2005 Biochemistry Final Exam PDF

Final Exam, Biochemistry, Fall 2005 Pin #_______________ Place your PIN# in the last 4 cells of the student number section of the scantrons as shown below, but fill the initial digits, too: 0 1...

Final Exam, Biochemistry, Fall 2005 Pin #_______________ Place your PIN# in the last 4 cells of the student number section of the scantrons as shown below, but fill the initial digits, too: 0 1 0 0 x x x x Multiple choice (2 points each, 100 points total). NUCLEOTIDES AND NUCLEIC ACIDS - Dr. MacKerell 1. How do a nucleotide and a nucleoside differ? A) A nucleoside is found in DNA, whereas nucleotides are found in RNA. B) Purines are only found in nucleotides. C) Nucleosides contain only deoxyribose sugars. D) A nucleotide is a nucleoside with a phosphate ester linked at the sugar 5' residue. E) None of the above. 2. The difference in RNA bases compared to DNA bases is A) A instead of T. B) U instead of G. C) U instead of T. D) A instead of U. E) none of the above. 3. The most abundant type of RNA found in the cell is A) mRNA. B) rRNA. C) tRNA. D) snRNA. E) none of the above. 4. Which is the smallest RNA molecule? A) mRNA B) rRNA C) tRNA D) prokaryotic mRNA E) none of the above PROTEINS AND PEPTIDES - Dr. Batchelor 5. Why is the peptide bond planar? A) Bulky side chains prevent free rotation around the bond. B) It contains partial double bond character, preventing rotation. C) Hydrogen bonding between the NH and C=O groups limits movement. D) None of the above. E) All of the above. 6. The neurotransmitter serotonin is synthesized from which amino acid ? A) trosine B) arginine C) glutamine D) phenylalanine E) tryptophan 7. Which amino acids contain reactive aliphatic hydroxyl groups? A) serine and methionine B) serine and threonine C) methionine and threonine D) cysteine and methionine E) cysteine and threonine 8. What determines a protein’s function? A) structure B) gene sequence C) N-terminal amino acids D) none of the above E) all of the above ENZYMES: CONCEPTS, KINETICS, AND CATALYTIC AND REGULATORY STRATEGIES - Drs. Rosen, Butko, Shapiro 9. The formula log K'eq = DG°/1.36 indicates the relationship between A) the free energy and the equilibrium constant. B) the reaction equilibrium and the isomerization rate. C) the equilibrium constant and standard free energy. D) all of the above. E) none of the above. 10. What is the common strategy by which catalysis occurs? A) increasing the probability of product formation B) shifting the reaction equilibrium C) stabilization of transition state D) all of the above E) none of the above 11. Enzyme catalysts can be A) RNA. B) lipids. C) proteins. D) a and c. E) none of the above. 12. The Km is A) equal to the product concentration at initial reaction conditions. B) equal to the substrate concentration when the reaction rate is half its maximal value. C) proportional to the standard free energy. D) all of the above. E) none of the above. 13. Given are five Km values for the binding of substrates to a particular enzyme. Which has the strongest affinity when k 1 is greater than k2? A) 150 mM B) 0.15 mM C) 150 µM D) 1.5 nM E) 15000 pM 14. The Gibbs free energy of activation is A) the difference between the substrate and the transition state. B) the difference between the substrate and the product. C) the difference between the product and the transition state. D) all of the above. E) none of the above. 15. The vitamin nicotinic acid is necessary for _______________ reactions. A) one carbon transfer B) methyl group transfer C) oxidation-reduction D) all of the above E) none of the above 16. Which amino acids in chymotrypsin are found in the active site and are participants in substrate cleavage? A) his, ser, asp B) his, ser C) asp, lys  D) lys, arg E) his, ser, arg 17. The most common strategy(ies) for enzymatic regulation: A) multiple enzyme forms B) allosteric control C) reversible covalent modification D) proteolytic activation E) all of the above 18. Zymogen example(s): A) pepsinogen B) procarboxypeptidse C) preproinsulin D) a and b E) all of the above 19. A regulatory mechanism that is NOT readily reversible: A) phosphorylation B) allosteric control C) proteolytic cleavage D) all of the above E) none of the above CARBOHYDRATES - Dr. MacKerell 20. The nutritional storage form(s) of glucose in mammals. A) glycogen B) amylose C) amylopectin D) b and c E) all of the above LIPIDS AND MEMBRANES - Dr. Butko 21. How many molecules thick are membranes? A) two B) one C) infinite D) varying thickness, depending on structure E) none of the above 22. Molecule that helps regulate membrane fluidity in animals: A) protein B) cholesterol C) ATP  D) magnesium ion E) none of the above METABOLISM: CONCEPTS - Dr. Butko 23. The major purpose(s) for which organisms require energy: A) performance of mechanical work B) active transport C) synthesis of biomolecules D) a and c E) a, b, and c 24. Reaction pathways that transform fuels into cellular energy: A) anabolic B) catabolic C) allobolic D) all of the above E) none of the above 25. The free energy change for hydrolysis of ATP to ADP is: A) 9.20 kJ/mol. B) 136 kJ/mol. C) 30.5 kJ/mol. D) 61.0 kJ/mol. E) 31.8 kJ/mol. 26. Fats are a more efficient energy source than carbohydrates because they are more A) oxidized. B) polarized. C) reduced. D) all of the above. E) none of the above. 27. An example of an oxidation reaction would be A) the conversion of succinate to fumarate using FAD. B) the addition of carbon dioxide to pyruvate to form oxaloacetate. C) the conversion of citrate to isocitrate. D) the hydrolysis of a peptide bond. E) none of the above. 28. An example of an isomerization reaction would be A) the conversion of succinate to fumarate using FAD. B) the addition of carbon dioxide to pyruvate to form oxaloacetate. C) the conversion of citrate to isocitrate. D) the hydrolysis of a peptide bond.  E) none of the above. GLYCOLYSIS AND GLUCONEOGENESIS - Dr. Butko 29. The commited step in glycolysis – and the most important control point – is catalyzed by the enzyme A) phosphoglucose isomerase B) hexokinase C) phosphofructokinase D) aldolase E) phosphoglycarate kinase 30. What two 3-carbon molecules are generated by the cleavage of fructose-1,6- bisphosphate? A) glyceraldehyde-3-phosphate and 3-phosphoglycerate B) glyceraldehyde-3-phosphate and dihydroxyacetone phosphate C) pyruvate and phosphoenolpyruvate D) enolase and 2-phosphoglycerate E) glyceraldehyde-3-phosphate and pyruvate 31. How is pyruvate kinase activity regulated? A) b, c, d, and e, below B) Alanine allosterically inhibits the enzyme. C) Fructose 1,6-bisphosphate activates both isozyme forms. D) The enzyme binds phosphoenolpyruvate cooperatively. E) Two different isoforms exist that differ in their phosphorylation regulation. 32. The primary raw materials (not the initial intermediates) for gluconeogenesis are A) galactose and sucrose. B) pyruvate and oxaloacetate. C) lactate and alanine. D) fructose and alanine. E) lactose and lactate. THE TRICARBOXYLIC ACID CYCLE - Dr. Butko 33. What is the primary function of the citric acid cycle? A) Substrate-level phosphorylation to produce ATP B) Extraction of electrons from carbon fuels. C) Synthesis of tricarboxylic acids. D) Production of CO2. E) Keeping the redox balance inside the mitochondria. 34. What molecule initiates the TCA cycle by reacting with oxaloacetate? A) Pyruvate  B) Acetyl CoA C) Oxaloacetate D) All of the above E) None of the above 35. What enzyme(s) is (are) responsible for this reaction: Pyruvate + CoA + NAD+ ® acetyl CoA + NADH + CO2 A) Acetyl CoA synthetase B) Pyruvate dehydrogenase C) Pyruvate dehydrogenase complex D) a and b E) a, b, and c 36. Which enzymes catalyze the control point reactions of TCA cycle in mammals? A) Pyruvate dehydrogenase complex, isocitrate dehydrogenase, and a- ketoglutarate dehydrogenase complex B) Isocitrate dehydrogenase, malate dehydrogenase, and fumarase C) Isocitrate dehydrogenase, malate dehydrogenase, a-ketoglutarate dehydrogenase complex, and succinate dehydrogenase D) All of the above E) None of the above 37. What are the approximate stoichiometries of ATP derived per NADH and FADH2 from the electron transport chain and oxidative phosphorylation? A) 1.5 ATP per NADH, 1.5 ATP per FADH2 B) 3 ATP per NADH, 2 ATP per FADH2 C) 2 ATP per NADH, 1 ATP per FADH2 D) 2.5 ATP per NADH, 2.5 ATP per FADH2 E) 2.5 ATP per NADH, 1.5 ATP per FADH2 38. Approximately how many ATP or GTP equivalents are made during one turn of the citric acid cycle? A) 10 B) 6 C) 9 D) 12 E) none of the above 39. What are some of the biosynthetic precursors provided by the citric acid cycle? A) a-Ketoglutarate B) Succinyl CoA C) Citrate D) all of the above E) none of the above  OXIDATIVE PHOSPHORYLATION - Dr. Butko 40. The type of gradient critical to ATP formation by oxidative phosphorylation. A) sodium ion B) chloride ion C) proton D) potassium ion E) none of the above 41. In oxidative phosphorylation the electron transfer potential of ______________ is (are) converted to phosphoryl transfer potential of ATP. A) NADH and FADH2 B) glucose C) GTP D) all of the above E) none of the above 42. Electron flow within the electron transport chain leads to A) transport of protons across the inner mitochondrial membrane. B) coupled synthesis of GTP. C) a dangerous imbalance. D) all of the above. E) none of the above. 43. Which of the following does not shuttle electrons? A) Complex I B) Complex II C) Complex III D) Complex IV E) All of the above 44. The net ATP obtained per NADH if the glycerol 3-phosphate shuttle is used is A) 2.5. B) 1.5. C) 2.0. D) 1.0. E) none of the above. 45. In the malate-aspartate shuttle, electrons from NADH are transferred to ________, forming malate. A) oxaloacetate B) aspartate C) acetate D) glutamate E) none of the above 46. What is the net estimate of ATP molecules made by the oxidation of glucose? (Assume the malate-aspartate shuttle is used.) A) 36 B) 30 C) 28 D) 20 E) None of the above PENTOSE PHOSPHATE PATHWAY - Dr. Butko 47. ATP is called the energy currency. The currency of reducing power is A) NADPH. B) NADH. C) AMP. D) ADP. E) none of the above. 48. The purpose of the pentose phosphate pathway is to A) generate ATP. B) generate NADPH. C) generate 5-carbon sugars. D) a and b. E) b and c. 49. Which of the following reactions is NOT part of the pentose phosphate pathway? A) C5 + C5 ® C3 + C7 B) C4 + C5 ® C3 + C6 C) C3 + C7 ® C6 + C4 D) C5 + C6 ® C2 + C9 E) All of the above are true. GLYCOGEN METABOLISM - Dr. Butko 50. The major site(s) of glycogen storage is (are) A) adipose tissue. B) liver. C) skeletal muscle. D) b and c. E) a, b, and c. 51. The key enzyme in glycogen degradation is A) glycogen phosphatase. B) glycogen phosphorylase. C) glucose 1-phosphate synthase.  D) all of the above. E) none of the above. 52. Conversion of glucose 1-phosphate to glucose 6-phosphate is carried out by the enzyme A) phosphoglucomutase. B) Kinase 1-P. C) phosphoglycerate mutase. D) all of the above. E) none of the above. 53. Phosphorylase kinase is regulated by A) calcium ions. B) cAMP activated PKA (Protein Kinase A). C) tyrosine levels. D) a, b, and c. E) a and b. 54. The key regulatory enzyme in glycogen synthesis is A) glycogen synthase phosphorylase. B) glycogen synthase. C) glycogen synthase kinase. D) all of the above. E) none of the above. 55. Which of the following occur after a carbohydrate-rich meal? A) Blood-glucose levels rise leading to glycogen storage in the liver. B) Blood-glucose levels rise leading to glycogen storage in the muscle. C) Glycogen storage in the muscle shuts down. D) All of the above. E) None of the above. 56. What is the normal glucose concentration in blood? A) 80-120 g/100 mL (4.4-6.7 M) B) 80-120 mg/100 mL (4.4-6.7 mM) C) 80-120 µg/100 mL (4.4-6.7 µM) D) all of the above E) none of the above FATTY ACID METABOLISM - Dr. Butko 57. Fatty acids are the building blocks of A) cholesterol. B) phospholipids. C) glycolipids. D) heme.  E) b and c. 58. Why are triacylglycerols an excellent design for energy stores? A) They are anhydrous. B) They are small. C) They are reduced. D) a and b. E) a and c. 59. Enzymes that digest the triacylglycerols into free fatty acids and monoacylglycerol are called A) hydrases. B) glyases. C) lipases. D) all of the above. E) none of the above. 60. The hormone ________ induces lipolysis, whereas the hormone _________ inhibits the process. A) glucagon; adrenocorticotropic hormone B) epinephrine; insulin C) insulin; norepinephrine D) glucagon; epinephrine E) epinephrine; glucagon 61. The function of the enzyme acyl CoA synthetase is A) lipolysis to release free glyceraldehyde. B) ATP-dependent reduction prior to activation. C) ATP-dependent activation of fatty acids using CoA. D) all of the above. E) none of the above. 62. The site of most fatty acid degradation in the cell is the A) mitochondria. B) nucleus. C) chloroplast. D) all of the above. E) none of the above. 63. How many rounds of b-oxidation would be required for fatty acid with an acyl chain of 16 carbons? A) 16 B) 8 C) 7 D) 15 E) none of the above 64. How many acetyl CoA molecules would be made from a fatty acid with an acyl chain of 16 carbons? A) 16 B) 8 C) 7 D) 15 E) none of the above 65. What is the committed step in fatty acid synthesis? A) binding of molecule to acyl carrier protein B) synthesis of malonyl CoA C) transacylase reaction D) all of the above E) none of the above 66. Intermediates in fatty acid synthesis are linked to A) an acyl carrier protein. B) carnitine. C) dolichol phosphate carrier. D) all of the above. E) none of the above. 67. Complete this reaction: Acetyl CoA + 7 malonyl CoA + 14 NADPH + 20 H+ ® A) palmitate + 6 CO2 + 12 NADP+ + 8 CoA + 6 H2O B) oleate + 7 CO2 + 14 NADP+ + 8 CoA + 6 H2O C) palmitate + 7 CO2 + 14 NADP+ + 6 H2O D) palmitate + 7 CO2 + 14 NADP+ + 8 CoA + 6 H2O E) none of the above PROTEIN TURNOVER AND AMINO ACID CATABOLISM - Dr. Batchelor 68. Surplus amino acids are A) stored in proteosomes. B) stored in protein scaffolds. C) used as metabolic fuel. D) all of the above. E) none of the above. 69. Amino acids that supply amino groups that can be converted directly to NH4+ include A) serine and threonine. B) serine, asparagine, and threonine. C) proline and threonine. D) serine and valine.  E) none of the above. 70. During the urea cycle, urea is synthesized on what ‘carrier’ molecule? A) ornithine B) citrilline C) arginine D) lysine E) none of the above 71. The two nitrogen atoms in urea arise from A) ammonia and aspartate B) glutamine and glutamate C) alanine and aspartate D) all of the above E) none of the above 72. Amino acids degraded to acetyl CoA are ____________ amino acids. A) glucogenic B) neogenic C) ketogenic D) all of the above E) none of the above 73. Vitamin B12: A) Is required for the catabolism of odd numbered amino acids B) Is required for the conversion of homocysteine to methionine C) Is a prosthetic group in only two of our enzymes D) All of the above E) None of the above 74. Taking vitamin B12 pills as a supplement is usually a waste of time because: A) A vitamin B12 deficiency is unlikely B) Methionine is a better supplement for the resulting methionine deficiency C) A vitamin B12 deficiency typically results from defective absorption D) All of the above E) None of the above 75. The preventive strategy for phenylketonuria in afflicted individuals is A) increase in tyrosine. B) elimination of phenylalanine in the diet. C) nutritional supplements of aspartame. D) all of the above. E) none of the above. AMINO ACID BIOSYNTHESIS - Dr. Batchelor 76. Glutamine synthetase adds NH3 to _________ to make glutamine. A) Schiff base B) glutamate C) ketoglutarate D) none of the above E) all of the above 77. Glutamate is the precursor for the amino acids glutamine and A) glutathione. B) proline. C) arginine. D) a and b. E) b and c. 78. Types of units that can be carried by tetrahydrofolate: A) CO2 B) methyl, methylene, formyl C) formyl, CO2 D) methyl, CO2 E) none of the above 79. Essential amino acids are synthesized by A) microorganisms. B) humans. C) plants. D) a and b. E) a and c. 80. Amino acid added to indole to form tryptophan: A) glutamine B) serine C) tyrosine D) all of the above E) none of the above NUCLEOTIDE BIOSYNTHESIS - Dr. Batchelor 81. The two nucleotides that can serve as energy currency in certain biomolecular paths: A) ATP and GTP B) ATP and UTP C) UTP and GTP D) dATP and dGTP E) none of the above 82. The source(s) of NH2 groups in synthesis of nucleotides: A) aspartate B) glutamine C) glycine D) a and b E) a, b, and c 83. Scaffolds for the ring systems in nucleotides are from the amino acid(s) A) glycine. B) glutamine. C) aspartate. D) a and b. E) a and c. 84. In de novo synthesis the pyrimidine ring is assembled using A) bicarbonate. B) aspartate. C) glutamine. D) a and b. E) a, b, and c. 85. What enzyme carries out this reaction? XDP + YTP ® XTP + YDP A) nucleoside triphosphate kinase B) nucleoside diphosphate kinase C) nucleoside diphosphate phosphorylase D) nucleoside triphosphate phosphorylase E) none of the above 86. The synthesis of CTP from UTP requires UTP and A) glutamine and ATP. B) glycine and ATP. C) glutamine, ATP, and NADH. D) all of the above. E) none of the above. 87. Tetrahydrofolate is generated from dihydrofolate by dihydrofolate reductase and uses the reductant A) FADH2. B) NADH. C) NADPH. D) riboflavin. E) none of the above. 88. Fluorouracil and aminopterin reduce the level of: A) dAMP  B) dUMP C) dTMP D) dGMP E) none of the above 89. NDPs are converted to dNDPs by: A) NDP kinase B) thymidylate synthase C) ALT D) ribonucleotide reductase E) none of the above 90. Allopurinol inhibits which enzyme? A) IMP synthase B) adenosuccinyl synthase C) xanthine oxidase D) XMP synthase E) none of the above BIOSYNTHESIS OF MEMBRANE LIPIDS AND STEROIDS - Dr. Butko 91. The first synthetic step in the pathway to form phospholipids and triacylglycerols is to make A) diacylglycerol. B) inosinic acid. C) phosphatidate. D) all of the above. E) none of the above. 92. The highest concentration of sphingolipids is found in the A) central nervous system. B) lymph system. C) serum. D) all of the above. E) none of the above. 93. Tay Sachs disease is caused by an inability to degrade A) sphingosene. B) gangliosides. C) dipalmitoyl phosphatidyl choline. D) all of the above. E) none of the above. 94. HMG CoA is synthesized from acetyl CoA and __________. A) oxaloacetate. B) acetoacetyl CoA.  C) acetyl CoA. D) all of the above. E) none of the above. 95. Feedback regulation of cholesterol synthesis is mainly controlled at this enzymatic step. A) 3-hydroxy-3-methylglutaryl CoA reductase B) geranyltransferase C) HMG transferase D) farnesyl reductase E) none of the above 96. Hydroxylation of cholesterol requires A) NADPH. B) activated O2. C) PLP. D) a and b. E) a and c. INTEGRATION OF METABOLISM – Dr. Butko 97. What is often the significance of the first irreversible step in a biosynthetic pathway? A) It always has low-affinity binding for the enzyme:substrate complex. B) The step usually requires a metal cofactor. C) It is often a regulatory step. D) All of the above. E) None of the above. 98. Pyruvate is derived from: A) Glucose-6-phosphate B) Lactate C) Alanine D) a and b E) a, b, and c 99. What are some of the metabolic fates of pyruvate? A) Transamination to alanine B) Carboxylation to oxaloacetate C) Reduction to lactate D) All of the above E) None of the above 100. Ethanol consumption leads to an increase in A) Glucose B) NADH C) Methanol D) Tyrosine E) Cholesterol