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INTRODUCTORY BIOCHEMISTRY BI 28 Name Second Midterm Examination KEY April 3, 2007 SIS # Make sure that your name or SIS # is on every page. This is the only way we have of matching you with your exam after grading it. Please work independently. Read each question carefully before answering. Unless otherwise indicated, there is only one correct answer for each multiple choice question. Points are indicated by the question within brackets [ ]. There are no calculators or other electronic devices needed or allowed on this exam. Page 2 total ____10______/ Page 3 total ____15______/ Page 4 total __________/ Page 5 total __________/ Page 6 total __________/ Page 7 total __________/ Page 8 total __________/ Page 9 total __________/ Extra Credit__________/ Exam total __________/100 1. [2] Which combination of cofactors is involved in the conversion of pyruvate to acetyl-CoA? A) B) C) D) E) Biotin, FAD, and TPP Biotin, NAD+, and FAD NAD+, biotin, and TPP Pyridoxal phosphate, FAD, and lipoic acid TPP, lipoic acid, and NAD+ 2. [2] Malonate is a competitive inhibitor of succinate dehydrogenase. If malonate is added to a mitochondrial preparation that is oxidizing pyruvate as a substrate, which of the following compounds would you expect to decrease in concentration? A) B) C) D) E) Citrate Fumarate Isocitrate Pyruvate Succinate 3. [2] Briefly describe the relationship of the pyruvate dehydrogenase complex reaction to glycolysis and the citric acid cycle. Ans: The pyruvate dehydrogenase complex converts pyruvate, the product of glycolysis, into acetyl-CoA, the starting material for the citric acid cycle. 4. [2] Most of the energy released in the citric acid cycle reactions is conserved in _________. A) GTP B) ATP C) NADH D) ADP 5. [2] The formation of oxaloacetate by malate dehydrogenase is endergonic (ΔG’0 = 29.7 kJ/mol), so the concentration of oxaloacetate would be much lower than that of the substrate L-malate at equilibrium. Explain why the reaction moves forward in the citric acid cycle. A: Oxaloacetate is effectively removed in step 1 of the cycle, which has a high affinity for axaloacetate and is highly exergonic ((ΔG’0 = -32.2kJ/mol). Alternative answer: exergonic step 1 drives the reaction forward. Points for removed, exergonic, step 1 2 6. [3] Indicate whether the following statements about the citric acid cycle are true or false by circling T or F. T / F The carbon atoms that enter the citric acid cycle via acetyl-CoA are the same ones released as carbon dioxide during one round of the citric acid cycle. T / F The overall goal of the citric acid cycle is to oxidize pyruvate, form reduced coenzymes, and produce ATP. T / F A racemic mixture of the enantiomeric forms of isocitrate is produced during the citric acid cycle reactions. 7. [2] Circle the enzyme(s) that are unique to the glyoxylate cycle A) malate synthase B) malate dehydrogenase C) isocitrate lyase D) citrate synthase E) isocitrate dehydrogenase 8. [2] In the respiratory electron transport chain electrons are passed from ___________. A) NADH and QH2 to O2 C) O2 to NADH B) O2 to NAD+ and Q D) NADH to ATP 9. [2] A lipid soluble cofactor that can diffuse freely in the membrane of the electron transport chain and carry electrons across the membrane is __________. A) ubiquinone C) FADH2 B) cytochrome c D) heme 10. [4] Explain why there are only 6 protons translocated for each FADH2 that is reduced by the succinate dehydrogenase complex. A: Electrons that enter the electron transport chain from succinate dehydrogenase bypass complex I (which transports 4 protons) 11. [2] During oxidative phosphorylation, NADH equivalents are transferred into the mitochondrial matrix via the __malate___-___aspartate_____ shuttle in liver cells and the __glycerol 3phosphate_ shuttle in muscle cells. 3 12. [2] Rotation of the ______ subunit of ATP synthase causes conformational changes in the catalytic sites that produce ATP. A) α B) β C) δ D) ε E) γ 13. [2] Heat can be generated in the brown fat tissue of hibernating mammals due to _______. A) increased ATP production by ATP synthase B) uncoupling by thermogenin C) a greater pH gradient across the inner mitochondrial membrane by complex IV D) insufficient NADH production during the citric acid cycle due to less active pyruvate dehydrogenase 14. [2] Per carbon atom fixed, operation of the complete Calvin cycle requires the reducing equivalents derived from oxidation of _2__ molecules of NADPH to NADP+ and the energy derived from hydrolysis of _3__ molecules of ATP to ADP. 15. [2] Plants that use the C4 mechanism to acquire CO2, compared to plants that do not use this mechanism (C3 plants), need an additional amount of energy equivalent to that derived from hydrolysis of _2__ molecules of ATP to ADP, and an additional amount of reducing equivalents equivalent to the amount derived from oxidation of _0__ molecules of NADPH to NADP+. 16. [9] For each process or component listed below, indicate in the space provided whether it is associated with Photosystem I, Photosystem II, or both Photosystems. Pheophytin ___II____ Ferredoxin ____I_____ Chlorophyll b __I,II____ Oxygen-evolving complex ____II____ Cyclic photophosphorylation ___I______ Noncyclic photophosphorylation __I,II____ Plastoquinone ___II_____ 4 17. [2] Indicate with an asterisk (*) which atom or atoms of the compound shown below would be radioactively labeled when 14CO2 is fixed during one turn of the Calvin cycle. *CH2OH | H-C-OH | CH2OPO3H218. [2] Gluconeogenesis shares some, but not all, enzymes with the glycolytic pathway. It would appear to be more efficient if both pathways used all of the same enzymes since the pathways are essentially the reverse of each other. Why don’t both pathways use all of the same enzymes? A) The reactions where enzymes differ occur in different parts of the cell for glycolysis versus gluconeogenesis B) Enzymes can catalyze a reaction only in one direction, so naturally the two pathways have some enzymes that differ. C) In tissues where gluconeogenesis occurs, the glycolytic enzymes are present at extremely low concentrations. D) Three of the reaction steps in gluconeogenesis would have prohibitively large, positive free energies if they used glycolytic enzymes for their catalysis. 19. [4] Function of fructose 2,6 bisphosphate in the regulation of glycolysis and gluconeogenesis. Mention which enzymes determine the cellular levels of this molecule, which enzymes are regulated by this molecule and which effect high concentrations of F2,6BP will have on glycolysis and gluconeogenesis. Function of F2,6BP: allosteric regulator of PFK1 and FBPase1, or reciprocally regulates glycolysis and gluconeogenesis Enzyme(s) determining cellular levels: PFK2/FBPase2 F2,6BP regulates: PFK1 and FBPase1 High [F2,6BP]: increase (activate, upregulate) glycolysis and decrease (inhibit, downregulate) gluconeogenesis 20. [2] The glycogen-branching enzyme catalyzes: A) B) C) D) E) degradation of (a1 → 4) linkages in glycogen formation of (a1 → 4) linkages in glycogen. formation of (a1 → 6) linkages during glycogen synthesis. glycogen degradation in tree branches. removal of unneeded glucose residues at the ends of branches. 5 21. [4] Explain the function of glycogenin A: Glycogenin is a protein that acts as a primer for the initiation of new glycogen molecules. It catalyzes the transfer of a glucose residue from UDP-glucose to a tyrosine residue of itself. It then adds seven more glucose residues and forms a complex with glycogen synthase, which further extends the growing glycogen chain. 22. [2] During polysaccharide breakdown, glycogen and starch are converted to _glucose 1phosphate_ by the enzyme ___glycogen phosphorylase_______. 23. [4] Indicate whether the following statements about fatty acid catabolism are true of false by circling T or F. T / F hydrolysis of glycerolipids releases glycerol 3-phosphate and fatty acids T / F The rate limiting step in fatty acid oxidation is the activation of free fatty acids with ATP T / F fatty acids are transported into mitochondria as acyl carnitine T / F β-oxidation of odd numbered fatty acids yields propionyl-CoA that is then further converted to succinyl-CoA 24. [2] In the human body, ketogenesis occurs in the ___liver____. Ketone bodies are synthesized from ____acetyl-CoA_____. 25. [6] Fatty acid biosynthesis: In the space provided below, enter which molecule is the carbon donor for synthesis, which enzyme synthesizes this carbon donor, which enzyme then synthesizes fatty acids, what functions as the acyl carrier during synthesis, which cofactor serves as the electron donor and which fatty acid is released from the synthesizing enzyme. Carbon donor for fatty acid synthesis: malonyl-CoA Synthesized by: ACC, acetyl-CoA carboxylase Enzyme that synthesizes fatty acids: fatty acid synthase Acyl carrier for synthesis: ACP, acyl carrier protein Electron donor cofactor: NADPH Fatty acid released: palmitate 6 26. [2] A 30-carbon precursor of the steroid nucleus (during cholesterol synthesis) is: A) B) C) D) E) farnesyl pyrophosphate. geranyl pyrophosphate. isopentenyl pyrophosphate. lysolecithin. squalene. 27. [2] Transamination from alanine to α-ketoglutarate requires the coenzyme: A) B) C) D) E) biotin. NADH. No coenzyme is involved. pyridoxal phosphate (PLP). thiamine pyrophosphate (TPP). 28. [2] Serine or cysteine may enter the citric acid cycle as acetyl-CoA after conversion to: oxaloacetate. propionate. pyruvate. succinate. E) succinyl-CoA A) B) C) D) 30. [6] Amino acid biosynthesis: In the empty boxes in the figure to the right, mark the correct position for the following molecules with the corresponding letter. A) oxaloacetate B) histidine C) pyruvate D) α-ketoglutarate E) ribose 5-phosphate F) serine 7 29. [2] During starvation, more urea production occurs. Explain this observation (in 50 words or less). Ans: During starvation, cellular proteins are degraded and their carbon skeletons are oxidized for energy. The first step in amino acid catabolism is removal of the amino groups, which are ultimately excreted as urea. 31. [2] Which of the following enzymes is not involved in the assimilation of inorganic nitrogen into an organic molecule? A) B) C) D) E) Arginase Glutamate dehydrogenase Glutamate synthase Glutamine synthetase Nitrogenase 32. [4] Indicate with a letter the cellular compartment where each of the following metabolic pathways takes place (indicate with “C”ytosol, “M”atrix, “B”oth compartments): _B__ urea synthesis _C__ glycolysis _C__ fatty acid synthesis _M__ β-oxidation 33. [2] Insulin is an example of a(n) ____________ hormone. A) B) C) D) E) catecholamine eicosanoid paracrine peptide steroid 34. [2] The largest energy store in a well-nourished human is: A) B) C) D) E) ATP in all tissues. blood glucose. liver glycogen. muscle glycogen. triacylglycerols in adipose tissue. 8 35. [2] When blood glucose is abnormally high, the pancreas releases: A) B) C) D) E) epinephrine. glucagon. glucose. insulin. trypsin. 36. [4] Which class of hormones acts via nuclear receptors? Briefly describe the mode of action of these hormones. Ans: Steroid hormones. Examples are the sex hormones testosterone and estradiol. They pass through the plasma membrane and interact with receptor proteins in the nucleus. The hormonereceptor complex interacts with DNA and alters the expression of specific genes. Challenge Question [4 extra credit] Preparation of an extract of muscle results in a dramatic decrease in the concentration of citric acid cycle intermediates compared to their concentrations in the tissue. However, in 1935, Szent-Gyorgi showed that the production of CO2 by the extract increased when succinate was added. In fact, for every mole of succinate added, many extra moles of CO2 were produced. Explain this effect in terms of the known catabolic pathways. Ans: Succinate is an intermediate in the citric acid cycle that is not consumed but is regenerated by the operation of the cycle. Its addition to an extract depleted in citric acid cycle intermediates allows the cycle to resume operating, oxidizing acetyl-CoA to CO2. 9