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DENF 1521 Biochemistry

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The Citric Acid Cycle

Lesson 4.1
Citric Acid Cycle

Instructions
  1. Please enter your name below to be sure you get credit (before doing anything else).
  2. Then study Lesson 4.1 at your own pace. When Practice Exercises appear, click the appropriate button to choose your answer. Then press the "Get Feedback..." button to find out how you did. Continue to try again if you miss.
  3. After studying Lesson 4.1, and responding to all practice exercises, follow instructions at the end to submit your responses for Lesson 4.1 participation credit.
NAME:
Dental Biochemistry Brush
DB Bullet Lesson 4.1 Glycolysis Overview

4.1 Reactions of the Citric Acid Cycle

4.1A Lesson objectives

The objectives of this lesson are to understand that:

  1. Pyruvate is converted to acetyl CoA
  2. Acetyl CoA condenses with oxaloacetate to form citrate
  3. The citric acid cycle results in the formation of GTP, NADH, FADH2, and CO2
  4. The citric acid cycle provides intermediates for various biosynthetic reactions
  5. These intermediates are replaced by anaplerotic reactions

4.1B Introduction

The citric acid cycle (CAC) is the final common pathway for oxidation of all fuel molecules including amino acids, sugars, and fatty acids. The CAC is also known as the tricarboxylic acid cycle or Kreb's cycle. The main point of entry for carbon molecules is as acetyl CoA which condenses with oxaloacetate to form citrate. The citric acid cycle generates the reduced coenzymes, NADH and FADH2, GTP, and provides intermediates for biosynthetic reactions. The citric acid cycle occurs in the mitochondrial matrix of the cell. The reduced coenzymes enter oxidative phosphorylation where the majority of the cell's ATP is synthesized.

4.1C Oxidative decarboxylation of pyruvate

The first reaction to be considered is the oxidative decarboxylation of pyruvate to form acetyl CoA. This reaction, catalyzed by the enzyme pyruvate decarboxylase, is not part of the citric acid cycle but generates the acetyl CoA that enters the CAC. This reaction provides the link between glycolysis and the CAC. The reaction is as follows.

Pyruvate + CoA + NAD+ acetyl CoA + CO2 + NADH
The Pyruvate Dehydrogenase Complex is responsible for carrying out this reaction. This complex contains 3 kinds of enzymes and many cofactors and four steps are required to convert pyruvate to acetyl CoA. This complexity is illustrated by the following table and illustration.

The E. coli pyruvate dehydrogenase complex
Enzyme Number of chains Cofactor Reaction catalyzed
Pyruvate dehydrogenase component 24 Thiamine pyrophosphate Oxidative decarboxylation of pyruvate
Dihydrolipoyl transacetylase 24 Lipoamide Transfer of acetyl group to CoA
Dihydrolipoyl dehydrogenase 12 FAD Regenerate oxidized lipoamide

The interaction of the different components is illustrated diagrammatically below.

One of the important cofactors necessary for the activity of the pyruvate dehydrogenase complex is thiamine pyrophosphate (TPP). TPP is derived from the vitamin thiamine, also called vitamin B1. The function of TPP in the pyruvate dehydrogenase complex is to destabilize the bond between the carbonyl and carboxyl groups of pyruvate. TPP is also a cofactor for the transketolase enzymes. The structure of TPP is shown below. A deficiency in thiamine results in the disease called beriberi. The oral manifestations of thiamine deficiency include "old rose" colored tongue, some depapillation at the periphery of the tongue, and a deeper than expected red color of the oral mucosa.

Lipoamide or lipoic acid contains 2 thiol groups which are essential for its function as a cofactor. Lipoic acid is linked to the dihydrolipoyl transacetylase component of the pyruvate dehydrogenase complex. The thiol groups can exist in the oxidized form (as shown in the figure below) or in the reduced form (2 free HS- groups). Because of its ability to undergo oxidative-reduction reactions, lipoate can serve as an electron carrier as well as an acyl carrier. The pyruvate dehydrogenase reaction depends on both of these functions.

TPP
Lipoate

Dental Biochemistry Brush
DB Bullet Lesson 4.1 Citric acid cycle

CAC introduction
Practice
Exercise 1: 		Large amounts of ATP are made directly by the citric acid cycle.

No Response
True
False

Practice
Exercise 2: 		The entry point for carbon atoms into the citric acid cycle is in the form of

No Response
Pyruvate
Acetyl CoA
Citrate
Oxaloacetate


Practice
Exercise 3: 		Two of the cofactors necessary for the pyruvate dehydrogenase complex to be active are

No Response
Thiamine pyrophosphate and biotin
Biotin and lipoamide
Lipoamide and thiamine pyrophosphate
Pyridoxal phosphate and thiamine pyrophosphate


Practice
Exercise 4: 		The disease beriberi is caused by a deficiency in thiamine.

No Response
True
False

Dental Biochemistry Brush
DB Bullet Lesson 4.1 Citric acid cycle

4.1D Overview of the citric acid cycle

The diagram below schematically illustrates the citric acid cycle (CAC). Note that a C-6 molecule (citrate) is formed from C-4 (oxaloacetate) and C-2 (acetyl CoA) molecules. One cycle of the citric acid cycle generates

4.1E Formation of citrate

The initial step of the CAC is the condensation of oxaloacetate and acetyl CoA to form citrate. This reaction is catalyzed by the enzyme citrate synthase. The reaction involves a condensation of reactants to form the intermediate citryl CoA followed by a hydrolysis reaction yielding citrate and CoA. This reaction and the citryl CoA intermediate are depicted below.

Dental Biochemistry Brush
DB Bullet Lesson 4.1 Citric acid cycle

CAC overview
Practice
Exercise 5: 		One round of the citric acid cycle directly generates all of the following molecules EXCEPT

No Response
NADH
FADH2
GTP
ATP


Practice
Exercise 6: 		Citryl CoA is the intermediate in the formation of citrate.

No Response
True
False


Dental Biochemistry Brush
DB Bullet Lesson 4.1 Citric acid cycle

4.1F The complete citric acid cycle

The net reaction for the citric acid cycle is:

Acetyl CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O
2 CO2 + 3 NADH + FADH2 + GTP + H+ + CoA
Many of the reactions of the citric acid cycle result in the formation of important molecules. It is important to know the reactions which produce these molecules.

Sites of CO2 production

Sites of NADH production

Sites of FADH2 production

Sites of GTP production

  • Isocitrate dehydrogenase
  • -ketoglutarate dehydrogenase
  • Isocitrate dehydrogenase
  • -ketoglutarate dehydrogenase
  • Malate dehydrogenase
  • Succinate dehydrogenase
  • Succinyl CoA synthetase

Note that 1 additional molecule of CO2 and 1 additional molecule of NADH are also formed by the pyruvate dehydrogenase reaction. However, this reaction is not considered a part of the citric acid cycle.

CAC

The net ATP yield from the citric acid cycle and glycolysis can be summarized as follows.

Reactions Reduced coenzymes ATP equivalent
Pyruvate Dehydrogenase 1 NADH 2.5
Citric Acid Cycle 3 NADH
1 FADH2
. 		7.5
1.5
1 GTP=1
. Subtotal/glucose 12.5 x 2 = 25/glucose
Glycolysis 2 NADH
. 		5 (or 3)
Anaerobic ATP=2
. NET 30 (or 32)

Note: new value for ATP/NADH is 2.5; ATP/ FADH2 is 1.5. You may see the numbers ATP/NADH=3; ATP/ FADH2=2 in some older texts. For more information on the reevaluation of the number of ATP's/nucleotide coenzyme see Hinkle, et al. Mechanistic stoichiometry of mitochondrial oxidative phosphorylation. Biochemistry 30:3576-82, 1991.

The different values of 30 or 32 ATP/glucose depend on the method used to transport cytoplasmic NADH, formed by glycolysis, into the mitochondria. See lesson 5.3 for more details.

Dental Biochemistry Brush
DB Bullet Lesson 4.1 Citric acid cycle

Details of the CAC
Practice
Exercise 7: 		Which of the following compounds is NOT a product of the reaction catalyzed by the enzyme isocitrate dehydrogenase?

No Response
FADH2
CO2
NADH
-ketoglutarate


Practice
Exercise 8: 		The products of the reaction catalyzed by succinyl CoA synthetase are succinate and GTP.

No Response
True
False


Practice
Exercise 9: 		The total number of NADH molecules resulting from 1 round of the citric acid cycle is

No Response
One
Two
Three
Four


Practice
Exercise 10: 		Which of the following reactions does NOT result in the production of both CO2 and NADH?

No Response
Pyruvate dehydrogenase
Malate dehydrogenase
Isocitrate dehydrogenase
Succinate dehydrogenase


Dental Biochemistry Brush
DB Bullet Lesson 4.1 Citric acid cycle

4.1G Summary

After completing this lesson you should understand the following about the citric acid cycle.
  1. Pyruvate is converted to acetyl CoA by the pyruvate dehydrogenase complex
  2. The pyruvate dehydrogenase complex contains several enzyme activities and cofactors and is the key step regulating the flow of C-2 units into the citric acid cycle.
  3. Acetyl CoA condenses with oxaloacetate to form citrate as the first step of the actual cycle
  4. One round of the citric acid cycle results in the formation of 1 GTP, 3 NADH, 1 FADH2, and 2 CO2

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Final Instructions

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End Lesson 4.1
Overview of the citric acid cycle



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