Advanced Biochemistry I Study Questions PDF Fall 2023

BCH 361 Advanced Biochemistry I Fall 2023 Study Questions for Final Exam These are questions from the notes. They may or may not have any similarity to questions on the final exam. This is not an exhaustive...

BCH 361 Advanced Biochemistry I Fall 2023 Study Questions for Final Exam These are questions from the notes. They may or may not have any similarity to questions on the final exam. This is not an exhaustive list. No answers are provided. Look in your notes for these or do the calculations. Carbohydrate metabolism 1. In glycolysis, why doesn’t oxidation of glucose to pyruvate occur in one step? (think primarily about the energetics, but you could also think about the feasibility of the reaction) 2. Why is it necessary to invest two ATP in the beginning reactions of glycolysis? 3. Why is it necessary to convert G6P to F6P? 4. What would happen if DHAP is not converted to GAP? 5. What are the high energy intermediates in glycolysis? 6. What is the role of the high energy intermediates in glycolysis? How are they used to achieve this? 7. Using the ΔG°’ values for each of the reactions, calculate each Keq. 8. What are the differences between hexokinase and glucokinase? 9. What is the role of the divalent metal ion in the hexokinase reaction? 10. Some reactions are thermodynamically unfavourable. What allows them to occur in a cell? 11. Where, why and how is glycolysis regulated? 12. What are the different ways that enzymes can be regulated? 13. What are typical roles for amino acids found in carbohydrate metabolism? 14. What is the purpose of PFK-2? 15. What are the ways that C-C bonds are broken? 16. What is the significance of the GAPDH reaction? 17. How does 1,3-BPG generate ATP? 18. Why does 3PG need to be converted to 2PG? 19. What is the fate of each C of glucose in glycolysis? 20. High fructose diets are unhealthy for us. Why do you think this is? 21. How does galactose enter glycolysis? How is metabolism of galactose regulated? 22. UDP-Gal 4-epimerase uses a different mechanism than other isomerases we have seen. What is a more typical isomerization strategy? Why can’t this be used here? 23. How is phosphoglucomutase activated? 24. Why are fermentation reactions necessary? 25. What happens to lactate formed in muscle cells? 26. What is the role of TPP? 27. How do dehydrogenases work? 28. How are gluconeogenesis and glycolysis different? Why must they be different? 29. Where in the body does gluconeogenesis take place? How is this advantageous for regulation? 30. Where in the cell does the pyruvate carboxylase reaction take place? 31. What problems does this location pose for gluconeogenesis? How is this overcome? 32. How is oxaloacetate used to generate PEP? 33. What cellular structure(s) is glucose-6-phosphatase associated with? 1 BCH 361 Advanced Biochemistry I Fall 2023 34. How is gluconeogenesis regulated? 35. Why do the regulation of glycolysis and gluconeogenesis need to be coordinated? 36. What is the purpose of the pentose phosphate pathway? 37. What happens to the products of the pentose phosphate pathway? 38. How is the pentose phosphate pathway regulated? 39. How does the rate of a reaction relate to the energetics of the reaction? 40. What is the minimum amount of energy released by the oxidation of G6P to 6- phosphonogluconate if the reduction potential of NADP+ is -0.324 V? 41. Transketolase occurs twice in the pentose phosphate pathway. Does this appear to be an enzyme with high substrate specificity? Why/why not? 42. Why is decarboxylation of β-ketoacids relatively easy? 43. What is the driving force for decarboxylation reactions? 44. Ru5P 3-epimerase uses two Asp residues in its mechanism. Why is this important? Why can’t it use just one? 45. What is occurring in the reaction catalyzed by transaldolase, just looking at the substrates and products? 46. How is this achieved (mechanism) 47. How do Schiff bases facilitate cleavage between the α and β carbons? 48. What is the purpose of glycogen? 49. Why is the branched structure of glycogen important? 50. How is glycogen synthesis different from glycogen breakdown? 51. Why can’t glycogen synthesis and degradation use the identical reactions? 52. How is energy used to facilitate glycogen synthesis? Chemically, what makes the synthetic reactions spontaneous? 53. What is the core of glycogen? 54. Why does glycogen degradation make use of phosphate instead of water to break the glycosidic bonds? 55. Why is phosphoglucomutase required in glycogen metabolism? 56. Compared to glycogen, cellulose, also an α1 → 4 linked glucose polymer, is relatively chemically inert. Why? 57. Why is debranching enzyme required? 58. What happens to the glucose residue that is linked α1 → 6 (ie to the branch point)? 59. How is glycogen metabolism regulated? 60. How are the muscle and liver glycogen metabolism enzymes different? 61. How is regulation of glycogen degradation and synthesis coordinately regulated? 62. What role do hormones play in glycogen metabolism? TCA cycle metabolism 1. Where in the cell do these reactions occur? 2. What is the importance of the TCA cycle? 3. How does pyruvate enter the TCA cycle? 4. What are the roles of the cofactors in the pyruvate dehydrogenase complex? 5. What is the significance of the pyruvate dehydrogenase complex? 2 BCH 361 Advanced Biochemistry I Fall 2023 6. Why are the last two reactions catalyzed by the PDH complex required? 7. Why is pyruvate converted to acetyl-CoA instead of simply acetate? 8. Why can’t the C-C bonds in acetyl-CoA (or acetate) be cleaved using any of the reactions we have seen in carbohydrate degradation? 9. Why are thioesters high energy functional groups? 10. Why is the reaction catalyzed by citrate synthase favourable? 11. Why must citrate be converted to isocitrate? 12. What is the role of the [4Fe-4S] cluster in the aconitase reaction? 13. How does the mechanism of aconitase compare to other isomerizations we have seen? 14. In the reaction catalyzed by isocitrate dehydrogenase, which happens first, reduction of NAD+ or decarboxylation? Why is this order important? 15. How does the reaction catalyzed by α-KG dehydrogenase work? 16. Succinyl-CoA synthetase is also known as succinate thiokinase. Why might this enzyme have these two names? 17. If the hydrolysis of GTP has a ΔG°’ value of -30.5 kJ/mol, what must the be the ΔG°’ value for the hydrolysis of succinyl-CoA? 18. What is the importance of the thioester function group of succinyl-CoA in generating GTP? 19. C1 and C4 of succinate cannot be distinguished in solution. Why not? 20. Why is FAD used as a cofactor in the succinate dehydrogenase reaction instead of NAD+? 21. How and why is succinate dehydrogenase inhibited by malonate? 22. A typical hydration reaction is an anti reaction, with the hydroxyl group and proton being attached to opposite faces of the alkene. Yet the reaction catalyzed by fumarase is a syn addition. How does this enzyme achieve this stereochemistry? 23. The ΔG°’ value for the malate dehydrogenase reaction is highly unfavourable, yet, this reaction must occur for the citric acid cycle to continue. What drives this reaction forward? 24. What is the purpose of the last three reactions of the citric acid cycle? 25. What is the fate of the carbonyl carbon of acetyl-CoA in the TCA cycle? 26. What is the fate of the methyl carbon of acetyl-CoA in the TCA cycle? 27. Where and how is the TCA cycle regulated? 28. TCA cycle intermediates are used in other metabolic pathways. How are the intermediates regenerated? 29. What would happen if they were not regenerated? 30. What would control the rate of regeneration? Electron Transport and Oxidative Phosphorylation 1. What is the purpose of the electron transport chain? 2. Some anaerobic organisms also have an electron transport chain. Since they do not live in the presence of O2, what must they use as their ultimate electron acceptor(s)? 3. Where is the ETC located? 4. How can we use standard electron potentials to determine probable orders of electron acceptors in the ETC complexes? 5. Why is the energy from NADH and FADH2 not transferred directly to O2? 6. Overall, what happens in Complex I? 3 BCH 361 Advanced Biochemistry I Fall 2023 7. How does the oxidation of NADH result in reduction of ubiquinone (CoQ or UQ)? 8. How does Complex I translocate protons? 9. FMN and CoQ can accept and donate one or two electrons. How is this possible? 10. Overall, what happens in Complex II? 11. How does the oxidation of FADH2 result in the reduction of ubiquinone? 12. Why does Complex II not translocate protons? 13. What role do Fe-S clusters play in the ETC? 14. Overall, what happens in the Complex III? 15. How does the Q-cycle work? 16. Why are there two different active sites in Complex III? 17. How are the electrons bifurcated (sent in different directions) in the Q-cycle? 18. Why must the electrons be split apart from each other? 19. What is the role of porphyrin structures in the ETC? 20. Where in a cell would one find ubiquinone? 21. Where does cytochrome c exist? 22. Overall, what does Complex IV do? 23. How does Complex IV use the energy transferred from Cytochrome c to translocate protons? 24. What is remarkable about the chemistry of O2 reduction by Cytochrome c? 25. What is a respirasome? 26. What are normal functions of multi-enzyme complexes? 27. What happens if an ETC complex is inhibited? 28. How can inhibitors be used to determine the sequence of electron carriers in the ETC? 29. NADH produced in glycolysis must enter the mitochondrial matrix in order to interact with Complex I. How does this happen? 30. How is respiration coupled to ATP synthesis? 31. Why is an intact inner mitochondrial membrane important? 32. How does the Fo portion of the ATP synthase function? 33. How does the F1 portion of the ATP synthase function? 34. What does an uncoupling agent do? 35. What features do uncoupling agents have in common? 36. Why would ingesting an uncoupling agent lead to weight loss? 37. How would ingesting large amounts of an an uncoupling agent lead to death? 38. What is the role of thermogenin? 39. How is thermogenin regulated? 40. Why is it important to regulate thermogenin? 41. Why would plants need to have an uncoupling mechanism? 42. How does the uncoupling mechanism in plants operate? 43. Where in the mitochondrion is ATP synthesized? 44. How is the ATP generated by the FoF1 ATP synthase transferred to the cytosol? 45. What is a P/O ratio? 46. Aerobic bacteria are able to synthesize more ATP per mole of glucose than eukaryotic cells. Why? 47. How does respiratory control regulate metabolic pathways? 48. How is oxidative phosphorylation regulated? 4 BCH 361 Advanced Biochemistry I Fall 2023 49. If ATP synthase is inhibited, what would happen (in the mitochondrion and ETC)? 50. If uncouplers don’t bind to ATP synthase, how do they affect its action? 51. Why isn’t the inner mitochondrial membrane leaky? 52. What would happen to a cell if the inner mitochondrial membrane was “leaky”? 5