Draw anaplerotic reactions for each of the two glycolytic intermediates that can be directly converted to citric acid cycle intermediates (include carbon skeleton structures, but not cofactor structures). Briefly describe two distinct conditions that contribute to these reactions forming citric acid cycle intermediates in their respective tissues/organisms.
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- . Briefly describe the biological rationale for cach of the following allosteric phenomena: (a) activation of pyruvate carboxylase by acetyl-CoA; (b) acti- vation of pyruvate dehydrogenase kinase by NADH; (c) inhibition of isoci- trate dehydrogenase by NADH; (d) activation of isocitrate dehydrogenase by ADP; (e) inhibition of a-ketoglutarate dehydrogenase by succinyl-CoA; (f) activation of pyruvate dehydrogenase phosphatase by Ca*.(b) ☐ The exergonic reactions catalyzed by isocitrate dehydrogenase (ICDH) and α- ketoglutarate dehydroge-nase (aKGDH) are regu- lated by metabolites, in addition to the reaction catalyzed by citrate synthase. The diagram to the right illustrates the activity of ICDH (A,▲) and aKGDH (O,●) in the presence of 1.5 mM ADP (O,A) or 1.5 mM ATP (●,▲). In muscle tissue contraction of sarcomeres initiated by a nerve im- pulse results first in the release of Ca 2+ from the sarcoplasmic reticulum. As indicated by the chang- es in velocity of the two enzymes, what are the flux changes of the TCA cycle in muscle tissue upon release of Ca2+ under the influence of ADP viz. ATP and under the influence of NAD+ viz. NADH on cit- rate synthase? 100 75 Stimulation of activity (% of maximum) ŏ 25 1. -8 -7 -6 log {[Ca2+] (M)}a) describe the overall reaction catalyzed by the pyruvate dehydrogenase Situational Problems I. Oxidative decarboxylation of pyruvate and the TCA cycle in muscles are stimulated by increased aerobic excrcise. These processes operate only when O, is present, although oxygen does not participate directly in these processes. Explain why oxidative decarboxylation of pyruvate is activated under aerobic conditions. For the answer: a) describe the overall reaction catalyzed by the pyruvate complex (PDH) and its regulation; b) outline the intermediates and enzymes of the TCA cycle; c) explain the relationship between the reactions of PDH and the TCA cycle and the respiratory chain.
- 2. (a) ( In contrast to the pyruvate dehydrogen- ase complex, the a-ketoglutarate dehydrogenase (aKGDH) complex is not up- or downregulated by phosphorylation or dephosphorylation. However, the complex exhibits cooperativity modulated by the presence of ADP, ATP, inorganic phosphate (Pi), and Ca2+, as illustrated by the diagram on the right for the bovine kidney enzyme complex. Note in the diagram how the addition of 10 μM Ca2+ shifts the affinity of the enzyme complex for aKG from 20 mM Pi/-Ca2+ to 20 mM Pi/+Ca2+. Calcium especially en- hances the cooperative influence of ADP and ATP. Using the expanded copy of the diagram at the end of the problem set, estimate the change in S0.5 (re- member that for allosteric enzymes S0.5 corresponds to KM of a nonallosteric enzyme) for the enzyme complex in the presence of 20 mM Pi/-Ca2+ and in the presence of 20 mM Pi/+Ca2+. Compare similarly the change in S0.5 for the enzyme in the presence of 20 mM Pi/-Ca2+ plus 1.6 mM ADP to the enzyme in the…Compare and contrast Pyruvate Dehydrogenase with a-ketoglutarate dehydrogenaseOutline the mechanisms of both enzymes. Discuss the functions of the coenzymes. List the similarities and the differences between the 2 enzymes. Both are very large membrane bound complexes. What are the advantages of this strategy?How detailed is the enzyme structure known below(It's Pyruvate Dehydrogenase )? What insight(s) does this structural detail give you about the enzyme mechanism.A. Identify different types of organic reaction mechanims in the followingmetabolic pathways.1. Catabolism of triacylglycerols- beta-oxidation pathway2. Biosynthesis of fatty acids from Acetyl CoA3. Glycolysis (from glucose to two molecules of pyruvate)4. Conversion of Pyruvate to Acetyl CoA5.Citric acid cycle6. Gluconeogensis pathway (pyruvate to glucose) B. Identify at most 5 organic reactions for each metabolic pathway.
- Page of 6 ZOOM + name: 3. In the last reaction of the citric acid cycle, malate is dehydrogenated to regenerate the oxaloacetate necessary for the entry of acetyl-CoA into the cycle: L-Malate + NAD+ → oxaloacetate + NADH + H* AG'° = 30.0 kJ/mol (a) Calculate the equilibrium constant for this reaction at 25 °C. (b) Because AG°' assumes a standard pH of 7, the equilibrium constant calculated in (a) corresponds to [oxaloacetate][NADH] Keq [L-malate][NAD*] The measured concentration of L-malate in rat liver mitochondria is about 0.20 mM when [NAD*]/[NADH] is 10. Calculate the concentration of oxaloacetate at pH 7 in these mitochondria. (c) To appreciate the magnitude of the mitochondrial oxaloacetate concentration, calculate the number of oxaloacetate molecules in a single rat liver mitochondrion. Assume the mitochondrion is a sphere of diameter 2.0 microns.1. Consider the oxidation of the fatty acid with the common name arachidic acid. a. Draw the structure of arachidic acid. b. How many turns of the fatty acid oxidation cycle is required for the complete oxidation of arachidic acid? c. How many moles of ATP are formed from one mole of arachidic acid if the acetyl CoA produced go to the citric acid cycle and oxidative phosphorylation? Assume 1 mole of NADH is equivalent to 3 moles ATP and 1 mole FADH2 is equivalent to 2 moles of ATP. Show how you arrived at your answerShow that the free energy change for the succinate dehydrogenase reaction catalyzed by Complex II is insuffi cient to drive ATP synthesis under standard conditions.
- Describe the mechanism of a-chymotrypsin. Explain the roles of constituents of the catalytic triad, their modes of catalysis, and the significance of the oxyanion hole in the catalysis.Based on the action of thiamine pyrophosphate in catalysis of the pyruvate dehydrogenase reaction, suggest a suitable mechanism for the fourth step in the pyruvate decarboxylase reaction in yeast:. Using the principles described in the text regarding pyridoxal phos- phate mechanisms, propose a mechanism for the reaction catalyzed by serine hydroxymethyltransferase.