S/A CAC

Question 1

The citric acid cycle begins with the condensation of acetyl-CoA with oxaloacetate. Describe three possible sources for the acetyl-CoA.

Answer 1

: Acetyl-CoA is produced by (1) the pyruvate dehydrogenase complex, (2) β oxidation of fatty acids, or (3) degradation of certain amino acids.

Question 2

Briefly describe the relationship of the pyruvate dehydrogenase complex reaction to glycolysis and the citric acid cycle.

Answer 2

The pyruvate dehydrogenase complex converts pyruvate, the product of glycolysis, into acetyl- CoA, the starting material for the citric acid cycle.

Question 3

Describe the enzymes, cofactors, intermediates, and products the pyruvate dehydrogenase complex.

Answer 3

The pyruvate dehydrogenase complex consists of multiple copies of each of three enzymes.

The first enzyme to act is pyruvate dehydrogenase (E1), which converts pyruvate to CO2 and the hydroxyethyl derivative of thiamine pyrophosphate (TPP).
The same enzyme then oxidizes the hydroxyethyl group to an acetyl group attached to enzyme-bound lipoate through a thioester linkage.

The second enzyme, dihydrolipoyl transracetylase (E2), transfers the acetyl group to coenzyme A, forming acetyl-CoA.

The third enzyme, dihydrolipoyl dehydrogenase (E3), oxidizes the dihydro- lipoate to its disulfide form, passing the electrons through FAD to NAD+. (See Fig. 16-6, p. 605.)

Question 4

Suppose you found an overly high level of pyruvate in a patient’s blood and urine. One possible cause is a genetic defect in the enzyme pyruvate dehydrogenase, but another plausible cause is a specific vitamin deficiency. Explain what vitamin might be deficient in the diet, and why that would account for high levels of pyruvate to be excreted in the urine. How would you determine which explanation is correct?

Answer 4

The most likely explanation is that the patient has a deficiency of thiamine, without which the cell cannot make thiamine pyrophosphate, the cofactor for pyruvate dehydrogenase. The inability to oxidize pyruvate produced by glycolysis to acetyl-CoA would lead to accumulation of pyruvate in blood and urine. The most direct test for this deficiency is to feed a diet supplemented with thiamine and determine whether urinary pyruvate levels fall.

Question 5

Page: 605 Difficulty: 2
Match the cofactors below with their roles in the pyruvate dehydrogenase complex reaction.
Cofactors:
A. Coenzyme A (CoA-SH)
B. NAD+
C. Thiamine pyrophosphate (TPP) D. FAD
E. Lipoic acid in oxidized form
Roles:
_______ Attacks and attaches to the central carbon in pyruvate.
_______ Oxidizes FADH2.
_______ Accepts the acetyl group from reduced lipoic acid.
_______ Oxidizes the reduced form of lipoic acid.
_______ Initial electron acceptor in oxidation of pyruvate.

Answer 5

Ans:C; B; A; D; E

Question 6

Two of the steps in the oxidative decarboxylation of pyruvate to acetyl-CoA do not involve the three carbons of pyruvate, yet are essential to the operation of the pyruvate dehydrogenase complex.

Answer 6

The two steps catalyzed by dihydrolipoyl dehydrogenase (E3) are required to regenerate the oxidized form of lipoate, bound to dihydrolipoyl transacetylase, from the dihydrolipoyl (reduced) form produced in the oxidation of pyruvate. First, FAD is reduced to FADH2 to reoxidize the dihydrolipoate, then NAD+ is reduced to NADH to reoxidize the FADH2 to complete the reaction.

Question 7

What is the function of FAD in the pyruvate dehydrogenase complex? How is it regenerated?

Answer 7

FAD serves as the electron acceptor in the re-oxidation of the cofactor dihydrolipoate. It is converted to FADH2 by this reaction and is regenerated by the passage of electrons to NAD+.

Question 8

The human disease beriberi is caused by a deficiency of thiamine in the diet. People with severe beriberi have higher than normal levels of pyruvate in their blood and urine. Explain this observation in terms of specific enzymatic reaction(s).

Answer 8

Thiamine is essential for the synthesis of the cofactor thiamine pyrophosphate (TPP). Without this cofactor the pyruvate dehydrogenase complex cannot convert pyruvate into acetyl-CoA, so the pyruvate produced by glycolysis accumulates.

Question 9

Draw the citric acid cycle from isocitrate to fumarate only, showing and naming each intermediate. Show where high-energy phosphate compounds or reduced electron carriers are produced or consumed, and name the enzyme that catalyzes each step.

Answer 9

This part of the citric acid cycle includes the reactions catalyzed by isocitrate dehydrogenasethe α-ketoglutarate dehydrogenase complex, succinyl-CoA synthetase, and succinate dehydrogenase.

Question 10

Show the three reactions in the citric acid cycle in which NADH is produced, including the structures. None of these reactions involves molecular oxygen (O2), but all three reactions are strongly inhibited by anaerobic conditions; explain why.

Answer 10

NADH is produced in the reactions catalyzed by isocitrate dehydrogenase, the α-ketoglutarate dehydrogenase complex, and malate dehydrogenase. These reactions are indirectly dependent on the presence of O2 because the NADH produced in the reactions is normally recycled to NAD+ by passage of electrons from NADH through the respiratory chain to O2. See also Fig. 16-7, p. 607.

Question 11

Show the reactions by which α-ketoglutarate is converted to malate in the citric acid cycle.

Answer 11

The reactions are those catalyzed by the α-ketoglutarate dehydrogenase complex, succinyl-CoA synthetase, succinate dehydrogenase, and fumarase

Question 12

Show the steps of the citric acid cycle in which a six-carbon compound is converted into the first four-carbon intermediate in the path. For each step, show structures of substrate and product, name the enzyme responsible, and show where cofactors participate.

Answer 12

he reactions are those catalyzed by isocitrate dehydrogenase, the α-ketoglutarate dehydrogenase complex, and succinyl-CoA synthetase.

Question 13

Show the structures of the reactants and products for two of the four redox reactions in the citric acid cycle. Indicate where any cofactors participate, and label the reactants, products, and cofactors as oxidants or reductants in the reaction.

Answer 13

The four oxidation-reduction reactions are those catalyzed by isocitrate dehydrogenase, the α- ketoglutarate dehydrogenase complex, succinate dehydrogenase, and malate dehydrogenase. (

Question 14

Show the steps of the citric acid cycle from succinyl-CoA to oxaloacetate only.

Answer 14

These are the steps catalyzed by succinyl-CoA synthetase, succinate dehydrogenase, fumarase, and malate dehydrogenase.

Question 15

Explain why fluorocitrate, a potent inhibitor of the enzyme aconitase, is a deadly poison.

Answer 15

By inhibiting aconitase, fluorocitrate prevents the citric acid cycle from operating. This prevents the oxidation of acetyl-CoA and dramatically reduces the yield of ATP from carbohydrate and lipid catabolism. The resulting drop in ATP levels is lethal.

Question 16

The citric acid cycle is frequently described as the major pathway of aerobic catabolism, which means that it is an oxygen-dependent degradative process. However, none of the reactions of the cycle directly involves oxygen as a reactant. Why is the pathway oxygen-dependent?

Answer 16

The citric acid cycle produces NADH, which normally is recycled by passage of electrons from NADH to O2 via the respiratory chain. With no O2 to accept electrons from NADH, the accumulation of NADH effectively stops the citric acid cycle.

Question 17

In the citric acid cycle, a five-carbon compound is decarboxylated to yield an activated four-carbon compound. Show the substrate and product in this step, and indicate where any cofactor(s) participate(s).

Answer 17

The oxidation of α-ketoglutarate to succinyl-CoA involves five cofactors: lipoate, thiamine pyrophosphate (TPP), FAD, NAD+, and CoA-SH. (See p. 610.)

Question 18

CO2 is produced in two reactions in the citric acid cycle. For each of these reactions, name and show the structures of reactant and product, name the enzyme, and show how any cofactors participate.

Answer 18

See the isocitrate dehydrogenase and α-ketoglutarate dehydrogenase reactions

Question 19

In which reaction of the citric acid cycle does substrate-level phosphorylation occur?

Answer 19

Substrate-level phosphorylation of GDP to GTP occurs in the succinyl-CoA synthetase reaction in which succinyl-CoA is converted to succinate during the citric acid cycle.

Question 20

You are in charge of genetically engineering a new bacterium that will derive all of its ATP from sunlight by photosynthesis. Will you put the enzymes of the citric acid cycle in this organism? Briefly explain why or why not.

Answer 20

Yes; even though the citric acid cycle is not needed for catabolic reactions in this organism, the enzymes of the cycle are still essential. They produce precursors of amino acids (such as α-keto- glutarate and oxaloacetate), of heme (succinyl-CoA), and of a variety of other essential products.