Degradation of γ-linolenic Acid Answer Key

Answer Key No. on Test 38 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 T F T F F T T T T F T F T T T T T T F T 2,5 1 3 4 x x x 1. Carbamoyl-phosphate synthetase 2. Ornithine transcarbamylase x x 3. Arginino-succinate synthetase 4. Arginino-succinase 5. Arginase Bond broken E D B J D D B D C D C C A C D Bond made 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 36 Mechanism #2 is more easily converted to a citric acid cycle intermediate than #1. Pathway: Succinyl-semialdehyde is oxidized to succinate using NAD+, which is reduced to NADH. #1 #2 Glutamate Dehydrogenase 4-amino butyrate succinyl-semialdehyde No. on Test Answer Key 37 39 A. Stearate gives 9 acetyl-CoA = 9x12=108 ATP (each acetyl-CoA gives (3NADH=9) +(1FADH2=2)+(1GTP=1)=12 from th TCA cycle and OxPhos). β-oxidation gives 8 NADH each round (8x3=24 ATP) and FADH2 (8x2=16 ATP). Total is 108+24+16=148; minus 2 ATP for activation is 146. | | | | | | | | B. GLA gives 9 acetyl-CoA for 108 ATP equivalents, as above. But during βoxidation, the first DblBond is at an even carbon (∆4), so when fatty-acylCoA dehydrogenase (FACDH) puts in the ∆2 DblBond, it becomes a conjugated system and needs the reductase (-1 NADH) to make it a single ∆3 dblbond; then the isomerase will make it ∆2. The second DblBond is cis at odd carbon (∆3), so FACDH can't work, so the isomerase (-1 FADH2) is needed to make it even at ∆2 and trans. After the 4th acetyl-CoA is produced, the third DblBond is again at an even carbon (∆4)(carbon-12), so when FACDH puts in the ∆2 DblBond, it becomes a conjugated system and needs the reductase (-1 NADH) to make it a single ∆3, then an isomerase to make it a ∆2 dblbond at carbon-10. β-oxidation the gives just 6 NADH (8-2) overall, or 6x3=18 ATP, and 7 FADH2 (losing 1 for the middle Dblbond) (7x2=14). The total ATP equivalents are then 108 + 18 + 14 = 140; minus 2 ATP for activation is 138. C. Thr ends up as succinate and the 4 carbons are burned in two rounds of TCA cycle (6NADH=18ATP) + (2FADH2=4ATP) + (2GTP) = 24 ATP equivalents, minus 1 for carboxylation in the propionyl-CoA pathway, so 23. Ala ends up as pyruvate and the 3 carbons are burned in one round of TCA cycle after PyrDH (4NADH=12ATP( + (1FADH2=2ATP) + (1GTP) = 15 ATP. The total is 38, minus 4 for the urea cycle is 34. Biochemistry I. MULTIPLE CHOICE. (45 points; 3 points each answer) Choose the BEST answer to the question by WRITING the appropriate letter in the BOX to the left of each question. 1. Which of the following conversions requires more than one step? 1. alanine 2. glutamate 3. aspartate 4. proline 5. phenylalanine A. B. C. D. E. 2. 1, 2, 1, 3, 2, 4, 1 and 4 and a-ketoglutarate oxaloacetate glutamate succinate and 4 and 5 and 5 4 5 Choose a correctly balanced equation for the degradation of γ-linolenic acid (GLA) (C18:∆6,∆9,∆12) via the β-oxidation pathway. A. B. C. D. E. 3. pyruvate GLA + 8FAD + 8NAD+ + 9CoA-SH + 8H2O + ATP 9 Acetyl-CoA + 8FADH2 + 8NADH + 8H+ + AMP + PPi GLA + 5FAD + 7NAD+ + 9CoA-SH + 8H2O + ATP 9 Acetyl-CoA + 5FADH2 + 7NADH + 7H+ + AMP + PPi GLA + 5FAD + 6NAD+ + 9CoA-SH + 8H2O + ATP 9 Acetyl-CoA + 5FADH2 + 6NADH + 6H+ + AMP + PPi GLA + 7FAD + 6NAD+ + 9CoA-SH + 8H2O + ATP 9 Acetyl-CoA + 7FADH2 + 6NADH + 6H+ + AMP + PPi GLA + 8FAD + 8NAD+ + 9CoA-SH + 8H2O + ATP 8 Acetyl-CoA + Propionyl-CoA + 8FADH2 + 8NADH + 8H+ + ADP + Pi Urea synthesis in mammals takes place primarily in: A. skeletal muscle. B. liver. C. kidney. D. small intestine. E. brain. Page 2 + 4. Which metabolic intermediate provides free NH4 for the production of urea from via the urea cycle? A. B. C. D. E. F. G. H. I. J. K. L. Histidine Glutamine Glutamate Aspartate AMP Glycine Threonine All of the above B & F All except C & D B & F & G All except C & D & E 5. Serine or cysteine may enter the citric acid cycle as acetyl-CoA after conversion to: A. B. C. D. E. 6. oxaloacetate. succinate. succinyl-CoA. pyruvate. propionate. The standard reduction potentials (E o') for the following half reactions are given. Fumarate + 2H+ + 2eFAD + 2H+ + 2e- succinate FADH2 Eo' = +0.031 V Eo' = -0.219 V If you mixed succinate, fumarate, FAD, and FADH2 together, all at l M concentrations and in the presence of succinate dehydrogenase, which of the following would happen initially ? A. B. C. D. E. Succinate would become oxidized, FAD would become reduced. Succinate would become oxidized, FADH2 would be unchanged because it is a cofactor, not a substrate. Both fumarate and succinate would become oxidized; both FAD and FADH2 would become reduced. Fumarate would become reduced, FADH2 would become oxidized. No reaction would occur, because all reactants and products are already at their standard concentrations. 7. If a person's urine contains unusually high concentrations of urea, which of the following diets has he or she probably been eating recently? A. B. C. D. very very very very high carbohydrate, very low protein low carbohydrate, very high protein high fat, very low protein high fat, high carbohydrate, no protein 8. Page 3 Which substance is not involved in the production of urea via the urea cycle? A. B. C. D. E. 9. aspartate ATP ornithine malate carbamoyl phosphate In muscle, the oxidation of branched-chain amino acids can provide a significant amount of energy. The number of net ATP equivalents per mole of Ile is ______ when burned competely to CO2 and water and the energy from the TCA cycle is used by oxidative phosphorylation to make ATP in the mammalian mitochondria. Relative to glucose, this is _____ ATP equivalents. A. B. C. D. E. 30-34; 30-34; 30-34; 10-15; 50-60; much less much more about the same about the same about the same 10. The degradation of tryptophan is both ketogenic and glucogenic. products acetyl-CoA, acetoacetyl-CoA, and ______. A. B. C. D. E. It yields the Cys Ser N10-formyl-THF Ala Gly 11. If an aerobic organism (e.g., the bacterium E. coli ) were fed each of the following four compounds as a source of energy, the energy yield from these substrates, in terms of ATP/mole, would be in the order: A. B. C. D. E. glucose > palmitate palmitate glucose > succinate alanine > succinate > > succinate > glucose > glucose > alanine > palmitate > succinate > glucose > alanine > palmitate (16:0) > alanine succinate > alanine palmitate 12. Which of the following statements concerning the b oxidation of fatty acids is true? A. B. C. D. Two NADH are produced for each acetyl-CoA produced. The free fatty acid must be carboxylated in the b position by a biotindependent reaction before the process of b oxidation commences. If electron transfer to oxygen were blocked as a result of cyanide poisoning, b oxidation would also cease because the FADH2 generated in the process (by acyl-CoA dehydrogenase) could not be oxidized. About 1200 ATP molecules are ultimately produced per 20-carbon fatty acid oxidized. 13. Page 4 Which of these amino acids is (are) both ketogenic and glucogenic? 1. 2. 3. 4. 5. A. B. C. D. E. isoleucine valine histidine arginine tyrosine 1 and 2 and 2, 3, 1, 3, 2, 4, 5 4 and 4 and 5 and 5 14. Glutamate is metabolically converted to a-ketoglutarate and NH4+ by a process described as: A. B. C. D. E. hydrolysis. deamination. oxidative deamination. reductive deamination. transamination. Extra Credit What is the name of this enzyme? 15. The PLP cofactor is used by a number of enzymes in amino acid metabolism, but not just for transaminations. It is used for enzymes that do decarboxylations, racemizations, and various eliminations. This versatility of PLP can be explained by __________. A. PLP has an electron sink that is partially filled with each of the different reactions. B. PLP is phosphorylated, and the degree of binding to this group by each enzyme dictates which kind of chemistry it will catalyze. C. PLP has a pi-orbital of the filled nitrogen in the ring, and the orientation of the sessile bond relative to this nitrogen changes its reactivity D. PLP has aromatic pi-orbitals that extend into the aldehyde/Schiff-base, and the orientation of the sessile bond at the alpha-carbon changes its reactivity E. PLP is not really important for these enzymes. II. TRUE-FALSE. (20 points) Place a "T" of "F" in the box on the left. No other answer will be accepted. 16. Mobilization of fatty acids stored in adipose is dependent on hormone signals that leads to the activation of protein kinase A. 17. Fatty acids are activated to their CoA-thioesters by Fatty Acyl-CoA Synthetase and then transported into the mitochondria using the citruline/ornithine carrier. 18. Ketone bodies are formed in the liver mitochondria CoA and not enough activity of the TCA cycle. 19. Peroxisomal oxidation of fatty acids is identical to the way they are oxidized in the mitochondria. when there is too much acetyl- Page 5 20. Pyrimidine degradation produces a dead-end product that does not contribute to the citric acid cycle and energy production, and is rather excreted as an oxidized pyrimidine ring; uridine. 21. Hyperuricemia can be caused by energy depletion. 22. Urate oxidase is missing in humans, whereas most animals possess this enzyme. This enzyme is mis-named and is more properly called urate dioxygenase. 23. Vitamin B12 (Cbl) is used in enzymes that need the help of a free radical to perform the chemistry that they catalyze. 24. The degradation of CMP contributes to the urea cycle 25. The 26S proteosome comes in two forms, a smaller form, made of a 19S core plus other proteins, or a larger form made of a 20S core plus these other proteins. Both forms regulate proteolysis, bind to ubiquinated proteins, and unfold the protein as the removes the ubiquitin proteins, but do not catalyze peptidebond hydrolysis. 26. In animals, acetoacetate, beta-hydroxybutyrate, and acetone are derived from hydroxy-methylglutaryl-CoA, which comes exclusively from excess fatty acid degradation when sugar is unavailable. 27. Ubiquitin can be polymerized using the C-terminal carboxylate and lysine-11. When these polymers are attached to a lysine on any protein in the cell, it will be degraded by the proteosome. 28. Ketone bodies arise from amino-acid degradation 29. If you had a deficiency of 2,4 dienoyl-CoA reductase there would be difficulty utilizing fat compared to plant oils. 30. The N-end rule predicts protein half-life in cells based on their aminoterminal residue. 31. The proteosome requires ATP hydrolysis, which is used mostly for the unfolding and de-ubiquination steps performed by the 19S portion of the 26S proteosome. 32. One-carbon metabolism involves various oxidation states of a single carbon atom attached either to tetrahydrofolate (THF) or S-adenosylhomocysteine (these are the cofactors WITHOUT a one-carbon unit attached). 33. The conversion of either Ser to Gly, or the cleavage of Gly to NH3+ and CO2, are the major sources of one-carbon units in the pool of one-carboncontaining forms of THF. They initially form N5,N10-methylene-THF. 34. The first step in proline degradation uses and oxygenase, whereas the first step in phenylalanine degradation uses an oxidase. 35. Most purines and pyrimidines from nucleic acids ingested in the diet are recovered in a "salvage pathway" rather than used for degradation to produce energy. III. MECHANISMS. (8 points) Page 6 36. In the diagram draw arrows to indicate the movement of electrons for the decarboxylation of this glutamate-PLP aldimine intermediate. Mechanism #1: If the resulting quinoid intermediate is protonated at the stabilized carbanion, followed by hydrolysis of the PLP=AA Schiff base, NAME the resulting compound. Mechanism #2: If the resulting quinoid intermediate is NOT protonated at this stabilized carbanion, but rather the quinoid-Schiff base is hydrolyzed, NAME the resulting compound. Choose which of these two mechanisms is more likely based on which of these products could more readily (fewer steps) be used for energy production. Explain very briefly in the box by diagraming the pathway to a citric acid cycle intermediate. IV. Page 7 PATHWAYS. (18 points) 37. You live on a ranch in Australia, and decide to go on a high fat diet. You are told that you need to eat some carbohydrate to digest all the fat, but there is no source of sugar on the ranch. In addition, all you have available to eat is sheep skin. One of the common fatty acids in the fat in sheep skin is shown below (valerate (5:0)). Complete the pathway for energy production from this fatty acid to TCA cycle intermediates by entering the information in the labeled boxes. In the box just below on the right, name which product, acetyl-CoA or product A, explains why are you not concerned about the lack of sugar on the ranch? (13 pt) H3 H Enzyme names: Draw structure of intermediate + ATP + NAME an amino acid whose catabolic pathway converges with the product below Draw structure of intermediate Draw structure of intermediate Draw & NAME the structure of the product + H+ Draw structure of intermediate Cofactor Acetyl-CoA + Draw & NAME the structure of the product CO2 Cofactor Product A Page 8 38. Below is the structure of Arginosuccinate with several BONDS noted with a box next to it. To the right is a numbered list of urea-cycle enzymes and two boxes, one for making a bond and one for breaking a bond. First, place the correct number for the enzyme that catalyzes the reaction that made or broke one of the bonds designated with a box. Second, indicate in the appropriate box for each numbered enzyme. (5pts) 1. Carbamoyl-phosphate synthetase 2. Ornithine transcarbamylase 3. Arginino-succinate synthetase 4. Arginino-succinase 5. Arginase Bond broken Bond made V. SHORT ANSWER. (9 points) Give a number in the box as directed for each problem or question below. For easier calculation, assume 3ATP equivalents per NADH and 2ATP equivalents per FADH2 during electron transport and oxidative phosphorylation. 39. A. How many ATP equivalents are derived from the complete oxidation of stearic acid (C18:0)? (start from the free fatty acid) B. How many ATP equivalents are derived from the complete oxidation of γ-linolenic acid? (start from the free fatty acid)(HINT: see #2) C. How many ATP equivalents are derived from the complete oxidation of one Alanine and one Threonine in the liver? Be sure to account for disposing of the nitrogens.