* 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
Artificial gene synthesis wikipedia , lookup
Point mutation wikipedia , lookup
Mitochondrion wikipedia , lookup
Photosynthesis wikipedia , lookup
Microbial metabolism wikipedia , lookup
Basal metabolic rate wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Nicotinamide adenine dinucleotide wikipedia , lookup
Peptide synthesis wikipedia , lookup
Proteolysis wikipedia , lookup
Genetic code wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Butyric acid wikipedia , lookup
Adenosine triphosphate wikipedia , lookup
Metalloprotein wikipedia , lookup
Oxidative phosphorylation wikipedia , lookup
Glyceroneogenesis wikipedia , lookup
Fatty acid synthesis wikipedia , lookup
Fatty acid metabolism wikipedia , lookup
Amino acid synthesis wikipedia , lookup
Citric acid cycle wikipedia , lookup
BIS103-002 (Spring 2008) Final Exam (June 9) Instructor: Abel Name_____________________________________ 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 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 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 23 3 12 4 12 5 11 6 20 (+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 BIS103-002 (Spring 2008) Final Exam (June 9) 1. (22 pts.) Name_____________________________________ Questions on fatty acid metabolism. a) Calculate how many moles of ATP and NADPH are required for the synthesis of lauric acid (a 12:0 fatty acid) from acetyl-CoA. Consider that the acetyl-CoA building blocks need to be exported out of the mitochondria. You must show your work for full credit. (6 pts) 1. Transport of 6 acetyl-CoA from mitochondria to cytosol (citrate shuttle): 6 ATP 2. Conversion of 5 acetyl-CoA to 5 malonyl-CoA: 5 ATP 3. Five rounds of fatty acid biosynthesis (2 NADPH per round): 10 NADPH Moles of ATP: 11 Also correct: 11 ATP 4 NADPH Moles of NADPH: 10 b) Assume that the 12:0 fatty acid is further oxidized to the 12:0(Δ6) desaturated fatty acid using molecular oxygen as the oxidant. Provide a balanced equation for this desaturation step by filling in the blanks. (3 pts) 12:0 + O2 + NADPH Î 12:0(Δ6) + 2H2O + NADP+ (+H+) c) Which major pathway discussed in class provides most of the NADPH needed for fatty acid biosynthesis? (1 pt) Pathway: Pentose Phosphate Pathway (PPP) d) A minor process of NADPH formation takes place in the cytosol and may convert the NADH from glycolysis to NADPH for fatty acid synthesis. First, provide the common name of the enzyme that catalyzes the NADH-producing reaction in glycolysis. (2 pts) Partial credit for enzyme class (1 pt) Common name: Glyceraldehyde-3-P Dehydrogenase ( or G3P Dehydrogenase) 2 BIS103-002 (Spring 2008) Final Exam (June 9) Name_____________________________________ Second, provide balanced equations for the reactions catalyzed by malate dehydrogenase and the malic enzyme that can convert NADH produced in glycolysis to NADPH for fatty acid biosynthesis. Use names or common abbreviations for substrates and products. (4 pts) Reaction 1: OAA + NADH Ù Malate + NAD+ Reaction 2: Malate + NADP+ Î Pyruvate + CO2 + NADPH e) The conversion of NADH to NADPH in the cytosol by the two enzymes above could provide a way to regenerate NAD+ for maintaining glycolysis. Why is this alternative not used in tissues or organs undergoing anaerobic glycolysis to regenerate NAD+? (2 pts) Tissues that undergo anaerobic glycolysis (e.g., skeletal muscles) are in desperate need of ATP (no or only very low ATP production by oxidative phosphorylation), which is not used for biosynthetic processes (requiring NADPH). Tissues would not be regulated so that the PPP pathway is activated at the same time as anaerobic glycolysis. f) The synthesis of triacylglycerides involves the formation of ester bonds between glycerol and fatty acids, an energy-requiring process. What renders the ester bond formation in triacylglycerol synthesis energetically feasible? (2 pts) The hydrolysis of the thioester bond of “activated fatty acids”, which are acyl-CoA. g) Activated fatty acids (acyl-CoA) are produced in the cytosol as the first and last step of fatty acid degradation and fatty acid synthesis, respectively. How is the transport of newly synthesized acyl-CoA into the mitochondria for degradation by β-oxidation effectively prevented? (2 pts) The early intermediate of fatty acid biosynthesis, malonyl-CoA, allosterically inhibits carnitine acyltransferase I, which imports acyl-CoA from the cytosol into the mitochondria for β-oxidation. 3 BIS103-002 (Spring 2008) Final Exam (June 9) 2. (23 pts.) Name_____________________________________ Questions related to the metabolism of amino acids a) The chemical structure in the box depicts an amino acid. Provide the common name for this amino acid. (1 pt) COO HC NH2 CH2OH Name: Serine b) Three reactions can produce the amino acid shown above (a) from 3-phosphoglycerate (3-PGA), an intermediate of glycolysis. Draw the structure of 3-PGA and provide common and simplified names for each enzyme (e.g., ‘kinase’ or ‘oxidase’). The order of the enzymes is not important. (4 pts) Draw the structure of 3-PGA into the box: Enzyme 1: Dehydrogenase Enzyme 2: Phosphatase Enzyme 3: Transaminase c) Several co-factor discussed in class are involved in the transfer of carbon groups. The amino acid shown in (a) can be converted into glycine. Which co-factor ‘rescues’ the remaining carbon unit? (1 pt) Circle one! Biotin TPP PLP SAM THF CoA d) Glycine can be further decomposed to NH3 and CO2. Which co-factor ‘rescues’ the reduced carbon of glycine? (1 pt) Circle one! Biotin TPP PLP SAM THF CoA e) The enzyme that catalyzes the initial decarboxylation of glycine (glycine decarboxylase) has a requirement for which of the co-factors listed below? (1 pt) Circle one! Biotin TPP PLP SAM THF CoA 4 BIS103-002 (Spring 2008) Final Exam (June 9) Name_____________________________________ f) Assume that the NH3 derived from glycine decarboxylation is used for the production of urea. Provide a balanced equation for the reaction that generates carbamoyl-phosphate. Fill in the blanks and draw the chemical structure of carbamoyl-P into the box. (4 pts) See booklet NH3 + HCO3- + 2ATP Î Carbamoyl-P + 2ADP + 1Pi g) In addition to urea, fumarate is also produced in the urea cycle of mammals. This fumarate is converted by three reactions to aspartate, which is a substrate of a previous urea cycle reaction. Sketch out the reactions for the conversion of fumarate to aspartate. Include co-factors if they are required. (6 pts) Reaction 1: Fumarate + H2O Î Malate Reaction 2: Malate + NAD+ Ù Oxaloacetate (OAA) + NADH Reaction 3: OAA + Glutamate (Glu) Ù Aspartate (Asp) + α-Ketoglutarate (KGA) h) Two groups of experimental rats were fed different amino acids as the sole source of carbon for about one month. Group A was fed with lysine and leucine, and group B received aspartate and glutamate. Rats of both groups were examined after one month and a striking difference was noticed. One group of rats was healthy and gained some weight, whereas the other group of animals showed poor health and lost weight because of a decline in muscle mass. Which animal group was the healthiest? (1 pt) Circle one! A B Justify your choice by explaining the underlying biochemistry! (4 pts) Lysine and leucine are ketogenic amino acids, whereas aspartate and glutamate are glucogenic amino acids. That means that the animals fed with aspartate and glutatmate can produce glucose and other carbohydrates to stay reasonably healthy for some time. On the other hand, the group fed with lysine and leucine cannot produce glucose from this diet as it will be converted exclusively to acetyl-CoA. Since acetyl-CoA can only be used for lipid biosynthesis (and ketogenesis), maintenance of blood glucose levels is achieved by degradation of muscle protein, thus the loss of weight. 5 BIS103-002 (Spring 2008) Final Exam (June 9) 3. (12 pts.) Name_____________________________________ Short questions on nucleotide metabolism. a) Draw into the boxes the structures of the aromatic pyrimidine and purine ring system. Do not draw any R-groups. (4 pts). Pyrimidine Purine b) Briefly describe the difference between “de novo” and “salvage” pathways of nucleotide biosynthesis. (2 pts) De novo synthesis assembles the constituents of nucleotides “one-by-one” from simple precursors, whereas the salvage pathway rescues nucleobases from nucleic acid degradation and converts them back to nucleotides. c) How is the ribose unit activated for nucleotide biosynthesis (provide a balanced equation of the reaction) and briefly point out the major difference between the de novo synthesis of pyrimidine and purine nucleotides. (4 pts) Ribose activation: Ribose-5-P + ATP Î PRPP (5-phospho-ribosyl-1-pyrophosphate) + AMP Difference: De novo synthesis of pyrimidines first assembles the pyrimidine nucleobase ring and then attaches it ribose-5-P via activated ribose (PRPP). The opposite occurs in purine nucleobase synthesis; the purine ring system is assembled on the ribose-5-P scaffold (initially provided by PRPP). d) In addition to their role in nucleic acid biosynthesis, the purine ring system can be modified by “methoxylation”. This modification requires the sequential action of a “monooxygenase” (which inserts a –OH function) and a methyltransferase (which forms the –OCH3 function). What is the most likely oxidant for the monooxygenase reaction, and what is the most likely co-factor for the methyltransferase reaction? (2 pts) Oxidant (monooxygenase): Molecular oxygen (O2) Co-factor (methyltransferase): S-Adenosylmethionine (SAM) 6 BIS103-002 (Spring 2008) Final Exam (June 9) 4. (12 pts.) Name_____________________________________ Questions on metabolic regulation. a) When a dog confronts a “fight-or-flight” situation, the release of epinephrine promotes glycogen breakdown in the liver and skeletal muscle. The end product of glycogen breakdown in the liver is glucose; however, the end product in skeletal muscle is pyruvate, which then enters the mitochondria. What is the biochemical reason for the different end products in the two tissues? (2 pts) Glucose-6-P phosphatase in the liver produces glucose from G6P, an intermediate of glycogen degradation. However, this enzyme (G6P phosphatase) is not present in skeletal muscles. Therefore, in skeletal muscles G6P will enter glycolysis to be converted into 2x pyruvate. What is the advantage of these two different glycogen breakdown routes? (2 pts) The liver will export the glucose (derived from glycogen) into the blood where it reaches the skeletal muscles to supplement their increased fuel requirement for producing ATP. Degradation of muscle glycogen to pyruvate (and then to CO2 and H2O) provides ATP for physical activity. b) Caffeine is an inhibitor of the cyclic nucleotide phosphodiesterase. Predict the effect of a cup of coffee on the activity of the following key regulatory enzymes. (4 pts) Circle. Triacylglycerol lipase (adipose) higher lower Glycogen synthase (muscle) higher lower Glycogen phosphorylase (muscle) higher lower Phosphofructokinase-2 (liver) higher lower c) Given below are the names of regulated enzymes. Predict the effect of each of the allosteric effectors on the activity of the enzymes (write “activator” or “inhibitor” on the line provided). (4 pts) Phosphofructokinase-1: ATP: Inhibitor H+ (decreasing pH): Inhibitor Citrate Synthase: ADP: Activator Succinyl-CoA: Inhibitor 7 BIS103-002 (Spring 2008) Final Exam (June 9) 5. (11 pts.) Name_____________________________________ Short answer questions. a) Microorganisms have the ability to convert ethanol into glucose, which, unfortunately, humans can not do. The blank lines below stand for major biochemical pathways (or segments thereof) that accomplish this conversion. Write the names of the respective pathways above the lines. (3 pts) Glyoxylate Cycle TCA Cycle Gluconeogenesis (GNG) Ethanol ÎÎ____________ Î Succinate Î _____________Î OAA Î______________Î Glucose b) Dihydroxyacetone-P (DHAP), an intermediate of glycolysis, has at least two additional purposes in metabolism as discussed in class. What are two purposes other than being metabolized in glycoslysis? (2 pts) 1. Glycerol-3-P shuttle (transfer of reducing equivalents from cytosol into mitochondria) 2. Production of glycerol-3-P for triacylglyceride (lipid) synthesis c) Vegetarians who do not complement their diet with egg or milk products are highly advised to eat different types of plant protein. What is the biochemical basis for this recommendation? (2 pts) Proteins from animal sources contain a balanced set of essential amino acids. However, plant proteins are often deficient in certain essential amino acids, depending on the source of the plant diet (crop species; tissues, seeds or fruits consumed). d) The aromatic amino acids tryptophan and phenylalanine are essential to humans; however, tyrosine is not. What is the reason? Be specific. (2 pts) Tyrosine can be produced from phenylalanine in one reaction, which involves the hydroxylation of the ring system. e) Leaf cells of plants have particularly high concentrations of antioxidants, such as ascorbic acid or glutathione, to detoxify reactive oxygen species (ROS). What major metabolic processes generate by side-reactions ROS in plants? (2 pts) Mitochondrial electron transport chain (ETC) and light reactions of photosynthesis (PSN) 8 BIS103-002 (Spring 2008) Final Exam (June 9) Name_____________________________________ 6. (20 + 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. The final product(s) of amino acid catabolism excreted in the urine of humans are: i Urea and uric acid ii Ammonia and urea iii Urea and glutamine iv Ammonia and glutamine v Uric acid and ammonia Carbon dioxide derived from carbohydrate catabolism is generated in what cellular compartment(s)? i Cytosol ii Mitochondria iii Cytosol and Mitochondria iv Chloroplasts v Cytosol and Mitochondria and Chloroplasts Excess carbohydrate intake by physically exhausted adults is converted to: i Glycogen ii Glycogen and protein iii Triacylglycerides iv Triacylglycerides and glycogen v Triacylglycerides and glycogen and protein Which substance is NOT involved in the production of urea from ammonia via the urea cycle? i ATP ii Aspartate iii Ornithine iv Arginine v Lysine 9 BIS103-002 (Spring 2008) Final Exam (June 9) e. f. g. h. Name_____________________________________ Which one of the following oxygen compounds is the most reactive? i Oxygen ii Superoxide radical iii Hydrogen peroxide iv Hydroxyl radical v Water Which one of the following dietary polymers is the least effective source of chemical energy? i Starch ii Protein iii Lipids iv Nucleic Acids v Glycogen The methyl cycle serves the following primary purpose: i DNA methylation ii Regeneration of S-Adenosylmethionine iii Regeneration of N5-Methyl THF iv Regeneration of pyridoxal-P v Synthesis of cysteine from methionine Which one of the following processes is inhibited by insulin in the muscle? i Glycogen degradation ii Fatty acid synthesis iii Glycolysis iv Glycogen synthesis v Pentose phosphate pathway 10 BIS103-002 (Spring 2008) Final Exam (June 9) i. j. Name_____________________________________ All of the compounds listed below can be considered “activated” because their hydrolysis is thermodynamically favored. Which one of the following compounds is “least activated” or has the lowest ΔGo’ of hydrolysis based on simple chemical principles. i Acetyl-CoA ii O-Acetylserine iii Carbamoyl-phosphate iv Creatine-phosphate v UDP-Glucose Homoarginine (a homolog of arginine containing one additional methylene group) is synthesized by several microorganisms. A major portion of the carbon skeleton of homoarginine is most likely derived from: i Lysine ii Ornithine iii Asparagine iv Glutamine v Leucine Bonus question (2 extra pts). How many moles of ‘reducing equivalents’ and ‘ATP equivalents’ does it take for bacteria to reduce 1 mole of sulfate (SO42-) to 1 mole sulfhydryl groups (-SH) present in cysteine? i “1 ATP” and 8 Ferredoxin ii “2 ATP” and 6 Ferredoxin iii “3 ATP” and 6 Ferredoxin iv “2 ATP” and 8 Ferredoxin v “1 ATP” and 6 Ferredoxin 11 BIS103-002 (Spring 2008) Final Exam (June 9) Name_____________________________________ Use as scratch paper, if necessary. 12