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BIS103-001 (Winter 2007) Final Exam (March 20) Name_____________________________________ Instructor: Abel Student ID # ANSWER KEY Pls., check appropriate box below. Undergraduate Student Completing Incomplete Open Enrollment Student Graduate Student This exam consists of 8 questions. A maximum of 100 points can be earned. Partial credit will be given. There are a total of 12 pages, including the cover page and one blank sheet at the end for notes. However, do not use the blank sheet for your final answers. If you need more space, use the back of pages 2-11. Write your name on top of each page! Petitions for regrading will be considered only if you have used permanent ink, unless an addition error has occurred. *IT IS YOUR RESPONSIBILITY TO WRITE LEGIBLE! No extra effort will be made to decipher your handwriting. Question Value 1 22 2 12 3 12 4 12 5 9 6 7 7 12 8 14+2 TOTAL 100 (+2) Score T = 25 oC (298 K) T = 37 oC (310 K) R = 8.315 J mol-1 K-1 F = 96.5 kJ mol-1 V-1 n = equivalents of electrons Z = charge of proton ΔG = ΔGo’ + RTln[Prod.]/[React.] ΔG = ΔGo’ + 2.303RTΔpH + ZFΔΨ ΔGo’ = – nFΔEo’ ΔEo’ = Eo’Oxidant – Eo’Reductant I,_______________________________________, authorize the University to distribute publicly this graded exam (e.g., handed out in class or left in a bin for pick up). I am aware of the fact that violations of the Academic Code of Conduct1 may be reported to UC Davis Student Judicial Affairs. 1 Examples of academic misconduct include: receiving or providing unauthorized assistance on examinations, using unauthorized materials during an examination, altering an exam and submitting it for re-grading, or using false excuses to obtain extensions of time (http://sja.ucdavis.edu/cac.htm). Signature________________________________________ Date____________________________ 1 BIS103-001 (Winter 2007) Final Exam (March 20) 1. (22 pts.) Name_____________________________________ Short answer warm-up questions. a) Triglycerides are synthesized from glycerol-3-P and from activated fatty acids. How is glycerol-3-P produced from an intermediate of glycolysis? How are fatty acids activated? (4 pts) Balanced reaction generating glycerol-P from a glycolysis intermediate: Dihydroxyacetone-P (DHAP) + NADH Ù Glycerol-3-P + NAD+ Reaction that activates fatty acids for triacylglyceride synthesis: Fatty Acid + ATP + CoA-SH Î Acyl-CoA + AMP + PPi (Î 2Pi) b) Humans do not have the glyoxylate cycle. Describe in one sentence its purpose in plants and microorganisms. Give the structure of glyoxylate. Give the reaction catalyzed by malate synthase (names of reactants and products only) (4 pts) Purpose: To convert lipids (fatty acids) into carbohydrates. Glyoxylate structure: See booklet Malate synthase reaction: Acetyl-CoA + Glyoxylate + H2O Î Malate c) Draw the structure of urea and indicate the two precursor molecules from which the N and C atoms are derived. (3 pts) See booklet for structure. 1) Carbamoyl-P (made from ammonia and bicarbonate) 2) Aspartate d) Describe in one sentence the role of the “Methyl cycle”. (1 pts) To regenerate S-Adenosylmethionine (SAM). 2 BIS103-001 (Winter 2007) Final Exam (March 20) Name_____________________________________ e) Describe in one sentence the difference between oxidases and oxygenases. (2 pts) Oxidases use molecular oxygen as electron acceptor and do not incorporate the “O” into the substrate, whereas oxygenases introduce one or both O atoms into the substrate. f) Acetyl-CoA (or “activated acetate”) is a central intermediate in metabolism. There is a chemical reason why each carbon of acetyl-CoA is considered to be “activated” (or reactive). (2 pts) Reason 1: Hydrolysis of the CoA-thioester bond. Reason 2: The C-H bonds of the methyl group are more polarized (acidic). g) Given below are the names of three “activated” precursor molecules. For each precursor, indicate one biochemical pathway that utilizes it. Give also the reason why the initial reaction (in which the activated precursor is a reactant) is driven into the direction of product formation. (6 pts) AMP-Sulfate (APS) Pathway: Sulfate assimilation Reaction driven by: Release of AMP UDP-Glucose Pathway: Synthesis of carbohydrates (disaccharides, polysaccharides, glycogen) Reaction driven by: Release of UDP 5-Phosphoribosyl-1-pyrophosphate (PRPP) Pathway: Synthesis of nucleotides (salvage pathway, de novo synthesis) Reaction driven by: Release and hydrolysis of pyrophosphate (PPi) 3 BIS103-001 (Winter 2007) Final Exam (March 20) 2. (12 pts) Name_____________________________________ Shown below are several reactions discussed in class. Give the names for the provided chemical structures of substrate and product, for any missing co-factor that would be part of the written reaction or for covalently-bound co-factors if required by the enzyme, and the name of the enzyme catalyzing the reaction (enzyme class is sufficient). COO- a) O C H C COO- + H C NH2 H C H Glu H H + α-KGA H Substrate: Pyruvate Product: Alanine Co-factor: PLP (pyridoxal-P) Enzyme: (Ala) Transaminase/ Transferase b) NO 3- N O 2- Substrate: Nitrate Product: Nitrite Co-factor: NAD(P)H Enzyme: Nitrate reductase (Oxidoreductase) COO- c) C CH2 S-CoA O C + CoA-SH O CH2 CH2 CH2 COO- COO- + CO2 Substrate: α-KGA Product: Succinyl-CoA Co-factors: NAD+, TPP, Lipoic acid, FAD Enzyme: α-KGA Dehydrogenase (Oxidoreductase) 4 BIS103-001 (Winter 2007) Final Exam (March 20) 3. (12 pts) Name_____________________________________ The metabolic pathways and enzymes discussed this quarter are not all localized in the same subcellular compartment in eukaryotes. Indicate the subcellular location for the pathways or enzymes listed below (disregard transporters and shuttles). If a pathway occurs in more than one location, indicate all subcellular compartments. Each compartment may also be used more than once. Do not guess! You will loose 0.5 point for each wrong additional answer. A. B. C. D. E. Nucleus Cytosol Mitochondrial matrix Inner Mitochondrial Membrane Lysosome F. G. H. I. J. Chloroplast (thylakoid lumen) Chloroplast (stroma) Glyoxysome Peroxisome Secretory vesicles C, D TCA Cycle C β-oxidation of fatty acids F Oxygen evolution B, C Substrate level phosphorylation H Glyoxylate cycle (plants) B Pentose phosphate pathway (animals) B Anaerobic glycolysis G Calvin cycle B Fatty acid synthesis F Plastocyanin D Cytochrome c oxidase B, C Urea cycle 4. (12 pts) Fretting over a cup of coffee… a) Caffeine (see structure below) belongs to which class of compounds? Circle only one! (1 pt) H 3C O H 3C Amino Acids Pyrimidines Nucleotides Purines Nucleosides Peptides N N N N O CH 3 5 BIS103-001 (Winter 2007) Final Exam (March 20) Name_____________________________________ b) Which co-factor is the most likely the donor of the three methyl groups of caffeine? (1 pts) Full name of co-factor: S-Adenosylmethionine (SAM) c) Caffeine is an inhibitor of the enzyme cyclic nucleotide phosphodiesterase that participates in the adrenaline-mediated regulation of protein kinase A activity. Give the balanced reaction catalyzed by cyclic nucleotide phosphodiesterase. (2 pts) Reaction: 3’:5’-cyclic-AMP + H2O Î 5’-AMP d) What will be the consequence of increased coffee (caffeine) consumption on protein kinase A activity? Briefly explain your answer. (3 pts) Protein kinase A activity will be (circle): Brief explanation: increased decreased Since caffeine inhibits the cyclic nucleotide phosphodiesterase, 3’:5’-cyclic-AMP levels will remain elevated, which in turn leads to a prolonged activation of protein kinase A. e) A Google search for “coffee and antioxidants” indicates that coffee is an excellent source of antioxidants that help to detoxify “reactive oxygen species (ROS)”. What major metabolic process generates ROS in the cell? (1 pt) Mitochondrial ETC f) Diagram the process of ROS detoxification that involves glutathione. (4 pts) See p. 109 of booklet. 6 BIS103-001 (Winter 2007) Final Exam (March 20) 5. (9 pts) Name_____________________________________ Arginine can be synthesized from ornithine in the urea cycle. Therefore, arginine is an essential amino acid only under certain circumstances when the metabolic demand for arginine is exceedingly high, such as during childhood, pregnancy, or recovery from illnesses. Ornithine (see below, compound on the right) can be synthesized in three reactions from the compound shown on the left. NH2 - COO CH2 CH2 I. CH2 H C CH2 II. COO - CH2 H NH3+ C COO- NH3+ Ornithine a) Name the precursor of ornithine shown on the left (1 pts) Name of ornithine precursor: Glutamate b) How does the synthesis of ornithine proceed, taking into consideration that one reaction requires NAD+, another is catalyzed by a transaminase, and yet another produces ADP as one of its products (Note: all reactions have been discussed in class in a different context)? Draw the structures of the intermediates in the boxes below, write all co-factors and their products above each arrow, and give the enzyme class below each arrow. (8 pts) Kinase (Transferase) Dehydrogenase (Oxidoreductase) Acyl-phosphate Precursor Glu Î α-KGA PLP NAD+ Î NADH ATP Î ADP Intermediate I Transaminase (Transferase) (Semi)-Aldehyde Intermediate II Ornithine 7 BIS103-001 (Winter 2007) Final Exam (March 20) 6. (7 pts) Name_____________________________________ Questions on the tetrahydrofolate (THF) co-factor. a) Name the dietary precursor to THF? (1 pt): Folic Acid b) N5, N10-methylene-THF can be generated from serine. How is serine produced from an intermediate of glycolysis? Give the chemical structures of the precursor, intermediates and serine in the boxes below (co-factors or other substrates that are required in the written direction are give above each arrow). (4 pts) NAD+ Glu H2O Precursor Serine 3-Phosphoglycerate 3-Phosphohydroxy pyruvate 3-Phospho serine See Booklet for structures c) The formation of dTMP from dUMP requires a methylation step. Draw the form of THF on the frame below that participates in this conversion? (2 pt) N10 N5 CH2 N5, N10-Methylene-THF 8 BIS103-001 (Winter 2007) Final Exam (March 20) Name_____________________________________ 7. (12 pts) Questions on regulation. a) It was recently discovered that xylulose-5-P is an allosteric activator of the phosphoprotein phosphatase that is responsible for the dephosphorylation of the bifunctional enzyme PFK-2/F2,6BPase. Dephosphorylation of the PFK-2/F2,6BPase isoenzyme in the liver results in the activation of its kinase activity. Briefly explain the logic of this regulatory loop with respect to the degradation of excess dietary xylulose in the liver. (4 pts) Activation of PFK-2 will lead to the increased formation of F2,6P, which is an allosteric activator of PFK-1 (phosphofructo kinase 1) and consequently of glycolysis. Xylulose will be converted to F6P and GA3P by the pentose phosphate pathway. Thus, activation of glycolysis by xylulose via PFK-2 will metabolize excess dietary xylulose. b) Why is the hormonal regulation of glycolysis and gluconeogenesis different between the skeletal muscles and the liver? On the other hand, why is it similar for glycogen synthesis and breakdown? Mention the metabolic roles of both organs in carbohydrate metabolism. (4 pts) These two organs have different metabolic roles. One of the major tasks of the liver is to produce glucose that can be used as a fuel by the other cells of the body. On the other hand, the skeletal muscles are specialized for energy production (ATP). Thus, if glycolysis is activated in the muscles (ATP production), gluconeogenesis will be activated in the liver to produce glucose for the muscles and to recycle the lactate produced during anaerobic glycolysis (muscles). Glycogen breakdown will be activated in both organs to feed glycolysis in the muscles and to export glucose from the liver to the muscles. c) ATP, AMP, and NAD(P)H often act as allosteric regulators of key enzymes in metabolism. Predict the effect of each regulator of the activities of the following enzymes (use “+” for activation and “-“ for inhibition). (4 pts) ATP AMP NAD(P)H Citrate Synthase - + - Fructose-1,6,-bisphosphatase + - + ATP:Citrate Lyase + - + - + - Pyruvate Dehydrogenase 9 BIS103-001 (Winter 2007) Final Exam (March 20) Name_____________________________________ 8. (14 + 2 pts) Multiple-choice questions. Circle the best answer. There is only one best answer per question. Each question is worth 2 pts. a. b. c. d. Which of the following enzyme is NOT part of the glyoxylate cycle? i Isocitrate Dehydrogenase ii Malate Dehydrogenase iii Malate Synthase iv Citrate Synthase v Isocitrate Lyase Which of the following metabolites is NOT an intermediate of the urea cycle? i Ornithine ii Arginine iii Alanine iv Fumarate v Citrulline Which of the following C1-groups cannot be transferred by tetrahydrofolate? i –CH2– ii –CH3 iii –CHO iv –COOH v =CH– Which of the following processes in the liver is inhibited by insulin? i Glucose uptake ii Glycolysis iii Glycogen synthesis iv Fatty acid synthesis v Glycogen degradation 10 BIS103-001 (Winter 2007) Final Exam (March 20) e. f. g. h. Name_____________________________________ Which of the following carboxylases occurs ONLY in photosynthetic organisms? i Pyruvate carboxylase ii Ribulose-1,5-bisphosphate carboxylase iii Acetyl-CoA carboxylase iv Propionyl CoA carboxylase v Phosphoenolpyruvate carboxylase Which of the following enzyme-catalyzed reactions generates urea as a product? i Asparaginase ii Glutaminase iii Argininosuccinase iv Arginase v Urease Pyridoxal phosphate is a cofactor in this class of reactions: i methylation ii acetylation iii decarboxylation iv phosphorylation v adenylylation Bonus question (2 extra points)! The acceptor molecule for incorporating reduced sulfur provided by the reduced carrier molecule (carrier-S-S-) is formed by the combination of: i Cysteine + Homoserine ii Homoserine + Methionine iii Serine + Cysteine iv Acetate + Serine v None of the above 11 BIS103-001 (Winter 2007) Final Exam (March 20) Name_____________________________________ 12