Biochemistry Exam 4

NAME: For GradeScope, please write your FIRST and LAST name in CAPITAL letters WITHIN the box: EXAM IV Biochemistry II I. _________________/54 II. _________________/10 III. _________________/10 IV. _________________/26 _________________/100 TOTAL I. MULTIPLE CHOICE. (54 points; 2 points each) Choose the BEST answer to the question by WRITING the appropriate letter in the BOX to the left of each question. 1. The use of Schiff-base formation is part of the enzyme mechanism for all of the following enzymes, except ___. A. B. C. D. E. 2. Which of the following statements about gluconeogenesis is true? A. B. C. D. E. 3. Gluconeogenesis uses the same glycolytic enzymes except for two in the beginning which are used to circumvent the exergonic pyruvate kinase reaction, and to synthesize PEP. Regulation of gluconeogenesis uses the allosteric effector, Fru 1,6P2, whereas glycolysis is regulated by the effector, Fru 2,6P2. Pyruvate carboxylase fixes CO2 in much the same way as rubisco. Since both glycolysis and gluconeogenesis involve enzymes only in the cytosol, they must be coordinately regulated. The exergonic nature of the fructose bisphosphatase step is sufficient to drive the whole gluconeogenesis pathway. Which of these chloroplast enzymes is not thioredoxin? A. B. C. D. E. 4. acetoacetate decarboxylase transaldolase transketolase aldolase aspartate transaminase regulated by light through the use of rubisco fructose-1,6-bisphosphatase ribulose-5-phosphate kinase glyceraldehyde-phosphate dehydrogenase sedoheptulose-1,7-bisphosphatase Absorption of a photon in the chloroplast of a photosynthetic organism is not associated with which one of the following? A. B. C. D. E. release of most of the energy as fluorescence antenna molecules exciton transfer eventual transfer of energy to a photochemical reaction center transfer of energy from a chlorophyll molecule in a light-harvesting complex to another chlorophyll or to a phycoerythrobilin molecule Page 2 5. Which of the following statements about the pentose-phosphate pathway is true? A. B. C. D. E. The pentose-phosphate pathway has two main roles, to make reduced NADH and ribose 5-phosphate for nucleotide biosynthesis. After the oxidative phase of the pentose-phosphate pathway, the ribulose 5-phosphate is isomerized to ribose 5-phosphate using an enediol mechanism much like the glycolytic enzyme phosphoglucoisomerase that converts glucose 6-phosphate to fructose 6-phosphate. Ribose 5-phosphate is either recycled into glucose 6-phosphate or used to synthesize phosphoribosyl pyrophosphate (PRPP) using UTP. The pentose-phosphate pathway enzyme transaldolase transfers a 2carbon moiety from a ketose to an aldose. The reducing capacity generated by the pentose-phosphate pathway is essential for regulation of the light-independent reactions in the Calvin cycle. 6. An enzyme used in both glycolysis and gluconeogenesis is: A. B. C. D. E. hexokinase. glucose-6-phosphatase. 3-phosphoglycerate kinase. phosphofructokinase-1. pyruvate kinase. 7. The sequence of events in the response of hepatocytes to elevated epinephrine is: 1. phosphorylated phosphorylase-a rapidly degrades glycogen 2. adenylate cyclase is activated 3. epinephrine binds to its receptor on the cell surface 4. PKA phosphorylates phosphorylase kinase 5. cAMP-dependent protein kinase (PKA) is activated A. B. C. D. E. 2, 3, 3, 3, 5, 4, 2, 2, 5, 2, 1, 4, 5, 4, 3, 3, 5, 4, 2, 1, 5 1 1 1 4 8. The glycogen-branching enzyme catalyzes: A. B. C. D. E. glycogen degradation in tree branches. formation of (a1Æ6) linkages during glycogen synthesis. formation of (a1Æ4) linkages in glycogen. removal of unneeded glucose residues at the ends of branches. the synthesis of the initial 6 glucose residues of glycogen 9. Which of these compounds is not directly involved in the Calvin cycle? A. B. C. D. E. sedoheptulose-7-phosphate glyceraldehyde-3-phosphate erythrose-4-phosphate mannose-6-phosphate ribulose-5-phosphate Page 3 10. Glucagon (in liver) and epinephrine (in muscle): A. B. C. D. E. activate glycogen phosphorylase and inactivate glycogen synthase. inhibit glycogen synthesis and activate glycogenolysis. act by raising the concentration of cyclic AMP (cAMP). act through a protein kinase all of the above. 11. Glycogenin: A. B. C. D. E. is the gene that encodes glycogen synthase. contains a Tyr on which new glycogen chains are initiated. is the enzyme responsible for forming branches in glycogen. regulates the synthesis of glycogen. catalyzes the conversion of starch into glycogen. 12. In Gluconeogenesis, which compound is not considered a precursor for making glucose via gluconeogenesis in humans? A. B. C. D. E. acetyl‑CoA pyruvate glycerol succinyl‑CoA lactate 13. A person who cannot synthesize liver fructose-1,6-bisphosphatase would probably experience: A. failure to synthesize fats when the diet contained excess carbohydrate. B. inability to metabolize fructose. C. inability to convert fructose-1,6-bisphosphate into triose phosphates. D. inability to resynthesize glucose from lactate produced during exercise. E. none of the above. 14. The known mechanisms of activation of rubisco, or of other enzymes of the Calvin cycle, during illumination include all of these except : A. B. C. D. E. carbamylation of a Lys residue by CO2. relief of the inhibition by the "nocturnal inhibitor," 2carboxyarabinitol-1-phosphate. light-driven entry of Mg2+ into the stroma. phosphorylation by cAMP-dependent protein kinase. reduction of a disulfide bridge by thioredoxin. 15. The compound that condenses with CO2 in the first reaction of carbon dioxide fixation is: A. ribose-1,5-bisphosphate. B. ribulose-1,5-bisphosphate. C. ribulose-5-phosphate. D. 3-phosphoglycerate. E. rubisco. 16. In the light-independent ("dark") reactions of photosynthesis, the biosynthesis of 1 mole of hexose from 6 moles of carbon dioxide requires: A. B. C. D. E. 18 18 12 12 no moles moles moles moles NADPH of NADPH and of NADPH and of NADPH and of NADPH and and 12 moles 18 12 18 12 of moles moles moles moles ATP. of of of of ATP. ATP. ATP. ATP. 17. The Cori cycle is: A. B. C. D. E. Page 4 the interconversion between glycogen and glucose-l-phosphate. the synthesis of alanine from pyruvate in skeletal muscle and the synthesis of pyruvate from alanine in liver. the synthesis of urea in liver and degradation of urea to carbon dioxide and ammonia by bacteria in the gut. the production of lactate from glucose in peripheral tissues with the resynthesis of glucose from lactate in liver. none of the above. 18. Which of the following statements about the light reactions in photosynthetic plants is false ? A. B. C. D. E. There are two distinct photosystems, linked together by an electron transfer chain. A membrane-bound ATPase couples ATP synthesis to electron transfer. The ultimate source of electrons for the process is H2O. The ultimate electron acceptor is O2. No CO2 is fixed during the light reactions. 19. The fixation of CO2 into organic compounds (triose phosphates) in green plants: A. takes place in the cytosol. B. results in the production of ATP. C. involves condensation of the two-carbon compound acetate with CO2 to form 3-phosphoglycerate. D. requires NADPH. E. takes place at equal rates in light and darkness. 20. Which of the following is true of glycogen synthase? A. B. C. D. It catalyzes addition of glucose residues to the nonreducing end of a glycogen chain through (a1Æ4) bonds. The conversion of an active to an inactive form of the enzyme is controlled by the concentration of cAMP. Activation of the enzyme involves a phosphorylation. The enzyme has measurable activity only in liver. 21. Transketolase requires the coenzyme: A. B. C. D. pyridoxal phosphate. thiamine pyrophosphate. cobalamin (vitamin B12). tetrahydrofolic acid. 22. Glucokinase, an isozyme of hexokinase, is _____________ A. B. C. D. E. more active when blood glucose concentrations are high. has a lower Km value for glucose than the other hexokinase isozymes. is found in muscle and is important for partitioning glucose between glycolysis and gluconeogenesis. is inhibited by glucose 6‑phosphate. is sequestered in the mitochondria and released when Fru 1-P binds to the complex, allowing its migration to the cytosol. Page 5 23. Photosynthetic phosphorylation and oxidative phosphorylation appear to be generally similar processes, both consisting of ATP synthesis coupled to the transfer of electrons along an electron-carrier chain. Which of the following is not true of both processes? A. B. C. D. E. Both make use of oxygen as a terminal electron acceptor. Both contain cytochromes and flavins in their electron carrier chains. Both processes are associated with membranous elements of the cell. Each represents the major route of ATP synthesis in those cells in which it is found. Both contain a membrane complex with a "Q-cycle" that helps create the proton-motive force. 24. The process of photophosphorylation in chloroplasts use all of the following reactions except _______. A. B. C. D. E. a membrane-bound complex containing cytochromes f and b6 and binding sites for plastoquinone and plastocyanin, which leads to establishment of a proton gradient. multiple light-absorbing molecules in the appropriate distances for efficient energy transfer a photosystem that creates reduced ferrodoxin with a reduction potential sufficient for subsequent reduction of NADPH or plastiquinone. a photosystem that uses H2O2 as a source of electrons. a photosystem with a special pair of chlorophyll molecules that don't perform energy transfer, but perform electron transfer. 25. André Jagendorf showed _______. A. that the pH gradient across the drive ATP synthase. B. that the pH gradient across the ATP synthase. C. that the pH gradient across the drive ATP synthase. D. that the pH gradient across the drive ATP synthase and requires E. that the pH gradient across the drive ATP synthase. mitochondrial membrane is sufficient to plasma membrane is sufficient to drive lysosomal membrane is sufficient to thylakoid membrane is insufficient to a membrane potential. thylakoid membrane is sufficient to 26. Gout is caused by excess production of uric acid, which forms rather insoluble salts and gets depsited in the joints. Blocking the production of uric acid would involve the inhibition of ______________, one of the enzymes in purine degradation, by the well known drug called __________. A. B. C. D. E. AMP deaminase; coformycin Xanthine oxidase; coformycin AMP deaminase; allopurinol Xanthine oxidase; allopurinol purine nucleoside phophorylase; ribitol 27. Which of the following is true about xanthine oxidase? A. B. C. D. E. contains a molybdenum ion complex involved in redox reactions with oxygen oxidizes both xanthine and adenine is inhibited by coformycin is inhibited by allantoin oxidizes both purines and pyrimidines II. True/False. (10 points) TYPE/WRITE EITHER "T" or "F" in the BOX to the left of each question. Page 6 28. Glutathione is important in combating the ROS generated in metabolism. 29. The degradation of CMP contributes to the urea cycle. 30. Pyrimidine degradation produces a dead-end product that does not contribute to the citric acid cycle and energy production, and is rather excreted as an oxidized pyrimidine ring; uridine. 31. Hyperuricemia can be caused by energy depletion. 32. Urate oxidase is missing in humans, whereas most animals possess this enzyme. This enzyme is mis-named and is more properly called urate dioxygenase. 33. Plastocyanin is different from ferrodoxin in that it contains an essential copper ion. 34. While the 1.8 V of energy in a photon is sufficient to drive the synthesis of at least 5 ATP molecules from ADP + Pi, it is not sufficient for both driving ATP synthesis and creating the chemical species with reduction potentials for redox reactions to both create an electron acceptor capable of splitting water (ca. +1.4V) and an electron donor capable of reducing NADPH (ca. –1.4V). Hence the need to evolve two photosystems. 35. NADPH reductase has a TPP cofactor for transferring electrons one at a time to NADPH. 36. Many diabetics do not respond to insulin because of a deficiency of insulin receptors on their cells. This lack of insulin response lowers the rate of glycogen synthesis in muscle by the inability to activate PP-1, which normally converts glycogen synthase to its active form. 37. Many diabetics do not respond to insulin because of a deficiency of insulin receptors on their cells. This lack of insulin response lowers the rate of glycolysis in muscle by the inability to activate PP-1, which normally converts PFK-2/FBPase-2 to its active kinase form, which would have provided sufficient Fru2,6P2 to allosterically activate PFK-1. III. MATCHING. (10 points) WRITE the best choice as a LETTER in the BOX(s) to the left of each number. 38. Pathways: For each pathway on the left, match it to an enzyme that operates in that pathway. Items on the right column will be used only once or not at all.(10 pts) 1. Nucleic acid degradation 2. Photosynthesis (light rxns) 3. Glycolate Cycle 4. ATP synthesis 5. Glyoxylate/Kornberg Cycle 6. Calvin Cycle 7. Gluconeogenesis 8. Glycogen synthesis 9. Pentose phosphate pathway A. B. C. D. E. F. G. H. I. J. K. water-splitting complex in PSII phosphoenolpyruvate carboxykinase ATP synthase xanthine oxidase glucose-6-phosphate dehydrogenase 3-phosphoglycerate dehydrogenase uricanase glycine cleavage enzyme glycogen synthase rubisco malate synthase IV. Page 7 SHORT ANSWER/FILL IN. (26 points) Give a brief answer or fill in the blanks as directed to each problem or question below. Put your answers WITHIN the boxes provided. 39. H218O is added to a suspension of chloroplasts capable of photosynthesis. Where does the 18O label appear when the suspension is exposed to light? Explain. (2 pts) 40. During photophosphorylation, charge separation occurs at special pairs (SP) of chlorophyll molecules in the photosystems. This initiates electron flow through a series of carriers in the chloroplast. Identify the donors of electrons to fill the holes created the enter each photosystem, and the acceptor of the electrons created that leave each photosystem. Also, name the cofactor in each photosystem that immediately attains these excited electrons. Lastly, indicate what causes this charge separation and how much energy is created? (8 pts) PS-II PS-I SP SP Cofactor accepting electron Cofactor accepting electron Fills electron hole in PS-II Fills electron hole in PS-I Receives electron from PS-II Cause of charge separation Receives electron from PS-I Energy created per einstein 41. Four possible immediate products are produced from glucose-6-phosphate in the liver. Each is indicated with the end product, pathway, or location listed near each box. Name the intermediate and the enzyme that catalyzes its production in the boxes. Put a check mark in the small box if the enzyme is regulated in its activity. (10 pts) Blood Glycogen Glucose 6-phosphate Pyruvate Rib 5-P Page 8 42. Draw the structure of 3-phosphoglycerate. Circle the atom(s) that would be labeled first in plants grown in CO2 labeled with radioactive carbon. Indicate with an arrow the atom(s) that would end up on the C-l of Ribulose 1,5-bisphosphate after completion of the Calvin cycle starting from 3phosphoglycerate. (4 pts) 43. Draw the R-group of Lys-210 as it is in active Rubisco. Recall this modified Lys becomes negatively charged and complexes with the magnesium cofactor. It initiates the carboxylation reaction by acting as a base. (2 pts) Page 1 No. on Test Correct Answer 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 C E A A B C C B D E B A D D B C D D D A B A A D E D A 28 29 30 31 32 33 34 35 36 37 T T F T T T T F T T 38 1. D, G 2. 3. A H 4. C 5. K 6. J 7. B 8. I 9. E Page 2 No. on Test Correct Answer 39. The label appears as 18O: oxygen H218O + CO2 + light -----> (CH2O) + 18O 2 40. A0 Pheophytin H2 O Plastocyanin (PC) Plastoquinone (PQ) photon absorption (Light) 41. Glc 1-P Ferrodoxin (Fd) 1.5 V Glucose Phosphoglucomutase X phosphohexosisomerase X Glc-6-Pase Glc-6-P dehydrogenase 6-phospho gluconolactone Fru 6-P 42. 43. Carbamate