CITRIC ACID CYCLE. 1. Briefly describe the biological rationale for each of the
ID: 45710 • Letter: C
Question
CITRIC ACID CYCLE.
1. Briefly describe the biological rationale for each of the following allosteric phenomena: a)activation of pyruvate carboxylase by acetyl-CoA; b)activation of pyruvate dehydrogenase kinase by NADH; c) inhibition of isocitrate dehydrogenase by NADH; d)activation of isocitrate dehydrogenase by ADP; e)inhibition of alpha-ketoglutarate dehydrogenase by succinyl-CoA; f) activation of pyruvate dehydrogenase phosphotase by Ca2+
2. Predict which one of the 5 steps of the alpha-ketoglutarate dehydrogenase complex reaction is metabolically irreversible under physiological conditions and explain why?
Explanation / Answer
a) Acetyl CoA allosterically activates pyruvate carboxylase and the conversion of pyruvate to oxaloacetate and oxaloacetate is the limiting factor for Krebs cycle. So oxaloacetate depletion will hinders acetyl CoA entry into Krebs cycle.
b) Pyruvate Dehydrogenase Kinases are activated by NADH and acetyl-CoA. PDK is a part of the pyruvate dehydrogenase complex, phosphorylates three specific E1 serine residues, and thus causes inactivation of pyruvate dehydrogenase. Pyruvate dehydrogenase phosphatase dephosphorylates the serines by hydrolyzing the phosphates from the E1 subunit of the pyruvate dehydgrogenase complex, thus activates the complex.
c) These three reactions of the cycle catalysed by citrate synthase, isocitrate dehydrogenase and -ketoglutarate dehydrogenase operate with large negative free energy changes. The Isocitrate dehydrogenase is inhibited by the powerful negative allosteric effector like NADH. The oxidation of isocitrate and alpha ketoglutarate produces lots of NADH and which in turn affects the Isocitrate dehydrogenase and thus stops the conversion of Isocitrate to alpha ketoglutarate. So, the presence of NADH will have major impact on the flux of carbon through the TCA cycle.
d)Isocitrate dehydrogenase is allosterically regulated positively by ADP, and the inhibitionof IDH can be seen in the presence of ATP, NADPH or NADH. The IDH which is under the allosteric regulation, cannot catalyze the reaction unless levels of ADP are low. Isocitrate dehydrogenase is involved in the conversion of Isocitrate into alpha ketoglutarate.
e) -KGD catalyzes the conversion of -KG to succinyl-CoA, is a highly regulated enzyme, which could determine the metabolic flux through the Krebs cycle and is thermodynamically favorable. So its use has to be regulated in order to ensure efficiency. Succinyl-CoA also inhibits citrate synthase and it is useful as a regulatory molecule to indicate flow through the middle of the TCA cycle.
f) Whenever NADH and acetyl CoA comes down, the activation of kinase activity is needed which was inhibited allosterically by pyruvate. The
Ca2+ activated pyruvate dehydrogenase phosphatase will go and bind to the dehydrogenase complex, thus cause the hydrolysis of phosphorylated serine residue and thus activates the enzyme. Thus the conversion of pyruvate to acetyl CoA can be seen.