Citric Acid Cycle - General

Question 1

Where does the citric acid cycle occur?

Answer 1

In the mitochondrial matrix.

Question 2

Why is the reaction catalyzed by pyruvate dehydrogenase complex a crucial juncture in metabolism?

Answer 2

The reaction converts pyruvate, CoA and NAD+ into acetyl CoA, CO₂, NADH and H+. Acetyl CoA and NADH will continue on to the Citric Acid Cycle and ETC respectively, producing ATP.

Question 3

The pyruvate dehydrogenase complex consists of how many enzymes and how many coenzymes? What are the coenzymes?

Answer 3

3 enzymes and 5 coenzymes.

Coenzymes:

1. TPP (prosthetic group)
2. Lipoamide (prosthetic group)
3. FAD (prosthetic group)
4. NAD (substrate)
5. CoA (substrate)

Question 4

What kind of reaction does pyruvate dehydrogenase catalyze? Why is it called this?

Answer 4

An oxidative decarboxylation reaction. It is called this because it is a combination of a redox reaction (electrons from pyruvate are gained by NAD+) and decarboxylation reaction (pyruvate loses a carbon when converted to acetyl CoA).

Question 5

Acetyl CoA produced by any means is able to enter the citric acid cycle. What are the 3 means?

Answer 5

1. Glucose
2. Fats
3. Some amino acids

Question 6

Besides ATP synthesis, what are other possible metabolic fates of acetyl CoA? (3)

Answer 6

KFC

1. Cholesterol synthesis.
2. Fatty acids.
3. Ketone bodies.

Question 7

What are the 5 steps of the pyruvate dehydrogenase complex reaction?

Answer 7

1. Pyruvate enters complex, combines with TPP on E₁, undergoes a decarboxylation, leaving an acetyl group attached to TPP.
2. The oxidized form of lipoamide attached to E₂ moves to the active site on E₁, where E₁ catalyzes the transfer of the acetyl group to lipoamide.
3. The lipoamide brings the acetyl group to E₂ where it is transferred to CoA, reducing the lipoamide.
4. The reduced lipoamide is brought to E₃ where FAD is able to oxidize the -SH groups to a disulfide bond.
5. Now reduced to FADH₂, NAD+ comes in becomes reduced by FADH₂, converting it to FAD and NADH, where FAD can continue to oxidize lipoamides.

Question 8

What two mechanisms regulate the PDC? Describe briefly.

Answer 8

1. Covalent modification, specifically phosphorylation
   
   • Phosphorylation is done by pyruvate dehydrogenase kinase on E₁, inactivating it.
   • Dephosphorylation is done by a phosphatase on E₁, activating it.
2. Allosteric regulation by molecules that reflext high or low energy change

Question 9

What is the Warburg effect? What gene regulator is thought to play a factor.

Answer 9

The phenomenon for tumours to metabolize glucose to lactate through glycolysis in aerobic conditions. This does not happen normally unless the cells are under hypoxic conditions. The regulator is called hypoxia inducible factor-1 (HIF-1).

Question 10

The citric acid cycle consists of ___ reactions, producing ___ NADH, ___ FADH₂, ___ ATP and ___ CO₂.

Answer 10

8, 3, 1, 1, 2.

Question 11

In the conversion of citrate to isocitrate, what does aconitase do? Why is this important?

Answer 11

It changes the position of the hydroxyl group, allowing the subsequent reactions of the cycle to take place.

Question 12

Every NADH yields ___ ATP, every FADH₂ yields ___ ATP. Overall the citric acid cycle generates ___ ATP.

Answer 12

2.5, 1.5, 10.

Question 13

Which two key enzymes of the citric acid cycle are regulated and how? Why these enzymes?

Answer 13

1. Isocitrate dehydrogenase
   
   • Inhibited: NADH, ATP
   • Activated: ADP
2. a-ketoglutarate dehydrogenase
   
   • Inhibited: ATP, NADH, succinyl CoA

These enzymes link the citric acid cycle with other pathways.

Question 14

How does inhibition of the two key enzymes in the citric acid cycle effect the cell?

Answer 14

1. Isocitrate dehydrogenase inhibition causes citrate buildup, inhibiting PFK, inhibiting glycolysis.
2. a-KG dehydrogenase inhibition causes a buildup of a-KG causing the synthesis of amino acids and other biomolecules.

Question 15

Oxaloacetate, succinyl CoA, a-KG and citrate all provide biosynthetic precursors. What do each make?

Answer 15

• Oxaloacetate
  
  • Glucose
  • Aspartate → other amino acids, purines, pyrimidines
• a-KG
  
  • Glutamate → other amino acids → purines
• Succinyl CoA
  
  • Porphyrins, heme, chlorophyll
• Citrate
  
  • Fatty acids, sterols

Question 16

What is an anaplerotic reaction? Give an example from the citric acid cycle.

Answer 16

A reaction that replenishes intermediates of the cycle. An example is the synthesis of oxaloacetate from acetyl CoA and CO₂ by pyruvate carboxylase.

Question 17

What is the glyocylate cycle used for? What are its steps? (4)

Answer 17

It is used by plants and microorganisms to create glucose from acetyl CoA.

1. Acetyl CoA condenses with oxaloacetate to form citrate which is then converted to isocitrate
2. Isocitate is cleaved by isocitrate lyase to succinate and glyoxylate (2C)
3. Glyocylate combines with a molecule of acetyl CoA to form malate using malate synthase
4. Malate is converted to oxaloacetate, leaving the succinate from step 2, which can be converted into glucose