MBioS 303 Recitation Introductory Biochemistry, Summer 2008 Practice Problem Set #7: General Metabolism Concepts, Glycolysis and the TCA Cycle
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1 MBioS 303 Recitation Introductory Biochemistry, Summer 2008 Practice Problem Set #7: General Metabolism Concepts, Glycolysis and the TCA Cycle (1) Glucose 1-pohsphate is converted to fructose 6-phosphate in two successive reactions: Glucose-1-P glucose-6-p Glucose-6-P fructose-6-p ΔG⁰ = -1.7 kcal/mol ΔG⁰ = -0.4 kcal/mol What is the ΔG⁰ for the overall reaction? A. ΔG⁰ values are additive. a kcal/mol b kcal/mol c kcal/mol d. 1.3 kcal/mol e. 2.1 kcal/mol (2) Which of the following are ways by which two reactions can be coupled energetically to each other? B, C and D. Being in the same compartment does not necessarily couple two reactions. a. As common intracellular components of a compartment, two reactions become automatically coupled. b. An ionic gradient across a membrane that is formed by one reaction can drive another reaction that uses the gradient to render it exergonic. c. A shared, common intermediate can couple two reactions. d. A protein that is activated by binding another molecule or by being covalently modified can provide energy to drive another reaction. (3) Which of the following are high-energy compounds? B, D a. Glucose-6-phosphate b. Adenosine diphosphate c. Fructose-6-phosphate d. 1,3-bisphosphoglycerate e. Dihydroxyacetone phosphate (4) Which of the following answers complete the sentence correctly? NAD + B, C, D a. is a flavin nucleotide. b. is the major electron acceptor used in fuel metabolism. c. contains a nicotinamide ring that accepts a hydride ion during reduction. d. loses a plus charge upon reduction. e. contains ATP as a part of its structure.
2 (5) Match the four cofactors in the left column with the appropriate structural features and properties from the right column. a. ATP 2, 3, 5, 7 (1) nicotinamide ring (5) ribose group b. FAD 2, 3, 4, 5, 6 (2) adenine group (6) electron transfer c. NAD + 1, 2, 3, 5, 6 (3) phosphoanhydride bond (7) phosphate transfer (4) isoalloxazine ring (6) ATP and NADH release large amounts of free energy upon the transfer of the phosphate group to H 2 O and electrons to O 2, respectively. However, both molecules are relatively stable in the presence of H 2 O or O 2. Explain why. Although the transfer reactions of the cofactors ATP and NADH have large negative free-energy changes, there are high activation-energy barriers that greatly slow spontaneous reactions with H 2 O or O 2, respectively. In other words, cofactors with high group transfer potentials and fuel molecules are thermodynamically unstable yet kinetically stable. Consequently, specific enzymes are required to catalyze their reactions. (7) What are the three primary fates of pyruvate? Ethanol, lactate, and CO 2 /water (8) For each of the following types of chemical reactions, give at least one example of a glycolytic enzyme that carries out such a reaction. a. Aldol cleavage Aldolase b. Dehydration Enolase c. Phosphoryl transfer Hexokinase, phosphofructokinase, phosphyglycerate kinase, or pyruvate kinase d. Phosphoryl shift phosphoglycerate mutase e. Isomerization phosphohexose isomerase, triosephosphate isomerase f. Phosphorylation coupled to oxidation glyceraldehyde 3-phosphate dehydrogenase (9) The steps of glycolysis between glyceraldehyde 3-phosphate and 3-phosphyglycerate involve all of the following except: C a. ATP synthesis. b. Utilization of P i. c. Oxidation of NADH to NAD +. d. Formation of 1,3-bisphosphyglycerate. e. Catalysis by phosphoglycerate kinase. (10) Which of the following answers complete the sentence correctly? The phosphofructokinase and the pyruvate kinase reactions are similar in that D a. Both generate ATP. b. Both involve a high-energy sugar derivative. c. Both involve three-carbon compounds. d. Both are essentially reversible.
3 (11) If the C-1 carbon of glucose were labeled with 14 C, which of the carbon atoms in pyruvate would be labeled after glycolysis? C a. The carboxylate carbon c. The methyl carbon b. The carbonyl carbon (12) Starting with fructose 6-phosphate and proceeding to pyruvate, what is the net yield of ATP molecules? C a. 1 b. 2 c. 3 d. 4 e. 5 (13) Since lactate is a dead-end product of metabolism in the sense that its sole fate is to be reconverted into pyruvate, what is the purpose of its formation? The reduction of pyruvate to lactate converts NADH to NAD+, which is required in the glyceraldehyde 3-phosphate dehydrogenase reaction. This prevents glycolysis from stopping owing to too low a concentration of NAD+ and allows continued production of ATP. (14) The essentially irreversible reactions that control the rate of glycolysis are catalyzed by which of the following enzymes? A, D, E a. Pyruvate kinase b. Aldolase c. Glyceraldehyde 3-phoosphate dehydrogenase d. Phosphofructokinase e. Hexokinase f. Phosphyglycerate kinase (15) What are the potential advantages of a multienzyme complex with respect to the isolated enzyme components? A multienzyme complex can carry out the coordinated catalysis of a complex reaction. The intermediates in the reaction remain bound to the complex and are passed from one enzyme component to the next, which increases the overall reaction rate and minimizes side reactions. In the case of isolated enzymes, the reaction intermediates would have to diffuse randomly between enzymes. (16) Examine Figure 1 (near the bottom). Without using your notes or textbook, can you go through the figure and label the metabolic intermediates (labeled A through J) and the enzymes (labeled 1 through 10)? Also be sure to label where ADP and ATP are used and formed, and where NAD + and NADH are oxidized or reduced (indicated by red boxes). (17) Examine Figure 2 (near the bottom). Without using your notes or textbook, can you go through the figure and label the metabolic intermediates (labeled A through K) and the enzymes (labeled 1 through 8)? Also be sure to label where energy (in the form of ATP or GTP)
4 and electron carriers (in the form of NAD + /NADH or FAD/FADH 2 ) are oxidized and reduced (indicated by red boxes). You do need to know which specific energy molecule or electron carrier is used at each step! You should be able to determine the correct answers for questions 16 and 17 by using your textbook or lecture notes. Therefore, I am not providing the answers for these questions. FIGURE 1
5 FIGURE 2
Coupled, interconnecting reactions
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