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BANNER ID B 0 0 __ __ __ __ __ __ 1 INTRODUCTORY BIOCHEMISTRY BIOL0280 Second Midterm Examination April 2, 2015 Enter Legible BANNER ID: B 0 0 __ __ __ __ __ __ DO NOT WRITE YOUR NAME ON THIS EXAM Make sure that your Banner ID 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 for each question are indicated within brackets []. There are no calculators or other electronic devices needed or allowed on this exam. All hats must be removed during the exam. Exams will be scanned electronically before being returned. Page 2 total __________/ 10 Page 3 total __________/ 9 Page 4 total __________/ 12 Page 5 total __________/ 11 Page 6 total __________/ 12 Page 7 total __________/ 11 Page 8 total __________/ 12 Page 9 total __________/ 10 Page 10 total _________/ 13 Exam total __________/ 100 BANNER ID B 0 0 __ __ __ __ __ __ 2 1. [4 points] Name the molecules shown in the figures. ___________________________ _______________________ 2. [2 points] Which of the following is not true of the reaction catalyzed by the pyruvate dehydrogenase complex? A) Both NAD+ and a FAD act as electron carriers. B) The reaction occurs in the mitochondrial matrix. C) The substrate is held by the lipoyl-lysine “swinging arm.” D) Biotin participates in the decarboxylation. E) Two different cofactors containing —SH groups participate. Circle the correct answer. 3. [4 points] In the citric acid cycle, we encountered a three-step mechanism to oxidize an alkyl chain (shown in the figure). Name the four citric acid cycle intermediates (indicated with letters next to the figure) that are involved in this mechanism. _________________________________ A. _________________________________ B. _________________________________ C. _________________________________ D. BANNER ID B 0 0 __ __ __ __ __ __ 3 4. [2 points] The oxidative decarboxylation of α-ketoglutarate proceeds by means of multistep reactions in which all but one of the following cofactors are required. Which one is not required? A) Coenzyme A B) ATP C) Lipoic acid D) NAD+ E) Thiamine pyrophosphate Circle the correct answer. 5. [2 points] Indicate whether the following statements are true or false by circling True or False. True / False The citric acid cycle completely reduces the products of glycolysis to CO2 and generates oxidized cofactors as well as some ATP. True / False Anaplerotic reactions convert two-carbon molecules into four-carbon molecules. 6. [3 points] List at least three factors that mitochondria and bacteria have in common. 7. [2 points] Which of the following statements about the chemiosmotic theory is false? A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane. B) Energy is conserved as a transmembrane pH gradient. C) The membrane ATPase, which plays an important role in other hypotheses for energy coupling, has no significant role in the chemiosmotic theory. D) Oxidative phosphorylation cannot occur in membrane-free preparations. E) The effect of uncoupling reagents is a consequence of their ability to carry protons through membranes. Circle the correct answer. BANNER ID B 0 0 __ __ __ __ __ __ 4 8. [4 points] Indicate whether the following statements are true or false by circling True or False. True / False The energy gained from NADPH re-oxidation is conserved in a proton gradient. True / False Electrons that enter the electron transport chain from succinate dehydrogenase bypass Complex I. True / False Cytochrome C is a small membrane anchored protein that transfers electrons from Complex III to Complex IV. True / False The isolated F1 complex catalyzes ATP hydrolysis. 9. [2 points] Which of the following is not a feature of complex IV? A) B) C) D) Cytochrome c is a one-electron donor. Oxygen is a substrate. Copper is an essential metal for the reaction. For every electron passed to complex IV, two protons are consumed from the matrix (N) side. E) In order to generate two water molecules, complex IV must go through the catalytic cycle two times. Circle the correct answer. 10. [4 points] Glycolysis, the citric acid cycle, and oxidative phosphorylation are inhibited by ATP. Briefly explain the purpose of this regulation by ATP. 11. [2 points] Rotation of the ______ subunit of ATP synthase causes conformational changes in the catalytic sites that produce ATP. A) α B) β C) δ Circle the correct answer. D) ε E) γ BANNER ID B 0 0 __ __ __ __ __ __ 5 12. [4 points] Explain in one or two sentences what accessory pigments are. 13. [2 points] Oxidative phosphorylation and photophosphorylation share all of the following except: A) chlorophyll. B) involvement of cytochromes. C) participation of quinones. D) proton pumping across a membrane to create electrochemical potential. E) use of iron-sulfur proteins. Circle the correct answer. 14. [2 points] What is the soluble electron carrier in chloroplast photosystems, a molecule analogous to cytochrome c in mitochondria? A. Cytochrome c2 B. Cytochrome bc1 C. Plastocyanin D. Rhodopsin E. Ferredoxin Circle the correct answer. 15. [3 points] Fill in the blanks in the following sentence describing the Calvin cycle: For every 3 __________________ molecules fixed, 9 ATP and 6 _____________________ molecules are consumed and one molecule _______________________________________ is produced. BANNER ID B 0 0 __ __ __ __ __ __ 6 16. [4 points] Briefly describe the strategy used by C4 plants to circumvent photorespiration. 17. [2 points] In humans, gluconeogenesis: A) helps to reduce blood glucose after a carbohydrate-rich meal. B) is activated by the hormone insulin C) is essential in the conversion of fatty acids to glucose. D) requires the enzyme hexokinase. E) can result in the conversion of protein into blood glucose. Circle the correct answer. 18. [4 points] Fill in the blanks in the following sentences: The product of the enzyme PFK-2 is the molecule _______________________________. The main storage polysaccharide in animal cells is ______________________________. The enzyme that primes glycogen synthesis is called ____________________________. Glycogen phosphorylase and glycogen synthase are ____________________________ regulated. 19. [2 points] The glycogen-branching enzyme catalyzes: A) degradation of (α1 → 4) linkages in glycogen B) formation of (α1 → 4) linkages in glycogen. C) formation of (α1 → 6) linkages during glycogen synthesis. D) glycogen degradation in tree branches. E) removal of unneeded glucose residues at the ends of branches. Circle the correct answer. BANNER ID B 0 0 __ __ __ __ __ __ 20. [4 points] Briefly describe how fatty acids are transported from the cytosol into mitochondria. Mention potential activation reactions and the import systems being used. 21. [2 points] Which compound is an intermediate of the β oxidation of fatty acids? A) CH3—(CH2)20—CO—COOH B) CH3—CH2—CO—CH2—CO—OPO32– C) CH3—CH2—CO—CH2—OH D) CH3—CH2—CO—CO—S—CoA E) CH3—CO—CH2—CO—S—CoA Circle the correct answer. 22. [2 points] The cofactor of propionyl-CoA carboxylase is A) FAD B) NADH C) biotin D) coenzyme B12 E) TPP Circle the correct answer. 23. [3 points] Name the three molecules that function as ketone bodies in metabolism. 7 BANNER ID B 0 0 __ __ __ __ __ __ 8 24. [6 points] 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 the enzyme: _________________________________ Enzyme that synthesizes fatty acids: _________________________________ Acyl carrier for synthesis: _________________________________ Electron donor cofactor: _________________________________ Fatty acid released: _________________________________ 25. [2 points] Name the molecule shown in the figure. _________________________________ 26. [2 points] Fill in the missing word(s). Cholesterol-lowering drugs (statins) act as competitive inhibitors of the enzyme ___________________________________. 27. [2 points] Urea synthesis in mammals takes place primarily in tissues of the: A) brain. B) kidney. C) liver. D) skeletal muscle. E) small intestine. Circle the correct answer. BANNER ID B 0 0 __ __ __ __ __ __ 9 28. [2 points] If a person's urine contains unusually high concentrations of urea, which one of the following diets has he or she probably been eating recently? A) High carbohydrate, very low protein B) Very high carbohydrate, no protein, no fat C) Very low carbohydrate, very high protein D) Very, very high fat, high carbohydrate, no protein E) Very high fat, very low protein Circle the correct answer. 29. [4 points] Indicate whether the following statements are true or false by circling True or False. True / False Aminotransferases have a thiamine pyrophosphate prosthetic group. True / False Major excretory forms of nitrogen are ammonia, urea, and uric acid. True / False In amino acid biosynthesis, glycine and proline are derived from 3phosphoglycerate. True / False Denitrifying bacteria reduce NO3- to N2. 30. [4 points] Briefly describe the bacterial process of nitrogen fixation. BANNER ID B 0 0 __ __ __ __ __ __ 10 31. [3 points] List at least three factors affecting the activity of enzymes 32. [2 points] The molecule shown in the figure is A. carnitine B. ornithine C. arginine D. creatine E. glyoxylate Circle the correct answer. 33. [4 points] 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): _____ glycolysis _____ β-oxidation _____ fatty acid synthesis _____ urea synthesis 34. [4 points] In the space provided, name the energy sources (molecules) for muscle contraction during: Light activity or rest ________________________________________________ Bursts of heavy activity ________________________________________________