MCB102-07 exam

MCB102-07 exam - MCB102 Description of exam 2 given in Fall...

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Unformatted text preview: MCB102 Description of exam 2 given in Fall 2007 The following is part of the study guide given to students before the exam: 1. Calculation of free energy release from equilibrium constant. 3 points 2. Calculation of free energy release from difference in electrochemical potentials. 3 points For questions 1 and 2, formulae will be given on the cover phage of the exam, along with arithmetic calculations. Please do not bring a calculator. 3. Glycolysis 4 points 4. Recognizing a coenzyme and writing an important reaction and enzyme name. 8 points 5. Analysis of a branch-point in metabolism. 12 points 6. Hormone action and glycogen metabolism. 9 points 7. Quantitative analysis of photosynthesis light reactions. 6 points 8. Carbon dioxide fixation. 6 points 9. 14C labeling in the carbon shuffling part of the pentose phosphate pathway. No more than three steps are involved. 4 points 10. Diagram of electron and proton flow in electron transport (oxidative phosphorylation). Quantitative analysis of electron flow. Action of inhibitors. llpoints 11. 14C labeling in fatty acid synthesis. 4 points 12. A reaction of the B—oxidation scheme. 4 points 13. Synthesis of ketone bodies and cholesterol. 9 points 14. A reaction of the urea cycle. 9 points 15 and 16. Nucleotide metabolism. 12 points MCB102 Fall 2007 Exam 2 Metabolism Name 1____............_(3) SID 2MB) TA BWM) 4_____......_.__..(8) 5 (11) 6 (10) 7 W (6) 8____....._.___(6) 9_____..._._(4) 10 (11) 11 (4) 12 (4) 13 (9) 14 (5) 15 (3) 16 (9) Tota1________(100) AG") = -2.3 RT loglfiK’eq, where R is the gas constant, 8.8 Joules/m01-°K, and T = 298°K Arithmetic: 2.3 X 8.3 Joules/molpK X 298°K = 6 kJ/mol AG") = -nFAE’0} Where F is the Faraday constant, 96.5 kJ/Volt-mel, and n is the number of electrons transferred. 1. In the reaction S 9P, the ratio of P/S is 103 at standard reaction conditions. How much free energy is released by this reaction? Only two significant figures are necessary (3 points) 2. Below are two pieces of information from a table of standard electrochemical potentials: Half Reactions E’0 gyOltsz oxaloacetate + 2e' + 2 H+ 9 malate —O.17 NAD+ + Ze' + H+ 9 NADH -O.27 (fictional value) If the two pairs of reactants are mixed, will the electrons flow toward oxaloacetate or toward NAD“? (1 point) Calculate the standard free energy of this reaction. Only two significant figures are necessary. (2 points) Name SlD 3. If glycolysis in a cell extract is inhibited with iodoacetate or Hg“: fructose 1,6 bisphosphate accumulates. What enzyme is inhibited? (1 point) What amino acid side chain is inactivated? (1 point) Why does fructose 1,6 bisphosphate accumulate? Mention a second enzyme and equilibrium. (2 points) 4. Name the coenzyme shown below (1 point). 0 gN/C\NH Héww f This coenzyme is needed for a mitochondrial enzyme that is anaplerotic for the citric acid cycle and which begins gluconeogenesis. Write the reaction (names of substrates and products is sufficient) (6 points), and name the enzyme (1 point). Name SID 5. Glucose 6-phosphate has several metabolic options in a muscle cell. It can form glucose 1-phosphate, 6-ph0sphogluconolactone, or fructose 6-ph0sphate and then fructose 1,6 bisphosphate, as shown below. a. Name the ENZYMES that catalyze these reactions (A, B, C, D), using the spaces below. (1 point each) h. Name the additional reactant or unusual property of the enzyme involved in these reactions. (1 point each) 6-phosphogluconolactone(Lu—.m-~ glucose 6-P ~m~s§ glucose 1-P A B C Fructose 6-phosphate in Fructose 1, 6 bisphosphate Reaction A: Enzyme Additional reactant Reaction B: Enzyme Unusual property of the enzyme Reaction C: Enzyme Reaction D: Enzyme Additional reactant If glucose 1—phosphate proceeds toward the synthesis of glycogen; what other reactant Will be needed? (1 point) Name SID 5. Continued. Name a small molecule that will cause allosteric inhibition of the enzyme for reaction D? (1 point) Name a small molecule that will cause allosteric activation of the enzyme for reaction D? (1 point) Glucose 6-phosphate has an additional fate in liver cells. Name the enzyme involved. (1 point) 6. When the concentration of blood glucose drops, the pancreas releases a hormone called (1 point). What class of bio— molecule is this hormone? (1 point). Indicate the first steps in the effect of this hormone, that is, the steps that affect glycolysis, gluconeogenesis and glycogen metabolism, before the types of control diverge for the different pathways (4 points). Indicate the modifications of three enzymes for glycogen metabolism and Whether they are turned on or off by this modification. (3 points) Indicate the role of calcium ions. (1 point) Name SID 7. Write the reactants and products of the light reactions of photosynthesis in a balanced equation that yields one molecule of oxygen. Omit ATP. (5 points) How many photons are needed to drive this reaction? (1 point) 8. Write the reactants and products of the reaction that fixes carbon into carbohydrate in photosynthesis, and name the enzyme that catalyzes the reaction. Names of compounds are sufficient. An abbreviation of the enzyme name is sufficient. (6 points) Name SID 9. If ribulose 5-ph0sphate, which is the major product of the oxidative part of the pentose phosphate pathway, is labeled in carbon 2 with 14C and added to a plant cell extract, at which positions will this carbon appear in sedoheptulose 7-phosphate? Here is some space to sketch out the reactions, if you need it. (4 points) Name SID 10. When reduced cytochrome C is added to mitochondria along with ADP and phosphate, antimycin A and oxygen, cytochrome C becomes oxidized, and ATP is formed. In a very simple diagram, indicate the flow of electrons. Your diagram should include cytochrome C and a multi-protein complex, which you should name. You need not give any detail on electron flow through the individual components of a large protein complex. You need not include ATP formation, but indicate the direction of proton flow. Label the sub-cellular compartments on either side of the membrane. (4 points) Write a balanced equation for the overall reaction, omitting the formation of ATP. (5 points) Will rotenone inhibit this reaction? (I point) Will cyanide inhibit this reaction? (1 point) Name SID 11. The synthesis of palmitate (0-16) was carried out in the presence of malonyl-COA that was labeled With 14C in the middle carbon: HOG—MCI—Iz—C-SCoA In the structure of the resulting palmitate, circle the atoms that are labeled With radioactivity in the product. 2 points HBC-CH2-CH2—CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-COO‘ lf malonyl-CoA is labeled is labeled in carbon-3, as shown below, What be its fate? (2 points) H014C-CH2-C-SC0A 12. Consider the last round of the B-oxidation scheme, when only four carbons of palmitate remain. Write the last step in the sequence of four reactions in the fi-oxidation pathway of fatty acids. Names of compounds are sufficient. Name the enzyme. (4 points) Name SID 13. When the reaction of problem 12 is run in reverse, it is the first step in the synthesis of in mitochondria, as well as the first step in the synthesis of the membrane lipid in the cytoplasm. (3 points) Both of these biosyntheses have the same second reaction. Write this second reaction. Names of compounds are sufficient (5 points), and name the enzyme. (1 point) 14. Name this molecule. (1 point) if t“? ‘f (llvNH—CI)~CH2~‘COO ‘” 1TH cow (0142);), l + a ~~ Cl,~~—NH3 cot)“ In the urea cycle, write the reaction for which this molecule is one of the substrates, and name the products and the enzyme. Structures are not necessarywonly names of compounds (4 points). Name SID 15. N 31116: this molecule (1 point) This compound provides the major mode of nitrogen excretion for (a type of animal) (1 point) This compound precipitates (crystallizes) in the big toes of humans who suffer from a disease called .(1 point) 16. Name this compound (compound X). (4 points) The methylene group of this compound is donated from the amino acid , (1 point) which is converted to in the reaction (1 point). Name SID 16, continued. Name this compound. Abbreviations are encouraged in this question. (1 point) It reacts with compound X on the previous page to make the DNA precursor (1 point) on the surface of the enzyme (1 point). MCB102 Fall 2007 Exam 2 Answers 1. -18 kJ/mol 2. -19 kJ/mol (rounded off) or —19.3 kJ/mol (more exactly) 3. GAP dehydrogenase, Cys, GAP and DHAP accumulate and form fructose 1,6-bisphosphate, because the aldolase reaction has an equlibrium toward fructose 1,6 bisphosphate. 4. biotin; pyruvate carboxylase reaction: pyruvate + bicarbonate or carbon dioxide + ATP 9 oxaloacetate + ADP + Pi 5. A enzyme = Glucose 6-phosphate dehydrogenase, additional reactant = NADP+ B enzyme = phosphoglucomutase, unusual property: it is phosphorylated. C enzyme 2 phosphoglucose isomerase or phosphohexose isomerase D enzyme 2 phosphfructokinase-l or PFK-l, additional reactant = ATP To move glucose 1-phosphate toward glycogen synthesis UTP is needed. UDP-glucose is also an acceptable answer. Inhibitor of D = ATP and/or citrate Activator of D = AMP and/or ADP and/or fructose 2,6 bisphosphate In liver the additional reaction is catalyzed by glucose 6-phosphatase. 6. glucagon; peptide or polypeptide; glucagon binds a receptor, activates a G protein to release GDP and bind GTP. The activated G protein activates adenylyl cyclase, which makes cyclic AMP, which activates protein kinase A. Activated PKA phosphorylates and activates phosphorylase kinase, which phosphorylates and activates glycogen phosphorylase. PKA phosphorylates and inactivates glycogen synthase. Ca++ activates phosphorylase kinase. 7. 2 H20 + 2 NADP+ 9 02 + 2 NADPH + 2 H“; 8 photons 8. carbon dioxide + ribulose 1,5-bisphosphate + H20 9 2 8—phosphoglycerate The H20 is optional. The enzyme is RUBlSCO (ribulose bisphosphate carboxylase/oxygenase). 9. The label appears in carbons 2 and 4 of sedoheptulose 7-phosphate. 10. The electron flow is cth 9 Complex IV 9 02, giving H20. Protons flow from the mitochondrial matrix through Complex IV to the inter- membrane space. Here are 4 possible correct answers for the equation: 4 Cthreduced + 02 + 4 H+ '9 4 Cthoxidized + 2 H20 2 cthreduced + 1/2 02 + 2 H+ 9 2 Cytcoxidized + H20 4 cthreduced + 02 + 8 H+ '9 4 cytcoxidized + 2 H20 + 4H+ 2 cthreduced + 1/2 02 + 4 H+ 9 2 cthoxidized + H20 + 2H+ cthreduced could be written cthFe++, and cthoxidized could be written as cthFe+++. The reasons that there are four possible answers are because one can use a mole or a half mole of oxygen and because one can ignore the pumping of hydrogen, because it is imprecisely known, or one can include hydrogen pumping and increase the number of hydrogen ions on both sides of the equation, believing that the textbook knows that a certain number of hydrogen ions are pumped from the matrix to the inter-membrane space. The pumping of H’r might cause the third and fourth equations above to be written with negative side or positive side subscripts, as follows: 4 Cytcreduced + 02 + 8 H+N 9 4 Cthoxidized + 2 + 4HEPP 2 cytcreduced + 02 + 4 H+N '9 2 cytcoxidized + + 2H+P Rotenone will not inhibit this reaction, but cyanide will inhibit. 11. Carbons 2, 4, 6, 8, 10, 12, and 14 will be labeled. Carbon 16 will not be labeled (it comes from acetyl-CoA, rather than from malonyl-CoA). Label in carbon-3 goes to carbon dioxide or bicarbonate. 12. Thiolase catalyzes the following reaction: acetoactyl-COA + COASH 9 2 acetyl-CoA 13. ketone bodies; cholesterol The {3 hydroxy t3 methylglutaryl-COA synthase, or HMG-COA synthase (not synthetase) reaction is: acetoacetyl-COA + acetyl-CoA + H20 9 HMG-COA + CoASH 14. Arginosuccinate The arginosuccinase reaction is: arginosuccinate 9 arginine + fumarate. 15. Uric acid; birds or reptiles; gout. deoxythymiéyiate, m“ deoxythymidine monophosphate; thymiciylate synthaae deoxyuridylate or deoxyuridine menophosphate; dTMP or thymidylate or (not synthetaége}. 16. N5, N10 methylene tetrahydrofalate; serine; glycine; dUMP or mbdfi gfiuagwfi Eafisfim mfima wwgwmé m Emma gem 2am NchOE ...
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This note was uploaded on 02/22/2010 for the course MCB N/A taught by Professor Calendar,thorner during the Fall '08 term at Berkeley.

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MCB102-07 exam - MCB102 Description of exam 2 given in Fall...

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