Succinyl-CoA Synthetase mechanism Succinyl-CoA synthetase enzyme active site O Substrates bind to the active site of succinyl-CoA synthetase ÇOO CH2 CH2 OH His . Succinyl-CoA COA-S Guanosine O Phosphoryl group transfer to GDP to form GTP, which is released from the 2 Formation of succinyl-phosphate CoA GTP enzyme 3 Formation of phosphohistidine Guanosine COO Phosphohistidine P CH2 GDP GDP CH2 O-P=0 COO CH, I Succinate CH2 Succinyl-phosphate coo a) Which catalytic mechanism occurs in step 2? b) Why must phosphate first bind to succinyl-CoA before interacting with the His site and GDP?
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- Distinguishing the Mechanisms of Class I and Class I Aldolases Fructose bisphosphate aldolase in animal muscle is a class 1 aldolase, which forms a Schiff base intermediate between substrate (for example. fructose-1, 6-bisphosphate or dihydroxyacetone phosphate) and a lysine at the active site (see Figure I8.12). The chemical evidence for this intermediate conies from studies with aldolase and the reducing agent sodium borohydride, NaBH4. Incubation of the enzyme with dihydroxyacetone phosphate and NaBH4 inactivates the enzyme. Interestingly, no inactivation is observed if NabH4 is added to the enzyme in the absence of substrate. Write a mechanism that explains these observations and provides evidence for the formation of a Schiff base intermediate in the aldolase reaction.Extending the Mechanism of Methylmalonyl-CoA Mutase to Similar Reactions Based on the mechanism for the methylmalonyl-CoA mutase (see problem 14), write reasonable mechanisms for the following reactions shown.Regulation of Glutamine Synthetase by Covalent Modification Suppose at certain specific metabolite concentrations in vivo the cyclic cascade regulating E. coli glutamine synthetase has reached a dynamic equilibrium where the average state of GS adenylylation is poised atn=6. Predict what change in nwill occur if: [ ATP ] increases, PIIA/PIID increases, [ -KG ]/[ Gln ] increases, [ Pi ] decreases.
- Modeling the Regulation of AcetyI-CoA Carboxylase Based on the information presented in the text and in Figures 24.4 and 24.5, suggest a model for the regulation of acetyl-CoA carboxylase. Consider the possible roles of subunit interactions, phosphorylation, and conformation changes in your model.Using the ActiveModel for aldose reductase, describe the structure of the TIM barrel motif and the structure and location of the active site.The mechanism for the conversion from alpha kytoglutarate into succinyl CoA by alpha-ketoglutare dehydrogenase is analogous to the pyruvate dehydrogenase mechanism. Draw and show the major intermediates and arrow pushing for the enzyme-catalyze process for the conversion of alpha-ketoglutarate to succinyl CoA. Note: the carbanion of thiamine pyrophosphate nucleophillically attacks C-2 of the alpha-ketoglutarate, i.e., the carbonyl carbon of that substrate.
- The products of pyrimidine base catabolism, β-alanine and β-aminoisobutyrate, can be further degraded to acetyl-CoA and succinyl-CoA, respectively. Can you suggest the types of reaction required to accomplish these transformations?ATP is a (+) allosteric effector, and CTP is a (-) allosteric effector of theenzyme ATCase. Both of these heterotropic effectors bind to the regulatorysubunits on ATCase. The substrates of ATCase, aspartate and carbamoylphosphate, bind the enzyme active site with positive cooperativity (i.e.,they exert a “+” homotropic effect on activity). As the concentrations ofthe substrates change from values where [S] ≪ KM to values where [S] issaturating ([S]≫ KM), how will the binding constants for each of the twoallosteric effectors change? In other words, does ATP bind ATCase withhigher affinity when [S] is low or high? Does CTP bind ATCase with higheraffinity when [S] is low or high?Please draw out mechanism The formation of fructose 1, 6- biphophste from dihydroxyacetome phospahte (DHAP) and Glyceraldehyde 3- phosphate (GAP) catalyzed by alsolase.
- Explain biochemical pathways mechanistically. Describe the β-oxidation pathway. Describe the conversion of propionyl CoA to succinyl CoA. Describe the substrate activation processes in the urea cycle (CPS 1 and arginosuccinate synthetase).Digestion of plant materials generates phytanate (derived from chlorophyllmolecules; (a) Explain why phytanate cannot be catabolized by β oxidation.(b) Instead, phytanate is linked to CoA, then a peroxisomal dioxygenaseconverts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA. Draw the structure of this intermediate. (c) 2-Hydroxyphytanoyl-CoA lyase generates an aldehyde (pristanal) and formyl-CoA. Draw the structure of pristanal.Some bacteria use the citric acid cycle intermediate, α-ketoglutarate, plusacetyl-CoA, as the starting point for lysine biosynthesis. The first partof this biosynthetic pathway uses the same chemical strategy found inthe citric acid cycle. Propose a four-step pathway for the conversion ofα-ketoglutarate to 2-oxoadipate. Draw the three missing intermediates, andindicate the chemistry involved in each reaction. Include any cofactors thatyou think might be required for specific steps.