INTRODUCTORY BIOCHEMISTRY. BI 28 Second Midterm Examination April 3, 2007

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1 INTRODUCTORY BIOCHEMISTRY BI 28 Second Midterm Examination April 3, 2007 Name 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. Exams will be photocopied before being returned on Thursday. Please note: All regrade requests for this exam are due by Thursday April 12 th at 5pm. Regrades can lead to an overall lower score on the exam. Page 2 total /10 Page 3 total /15 Page 4 total /17 Page 5 total /10 Page 6 total /18 Page 7 total /12 Page 8 total /12 Page 9 total /6 Extra Credit /4 Exam total /100

2 1. [2] Which combination of cofactors is involved in the conversion of pyruvate to acetyl-coa? A) Biotin, FAD, and TPP B) Biotin, NAD +, and FAD C) NAD +, biotin, and TPP D) Pyridoxal phosphate, FAD, and lipoic acid E) 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) Citrate B) Fumarate C) Isocitrate D) Pyruvate E) Succinate 3. [2] Briefly describe the relationship of the pyruvate dehydrogenase complex reaction to glycolysis and 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. 2

3 6. [3] Indicate whether the following statements about the citric acid cycle are true or false by circling T or F for each question. 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 QH 2 to O 2 B) O 2 to NAD+ and Q C) O 2 to NADH 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 B) cytochrome c C) FADH 2 D) heme 10. [4] Explain why there are only 6 protons translocated for each FADH 2 that is reduced by the succinate dehydrogenase complex. 11. [2] During oxidative phosphorylation, NADH equivalents are transferred into the mitochondrial matrix via the - shuttle in liver cells and the shuttle in muscle cells. Enter the correct answer in the missing spaces provided 3

4 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 molecules of NADPH to NADP + and the energy derived from hydrolysis of molecules of ATP to ADP. Enter the correct number in the missing spaces provided 15. [2] Plants that use the C4 mechanism to acquire CO 2, compared to plants that do not use this mechanism (C3 plants), need an additional amount of energy equivalent to that derived from hydrolysis of molecules of ATP to ADP, and an additional amount of reducing equivalents equivalent to the amount derived from oxidation of molecules of NADPH to NADP +. Enter the correct number in the missing spaces provided 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 Ferredoxin Chlorophyll b Oxygen-evolving complex Cyclic photophosphorylation Noncyclic photophosphorylation Plastoquinone 4

5 17. [2] Indicate with an asterisk (*) which atom or atoms of the compound shown below would be radioactively labeled when 14 CO 2 is fixed during one turn of the Calvin cycle. CH 2 OH H-C-OH CH 2 OPO 3 H [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] Considering the function of fructose 2,6 bisphosphate (F2,6BP) in the regulation of glycolysis and gluconeogenesis, enter in the spaces provided below its function, which enzyme(s) determine the cellular levels of this molecule, which enzyme(s) are regulated by this molecule, and what effect high concentrations of F2,6BP will have on glycolysis and gluconeogenesis. Function of F2,6BP: Enzyme(s) determining cellular levels: F2,6BP regulates: High [F2,6BP]: 20. [2] The glycogen-branching enzyme catalyzes: A) degradation of (a1 4) linkages in glycogen B) formation of (a1 4) linkages in glycogen. C) formation of (a1 6) linkages during glycogen synthesis. D) glycogen degradation in tree branches. E) removal of unneeded glucose residues at the ends of branches. 5

6 21. [4] Explain the function of glycogenin 22. [2] During polysaccharide breakdown, glycogen and starch are converted to by the enzyme. Enter the correct answer in the missing spaces provided 23. [4] Indicate whether the following statements about fatty acid catabolism are true of false by circling T or F for each question. 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. Ketone bodies are synthesized from. Enter the correct answer in the missing spaces provided 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: Synthesized by: Enzyme that synthesizes fatty acids: Acyl carrier for synthesis: Electron donor cofactor: Fatty acid released: 6

7 26. [2] A 30-carbon precursor of the steroid nucleus (during cholesterol synthesis) is: A) farnesyl pyrophosphate. B) geranyl pyrophosphate. C) isopentenyl pyrophosphate. D) lysolecithin. E) squalene. 27. [2] Transamination from alanine to α-ketoglutarate requires the coenzyme: A) biotin. B) NADH. C) No coenzyme is involved. D) pyridoxal phosphate (PLP). E) thiamine pyrophosphate (TPP). 28. [2] Serine or cysteine may enter the citric acid cycle as acetyl-coa after conversion to: A) oxaloacetate. B) propionate. C) pyruvate. D) succinate. E) succinyl-coa 29. [6] Amino acid biosynthesis: In the empty boxes in the figure to the right, mark the correct box for the following molecules with the corresponding letter. A) oxaloacetate B) histidine C) pyruvate D) α-ketoglutarate E) ribose 5-phosphate F) serine 7

8 30. [2] During starvation, more urea production occurs. Explain this observation (in 50 words or less). 31. [2] Which of the following enzymes is not involved in the assimilation of inorganic nitrogen into an organic molecule? A) Arginase B) Glutamate dehydrogenase C) Glutamate synthase D) Glutamine synthetase E) 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): urea synthesis glycolysis fatty acid synthesis β-oxidation Enter the correct letter in the missing spaces provided 33. [2] Insulin is an example of a(n) hormone. A) catecholamine B) eicosanoid C) paracrine D) peptide E) steroid 34. [2] The largest energy store in a well-nourished human is: A) ATP in all tissues. B) blood glucose. C) liver glycogen. D) muscle glycogen. E) triacylglycerols in adipose tissue. 8

9 35. [2] When blood glucose is abnormally high, the pancreas releases: A) epinephrine. B) glucagon. C) glucose. D) insulin. E) trypsin. 36. [4] Which class of hormones acts via nuclear receptors? Briefly describe the mode of action of these hormones. 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 CO 2 by the extract increased when succinate was added. In fact, for every mole of succinate added, many extra moles of CO 2 were produced. Explain this effect in terms of the known catabolic pathways. 9