Biochemistry Old Exam Final

Biochemistry II I. /57 II. /23 III. /29 IV. /25 v. / 6 TOTAL /140 I. MULTIPLE CHOICE (57 points) Choose the best answer as requested in each question Ьу circling the approporitate letter(s). 3 points each. 1. Which of the following is true of glycogen synthesis and breakdown? А. в. с. D. Е. 2. If а cell were unaЫe to synthesize or obtain tetrahydrofolic acid (Н4 folate), it would рrоЬаЫу Ье deficient in the biosynthesis of: А. В. с. D. З. lysine. thymidylate (ТМР), malonate. leucine. When glycerol is converted to glucose via gluconeogenesis, the first glycolytic intermediate formed is: А. в. С, D. Е. 4. Synthesis is catalyzed Ьу the same enzyme that catalyzes breakdown. The immediate product of glycogen breakdown is free glucose. Phosphorylation activates the enzyme responsiЫe for breakdown, and inactivates the synthetic enzyme. Under normal circumstances glycogen synthesis and glycogen breakdown occur simultaneously and at high rates. The glycogen molecule "grows" at its reducing end. 1,3-bisphosphoglycerate. ribulose-1,5-bisphosphate. glycerol-1,3-bisphosphate. glycerol-3-phosphate. dihydroxyacetone phosphate. The synthesis of both glycerophospholipids and triacylglycerols involves: А. в. с. D. Е. CDP-diacylglycerol. phosphoethanolamine. phosphatidate. CDP-choline, phosphatidate phosphatase. Page 1 5, Which of the following is not true of the reaction catalyzed Ьу ribonucleotide reductase? А. в. С. D. Е. 6. Cholesterol is synthesized from: А. в. с. D. Е. 7. А. serine labeled at С-2 (Са)· С. D. glycine labeled at С-2 (Са)· glycine labeled at С-1 (Соо-). serine labeled at С-3 (СН2ОН). Precursors for the biosynthesis of the pyrimidine ring system include: А. в. с. D. 10. Biotin is required. Carbon dioxide is liberated. АТР is consumed. Mevalonate is an intermediate. NADPH is the electron donor. The carbon skeleton of several amino acids may Ье derived metabolically from glucose. If glucose labeled with 14с at С-1 were the starting material for amino acid biosynthesis, а product that would Ье readily formed is: в. 9. acetyl-CoA. malate. oxalate, lipoic acid. choline. Which of the following statements about the synthesis of isopentenyl pyrophosphate from acetate is not true? А. в. С. D. Е. 8. It acts on nucleoside diphosphates. Thioredoxin acts as an essential electron carrier. Its mechanism involves formation of а free radical. There is а separate enzyme for each nucleotide (ADP, CDP, GDP, UDP). Glutathione is part of the path of electron transfer. glutamate, NH3, and СО2, glycine, glutamine, со2, and aspartate. glycine and succinyl-CoA. carbamoyl phosphate and aspartate. Which of the following substrates cannot contribute to net gluconeogenesis in mammalian liver? А. в. С. D. Е. alanine palmitate a-ketoglutarate glutamate pyruvate Page 2 11. Which of the following statements is not true of the pathway Ьу which purine nucleotides are synthesized? А. В. С, D. 12. In comparing fatty acid biosynthesis with � oxidation of fatty acids, which of the following statements is incorrect? А. В. С. D. Е. 13. с. D. Е. adenosine-5'-phosphate. guanosine-5'-phosphate. 5-phosphoribosyl-1-pyrophosphate. ribulose-5-phosphate. ribose-5-phosphate. Humans cannot convert dietary: А. В. С. D. Е. 15. Fatty acid degradation is catalyzed Ьу cytosolic enzymes; fatty acid synthesis Ьу mitochondrial enzymes. А thioester derivative of crotonic acid (trans-2-butenoic acid) is an intermediate in the synthetic path, but not in the degradative path. А thioester derivative of D-�-hydroxybutyrate is an intermediate in the synthetic path, not in the degradative path. The condensation of two moles of acetyl-CoA in the presence of а crude extract is more rapid in bicarbonate buffer than in phosphate buffer at the same рН; the cleavage of acetoacetyl-CoA proceeds equally well in either buffer. Fatty acid biosynthesis uses exclusively NADPH, whereas � oxidation uses exclusively NAD+ . The ribosyl phosphate moiety needed for the synthesis of orotidylate, inosinate, and guanylate is provided most directly Ьу: А. в. 14. The amino acid glycine is one of the precursors. The first enzyme in the path is aspartate transcarbamoylase (ATCase). Inosinate is the purine nucleotide that is the precursor of both adenylate and guanylate. COz is required for one of the steps in this pathway. carbohydrate into stored lipid. amino acids into stored lipid. glucose into amino acids. amino acids into glucose. fatty acids into glucose. Photosynthetic phosphorylation and oxidative phosphorylation appear to Ье generally similar processes, both consisting of АТР synthesis coupled to the transfer of electrons along an electron carrier chain. Which of the following is not true of both processes? А. В. С. D. Both make use of oxygen as а 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 АТР synthesis in those cells in which it is found. Page 3 16. Which of the following molecules binds strongly to avidin, а protein found in raw eggs? А. в. с. D. Е. 17. Which of these statements about the regulation of cholesterol synthesis is not true? А. в. С. D. Е. 18. methanol. S-adenosylmethionine (adoMet or SAM). а tetrahydrofolate derivative. choline. serine. Which of the following enzymes is not involved in the assimilation of inorganic nitrogen into an organic molecule? А. В. С. D. II. 20. Insulin stimulates HMG-CoA reductase. High intracellular cholesterol stimulates formation of cholesterol esters. Cholesterol acquired in the diet has essentially no effect on the synthesis of cholesterol in the liver. Some metabolite or derivative of cholesterol inhiЬits HMG-CoA reductase. Failure to regulate cholesterol synthesis predisposes humans to atherosclerosis. In the synthesis of phosphatidylcholine from phosphatidylethanolamine, the methyl group donor is: А. в. С. D. Е. 19. pantothenic acid folic acid niacin lipoic acid Ьiotin glutamine synthetase nitrogenase arginase carbamoyl phosphate synthetase FILL-IN & MATCHING. ( 23 points) Indicate which of the following statements is true (Т), and which is false (F). For any statement that you say is false, explain why it is false. (4 pts) __ (а) In а reaction under standard conditions, only the reactants are fixed at 1 м. __ (Ь) When дG0 ' is positive, Keq ' > 1. __ (с) дG' and ЛG0 ' mean the same thing. __ (d) When дG0 ' = 1.0 kJ/mol, Keq ' = 1. Page 4 1. 2. 3. 4. 5. 6. 7. 8. 9. 1 О. 11. 12. 13. 14. 15. 16. 17. 18. 19. 2 О. 21. Energy Metabolism (9 pts) In energy metabolism, sugars are completely oxidized to А key _______ (а), mostly in the ______________ (Ь). intermediate of this metabolism is acetyl-CoA, а __ (с) carbon compound attached to coenzyme А. During the complete oxidation of а molecule of acetyl-CoA there are ____ (d) molecules of _______ (е) reduced to ________ (f) (а key electron carrier). In addition, FAD is reduced to _______ (g), Using the Р/O ratio of 3.0 and 2.0 for these two electron carriers, respectively, the mitochondria can produce ____(h) molecules of АТР from each acetyl-CoA that is oxidized. The complete process is called combustion because ________(i) is consumed Ьу reduction to form water. The oxidation of acetyl-CoA and the consumption of _____ (i) are different pathways; called the _________ (Ь) and oxidative-phosphorylation, respectively. However, both pathways are tightly coupled Ьу the ratios of ATP/ADP and Furthermore, the synthesis of АТР can Ье ____ (f)/ _____ (e). uncoupled from ___________ (j) Ьу compounds like _______________ (k), which destroy the _________ (1) gradient across the inner mitochondrial _______ (rn), 22. Regulation; cofactors and enzyme nomenclature: (10 pts) Match items on the left with the best answer from items on the right. All items on the right are used, some more than once. Column А Column В Allosteric effector for activation of phosphofructokinase-1 Allosteric effector for activation of protein kinase А Allosteric effector for inhiЬition of ribonucleotide reductase phosphorylation causes ___. adenylation causes ___. transfer of phosphoryl groups from АТР use of oxygen as an electron acceptor addition of oxygen to both the substrate and water addition of both oxygen atoms from oxygen to the substrate transfer of electrons interconversion of aldose and ketose sugars transfer of amino groups synthesis utilizing hydrolysis of АТР removal of carbon dioxide use pyridoxal phosphate use Ьiotin use NADH use tetrahydroЬiopterin use of SАМ substrate that is cleaved using Schiff base-enzyme mechanism Page 5 А. carboxylases В. decarboxylases С. transaminases D. Е. F. G. Н. I. kinases dehydrogenases oxidases mono-oxygenases dioxygenases isomerases J. К. L. М. N. О. Р. Q. inhiЬition of glutamine synthetase synthetases methylases fructose 2, 6-Ьisphosphate cyclic АМР dATP inhiЬition of glycogen synthase fructose 1, 6-Ьisphosphate III. SHORT ANSWER. (29 points) 23. The conversion of glucose into glucose-6-phosphate, which must occur in the breakdown of glucose, is thermodynamically unfavoraЫe (endergonic). How do cells overcome this proЫem? (2 pts) 24. Many diabetics do not respond to insulin because of а deficiency of insulin receptors on their cells. How does this affect (а) the levels of circulating glucose immediately after а meal and (Ь) the rate of glycogen synthesis in muscle? (4 pts) 25. А sample of glycogen from а patient with liver disease is incubated with Pi, normal glycogen phosphorylase, and normal debranching enzyme. The ratio of Glc 1-Р to glucose formed in the reaction mixture was 100. What is the patient's most рrоЬаЫе deficiency? (3 pts) 26. What is an oxidation? What is а reduction? Can an oxidation occur without а simultaneous reduction? Why or why not? (4 pts) Page 6 27. Many amino acids are broken down to intermediates of the citric acid cycle. (а) Why can't these amino acid "remanants" Ье directly oxidized to СО 2 in one round of the citric acid cycle? (Ь) Explain why amino acids that are broken down to pyruvate can have 1/3 of the carbon in pyruvate completely oxidized, but not the other 2/3 carbons in one round of the citric acid cycle. (с) Not all amino acids are anaplerotic for the citric acid cycle. Name three amino acids whose "remanants" are anaplerotic. (10 pts) 28. What are the biological functions of the pentose phosphate pathway? (2 pts) 29. Explain why the phosphorolysis of glycogen is more efficient than the hydrolysis of glycogen in mobilizing glucose for the glycolytic pathway. (2 pts) 30. Why do individuals who are undergoing chemotherapy with methotreaxate often temporarily go bald? (2 pts) Page 7 31. PATHWAY. IV. Write out the eight steps in the ТСА cycle starting from the condensation of acetyl-CoA with oxaloacetate. For each step give the name of the enzyme that catalyzes the reaction (no abbreviations), any cofactors required (abbreviations ОК), the name of each intermediate/product(s) and their structures (including acetyl-CoA with oxaloacetate; you can abbreviate phosphate and/or phosphoryl Ьу а circled "Р" and Coenzyme А as "СоА"). (25 points) Page 8 v. 32. LABORATORY (6 points) Match the staining method that best visualizes each of the following molecules. (3 pts) А. В. с. Periodate/Schiff Coomassie Blue Horseradish peroxidase conjugated anti-IgG/chloronapthol protein to which you have an antibody glycoprotein serum protein 33. In the laboratory, quantitative precipitation of а radioactive sample of protein and collection for scintillation counting can Ье done Ьу _. А, в. с. D. Е. F. use of а dye-binding assay use of а Spec-20 to measure the absorance at 260 nm use of а polyacrylamide gel asking your TF to do it for you using ТСА and filtration onto glass fiber filter disks using BSA and measuring the absorbance at 280nm in а UV spectrophotometer Page 9 No. in No. on Q-Bank Test Correct Answer 19 21 19 2 21 20 20 21 21 11 25 8 14 35 23 25 13 34 20 21 16 18 10 27 11 20 1 2 3 с 6 7 8 9 А А в Е \ \1 \ с D 12 А 13 с Е 14 15 А ·� Е 12 16 20 28 17 с в 20 21 18 21 78 19 с с; 13 29 20 iD (а) False; both reactants and products are fixed at 1 м. (Ь) False; дG 0 ' = -RT lnКeq', so when K eq ' > 1, the term -RT lnКeq' (i.e., дG 0 ') has а negative value. (с) False; дG is а variaЫe dependent upon the physical constant ЛG 0 and а term that includes Т and the concentrations of reactants and products: дG 30 ' дG 0 ' + RT ln [product] [reactant] (d) False; дG 0 ' = -RT lnКeq'· and дG 0 ' = О. а. carbon dioxide 1 21 ь. ТСА cycle с. 2 d. 3 е. NAD+ f. NADH g. FADH 2 h. 11 i. oxygen j. electron transport k. dinitrophenol l. proton m. membrane When Keq ' 1, the logarithmic term о, No. in No. on Q-Bank Test Correct Answer 30 2 22 1 \) 1 ·')· ' \, 1 м, N, о, Р, J, о; F, G, "i н, l, E/F/G/H,_ li 11 i.1 I' с, к, lv в, 1, С/В, А, 11 Е, tl! G, i?, L, Zt Q 1. 14 47 23 Cells often drive а thermodynamically unfavoraЫe reaction in the forward direction Ьу coupling it to а highly exergonic reaction through а common intermediate. In this example, to make glucose-6-phosphate formation thermodynamically favoraЫe, cells transfer phosphoryl groups from АТР to glucose. АТР "hydrolysis" is highly exergonic, making the overall reaction exergonic. (Numerical solution below not required.) Glucose + Pi---►�glucose-6-phosphate + Н2О +13.8 kJ/mo дG 0 ' 0 �•=5�k=J�/�m=o=l АТР + Hl�O===►�A�DP � �+:t__�Pi--------=д=G�0_'__-_3� Sum: АТР + glucose --�►�ADP + glucose-6-phosphate дG 0 22 19 13 ' = -16.7 kJ/mol 24 (а) Circulating [glucose] is high because cells do not respond to the insulin signal to take up glucose. (Ь) Insulin is unaЫe to activate phosphoprotein phosphatase-1 in muscle, so glycogen synthesis is not stimulated. Moreover, glycogen synthesis is much reduced Ьу the lack of availaЫe glucose in the cell. The deficiency is in branching enzyme (Туре IV glycogen storage 50 25 disease). The high ratio (normal is -1 0 ) of Glc 1-Р to glucose indicates abnormally long chains of a(l->4)-linked residues with few a(l->6)-linked branch points (which result in free glucose). Oxidation is the loss of electrons; reduction is the gain of 34 26 electrons. Free electrons are unstaЫe (do not occur), so whenever an electron is released Ьу oxidation of some species, an electron must Ье accepted Ьу reduction of another species. 46 No. in No. on Q-Bank Test Correct Answer 15 56 27 14 86 28 14 75 29 21 77 30 Methotrexate kills rapidly proliferating cells, such as cancer cells and those of hair follicles. \ Consequently, hair falls out. ? 49 31 А; В С; 2 32 6 33 Е 19 29 29 (а) These "remanants" do not get oxidi zed directly in one round of the citric acid cycle because they are a�or Д,;,compounds � each round of the citric acid cycle only produces 2 СО2 molecules. Those that make �c:lc:�1:y:L.:-C()A, c:1.re _11ot: q�,idize<:l in о�е J :i;ound because the carbons produced in one round come fromthe carboxylates of oxaloacetate, not acetyl-CoA. (Ь) The pyruvate qerived from amino acids is converted to acetyl-CoA ' ' '? Ьу the•·..P �XJ!'LG!&P�hY�.epc.i:1.� .�. C()l1l_FJi!x after oxidation of the carboxylate (1 of the\ 3 ca:rbфns!) to СО2• The remaining 2/ 3 carbons (as ( "•,,. J/ z acetyl СоА) are NOT с O'fllpletely oxidized t��nd ..OJ the citric acid . cycle for the same :r;ea�on tha \ t the 2/3 or pyruvate are not (see (а)). (с) Asp, Phe, Tyr, !·le,1 Met,' Val, �lf-, Glu, Gln, Asn, Pro 2 The pentose ph��phate p�thw:ay ;}oduces pentose phosphates (for nucleotide synt�e�is) NADtH (reducing agent for Ьiosynthetic processes) . / 't ) 1�l-phosphate, which can Ье Phosphorolysis yi:�ldi,/ gluqose , .. , ' ! converted into gfuc�se-6-phosphate without the investment of energy from АТР. 1., ,!Wdrolysis of glycogen yields free glucose, which must Ье converted into glucose-6-phosphate (at the expense of АТР) before it can enter glycolysis. уша 1N.,,,ti (0 )},t, tif,�I .:..J :J")\'\...- ' ,с...,{ 'L/1./ Page 3( \•,/,, ' t. j /