* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download BIS103-002 (Spring 2008) - UC Davis Plant Sciences
Basal metabolic rate wikipedia , lookup
Isotopic labeling wikipedia , lookup
Butyric acid wikipedia , lookup
Biochemical cascade wikipedia , lookup
Mitochondrion wikipedia , lookup
Biosynthesis wikipedia , lookup
Photosynthesis wikipedia , lookup
Photosynthetic reaction centre wikipedia , lookup
Phosphorylation wikipedia , lookup
Metalloprotein wikipedia , lookup
Light-dependent reactions wikipedia , lookup
Amino acid synthesis wikipedia , lookup
NADH:ubiquinone oxidoreductase (H+-translocating) wikipedia , lookup
Fatty acid synthesis wikipedia , lookup
Nicotinamide adenine dinucleotide wikipedia , lookup
Electron transport chain wikipedia , lookup
Lactate dehydrogenase wikipedia , lookup
Microbial metabolism wikipedia , lookup
Fatty acid metabolism wikipedia , lookup
Glyceroneogenesis wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Biochemistry wikipedia , lookup
Adenosine triphosphate wikipedia , lookup
BIS103-002 (Spring 2008) Midterm #2 (May 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 6 questions. A maximum of 100 points can be earned. Partial credit will be given. There are a total of 13 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 2-12. Write your name on top of each page! Petitions for re-grading 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 10 3 24 4 12 5 10 6 22+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 ΔGo’ = – RTlnKeq 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 BIS103-002 (Spring 2008) Midterm #2 (May 20) 1. (22 pts) Name_____________________________________ Questions related to the Tricarboxylic Acid (TCA) or Citric Acid cycle. a) The TCA cycle is sometimes referred to as an “amphibolic” pathway. Briefly explain why. (2 pts) The TCA cycle simultaneously serves two major functions: In its catabolic mode, products of carbohydrate, lipid or amino acid degradation, most prominently acetyl-CoA, are completely degraded to CO2 and NADH/FADH2. At the same time, the TCA cycle also provides the starting building blocks (also called ‘precursors’) for a number of anabolic (or biosynthetic) pathways and reactions. b) Briefly explain the purpose of the “anaplerotic reactions”. (2 pts) The purpose of the anaplerotic reactions is to maintain a minimal concentration of the TCA cycle intermediate oxaloacetate (OAA) to enable its catabolic function (degradation of acetyl-CoA) when other intermediates, including OAA, are withdrawn from TCA cycle reactions for biosynthetic purposes (e.g. OAA Î glucose or citrate Î fatty acids). c) Provide complete equations for the reactions catalyzed by pyruvate carboxylase and citrate synthase. (Name all substrates and products or use common abbreviations). (6 pts) Pyruvate Carboxylase: Pyruvate (Pyr) + ATP + HCO3- Î Oxaloacetate (OAA) + ADP + Pi Citrate Synthase: Oxaloacetate (OAA) + Acetyl-CoA + H2O Î Citric acid + Coenzyme A d) One of the two reactions above requires a covalently bound cofactor. Name the reaction and the required cofactor? (2 pt) Reaction: Pyruvate Carboxylase Name of co-factor: Biotin 2 BIS103-002 (Spring 2008) Midterm #2 (May 20) Name_____________________________________ e) Draw the structure of citric acid into the box. (2 pts) See booklet or text for structure. f) If 14CO2 is incorporated into the TCA cycle via the pyruvate carboxylase reaction, which one of the carbons of citric acid would be radioactively labeled? Encircle the carbon. (2 pts) One of the ‘flanking’ carboxylate groups, not the ‘central’ one. g) Although oxygen does not participate directly in the TCA cycle, the cycle operates only under aerobic conditions. Briefly explain why? (2 pts) The TCA cycle produces NADH and FADH2, which need to be regenerated to NAD+ and FAD in order to keep the TCA cycle operational. However, in the mitochondria, the regeneration of NAD+ and FAD is only possible by the ETC, which requires oxygen (aerobic conditions). h) Two reactions in glycolysis and one reaction of the TCA cycle generate ATP by substrate-level phosphorylation. The way ATP is produced in the TCA cycle by substrate-level phosphorylation is conceptually very similar to one of the two ATP-generating reactions in glycolysis. Briefly describe the common strategy that is used to capture chemical energy released during an oxidation step for the formation of ATP in glycolysis and the TCA cycle. (4 pts) The oxidation of an aldehyde to a carboxylate function yields enough energy to form an ATP from ADP by substrate level phosphorylation in glycoslysis (the combination of the reactions catalyzed by glyceraldehyde-3-P dehydrogenase and 3-phosphoglycerate kinase) and in the TCA cycle (the combination of the reactions catalyzed by α-ketoglutarate dehydrogenase and succinyl-CoA synthetase). Initially, the energy released during the oxidation step is captured to form a thioester (covalently linked to glyceraldehyde-3-P dehydrogenase in glycolysis; succinyl-CoA in the TCA cycle). This thioester is then converted into a high-energy acyl phosphate (1,3-bisP-glycerate in glycolysis; succinyl-P which remains tightly bound to succinyl-CoA synthetase). In both cases, the high phosphoryl group transfer potential of the acyl-phosphates allows the subsequent formation of ATP (GTP) from ADP (GDP). 3 BIS103-002 (Spring 2008) Midterm #2 (May 20) 2. (10 pts) Name_____________________________________ A recently discovered bacterium, Sulfospirillum arsenophilum, uses arsenate, AsO43- or As(V), as a respiratory oxidant for the oxidation of a variety of organic compounds, including acetate. Some components of its electron transfer chain are listed below with their standard reduction potentials Eo’. As(V) + 2e- Î As(III) Acetate + 2e- Î Acetaldehyde NAD+ + 2H+ + 2e- Î NADH + H+ CoQ + 2H+ + 2e- Î CoQH2 Flavoprotein cox (FPc) + 2H+ + 2e- Î FPcred Flavoprotein box (FPb) + 2H+ + 2e- Î FPbred Eo’ = Eo’ = Eo’ = Eo’ = Eo’ = Eo’ = + 0.16 V – 0.59 V – 0.32 V + 0.06 V – 0.19 V + 0.10 V a) Order the electron carriers listed above in such away that would allow spontaneous electron flow from the initial electron donor to the terminal electron acceptor. Write the appropriate compounds into the boxes given below (use the abbreviations underlined above). (4 pts) Initial e- donor Acetate Î Carrier 1 NAD+ Î Carrier 2 Î Carrier 3 Î Carrier 4 Î Terminal e- acceptor FPc CoQ FPb Arsenate, As(V) b) Calculate the maximum number of ATP molecules that could theoretically be synthesized under standard conditions per pair of electrons transferred from acetate to the terminal electron acceptor? Assume ΔGo’ = 30.5 kJ mol-1 for the reaction ADP + Pi Î ATP + H2O, and a coupling efficiency of 85%. For full credit you must show your work. (6 pts) ΔEo’ = Eo’(ox) - Eo’ (red) = +0.16V – (–0.59 V) ΔEo’ (ETC) = + 0.75 V ΔGo’ = – nF ΔEo’ = –2 x 96,500 Jmol-1 V-1 x 0.75 V ΔGo’ (ETC) = – 144,750 Jmol-1 or – 144.75 kJmol-1 ΔGo’(ETC) / ΔGo’(ATP) x 0.85 Number of ATPs: 4 ATP 4 BIS103-002 (Spring 2008) Midterm #2 (May 20) 3. (24 pts.) Name_____________________________________ Lactate, the product of anaerobic glycolysis in skeletal muscles, is converted in the liver to glucose by gluconeogenesis. In addition, some of the lactate from the muscles is diverted and used as a “fuel” molecule to meet the ATP demand of gluconeogenesis. Answer the following questions: a) Draw the structure of lactate into the provided box. (2 pts) See booklet or text for structure. b) Three reactions in gluconeogenesis have a requirement for ATP (or GTP). Name the enzymes (common name only) that catalyze these reactions. (3 pts) 1. Pyruvate Carboxylase (lyase) 2. Phosphoenolpyruvate (PEP) Carboxykinase (lyase) 3. Phosphoglycerate Kinase (transferase, kinase) c) In order to provide the 3 moles of ATP required per mole of lactate in gluconeogenesis, a portion of the recycled lactate from the blood can also be completely degraded to CO2 and H2O by “biological oxidation”. Below, give the common names of the enzymes (1. and 2.) and the names of the biochemical pathways (3. and 4.) that catalyze the complete oxidation of lactate in the liver. Do not use abbreviations, provide the full (common) names. (4 pts) 1. Lactate Î Pyruvate Lactate Dehydrogenase (oxidoreductase) 2. Pyruvate Î Acetyl-CoA Pyruvate Dehydrogenase (oxidoreductase) 3. Acetyl-CoA Î 2CO2 Tricarboxylic Acid (or citric acid) Cycle (TCA) 4. NADH or FADH2 Î H2O Electron Transport Chain (ETC) 5 BIS103-002 (Spring 2008) Midterm #2 (May 20) Name_____________________________________ d) Calculate how many moles of ATP can be generated per mole lactate during this oxidation process. Assume the following: NADH = 3 ATP; FADH2 = 2 ATP; and only the malate-oxaloacetate shuttle is operating. For full credit you must show your work. (8 pts) 1. Lactate Î Pyruvate: Yields 1 NADH 2. Pyruvate Î Acetyl-CoA: Yields 1 NADH 3. Acetyl-CoA Î 2CO2 : Yields 3 NADH 1 FADH2 1 GTP(=ATP) 4. ETC and ATP synthase: Yields 15 ATP (from 5 NADH) 2 ATP (from 1 FADH2) (indirectly transported to mitochondria via malate-OAA shuttle) ======================================================================== Total: 17 ATP + 1 GTP( or ATP) = 18 ATP Moles ATP produced per mole lactate: 18 moles ATP per mole lactate e) The complete oxidation of 1 mole lactate to CO2 generates enough energy (ATP) for how many moles of glucose to be formed from lactate by gluconeogenesis? (1 pt) Answer: 3 moles of glucose per mole lactate 6 BIS103-002 (Spring 2008) Midterm #2 (May 20) Name_____________________________________ f) After gluconeogenesis, glucose is transported from the liver to skeletal muscles where it is converted into glycogen by four reactions. Provide the names or commonly used abbreviations for the two missing glucose derivatives (write into the boxes below). Give the balanced equation for reaction 3, and explain how reaction 3 becomes essentially irreversible. (6 pts) Glucose Glc-1-P 1. 2. Glycogen 3. Glc-6-P 4. UDP-Glc Balanced equation for reaction 3: Glc-1-P + UTP Ù UDP-Glucose + PPi What renders reaction 3 irreversible? The subsequent hydrolysis of PPi to 2x Pi. 4. (12 pts) Questions related to the pentose phosphate pathway. a) Two major pathways in metabolism catalyze the “biological oxidation” of one mole glucose into six moles of CO2. These are: (i) the pentose phosphate pathway, and (ii) glycolysis followed by the PDH reaction and the TCA cycle. Compare both major metabolic routes as outlined below. (4 pts) Pentose-P Pathway GlycolysisÎPDHÎTCA Cellular compartment(s) of CO2 formation. Cytosol Mitochondria Cellular compartment(s) of ATP generation. None Cytosol and Mitochondria Which of the following reducing equivalents are formed? (FADH2, FMNH2, NADH, NADPH) NADPH NADH and FADH2 What is the major purpose of the reducing equivalents generated? Biosynthesis Production of ATP (ETC) 7 BIS103-002 (Spring 2008) Midterm #2 (May 20) Name_____________________________________ b) Mannoheptulose is a 7-carbon sugar found in high concentrations in avocado fruit, which can be can be converted to glucose by humans after avocado consumption via the pentose phosphate pathway and gluconeogenesis. Which phase(s) of the pentose phosphate pathway transform mannoheptulose into intermediates of gluconeogenesis (give their names, not numbers)? Give the names (or abbreviations) of the two initial intermediates of gluconeogenesis into which mannoheptulose is converted. (3 pts) Phase(s): Rearrangement phase (or carbon transfer reactions) Intermediate 1: Fructose-6-phosphate (F6P) Intermediate 2: Glyceraldehyde-3-phosphate (GA3P) c) Which phase of the Calvin cycle (CO2 assimilation in photosynthesis) is most similar to the pentose phosphate pathway? (1 pt) Phase: Regeneration phase (III. phase) d) The pentose phosphate pathway is particularly active in the erythrocytes. Briefly explain why? (2pts) Erythrocytes are exposed to high levels of oxygen, which generates toxic ‘reactive oxygen species’ (or ROS). NADPH, a major product of the pentose phosphate pathway, is used to fully reduce (or detoxify) those ROS. e) The pentose phosphate pathway is also very active in tumor cells. Metabolic labeling studies with 14 C-labeled glucose showed that more than 70% of the ribose in DNA is derived from this pathway. The ribose of DNA will be radioactively labeled if the C-6 position of administered glucose carries the 14Cisotope, but the ribose will not be labeled if the C-1 carbon is radioactive. How do you explain this observation? (2 pts) During the oxidation phase of the pentose phosphate pathway, the carbon-1 of glucose is lost as CO2. 8 BIS103-002 (Spring 2008) Midterm #2 (May 20) 5. (10 pts) Name_____________________________________ Questions related to the catabolism of lipids. a) Draw the common structure of a triacylglyceride. (2 pts) Something like this. b) What is the biological function of bile acids or bile salts? (1 pt) Bile salts are ‘biological detergents’ released from the gall bladder to emulsify lipid droplets in the intestine. c) Free fatty acids are activated by coenzyme A before their degradation by β-oxidation. You add a fatty acid and radioactively labeled [14C]coenzyme A to a rat liver homogenate. After an incubation period you isolate the cytoplasmic and mitochondrial fraction. A subsequent analysis reveals that both fractions contain the acyl-CoA product; however, the [14C]-label is only present in one of the two fractions. Which fraction contains acyl-[14C]CoA and why? (4 pts) Fraction: Cytosol Reason: The pools of CoA in the cytosol and mitochondria are separated and do not exchange. d) What is meant by the term “ketogenesis” and list two conditions under which it occurs. (3 pts) Ketogenesis is the formation of ketone bodies (acetoacetate, acetone, β-hydroxybutyrate) from acetyl-CoA during prolonged starvation or Diabetes mellitus. 9 BIS103-002 (Spring 2008) Midterm #2 (May 20) 6. (22 pts) a. b. c. d. Name_____________________________________ Multiple-choice questions. Circle the best answer. There is only one best answer per question. Each question is worth 2 pts. Which one of the following compounds is NOT an intermediate of the TCA cycle? i Acetyl-CoA ii Citrate iii Oxaloacetate iv Succinyl-CoA v Succinate Which one of the following substrates cannot be oxidized by isolated mitochondria (i.e. purified mitochondria that are incubated in buffer and substrate)? i Pyruvate ii Lactate iii Succinate iv Fumarate v Malate Vitamine B1 (or thiamine) is the precursor to the coenzyme thiamine pyrophosphate (TPP). Thiamine deficiency would decrease which one of the following enzyme activities? i Fumarase ii Isocitrate dehydrogenase iii Malate dehydrogenase iv Succinate dehydrogenase v α-Ketoglutarate dehydrogenase Which one of the following enzymes of the pentose-P pathway requires TPP as a coenzyme? i Transaldolase ii Transketolase iii Phosphopentose isomerase iv Phosphopentose epimerase v Glucose-6-P dehydrogenase 10 BIS103-002 (Spring 2008) Midterm #2 (May 20) e. f. g. h. Name_____________________________________ Biotin is a cofactor necessary for what type of enzymes? i Enzymes catalyzing the transfer of one carbon atom ii Enzymes catalyzing the transfer of two carbon atoms iii Enzymes catalyzing the transfer of three carbon atom iv Enzymes catalyzing oxidoreduction reactions v Enzymes catalyzing isomerization reactions During “oxidative phosphorylation” or “photophosphorylation” the proton motive force that is generated by electron transport is used to: i oxidize NADH to NAD+ ii induce a conformational change in the ATP synthase iii oxidize coenzyme QH2 to coenzyme Q iv provide ADP and Pi for ATP synthesis v to detoxify reactive oxygen species The relative concentrations of ATP and ADP control the cellular rates of: i the TCA cycle ii pyruvate dehydrogenase iii the electron transport chain iv gluconeogenesis v all of the above The cytochrome b6f complex of the ETC in chloroplasts is analogous to what complex of the mitochondrial ETC? i Complex I ii Complex II iii Complex III iv Complex IV v Complex V 11 BIS103-002 (Spring 2008) Midterm #2 (May 20) i. j. k. Name_____________________________________ What one is the most likely source of propionyl-CoA in metabolism (as discussed in class)? i a product of glycolysis ii a product of the PDH reaction iii a product of fatty acid degradation iv a product of ketone body degradation v a product of the pentose phosphate pathway Which one of the following enzymes does NOT catalyze a decarboxylation reaction? i 6-Phosphogluconate dehydrogenase ii α−Ketoglutarate dehydrogenase iii Pyruvate dehydrogenase iv Succinate dehydrogenase v Isocitrate dehydrogenase After drinking a pint of beer at Sudwerk’s, the ethanol in the blood is taken up by liver cells and converted into acetate, which is then activated like a fatty acid to form acetyl-CoA. The conversion of one mole ethanol into one mole acetyl-CoA requires one of the following: i 1 mole NAD+ and 1 mole ATP ii 2 moles NADP+ and 1 mole AMP iii 1 mole FAD and 1 mole ATP iv 2 moles NAD+ and 1 mole ATP v 1 mole NADP+ and 1 mole AMP Bonus Question (2 extra pts): The intermediates of glycolysis are phosphorylated, but those of the TCA cycle are not. Why? Justify your answer. All intermediates of the TCA cycles are carboxylic acids and thus negatively charged, which increases their recognition and binding by enzymes and minimizes diffusion across a membrane. The addition of a phosphate group to intermediates in glycolysis serves the same functions as the initial intermediates of glycolysis would not carry a negative charge if unphosphorylated, and prepares glycolytic intermediates for substrate-level phosphorylation. 12 BIS103-002 (Spring 2008) Midterm #2 (May 20) Name_____________________________________ Use blank sheet as scratch paper, if needed. 13