Flashcards in 16.1 production of Acetyl-CoA (activated Acetate) Deck (43):
Q # 1 The oxidative decarboxylation of pyruvate is a highly exergonic reaction. How is the energy released by this reaction conserved?
This energy is conserved by the generation of ATP. NADH formed in this reaction goes to the respiratory chain and gives up a hydride ion. 2.5 ATP per pair of electrons transferred.
Q # 2 Why is the thioester bond important to the function of coenzyme A?
Thioester bonds are high energy bonds that can be used to catalyze group transfer reactions.
Q # 3 What are the two possible roles of lipoate in enzymatic reactions?
Lipoate acts as an electron carrier or it can transfer electrons. (S-S) bond
What are the important enzymes in dehydrogenation and decarboxylation of Pyruvate?
TPP (thiamine pyrophosphate), Flavin adenine dinucleotide, (FAD), and Co-enzyme A, Nicotinamide adenine dinucleotide (NAD), Lipoate.
What four vitamins are vital components of the pyruvate dehydrogenase complex?
thiamine, riboflavin (in FAD), niacin (in NAD), panthothenate (in CoA)
What are the five co-factors in the pyruvate dehydrogenase complex? What are their roles?
NAD and FAD (electron carriers); Lipoate (redox reactions); CoA (facilitates transfer of groups, high energy thioester bond); TPP (functions as a coenzyme to remove CO2 from pyruvate)
(E1); has bound TPP
(E2) point of connection for the prosthetic group lipoate
(E3) has bound FAD and NAD
What are the three enzymes that make up the pyruvate dehydrogenase complex?
pyruvate dehydrogenase, dihydrolipoyl transacetylase and dihydrolipoyl dehydrogenase.
Q # 5 What is the result of the first three reactions of the overall pyruvate dehydrogenase complex? What is the source of energy for this set of reactions?
The decarboxylation of pyruvate, the reduction of lipoyllysine to produce two thiol groups, carbonyl is transferred to acetyl CoA
Q # 6 What is the results of steps 4 and 5 in this process?
FAD to FADH2 to NADH + H+
Q # 7 Why is it advantageous to have three different enzymatic activities clustered into a single enzyme complex?
Allow the reaction to occur quickly without diffusing or going away from one another; don't leave complex, prevents theft of intermediates and reactive groups.
Q # 8 Why is thiamine deficiency a serious conditions?
No thiamine, can't oxidize pyruvate (TPP is lacking), causes build up of pyruvate and lack of ATP.
Step 1 pyruvate dehydrogenase
C-1 released as CO2; C-2 attaches to TPP as hyrdoxyethyl group; rate limiting step
Q # 9 What are the roles of the citric acid cycle? Where in eukaryotes do these reactions take place? Where do they occur in prokaryotes?
Oxidize the carbon left in acetyl CoA; energy from oxidation is conserved in the reduced FADH2 and NADH + H + ; the four and five carbon products also serve as precursors for other compounds; CAC occurs in the mitochondria for eukaryotes vs. cytosol in prokaryotes
Q # 10 Why do the carbonyls groups "rule" in chemical transformation of metabolic pathways?
Methylene groups are reactive and are important in the transformation of succinate to oxaloacetate. methylene groups are readily metabolized by most organisms, methane is stabile and is not metabolized by most organisms. Acetyl CoA is not favorable to harvest from, because the methyl group is stable. The carbonyl in oxaloacetate is attacked by the methyl group of acetylC oA
Q # 11 What are the eight steps of the CAC?
1) Formation of Citrate ( catalyzed by citrate synthase) hydrolysis of the thioester makes this reaction highly exothermic and favorable. 2) Formation of isocitrate via cis-aconitate. 3) Oxidation of isocitrate to alpha ketoglutarate and CO2 4) oxidation of alpha ketoglutarate to succinyl-CoA and CO2 5) Conversion of succinyl-CoA to succinate. 6) Oxidation of succinate to Fumarate 7) Hydration of fumarate to malate 8) Oxidation of malate to oxaloacetate
Converts Acetyl CoA to Citrate in the presence of Oxaloacetate; Oxaloacetate increase the binding affinity for Acetyl CoA; uses induced fit; releases CoA-SH; binding order decreases likelyhood that the thioester bond is cleaved; uses cage effect; rate limiting step of CAC; highly favorable;
mediates the conversion of citrate to cis-aconitate to isocitrate; although unfavorable (∆G'˚ = 13.3 kj/mol) this reaction is pulled to the right because isocitrate is quickly consumed in the next step of the CAC; contains an iron sulfur center ( aids in removal of H2O and binding substrate at active site); citrate needs to be converted, because it is a tertiary alcohol and a poor substrate for oxidation; isocitrate is a secondary alcohol and a good candidate for substrate oxidation.
catalyzes the oxidative decarboxylation of isocitrate to form alpha ketoglutarate; Mn2+ in the active site interacts with the carbonyl of the intermediate.
alpha ketoglutarate dehydrogenase
mediates the conversion of alpha ketoglutarate to succinyl-CoA by oxidative decarboxylation; NAD+ serves as an electron carrier. CoA carries succinyl; very similar to pyruvate dehydrogenase ( it even has e1,2, and 3 complexes, TPP, lipoate, FAD, NAD, and coenzyme A); example of divergent evolution.
mediates the conversion of succinyl-CoA to succinate; GDP to GTP; removal of CoA-SH; made up of alpha and beta subunits (alpha binds succinyl-CoA), (beta confers specificity for either ADP GDP); generated by substrate level phosphorylation.
Nucleotide diphosphate kinase
responsible for the conversion for GTP + ADP to GDP and ATP.
catalyzes the oxidation of succinate to fumarate.
A competitive inhibitor of succinate dehydrogenase and its addition to the mitochondria blocks the activity of the citric acid cycle.
catalyzes the conversion of Fumarase to malate. Highly stereospecific; only catalyzes the conversion of the trans double bond.
L- malate dehydrogenase
Catalyzes the oxidation of L-malalte to oxaloacetate. (highly endergonic ∆G'˚= 29.7 Kj/mol, but is favorable because oxaloacetate is continually removed and used by the exergonic citrate synthase reaction;
Q # 26 What is the net equation for one turn of the citric acid cycle?
2 CO2 ( from the oxidation of isocitrate and a-ketoglutarate); Energy conserved in the formation of 3 NADH, 1 FADH2; and 1 ATP or GTP. (ATP or GTP is formed from the formation of Succinate from succinyl CoA);
Q # 27 What is the net energy yield per molecule of glucose for the combined reactions of glycolysis, the pyruvate dehydrogenase reaction, and the citric acid cycle?
32 ATP per glucose molecule.
Q # 30 Why is the oxidation of Acetate so Complicated?
It is so complicated, because the CAC is a intermediary hub of metabolism for a lot of 4 and 5 carbon molecules.
pathway that serves a catabolic and an anabolic pathway
Q # 32 Under What cellular circumstances is pyruvate carboxylase activity stimulated?
When the CAC is deprived of oxaloacetate.
produces oxaloacetate from pyruvate and CO2; inactivated by the presence of Acetyl-CoA;
reactions that served to replenish intermediates that are taken away from the CAC and used for other biosynthetic processes.
What are the four enzymes that mediate anaplerotic reactions?
Pyruvate carboxylase, PEP carboxykinase, PEP carboxylase, and malic enzyme
Q # 36 How does covalent modification regulate the pyruvate dehydrogenase complex?
Phosphorylation of specific ser residues on E1 inactivates PDH. mediated by pyruvate kinase dehydrogenase;
What molecules inhibit the pyruvate dehydrogenase complex?
ATP, Acetyl-CoA, and NADH; also inhibited by the phosphorylation of specific ser residues on the E1 portion (mediated by pyruvate dehydrogenase kinase)
What molecules activate the pyruvate dehydrogenase complex?
AMP, CoA, NAD+
Q # 37 Why are citrate synthase, isocitrate dehydrogenase, and alpha ketoglutarate dehydrogenase good candidates for regulatory enzymes?
Citrate synthase, isocitrate dehydrogenase, and a-ketoglutarate are strongly exergonic steps; succinyl coA inhibits a-ketoglutarate dehydrogenase and citrate synthase; citrate blocks citrate synthase; ATP inhibits citrate synthase and isocitrate dehydrogenase;
Q # 38 What is the role of calcium ions in regulation of the citric acid cycle?
Ca2+ signals for contraction and an increase in the demand for ATP; activates isocitrate dehydrogenase, alpha ketoglutarate, ad PDH complex
What three factors govern the rate of flux through a cycle?
Substrate availability, inhibition by accumulating products, and allosteric feedback inhibition of the enzymes that catalyze early steps in the cycle