Chapter 15: Glycolysis: [1-6, 8, 9, 15] 1. ATP yield. Each of the following molecules is processed by glycolysis to lactate.

How much ATP is generated from each molecule? A. Glucose-6-phosphate: 3 ATP B. Dihydroxyacetone phosphate: 2 ATP C. Glyceraldehyde 3-phosphate: 2 ATP D. Fructose: 2 ATP E. Sucrose: 4 ATP 2. Enzyme redundancy? Why is it advantageous for the liver to have both hexokinase and glucokinase to phosphorylate glucose? Glucokinase enables the liver to remove glucose from the blood when hexokinase is saturated, ensuring that glucose is captured for later use. 3. Corporate sponsors. Some of the early research on glycolysis was supported by the brewing industry. Why would the brewing industry be interested in glycolysis? Glycolysis is a component of alcoholic fermentation, the pathway that produces alcohol for beer and wine. The belief was that understanding the biochemical basis of alcohol production might lead to moreefficient means of producing beer. 4. Recommended daily allowance. The recommended daily allowance for the vitamin niacin is 15 mg per day. How would glycolysis be affected by niacin deficiency? The conversion of glyceraldehydes 3-phosphate into 1,2-bisphosphoglycertae would be impaired. Glycolysis would be less effective. 5. Whos on first? Although both hexokinase and phosphofructokinase catalyze irreversible steps in glycolysis and the hexokinase-catalyzed step is first, phosphofructokinase is nonetheless the pacemaker of glycolysis. What does this information tell you about the fate of the glucose 6phosphate formed by hexokinase? Glucose 6-phosphate must have other fates. Indeed, it can be converted into glycogen or be processed to yield reducing power for biosynthesis. 6. The tortoise and the hare. Why is the regulation of phosphofructokinase by energy charge not as important in the liver as it is in muscle? The energy needs of a muscle cell vary widely, from rest to intense exercise. Consequently, the regulation of phosphofructokinase by energy charge is vital. In other tissues, such as the liver, ATP concentration is less likely to fluctuate and will not be a key regulator of phosphofructokinase.

7. (8) Running in reverse. Why cant the reactions of the glycolytic pathway simply be run in reverse to synthesize glucose? The DeltaG for the reverse of glycolysis is +96kJ mol-1 (+23kcal mol-1_, far to endergonic to take place. 8. (9) Road blocks. What reactions of glycolysis are not readily reversible under intracellular conditions? The conversion of glucose into glucose 6-phosphate into fructose1,6-bisphosphate by phosphofructokinase; the formation of pyruvate from phosphoenolpyruvate kinase.

9. (15) Tracing carbon atoms. Glucose labeled with C14 at C-1 is incubated with glycolytic enzymes and necessary cofactors. a. What is the distribution of C14 in the pyruvate that is formed? (Assume that the interconvention of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate is very rapid compared with the subsequent step.) Label is in the methyl carbon atom of pyruvate. b. If the specific activity of the glucose substrate is 10mCi mmol-1, what is the specific activity of the pyruvate that is formed? 5mCi mM-1, the specific activity is halved because the number of moles of product (pyruvate) is twice that of the labeled substrate (glucose). Chapter 16: Gluconeogenesis [1-5, 8-11] 1. Road blocks. What reactions of glycolysis are not readily reversible under intracellular conditions? How are these reactions bypassed gluconeogenesis? In glycolysis, the formation of pyruvate and ATP by pyruvate kinase is irreversible. This step is bypassed by 2 reactions in gluconeogenesis: 1) formation of oxaloacetate from pyruvate and CO2 by pyruvate carboxylase and 2) formation of phosphoenolpyruvate from oxaloacetate and GTP by phosphoenolpyruvate carboxykinase. The formation of fructose 1,6- bisphophate by phosphofructokinase bypassed by fructose 1,6-bisophophatase into fructose 6-phosphate. Finally the hexokinase-catalyzed formation of glucose 6-phosphate in glycolysis is bypassed by glucose 6-phosphatase, but only in the liver. 2. Waste not, want not. Why is it in an organisms best interest to convert lactic acid from the blood into glucose in the liver? Lactic acid is capable of being further oxidized and is thus useful energy. The conversion of acid into glucose saves the carbon atoms for future combustion. 3. Metabolic mutant. What are the likely consequences of a genetic disorder rendering fructose 1,6-bisophosphatase in the liver less sensitive to regulation by fructose 2,6-bisphosphate? Fructose 2,6-bisphosphate, present at high concentration when glucose is abundant, normally inhibits gluconeogenesis by blocking fructose 1,6-bisphosphatase. In this genetic disorder, the phosphatase is active irrespective of the glucose level. Hence substrate cycling is increased. The level of fructose 1,6-bisphosphatase is consequently lower than normal. Less pyruvate is formed and thus less ATP is generated.

4. Biotin snatcher. Avidin, a 70-kd protein in egg white, has very high affinity for biotin. In fact, it is a highly specific inhibitor of biotin enzymes. Which of the following conversions would be blocked by the addition of avidin to a cell homogenate? a) Glucose pyruvate b) Pyruvate glucose c) Oxaloacetate glucose

d) Malate oxaloacetate e) Pyruvate oxaloacetate f) Glyceraldehyde 3-phosphate fructose 1,6- bisphosphate 5. Tracing carbon atoms. If cells synthesizing glucose from lactate are exposed to CO2 labeled with 14C will be distribution of label in the newly synthesized glucose? There will be no labeled carbons. The carbon dioxide added to pyruvate, formed from the lactate, to form oxaloacetate is lost with the conversion of oxaloacetate into phosphoenolpyruvate. 8. Different needs. Liver is primarily a gluconeogenic tissue, whereas muscle is primarily glycolytic. Why does this division of labor make good physiological sense. Muscle is likely to produce lactic acid during contraction. Lactic acid is a strong acid and cannot accumulate in muscle or blood. Liver removes the lactic acid from the blood and converts it into glucose. Glucose release is prevented by the absence of glucose 6-phosphatase. 9. Metabolic mutants. What would be the effect on an organisms ability to use glucose as an energy source if a mutation inactivated glucose 6-phosphate in the liver? Glucose produced by the liver could not be released into the blood. Tissues that rely on glucose as an energy source would not function as well unless glucose was provided in the diet. 10. Never let me go. Why does the lack of glucose 6-phosphatase activity in the brain and muscle make good physiological sense? Glucose is an important energy source for both tissues and essentially the only energy source for the brain. Consequently these tissues should never release glucose. Glucose release is prevented by the absence of glucose 6-phosphatase. 11. Match em 1. The following sequence is part of the sequence of reactions in gluconeogenesis. Pyruvate A oxaloacetate bmalatecoxaloacetateD phosphoenolpyruvate a) Takes place in mitochondria A,B b) Takes place in cytoplasm C,D c) Produces CO2 D d) Consumes CO2 A e) Requires NADH B f) Produces NADH C g) Requires ATP A h) Requires GTP D i) Requires thiamine none

j) Requires biotin A k) Is regulated by acetyl coA A Chapter 18: [1, 3, 5] 1. Flow of carbon atoms. What is the fate of the radioactive label when each of the following compounds is added to a cell extract containing the enzymes and cofactors of the glycolytic pathway, the citric acid cycle and the pyruvate dehydrogenase complex. A) After one round of the citric acid cycle, the label emerges in c-2 and c-3 of oxaloacetate b) the label emerges in co2 in the formation of acetyl coA from pyruvate. C) after one round of the citric acid cycle, the label emerges in c-1 and c-4 of oxaloacetate. (d and e). Same fate as that in part A 2. (3) Driving force. What is the change in G for the complete oxidation of the acetyl unit of acetyl CoA by the citric acid cycle. -41 kJmol-1 or -9.8 kcalmol-1 3. (5) Coupling reactions. The oxidation of malate by NAD+ to form oxaloacetate is a highly endergonic reaction under standard conditions. The reaction proceeds readily under physiological conditions. a. Why? The steady-state concentrations of the products are low compared with those of the substrates. b. Assuming an nad+/nadh ratio of 8 and a pH of 7, what is the lowest malate/oxaloacetate ratio at which oxaloacetate can be formed malate? The ratio of malate to oxaloacetate must be greater than 1.57*10^4 for oxaloacetate to be formed.

Chapter 19: [2, 6, 8, 9] 2. Thermodynamic constraint. Compare the DeltaG values for the oxidation of succinate by NAD+ and by FAD. Use the data given in 19.1 and assume that Enot for the FAD-FADH2 redox couple is nearly 0 V. Why is FAD rather than NAD+ the electron acceptor in the reaction catalyzed by succinate dehydrogenase? +DeltaG is +67mol-1 (+16.1 kcal mol-1) for oxidation by NAD+ and +47.7 kJmol-1 (11.4kcalmol) for oxidation by FAD. The oxidation of succinate by NAD+ is not thermodynamically feasible. 6. Six of one, half dozen of the other. How is the redox potential DeltaEnotrelated to the free-energy change of a reaction? DeltaG= -nFDeltaEnot 8. Line up. Place the following components of the electron transport chain in their proper order: C,E,B,A,D: NADH-Q Reductase, Ubiquinone, Q-cytochrome c oxidoreductase, cytochrome c, cytochrome c oxidase 9. Match em.

Complex I - NADH-Q oxidoreductase Complex II- Succinate Q reductase Complex III- Q-cytochrome c oxidoreductase Complex IV- Cytochrome c oxidase Ubiquinone- Coenzyme Q Chapter 20 [1-4, 6, 13, 14] 1. Energy harvest. What is the yield of ATP when each of the following substrates is completely oxidized to CO2 by a mammalian cell homogenate? Assume that glycolysis, the citric acid cycle and oxidative phosphorylation are fully active. a) Pyruvate= 12.5 b) Lactate= 14 c) Fructose 1,6- bisphosphate= 32 d) Phosphoenolpyruvate= 13.5 e) Galactose= 30 f) Dihydroxyacetone phosphate= 16 2. Potent poisons. What is the effect of each of the following inhibitors on electron transport and ATP formation by the respiratory chain? a) Azide- blocks electron transport and proton pumping at Complex IV b) Atractyloside- blocks electron transport and ATP synthesis by inhibiting the exchange of ATP and ADP across the inner mitochondrial membrane c) Rotenone- blocks electron transport and proton pumping at Complex I d) DNP- blocks synthesis without inhibiting electron transport by dissipating the proton gradient e) Carbon Monoxide- blocks electron transport and proton pumping at Complex IV f) Antimycin A- blocks electron transport and proton pumping at Complex III 3. A question of coupling. What is the mechanistic basis for the observation that the inhibitors of ATP synthase also lead to an inhibition of the electron-transport chain. If the proton gradient is not dissipated by the influx of protons into the mitochondrion with the generation of ATP, the outside of the mitochondrion eventually develops such a large positive charge that the electron-transport chain can no longer pump protons against the gradient. 4. O2 consumption. Oxidative phosphorylation in mitochondria is often monitored by measuring oxygen consumption. When oxidative phosphorylation is proceeding rapidly, the mitochondria will rapidly consume oxygen. If there is little oxidative phosphorylation, only small amounts of oxygen will be used. You are given a suspension of isolated mitochondria and directed to add the following compounds in order from a to h. With the addition of each

compound, all of the previously added compounds remain present. Predict the effect of each addition on oxygen consumption by the isolated mitochondria. a. Glucose- No effect, mitochondria cannot metabolize glucose b. ADP + P- No effect, no fuel is present to power the synthesis of ATP c. Citrate- The O2 falls because citrate is a fuel and ATP can be formed from ADP and P d. Oligomycin- Oxygen consumption stops because oligomycin inhibits ATP synthesis, which is coupled to the activity of the electron transport chain. e. Succinate- No effect, for the reason of D f. Dinitrophenol- O2 falls rapidly because the system is uncoupled and does not require ATP synthesis to lower the proton-motive force g. Rotenone- O2 falls, though at a lower rate. Rotenone inhibits Complex I, but the presence of succinate will enable electrons to enter Complex II h. Cyanide- Oxygen consumption ceases because Complex IV is inhibited and entire chain backs up. 13. Obeying the laws of Thermodynamics. Why will the isolated F1 subunits display ATPase activity but not ATP synthase activity? The patient has a deficiency of the branching enzyme. 14. Opposites attract. An arginine residue (Arg 210) in the a subunit of ATP synthase is near the aspartate residue (Asp 61) in the matrix-side proton channel. How might Arg 210 assist proton flow? A) Glycogen was too large to enter the gel and, because analysis was by Western blot with the use of an antibody specific to glycogenin, we should not expect to see background proteins. B) alpha-amylase degrades glycogen, releasing the protein glycogenin, we would not expect to see background proteins. C) Glycogen phosphorylase, glycogen synthase, and protein phosphatase I. These proteins might be visible if the gels were stained for protein, but a Western analysis reveals the presence of glycogenin only. Chapter 24: [14] 14. Glycogen isolation 1. The liver is a major storage site for glycogen. Purified from 2 samples of human liver, glycogen. Purified from two samples of human liver, glycogen was either treated or not treated with alpha-amylase and subsequently analyzed by SDS-PAGE and Western blotting with the use of antibodies to glycogenin. a) Why are no proteins visible in the lanes without amylase treatment? Glycogen was too large to enter the gel and, because analysis was by Western blot with the use of an antibody specific to glycogenin, we would not expect to see background proteins. b) What is the effect of treating the samples with alpha-amylase? Alpha-amylase degrades glycogen, releasing the protein phosphatase I, which can be visualized by Western blot. c) List other proteins that you might expect to be associated with glycogen. Why are other proteins not visible? Glycogen phosphorylase, glycogen synthase, and protein phosphatase I . These proteins might

be visible if the gels were stained for protein, but a Western analysis reveals the presence of glycogenin only. Chapter 25 [2-7, 9] 2. Watch your diet, Doctor. Noted psychiatrist Hannibal Lecter once remarked to FBI Agent Starling that he enjoyed liver with some fava beans and nice Chianti. Why might this diet be dangerous for some people? Fava beans contain pamaquine, a purine glycoside that can lead to the generation of peroxides- reactive oxygen species that can damage membranes as well as other biomolecules. Glutathione is used to detoxify the ROS. The regeneration of glutathione depends on an adequate supply of NADPH, which is synthesized by the oxidative phase of the pentose phosphate pathway. People with low levels of the dehydrogenase are especially susceptible to pamaquine toxicity. 3. Offal or awful? Liver and other organ meats contain large quantities of nucleic acids. In the course of digestion, RNA is hydrolyzed to ribose, among other chemicals. Explain how ribose can be used as a fuel. The nonoxidative phase of the pentose phosphate pathway can be used to convert three molecules of ribose 5-phosphate into two molecules of fructose 6-phosphate and one molecule of glyceraldehyde 3-phosphate. These molecules are components of the glycolytic pathway. 4. A required ATP. The metabolism of glucose 6-phosphate into ribose 5-phosphate by the joint efforts of the pentose phosphate pathway and glycolysis can be summarized the following equation. 5 glucose 6-phosphate + ATP - 6 ribose 5-phosphate + ADP. Which reaction requires ATP? The conversion of fructose 6-phosphate into fructose 1,6-bisphosphate by phosphofructokinase requires ATP. 5. Tracing glucose. Glucose labeled 14C at C-6 is added to a solution containing the enzymes and cofactors of the oxidative phase of the pentose phosphate pathway. What is the fate of the radioactive label? The label emerges at C-5 of ribulose 5-phosphate 6. Recurring decarboxylations. Which reaction in the citric acid cycle is most analogous to the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate? What kind of enzyme-bound intermediate is formed in both reactions? The oxidative decarboxylation of isocitrate to alphaketoglutarate. A beta-ketoacid intermediate is formed in both reactions. 7. Carbon Shuffling. Ribose 5-phosphate labeled with 14C at C-1 is added to a solution containing transketolase, transaldolase, phosphopentose epimerase, phosphopentose isomerase, and glyceraldehyde 3-phosphate. What is the distribution of the radioactive label in the erythrose 4phosphate and fructose 6-phosphate that are formed in this reaction mixture? C-1 and C-3 fructose 6phosphate are labeled, whereas erythose 4-phosphate is not labeled. 9. Reductive Power. What ratio of NADPH to NADP+ is required to sustain GSH= 10 mM and GSSG= 1 mM? Use the redox potentials given. DeltaEnot for the reduction of gluthatione by NADPH is +0.09 V. Hence DeltaG is -17.4kJ (-4.2 kcal) which corresponds to an equilibrium constant of 1126. The required NADPH/NADP+ ratio is 8.9*10^-5

Chapter 26: [2-4, 6-10, 13, 19] 2. Forms of energy. The partial reactions leading to the synthesis of acetyl CoA are freely reversible. The equilibrium constant for the sum of these reactions is close to 1, meaning that the energy levels of the reactants and products are about equal, even though a molecule of ATP has been hydrolyzed explain why these reactions are readily reversible. The ready reversibility is due to the high-energy nature of the thioester in the acyl coA. 3. Activation fee. The reaction for the activation of fatting acids before degradation is: This reaction is quite favorable because the equivalent of two molecules of ATP is hydrolyzed. Explain why, from a biochemical bookkeeping point of view, the equivalent of two molecules of ATP is used despite the fact that the left side of the equation has only one molecule of ATP. The return the AMP to a form that can be phosphorylated by oxidative phosphorylation or substrate-level phosphorylation , another molecule of ATP must be expended in the reaction: ATP + AMP 2 ADP (4) Proper sequence. Place the following list of reactions or relevant locations in the Beta oxidation of fatty acids in the proper order. a) b) c) d) e) f) g) h) Reaction with carnitine Fatty acid in the cytoplasm Activation of fatty acid by joining to coA Hydration NAD+ linked oxidation Thiolysis Acyl CoA in mitochondrion FAD-linked oxidation B, C, A, G, H, D, E, F

5. (6) A phantom of acetyl coA? In the equation for fatty acid degradation shown here, only seven molecules of coA are required to yield eight molecules of acetyl CoA. How is the difference possible? Palmitoyl CoA + 7 FAD + 7 NAD+ +7 CoASH +7 H2O- 8 acetyl coA + 7 FADH2 + 7 NADH + H+ The next to last degradation product, acetoacetyl coA, yields two molecules of acetyl coA with the thiolysis by one molecule of coA. 6. (7) Comparing yields. Compare the ATP yields from palmitic acid and palmitoleic acid. Palamitic acid yields 106 molecules of ATP. Palmitoelic acid has a double bond between carbon C-9 and C-10. When palmitoleic is processed in Beta oxidation, one of the oxidation steps (to introduce a double bond before the addition of water) will not take place, because a double-bound already exists. Thus FADH2 will not be generated, and

palmitoelic acid will yield 1.5 fewer molecules of ATP than palamitic acid, for a total of 104.5 ATP. 7. (8) Counting ATPs. What is the ATP yield for the complete oxidation of C17 (hetpadecanoic) fatty acid? Assume that the propionyl CoA ultimately yields oxaloacetate in the citric acid cycle. See C16 8. (9) Sweet Temptation. Stearic acid is a C18 fatty acid component of chocolate. Suppose you had a depressing day and decided to settle matters by gorging on chocolate. How much ATP would you derive from the complete oxidation of stearic acid to CO2? See C17 9. (10) The best storage form. Compare the ATP yield from the complete oxidation of glucose, a six carbon carbohydrate, and hexanoic acid, a six-carbon fatty acid. Hexanoic acid is also called caprioic acid and is responsible for the aroma of goats. Why are fats better fuels than carbohydrates? See C17 10. (13) Counting ATPs 2. How much energy is attained with the complete oxidation of the ketone body D-3-hydroxybutyrate? NADH produced with the oxidation to acetoacetate =2.5 ATP. Acetoacetate is converted into acetoacyl coA. 11. (19) Ill-advised diet. Suppose that, for some bizarre reason, you decided to exist on a diet of whale and seal blubber, exclusively. a) How would a lack of carbohydrates affect your ability to utilize fats? Fats burn in the flame of carbohydrates. Without carbohydrates there would be no anapleurotic reactions to replenish the components of the citric acid cylce. With the diet of fats only, the acetyl CoA from fatty acid degradation would build up. b) What would your breath smell like? Acetone from ketone bodies. c) One of your best friends, after trying unsuccessfully to convince you to abandon this diet, makes you promise to consume a healthy dose of odd-chain fatty acids. Does your friend have your best interest at heart? Explain. Yes. Odd-chain fatty acids would lead to the production of propionyl coA, which can be converted into succinyl coA, a citric acid cycle component. It would serve to replenish the citric acid cycle and mitigate the laitosis. Chapter 27 [2, 3, 5, 7, 9, 10] 2. The cost of cleanliness. Lauric acid is a 12-carbon fatty acid with no double bonds. The sodium salt of lauric acid (sodium laurate) is a common detergent used in a variety of products, including laundry detergent, shampoo, and toothpaste. How many molecules of ATP and NADPH are required to synthesize lauric acid? We still need 6 acetyl CoA units. One acetyl CoA unti will be used directly to become the two carbon atoms farthes from the acid end. The other five units must be converted into malonyl CoA molecule costs a molecule of ATP; so 5 molecules of ATP will be required. Each round of elongation requires 2 molecules of NADPH, one to reduce the double bond. As a result, 10 molecules of NADPH will be required. Therefore, 5 molecules of ATP and 10 molecules of NADPH are required to synthesize lauric acid. 3. Proper organization. Arrange the following steps in fatty acid synthesis in their proper order

a) dehydration b) condensation c) release of a c16 fatty acid d) reduction of carbonyl e) formation of malonyl ACP E, B, D, A, C 5. True or False a) Biotin is required for fatty acid synthase activity. False. Biotin is required for acetyl coA carboxylase activity. b) The condensation reaction in fatty acid synthesis is powered by the decarboxylation of malonyl coA. True c) Fatty acid synthesis does not depend on ATP False. ATP is required to synthesize malonyl CoA. d) Palmitate is the end product of fatty acid synthesis True e) All of the enzyme activities required for fatty acid synthesis in mammals are contained in single poplypetide chain True. f) Fatty acid synthase in mammals is active as a monomer. False. Fatty acid synthase is a dimer. g) The fatty acid arachidonate is a precursor for signal molecules True h) Acetyl CoA carboxylase is inhibited by citrate. False. Acetyl coA carboxylase is stimulated by citrate, which is cleaved to yield its substrate acetyl coA 7) Labels. Suppose that you had an invitro fatty acid synthesizing system that had all of the enzymes and cofactors required for fatty acid synthesis except acetyl coA. To this system, you added acetyl coA that contained radioactive hydrogen and carbon14. The ratio of h3/c14 is 3. What would be the h3/c14 ratio be after the synthesis of palamitic acid (c16) with the use of the radioactive acetyl coA? All of the labeled carbon atoms will be retained. Because we need 8 acetyl coA molecules and only 1 carbon atom is labeled in the acetyl group, we will have 8 labeled carbon atoms. The only acetyl CoA used directly will retain 3 tritium atoms. The 7 acetyl coA molecules used to make malonyl coA will lose 1 tritium atom on addition of the Co2 and another one at the dehydration step. Each of the 7 malonyl coA molecules will retain 1 tritium atom. Therefore the total retained tritium is 10 atoms. The ration of tritium to carbon is 1.25.

9) Alpha or omega? Only one acetyl coA molecule is used directly in fatty acid synthesis. Identify carbons atoms in palmitic acid that were donated by acetyl coA. The only acetyl coA used directly, not in the form of malonyl CoA provides the two carbon atoms at the w end of the fatty acid chain. Because palimitic acid is C16 fatty acid, acetyl coA will have provided carbon 15 and 16. 10) Now you see it, now you dont. Althought HCO3- is required for fatty acid synthesis, its carbon atom does not appear in the product. Explain how this possible. HCO3- is attached to acetyl CoA to from malonyl CoA. When malonyl CoA condenses with acetyl coA to form the 4-carbon keto acyl coA, HCO3- is lost as CO2

Chapter 29: [2-6, 9-11, 464-465] 2. Vital in the truest sense. Why are certain amino acids defined as essential for human beings? Human beings do not have the biochemical pathways to synthesize essential amino acids from simpler precursors. Consequently they must be obtained from the diet. 3. From few, many. What are seven precursors of the 20 amino acids? Oxaloacetate, pyruvate, ribose-5phosphate, phosphoenolpyruvate, erythose-4-phosphate, alpha-ketoglutarate, and 3phosphoglycerate 4. Common component. What cofactor is required by all transaminases (aminotransferases)? Pyridoxal phosphate (PLP) 5. One carbon at a time. What is the role of tetrahydrofolate in biochemical systems? Tetrahydrofolate is a carrier of one-carbon units 6. The same but different. Differentiate between S-adenosylmethione and tetrahydrofolate. Both carry one-carbon units. S-adenosylmethionine is more useful than tetrahydrofolate because it has a greater transfer potential. 9. Direct synthesis, which of the 20 amino acids can be synthesized directly from a common metabolic intermediate by a transamination reaction? Alanine from pyruvate; aspartate from oxaloacetate; glutamate from alpha-ketoglutarate 10. Lines of communication. For the following example of a branched pathway, propose a feed-back inhibition scheme that would result in the production of equal amounts of Y and Z. >>D>>E>>Y A- B>>C >>F>>G>>Z

You could inhibit CD step, Z could inhibit the CF step and C could inhibit AB. This scheme is an example of sequential feedback inhibition. Alternatively, Y could inhibit the CD step, Z could inhibit the CF step and the AB step would be inhibited only in the presence of both Y and Z. This scheme is called concerted feedback inhibition. 12. (11) Cumulative feedback inhibition. Consider the branched pathway in problem 10. The first common step (AB) is partly inhibited by both of the final products, each acting independently of the other. Suppose that a high level of Y alone decreased the rate of the AB step from 100 to 60s-1 and that a high level of Z zone alone decreased the rate from 100 to 40s-1. What would the rate be in the presence of high levels of both Y and Z? Synthesis from oxaloacetate and alpha-ketoglutarate would deplete the citric acid cycle, which would decrease ATP production. Anapleurotic reactions would be required to replenish the citric acid cycle.

Chapter 30 3. What is the activated reactant in the biosynthesis of each of the following compounds? a)Phosphoribosylamine PRPP b)Carbamoylaspartate carbamoyl phosphate c)Orotidylate(from oralate)PRPP 4. Amidotransferases are inhibited by the antibiotic and antitumor agent azaserine(O-diazoacetyl-Lserine), which is an analog of glutamine.Which intermediates in purine biosynthesis would accumulate in cells treated with azaserine? PRPP and formylglycinamide ribonucleotide 6. Bacterial growth is inhibited by the sulfanilamide and related sulfa drugs, and there is a concomitant accumulation of 5-aminoimidazole-4-carboxyamide-ribonucleotide. This inhibition is reversed by the addition of p-aminobenzoate. Propose a mechanism for the inhibitory effects of sulfanilamide. There is a deficiency of N10 formyltetrahydrofolate. Sulfanilamide inhibits the synthesis of folate by acting as an analog of p-aminobenzoate, one of the precursors of folate. 7. What major biosynthetic reactions use PRPP? PRPP is the activated intermediate in the synthesis of phosphoribosyamine in the de novo pathway of purine formation; in the synthesis of purine nucleotides from free bases by the salvage pathway; and in the synthesis of orotidylate in the formation of pyrimidines. 8. Mutant cells unable to synthesize nucleotides by salvage pathways are very useful tools in molecular and cell biology. Suppose that cell A lacks thymidine kinase, the enzyme catalyzing the phosphorylation of thymidine to thymidylate, and that cell B lacks hypozanthine-guanine phosphoribosyl transferase.

A) Cell A and Cell B do not proliferate in a HAT medium containing hypoxanthine, aminopterin or amethopterin, and thymine. However, cell C formed by the fusion of cells A and B grows in this medium. Why? Cell A cant grow in HAT medium because it cannot synthesize TMP either from thymidine or from dUMP. Cell B cant grow in the HAT medium because it cant synthesize purines by either the de novo pathway or the salvage pathway. Cell C can grow in a HAT medium because it contains active thymidine kinase from cell B(enabling it to phosphorylate thymidine to TMP) and hypoxanthine guanine phosphoribosyltransferase from cell A(enabling it to synthesize purines from hypoxanthine from the salvage pathway). b) Suppose you wanted to introduce foreign genes into cell A. Devise a simple means of distinguishing between cells that have taken up foreign DN and those that have not. Transform cell A with a plasmid containing foreign genes of interest and a functional kinase gene. The only cells that will grow in a HAT medium are those that have a thymidilate kinase gene; nearly all of these transformed cells will also contain the other genes on the plasmid.