Amino Acids is (are) Both Ketogenic and Glucogenic Biochemistry Answer Key

Biochemistry TOTAL I. MULTIPLE CHOICE. (38 points; 2 points each answer) Choose the BEST answer to the question by TYPING/WRITING the appropriate letter in the BOX to the left of each question. 1. Which of these amino acids is (are) both ketogenic and glucogenic? 1. 2. 3. 4. 5. isoleucine valine histidine arginine tyrosine A. B. C. D. E. 2. 5 4 and 4 and 5 and 5 Glutamate is metabolically converted to a-ketoglutarate and NH4+ by glutamate dehydrogenase, a process described as: A. B. C. D. E. 3. 1 and 2 and 2, 3, 1, 3, 2, 4, hydrolysis. deamination. oxidative deamination. reductive deamination. transamination. Which metabolic intermediate provides free NH4+ for the production of urea 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 Page 2 4. Which of the following statements is false in reference to the mammalian synthesis of urea? A. B. C. D. 5. Krebs was a major contributor to the elucidation of the pathway involved. The precursor to one of the nitrogens of urea is aspartate. The process of urea production is an energy-yielding series of reactions. The amino acid arginine is the immediate precursor to urea. 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. 6. Activation of protein-kinase A by glucagon Breakdown by triacylglyceride lipases to fatty acids and glycerol Transport of fatty acids in the blood by serum albumin Breakdown by lipases to phosphatidylglycerol Breakdown by Comparative Gene Identity-58-sctivated adipose triglyceride lipase Fatty Fatty Fatty Fatty Fatty acid acid acid acid acid + + + + + ATP + CoenzymeA ⇌ Fatty Acyl-CoA + AMP + PPi succinyl-CoA ⇌ Fatty Acyl-CoA + succinate ATP + CoenzymeA ⇌ Fatty Acyl-CoA + ADP + Pi ATP ⇌ Fatty Acyl-P + ADP ATP ⇌ Fatty Acyl-AMP + PPi Which steps in the TCA cycle are analogous to those of fatty-acid β-oxidation? A. B. C. D. E. F. G. H. I. 9. palmitate (16:0) > alanine > alanine > alanine palmitate Which reaction below is the proper reaction for activation of fatty acids? A. B. C. D. E. 8. alanine > succinate > > succinate > glucose > glucose > succinate palmitate > succinate > glucose > alanine > Which of the following is not needed for fat stores in the adipose to make their way into the liver mitochondria? A. B. C. D. E. 7. glucose > palmitate palmitate glucose > succinate malate dehydrogenase citrate synthase aconitase succinate dehydrogenase fumarase All of the above A, B, and D A, D, and E D and E only What additional enzyme would be required for oxidation of the unsaturated fatty acid C9:1∆7? A. B. C. D. E. Fatty acid unsaturase ∆1, ∆4-enoyl-CoA dehydrogenase ∆2, ∆3-enoyl-CoA isomerase 2,4-dienoyl-CoA dehydrogenase 2,4-dienoyl-CoA reductase Page 3 10. Ketone bodies include which of the following? A. B. C. D. E. 11. Which step of β-oxidation is different in peroxisomes; it generates peroxide and heat for the plant? A. B. C. D. E. 12. Acetone and acetic acid Acetone and acetoacetate acetic acid and β-hydroxybutyrate β-hydroxybutyrate and aspartic acid Hydroxy-methyl glutarate and β-hydroxybutyrate Fatty-acyl CoA Synthetase Acyl-CoA Dehydrogenase Enoyl-CoA Hydratase β-hydroxy-acyl-CoA dehydrogenase Thiolase Which of the modes of ubiquitination would target a protein to the proteasome? A. B. C. D. E. mono-ubiquitination at K-11 poly-ubiquitination at K-11 poly-ubiquitination at K-48 multi-ubiquitination at K-11, at K-48, and K-63 mono-ubiquitination at K-48 13. Ubiquitination of proteins was thought be analogous to ________ in the novel “Treasure Island?” A. Blue spot B. Coconuts full of gold coins C. Peter Pan D. Ace of spades E. A pirate 14. Which cofactor is utilized in aminotransferase enzymes? A. B. C. D. E. 15. What is the key enzyme that connects the pool of nitrogen for biosynthesis of proteins and nucleic acids, in the form of glutamate, and its use for degradation and energy production? A. B. C. D. E. 16. PLP TPP ATP FAD NAD+ Glutamate Aspartate Glutamine Glutamate Aspartate aminotransferase aminotransferase synthetase dehydrogenase transcarbamoylase If you wanted to demonstrate that the methyl groups on choline were from SAM, what carbon in which amino acid would you label with 14C? A. C-3 in Asp B. C-2(Cα) in Asp C. C-3 in Gly D. C-2(Cα) in Ser E. C-3 in Ser Page 4 17. If you were treating a patient with a folic-acid deficiency, which of the following symptoms would you be treating? A. B. C. D. 18. PLP is not involved in the catalysis of which of the following types of chemistry? A. B. C. D. E. F. G. 19. Hypoglycemia due to lack of blood sugar Anemia due to lack of phosphatidyl-choline for plasma membrane synthesis Mental retardation due to buildup of pyruvate from breakdown of Ser and Gly Cough due to allergies that folic acid alleviates amino-group transfer amino-acid racemization amino-acid β-elimination amino-acid decarboxylation glycogen phosphorolysis amino-acid γ-elimination amino-acid dehydrogenation For the following reaction, name the enzyme activity that would catalyze it: A. B. C. D. E. F. P-450 oxidase P-450 dioxygenase dioxygenase P-450 hydroxylase P-340 monooxygenase P-340 mixed-function oxidase Page 5 II. TRUE-FALSE. (16 points) Place a "T" of "F" in the box on the left. No other answer will be accepted. 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 is used in enzymes that need the help of a free radical to perform the chemistry that they catalyze. 24. The degradation of the pyrimidine 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, which in both forms regulate proteolysis, bind to ubiquinated proteins, and unfold the protein as they remove the ubiquitin from the proteins. 26. In animals, acetoacetate, beta-hydroxybutyrate, and acetone are derived from excess acetyl-CoA through the synthesis of hydroxy-methylglutaryl-CoA (HMGCoA), 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 in a linkage called an isopeptide linkage. 28. Ketone bodies can 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 degradation of the branched-chain amino acids utilize many of the kinds of reactions seen in the degradation of pyruvate by the mitochondria. 31. When ATP is depleted in the liver, the energy charge is maintained by depleting the AMP as well through the reaction of AMP deaminase. 32. Both methylmalonyl mutase and methionine synthase utilize cobalamin as a cofactor. 33. Chylomicrons help transport fat and cholesterol from the diet to tissues. 34. The lysosomal pathway is useful for protein turnover inside of cells and yields amino acids for use in metabolism. 35. Acyl-carnitine/carnitine transporter is an anti-porter for transport of fatty acids into the nucleus. Page 6 III. SHORT ANSWER. (15 points) Give a brief answer or fill in the blanks as directed to each problem or questionbelow in the boxes. 36. If you had labeled the 14C-6 of ATP in human cells that were depleted of energy, in what compound would you find the label? (2 pts) 37. How many ATP equivalents are derived from the complete oxidation of stearic acid (C18:0)? (use the back for your calculations) How many ATP equivalents are derived from the complete oxidation of a-linolenic acid (C18:3, ∆9,12,15)? NOTE: In both cases start from the free fatty acid for your calculation. [NOTE: use 3-ATP/NAD(P)H, 2-ATP/FADH2, and 1-ATP/GTP] (4 pt) 38. Cys, Gly, and Ser are amino acids whose degradation can yield pyruvate. Which, if any, of the remaining 17 amino acids can also do so? (2 pts) 39. Similar to the energy, in ATP equivalents, we calculated in class for 2 Alanines, calculate the net number of ATP equivalents you would get from 2 Isoleucine amino acids. As a hint, the intermediate calculations are provided: [NOTE: use 3-ATP/NAD(P)H, 2-ATP/FADH2, and 1-ATP/GTP] (7 pts) number Nitrogen from 2-Ile into the Urea Cycle (one through Glu-dehydrogenase and one through Asp) number Cost of the Urea Cycle: Carbon compounds after degradation of each Ile (include the number from TWO Ile): number name (2 carbon) name (3 carbon) number + ATP equivalents from each of the above carbons number + TOTAL Net Number of ATP equivalents: number number Page 7 40. IV. MECHANISMS. (8 points) Mechanism #1: In the diagram, draw an arrow pointing to the atom that will be protonated in the mechanism toward making the pyridoxamine-enzyme intermediate (E-PMP). Also draw arrows to indicate the movement of electrons for this protonation. After the step you diagramed above, the resulting pyridoxal-Schiff base will be hydrolyzed to yield that E-PMP and an α-keto acid. If the original amino acid used by this enzyme were alanine, what would be the name of that α-keto acid?. Mechanism #2: If this cofactor were in an alanine racemase instead of the alanine transaminase, circle the atom above that would be protonated instead of the one you indicated in Mechanism #1. V. PATHWAYS (23 points) 41. Fill in the blanks for the UREA cycle. For each step, give the name of the enzyme that catalyzes the reaction (NO abbreviations), DRAW the structure and name of each intermediate, and give any indicated co-substrates or products (abbreviations OK) as indicated in the appropriate boxes. Also, give; you can abbreviate phosphate as Pi, and a phosphoryl group by a circled-P. CO2 NH3 + Page 7 m. enzyme name a. n. f. structure & name b. enzyme name + L. structure & name g. o. k. structure & name structure & name e. enzyme name Asp c. enzyme name q. r. i. j. p. structure & name h. structure & name + d. enzyme name structure & name No. on Test Correct Answer 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 A D J C C D A H C B B C D A D E B G D 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 F T T T T F F T T F T T T T T F 40 41 No. on Test Correct Answer Uric Acid 36 37 A. Stearate gives 9 acetyl-CoA = 9x12=108 ATP (each acetyl-CoA gives (3NADH=9)+(1FADH2=2)+(1GTP=1)=12 from the 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. ALA gives 9 acetyl-CoA for 108 ATP equivalents, as above. But during βoxidation, the first DblBond is at an odd carbon (∆9), so when fatty-acylCoA dehydrogenase (FAcDH) cannot put in the ∆2 DblBond, so the isomerase (-1 FADH2) is needed to make it even at ∆2 and trans. The second DblBond is cis at an even carbon (∆12), so when FAcDH puts in the double bond 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 third DblBond is cis and at an odd carbon (∆15), so FAcDH can't work. Again, the isomerase (-1 FADH2) is needed to make it even at ∆2 and trans. β-oxidation the gives just 7 NADH (8-1) overall, or 7x3=21 ATP, and 6 FADH2 (losing 2 for the odd-carbon Dblbonds) (6x2=12). The total ATP equivalents are then 108 + 21 + 12 = 141; minus 2 ATP for activation is 139. 38 Trp, Ala 39 A. The two Ile are transaminated to move the nitrogens to 2 Glu with alpha-KG. One Glu is converted to ammonia and alpha-KG, and the other is converted to Asp and alpha-KG. There is a gain of one NADH from GluDH, and a gain of one NADH from fumarate as it gets re-cycled in the Bi-cycle to malate, and the malateDH takes malate to oxaloacetate. The 2 NADH yield 6 ATP. B. –4 ATP for making CP (2) and making arginosuccinate (2). Ile yields an acetyl-CoA and a propionyl-CoA. Since there are two Ile, you get 2 each of these 2-carbon and 3-carbon molecules. In the degradation, there is 2 NADH and an FADH2 per Ile, but this requires you to know the pathway, so it is ignored in the answer. It would add 16 more ATP equivalents. C. 2 Acetyl-CoA D. 2 Propionyl-CoA E. 2 Acetyl-CoA will give 6 NADH, 2 FADH2, and 2 GTP, which will + 2 ATP equivalents, which totals 24 ATP yield 18 + 4 F. 2 Propionyl-CoA will give 2 succinyl-CoA molecules, but will cost 2 ATPs for the carboxylase reaction, but each will take two rounds of the TCA cycle. So, 4 rounds of the TCA will give 12 NADH, 4 FADH2, and 4 GTP, which will yield 36 + 8 + 4 ATP equivalents, which totals 48-2 = 46 ATP. G. TOTAL = 6 + (–4) + 24 + 46 = 72 ATP