a dimer in the F 1 portion of ATP synthase. C) It prevents the F 1 portion from rotating relative to the F O portion. D) It interacts with the a and b subunits of the F O portion. E) It binds protons as part of the proton translocation process. 33. Which step is NOT part of the proton-translocation process in ATP synthase? A) A negatively charged amino acid in each c subunit becomes neutral upon proton binding. B) A positively charged amino acid in the a subunit forms an ion pair with a charged amino acid in a c subunit. C) Deprotonated c subunits are able to interact only with the a subunit. D) An arginine in the a subunit is reversibly protonated and deprotonated in each proton binding event. E) Proton direction is determined by the relative concentrations of protons on either side of the membrane.

Page 8 34. In which pairing are both transporters symports? A) adenine nucleotide translocase and phosphate translocase B) phosphate translocase and pyruvate translocase C) pyruvate translocase and adenine nucleotide translocase D) adenine nucleotide translocase and glutamate-aspartate transporter E) glutamate-aspartate transporter and phosphate translocase 35. Which statement explains why the [ATP]/[ADP][P i ] ratio is relatively stable in a cell? A) [ATP] is always relatively low. B) ATP consumption is balanced by ATP synthase activity. C) ATP is used to regulate protein kinases. D) ATPases ensure that ATP concentration does not become too large. E) Energy consumption is minimized to ensure ATP is not consumed. 36. Which statement does NOT describe characteristics of the protein inhibitor IF 1 ? A) This protein is relatively small (<100 amino acids). B) This protein has very little ordered structure at pH 7.0. C) This protein will bind to the F O portion of ATP synthase. D) This protein functions as a dimer when it is inhibiting ATP synthesis. E) This protein inhibits ATP hydrolysis by ATP synthase. 37. What will NOT occur when 2,4-dinitrophenol (an uncoupler of oxidative phosphorylation) is added to actively respiring mitochondria? A) The P:O ratio will increase. B) The rate of NADH reoxidation at Complex I will increase. C) The rate of oxidation of intermediates in the citric acid cycle will increase. D) Proton export from the matrix will occur. E) Heat will be released. 38. Cytochrome P-450 gets its name from what characteristic? A) It is a protein that is 450 amino acids long. B) It fluoresces at 450 nm. C) It absorbs light at 450 nm. D) It has a reduction potential of –450 mV. E) It contains a 450 Dalton prosthetic group.

Page 9 39. What is the role of cytochrome c in apoptosis? A) It acts as an allosteric effector for caspase-3. B) It transports electrons from mitochondria to the cytosol. C) It acts as a protease to activate various zymogens. D) It forms a complex with other proteins to generate an apoptosome. E) It activates pores in the outer mitochondrial membrane. 40. Which protein is NOT portion encoded in human mitochondrial DNA? A) Complex I (NADH dehydrogenase) B) Complex II (succinate dehydrogenase) C) Complex III (ubiquinone:cytochrome c oxidoreductase) D) cytochrome c E) Complex IV (cytochrome oxidase) 41. What mechanism accounts for mitochondrial inheritance in sexual reproduction in animals? A) Male gametes do not contain mitochondria. B) Mitochondria from male gametes do not enter the ovum. C) Female mitochondria are able to outcompete male mitochondria. D) Male mitochondria are degraded after fertilization. E) Male and female mitochondria merge after fertilization to form hybrids. 42. Almost all of the oxygen (O 2 ) one consumes in breathing is converted to: A) acetyl-CoA. B) carbon dioxide (CO 2 ). C) carbon monoxide and then to carbon dioxide. D) water. E) None of the answers is correct. 43. Which of the following electron carriers is NOT able to transfer one electron at a time? A) NADH B) FMN C) FAD D) ubiquinone E) heme

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Page 10 44. A new compound isolated from mitochondria is claimed to represent a previously unrecognized carrier in the electron transfer chain. It is given the name coenzyme Z. Which line of evidence do you feel is the LEAST conclusive in assigning this compound a position in the electron transfer chain? A) Alternate oxidation and reduction of the mitochondrion-bound coenzyme Z can be readily demonstrated. B) Removal of coenzyme Z from the mitochondria results in a decreased rate of oxygen consumption. C) The rate of oxidation and reduction of mitochondrion-bound coenzyme is of the same order of magnitude as the overall rate of electron transfer in mitochondria as measured by oxygen consumption. D) The reduction potential of Z is between that of two compounds known to participate in the electron transport chain E) When added to a mitochondrial suspension, coenzyme Z is taken up very rapidly and specifically by the mitochondria. 45. Antimycin A blocks electron transfer between cytochromes b and c 1 . If intact mitochondria were incubated with antimycin A, excess NADH, and an adequate supply of O 2 , which compound would be found in the oxidized state? A) coenzyme Q B) cytochrome a 3 C) cytochrome b D) cytochrome e E) cytochrome f 46. Reduced QH 2 is NOT formed by which of the following? A) Complex I and NADH B) Complex II and succinate C) Complex III and cytochrome c D) fatty acid oxidation E) oxidation of glycerol-3-phosphate

Page 11 47. In the reoxidation of QH 2 by purified ubiquinone-cytochrome c reductase (Complex III) from heart muscle, the overall stoichiometry of the reaction requires 2 mol of cytochrome c per mole of QH 2 because: A) cytochrome c is a one-electron acceptor, whereas QH 2 is a two-electron donor. B) cytochrome c is a two-electron acceptor, whereas QH 2 is a one-electron donor. C) cytochrome c is water soluble and operates between the inner and outer mitochondrial membranes D) heart muscle has a high rate of oxidative metabolism, and therefore requires twice as much cytochrome c as QH 2 for electron transfer to proceed normally. E) two molecules of cytochrome c must first combine physically before they are catalytically active. 48. Which statement is NOT a feature of Complex IV? A) Cytochrome c is a one-electron donor. B) Oxygen is a substrate. C) Copper is an essential metal for the reaction. D) For every electron passed to Complex IV, two protons are consumed from the matrix (N) side. E) In order to generate two water molecules, Complex IV must go through the catalytic cycle two times. 49. Which statement is NOT true of the proton motive force (pmf)? A) One component of the pmf is the chemical gradient of protons. B) One component of the pmf is the charge gradient of protons. C) Generation of the pmf in mitochondria requires succinate. D) The pmf is generated by the electron transport chain in mitochondria. E) The pmf drives ATP synthesis in mitochondria. 50. Cyanide, oligomycin, and 2,4-dinitrophenol (DNP) are inhibitors of mitochondrial aerobic phosphorylation. Which statement CORRECTLY describes the mode of action of the three inhibitors? A) Cyanide and 2,4-dinitrophenol inhibit the respiratory chain, and oligomycin inhibits the synthesis of ATP. B) Cyanide inhibits the respiratory chain, whereas oligomycin and 2,4-dinitrophenol inhibit the synthesis of ATP. C) Cyanide, oligomycin, and 2,4-dinitrophenol compete with O 2 for cytochrome oxidase (Complex IV). D) Oligomycin and cyanide inhibit synthesis of ATP; 2,4-dinitrophenol inhibits the respiratory chain. E) Oligomycin inhibits the respiratory chain, whereas cyanide and 2,4-dinitrophenol prevent the synthesis of ATP.

Page 12 51. If electron transfer in tightly coupled mitochondria is blocked (with antimycin A) between cytochrome b and cytochrome c 1 , then: A) all ATP synthesis will stop. B) ATP synthesis will continue, but the P/O ratio will drop to one. C) electron transfer from NADH will cease, but O 2 uptake will continue. D) electron transfer from succinate to O 2 will continue unabated. E) energy diverted from the cytochromes will be used to make ATP, and the P/O ratio will rise. 52. In normal mitochondria, the rate of NADH consumption (oxidation) will: A) be increased in active muscle, decreased in inactive muscle. B) be very low if the ATP synthase is inhibited, but increase when an uncoupler is added. C) decrease if mitochondrial ADP is depleted. D) decrease when cyanide is used to prevent electron transfer through the cytochrome a + a 3 complex. E) All of the answers are correct. 53. Which statement about the chemiosmotic theory is CORRECT? A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane. B) It predicts that oxidative phosphorylation can occur, even in the absence of an intact inner mitochondrial membrance. C) The effect of uncoupling reagents is a consequence of their ability to carry electrons through membranes. D) The membrane ATP synthase has no significant role in the chemiosmotic theory. E) All of the statements are correct. 54. Which statement about the chemiosmotic theory is FALSE? A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane. B) Energy is conserved as a transmembrane pH gradient. C) Oxidative phosphorylation cannot occur in membrane-free preparations. D) The effect of uncoupling reagents is a consequence of their ability to carry protons through membranes. E) The membrane ATPase, which plays an important role in other hypotheses for energy coupling, has no significant role in the chemiosmotic theory.

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Page 13 55. Upon the addition of 2,4-dinitrophenol (DNP) to a suspension of mitochondria carrying out oxidative phosphorylation linked to the oxidation of malate, what does NOT occur? A) Oxygen consumption decreases. B) Oxygen consumption increases. C) The P/O ratio drops from a value of approximately 2.5 to 0. D) The proton gradient dissipates. E) The rate of transport of electrons from NADH to O 2 becomes maximal. 56. Uncoupling of mitochondrial oxidative phosphorylation: A) allows continued mitochondrial ATP formation but halts O 2 consumption. B) halts all mitochondrial metabolism. C) halts mitochondrial ATP formation but allows continued O 2 consumption. D) slows down the citric acid cycle. E) slows the conversion of glucose to pyruvate by glycolysis. 57. 2,4-Dinitrophenol and oligomycin inhibit mitochondrial oxidative phosphorylation. 2,4-Dinitrophenol is an uncoupling agent; oligomycin blocks the ATP synthesis reaction itself. Therefore, 2,4-dinitrophenol will: A) allow electron transfer in the presence of oligomycin. B) allow oxidative phosphorylation in the presence of oligomycin. C) block electron transfer in the presence of oligomycin. D) diminish O 2 consumption in the presence of oligomycin. E) None of the answers is correct. 58. Which statement about energy conservation in the mitochondrion is FALSE? A) Drugs that inhibits the ATP synthase will also inhibit the flow of electrons down the chain of carriers. B) For oxidative phosphorylation to occur, it is essential to have a closed membranous structure with an inside and an outside. C) The yield of ATP per mole of oxidizable substrate depends on the substrate. D) Uncouplers (such as dinitrophenol) have exactly the same effect on electron transfer as inhibitors such as cyanide; both block further electron transfer to oxygen. E) Uncouplers “short circuit” the proton gradient, thereby dissipating the proton motive force as heat.

Page 14 59. Which statement is CORRECT concerning the mitochondrial ATP synthase? A) It can synthesize ATP after it is extracted from broken mitochondria. B) It catalyzes the formation of ATP even though the reaction has a large positive  G' °. C) It consists of F o and F 1 subunits, which are transmembrane (integral) polypeptides. D) It is actually an ATPase and only catalyzes the hydrolysis of ATP. E) When it catalyzes the ATP synthesis reaction, the  G' ° is actually close to zero. 60. When the  G' ° of the ATP synthesis reaction is measured on the surface of the ATP synthase enzyme, it is found to be close to zero. This is thought to be due to: A) a very low energy of activation. B) enzyme-induced oxygen exchange. C) stabilization of ADP relative to ATP by enzyme binding. D) stabilization of ATP relative to ADP by enzyme binding. E) None of the answers is correct. 61. During oxidative phosphorylation, the proton motive force that is generated by electron transport is used to: A) create a pore in the inner mitochondrial membrane. B) generate the substrates (ADP and P i ) for the ATP synthase. C) induce a conformational change in the ATP synthase. D) oxidize NADH to NAD + . E) reduce O 2 to H 2 O. 62. The oxidation of a particular hydroxy substrate to a keto product by mitochondria has a P/O ratio of less than 2. The initial oxidation step is very likely directly coupled to the: A) oxidation of a flavoprotein. B) oxidation of a pyridine nucleotide. C) reduction of a flavoprotein. D) reduction of a pyridine nucleotide. E) reduction of cytochrome a 3 . 63. The relative concentrations of ATP and ADP control the cellular rates of: A) glycolysis. B) oxidative phosphorylation. C) pyruvate oxidation. D) the citric acid cycle. E) All of the answers are correct.

Page 15 64. The rate of oxidative phosphorylation in mitochondria is controlled primarily by: A) feedback inhibition by CO 2 . B) the availability of NADH from the TCA cycle. C) the concentration of citrate (or) the glycerol-3-phosphate shuttle. D) the mass-action ratio of the ATD-ADP system. E) the presence of thermogenin. 65. Which factor is NOT controlled by hypoxia-inducible factor (HIF-1)? A) glucose transport B) glycolysis C) citric acid cycle D) Compex I of the respiratory chain E) Complex IV of the respiratory chain 66. Mammals produce heat by using which endogenous uncoupling agent? A) the small molecule 2-4-dinitrophenol synthesized by the cell B) the protein thermogenin C) the protein thioredoxin D) the protein cytochrome c E) a modified form of the F o F 1 ATPase 67. Which phrase BEST describes the role of mitochondria in apoptosis? A) escape of cytochrome c into the cytoplasm B) increased rate of fatty acid  oxidation C) an increase in permeability of outer membrane D) uncoupling of oxidative phosphorylation E) both escape of cytochrome c into the cytoplasm and an increase in permeability of outer membrane 68. Mutations in mitochondrial genes do NOT play a role in: A) adult onset diabetes. B) cystic fibrosis. C) hypertrophic cardiomyopathy. D) Leber's hereditary optic neuropathy. E) myoclonic epilepsy.

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Page 16 69. Which statement about human mitochondria is TRUE? A) About 900 mitochondrial proteins are encoded by nuclear genes. B) Mitochondrial genes are inherited from both maternal and paternal sources. C) rRNA and tRNA are imported from the cytoplasm and used in mitochondrial protein synthesis. D) The mitochondrial genome codes for all proteins found in mitochondria. E) The mitochondrial genome is not subject to mutations. 70. Cytochrome c can be reduced directly by small molecules such as ascorbate (vitamin C). If ascorbate is added to the following preparations of mitochondria (which include succinate and oxygen), what would you predict would be the effect on oxygen consumption in each case, and why? a. mitochondria that have been treated with oligomycin b. mitochondria that have been treated with cyanide c. mitochondria that have been treated with rotenone d. mitochondria that have been treated with antimycin A 71. How do the cytosolic and mitochondrial isozymes of glycerol 3-phosphate dehydrogenase differ from each other? 72. Cytochrome c interacts with multiple different proteins (for example: complex III, Complex IV, Apaf-1, sulfite oxidase and others). It is a small protein (~110 amino acids) and has a very low rate of mutation. Are these two aspects consistent with each other? Why or why not? 73. The ATP synthase F 1 portion contains many subunits arranged in a cyclic pattern, yet we cannot really describe it as having cyclic symmetry. Why? 74. Bovine ATP synthase contains 8 c subunits while yeast ATP synthase contains 10 c subunits. How many protons would be needed for each ATP in these two synthases, and how would it impact the P:O ratio? 75. Under standard conditions, NADH reoxidation by the electron-transport chain has a free-energy change equal to –220 kJ/mol. With 100% efficiency, how many ATP could be synthesized under standard conditions? What is the “actual” efficiency given these numbers?

Page 17 76. As you read and answer this question, you are (presumably) consuming oxygen. What single reaction accounts for most of your oxygen consumption? 77. Show the path of electrons from ubiquinone (Q or coenzyme Q) to oxygen in the mitochondrial respiratory chain. One of the two compounds (Q and O 2 ) has a standard reduction potential ( E' °) of 0.82 V, and the other, 0.045 V. Which value belongs to each compound? How did you deduce this? 78. Diagram the path of electron flow from NADH to the final electron acceptor during electron transport in mitochondria. For each electron carrier, indicate whether only electrons, or both electrons and protons, are accepted/donated by that carrier. Also, indicate where electrons from succinate oxidation enter the chain of carriers. 79. During electron transfer through the mitochondrial respiratory chain, the overall reaction is NADH + 1/2 O 2 + H +  NAD + + H 2 O. The difference in reduction potentials for the two half-reactions (  E' °) is +1.14 V. Show how you would calculate the standard free-energy change,  G' °, for the reaction as written above. (The Faraday constant,  , is 96.48 kJ/V · mol.) 80. The standard reduction potential for ubiquinone (Q or coenzyme Q) is 0.045 V, and the standard reduction potential ( E' °) for FAD is –0.219 V. Using these values, show that the oxidation of FADH 2 by ubiquinone theoretically liberates enough energy to drive the synthesis of ATP. The Faraday constant,  , is 96.48 kJ/V · mol.  G' ° for ATP synthesis is +30.5 kJ/mol.

Page 18 81. A recently discovered bacterium carries out ATP synthesis coupled to the flow of electrons through a chain of carriers to some electron acceptor. The components of its electron transfer chain differ from those found in mitochondria; they are listed below with their standard reduction potentials. (a) Place the electron carriers in the order in which they are most likely to act in carrying electrons. (b) Is it likely that O 2 (for which E' ° = 0.82 V) is the final electron acceptor in this organism? Why or why not? (c) How would you calculate the maximum number of ATP molecules that could theoretically be synthesized, under standard conditions, per pair of electrons transfered through this chain of carriers? (The Faraday constant,  , is 96.48 kJ/V · mol.)  G' ° for ATP synthesis is +30.5 kJ/mol. 82. Describe, in simple diagrams and a few words, the chemiosmotic theory for coupling oxidation to phosphorylation in mitochondria. 83. Compound X is an inhibitor of mitochondrial ATP synthesis. It was observed that when compound X was added to cells, the NAD + /NADH ratio decreased. Would you expect X to be an uncoupling agent or an inhibitor of respiratory electron transfer? Explain. 84. Cyanide ion (CN – ) blocks electron transfer in mitochondria at the level of cytochrome a + a 3 . 2,4-Dinitrophenol (DNP) is an uncoupler of mitochondrial oxidative phosphorylation. Draw graphs (ATP synthesized vs. time and O 2 consumed vs. time) with labeled curves to show the effects of adding each of these compounds separately to a suspension of mitochondria supplied with O 2 , succinate, ADP, and P i . Use an arrow to indicate the time of drug addition.

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Page 19 85. Give an example of (a) an uncoupler of oxidative phosphorylation, and (b) an inhibitor of respiration. (c) Describe the difference in the effects of such uncouplers and inhibitors on mitochondrial function. 86. Mitochondria carrying out oxidative phosphorylation consume oxygen. Explain what happens to this oxygen, and describe the effect of an uncoupling agent such as 2,4-dinitrophenol on the rate of oxygen consumption. Assume there is a sufficient supply of oxidizable substrate, ADP, and P i . 87. The compound 2,4-dinitrophenol (DNP), an uncoupler, was briefly used as a weight-loss drug. Some of its effects in people who took the drug included weight loss and higher than normal body temperature. Some people even died. Explain the first two effects of the compound in biochemical terms. 88. Although molecular oxygen (O 2 ) does not participate directly in any of the reactions of the citric acid cycle, the cycle operates only when O 2 is present. Explain this observation. 89. The skunk cabbage ( Symphocarpus foetidus ) can maintain a temperature of 10–25 °C higher than the temperature of the surrounding air. Suggest a mechanism for this. 90. Consider a liver cell carrying out the oxidation of glucose under aerobic conditions. Suppose that we added a very potent and specific inhibitor of the mitochondrial ATP synthase, completely inhibiting this enzyme. Indicate whether each of the following statements about the effect of this inhibitor is true or false; if false, explain in a sentence or two why it is false. ____ (a) ATP production in the cell will quickly drop to zero. ____ (b) The rate of glucose consumption by this cell will decrease sharply. ____ (c) The rate of oxygen consumption will increase. ____ (d) The citric acid cycle will speed up to compensate. ____ (e) The cell will switch to fatty acid oxidation as an alternative to glucose oxidation, and the inhibitor will therefore have no effect on ATP production. 91. When the F 1 portion of the ATP synthetase complex is removed from the mitochondrial membrane and studied in solution, it functions as an ATPase. Why does it not function as an ATP synthetase?

Page 20 92. When the  G' ° of the ATP synthesis reaction is measured on the surface of the ATP synthase enzyme, it was found to be close to zero. Describe briefly why this is so. 93. Explain briefly the current model for how the proton motive force that is generated by electron transport is used to drive the ATP synthesis reaction. 94. For each of the following explain whether they are transported into or out of the mitochondrion and comment briefly on the mechanism for each: (1) NADH (2) Inorganic phosphate (3) ADP 95. Describe and explain the two different ratios that affect the rate of respiration in mitochondria. What is accomplished by these control mechanisms? 96. In his studies of alcoholic fermentation by yeast, Louis Pasteur noted that the sudden addition of oxygen (O 2 ) to a previously anaerobic culture of fermenting grape juice resulted in a dramatic decrease in the rate of glucose consumption. This “Pasteur effect” can be counteracted by the addition of 2,4-dinitrophenol (DNP), an uncoupler of oxidative phosphorylation. (a) Why would the yeast cells consume less glucose in the presence of oxygen? Can you estimate how much less glucose they would use? (b) Why would DNP counteract or prevent the Pasteur effect? 97. Describe the role of hypoxia-inducible factor (HIF-1) in reducing reactive oxygen species (ROS). 98. Describe the role of cytochrome c in apoptosis. 99. Mutations in mitochondrial genes frequently produce diseases that affect the brain and skeletal muscle (mitochondrial encephalomyopathies). Why are these two tissues particularly sensitive to mitochondrial mutations? 100. Discuss three lines of evidence that support the theory that mitochondria evolved from endosymbiontic bacteria.

Page 21 Answer Key 1. D 2. C 3. D 4. D 5. C 6. B 7. A 8. C 9. E 10. B 11. C 12. A 13. D 14. A 15. D 16. B 17. C 18. C 19. E 20. D 21. D 22. D 23. D 24. C 25. B 26. B 27. B 28. C 29. D 30. D 31. E 32. A 33. D 34. B 35. B 36. C 37. A 38. C 39. D 40. D 41. D 42. D 43. A 44. E

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Page 22 45. B 46. C 47. A 48. E 49. C 50. B 51. A 52. E 53. A 54. E 55. A 56. C 57. A 58. D 59. E 60. D 61. C 62. C 63. E 64. D 65. D 66. B 67. E 68. B 69. A 70. 71. 72. 73. 74. 75. 76. 77. 78. 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90.

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Page 23 91. 92. 93. 94. 95. 96. 97. 98. 99. 100.

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Chapter 19- Oxidative Phosphorylation

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