Citric Acid Cycle Study Notes

The citric acid cycle is a crucial metabolic pathway, primarily aerobic, focusing on oxidation reactions.
Contains 8 reactions, with 4 being oxidations (contrasting with glycolysis, which has 10 reactions with a single oxidation).
Uses acetyl CoA as the source of carbon, producing carbon dioxide (CO₂).
- Carbon Input/Output: For every two molecules of CO₂ produced, two carbon atoms are introduced in the form of acetyl CoA.
- The cycle does not result in a net gain of carbon.

Glycolysis ends with pyruvate, which must convert into acetyl CoA.
This conversion is facilitated by the pyruvate dehydrogenase complex (PDH), a multi-enzyme complex.
During glycolysis, 2 ATP and 2 NADH are generated.
- Note: NADH's primary role will manifest later in the electron transport chain (ETC).
- In the ETC, electrons from NADH and other carriers (e.g., FADH₂) are transferred to oxygen, producing water and energy for ATP synthesis.

The conversion of pyruvate to acetyl CoA is termed an oxidative decarboxylation reaction.
Key components involved in this step:
- Coenzymes:
  - Thiamine pyrophosphate (TPP).
  - Lipoic acid (lipoate).
  - FAD.
  - Coenzyme A (CoA).
  - NAD⁺.
The process:
- Pyruvate is converted into acetyl CoA while releasing CO₂.
- CoA is transformed into acetyl CoA, and NAD⁺ is reduced to NADH.

Three main enzymes catalyze the conversion from pyruvate to acetyl CoA:
1. E1: Pyruvate dehydrogenase
  - Functions similar to yeast's pyruvate decarboxylase (converts pyruvate to acetaldehyde).
2. E2: Dihydrolipoamide transacetylase
  - Contains covalently bound lipoic acid, facilitating the transfer of carbon to CoA.
  - Lipoic acid is reduced during the reaction.
3. E3: Dihydrolipoamide dehydrogenase
  - Reoxidizes lipoic acid back to its oxidized form using FAD; transfers electrons to NAD⁺ to produce NADH.
Structure:
- PDH is a large complex with 24 E1 subunits on the exterior, E2 in the center, and E3 between subunits.
- This architecture allows substrates to seamlessly transition through the enzyme complex.

Regulation is primarily achieved through controlling E1, the pyruvate dehydrogenase.
Shutting down E1 halts the entire process since the subsequent enzymes depend on it to continue the reaction.

Step 1: Pyruvate enters E1.
- TPP releases CO₂.
- Hydroxyethyl group stays bound to TPP.
Step 2: Hydroxyethyl group transfers to the oxidized form of lipoic acid.
- Lipoic acid, covalently bound to lysine, acts as a flexible tether within the enzyme complex.
- Oxidation of the hydroxyethyl group to a carbonyl.
Step 3: CoA attacks the carbonyl to form acetyl CoA, regenerating lipoic acid.
Step 4: FAD oxidizes lipoic acid, resulting in FADH₂, which donates electrons to NAD⁺ forming NADH.

Begins with oxaloacetate (4 carbons) combined with acetyl CoA (2 carbons) to create citrate.
Sequence of reactions within the cycle:
1. Isomerization of citrate to isocitrate.
2. First oxidative decarboxylation: isocitrate to alpha-ketoglutarate, producing CO₂.
3. Second oxidative decarboxylation: alpha-ketoglutarate to succinyl CoA, also producing CO₂.
4. Conversion of succinyl CoA to succinate, yielding GTP (which can be converted to ATP).
5. Oxidation of succinate to fumarate (FAD to FADH₂).
6. Hydration of fumarate to malate.
7. Final oxidation: malate to oxaloacetate (NAD⁺ to NADH).
Production Summary per acetyl CoA:
- 2 CO₂.
- 3 NADH.
- 1 FADH₂.
- 1 ATP equivalent (GTP).

Converts acetate into 2 CO₂ in a controlled manner to extract energy efficiently.
Mechanisms require stepwise reactions rather than direct oxidation of acetate due to structural limitations.
Key decarboxylation reactions occur at isocitrate and alpha-ketoglutarate, where the presence of a ketone facilitates the breaking of the alpha-beta bond necessary for the decarboxylation.