TCA cycle

Office Hours:
- Note: No office hours on Friday.
- Available on Thursday from 12 PM to 1:30 PM in office BS426.

Definition: A metabolic process where glucose is oxidized to carbon dioxide (CO2) and water (H2O).
Process Details:
- Energy released during glucose oxidation is utilized for ATP generation through a sequence of five steps:
1. Pyruvate is produced from glucose.
2. Pyruvate is further oxidized to CO2 and acetyl-CoA.
3. Acetyl-CoA undergoes a series of reactions leading to the formation of NADH, FADH2, and ATP.
4. NADH and FADH2 undergo oxidation to pump protons, forming a proton gradient.
5. The proton gradient is used to produce ATP through chemiosmosis.

Under aerobic conditions:
- Pyruvate from glycolysis is oxidized to acetyl-CoA.
- Acetyl-CoA proceeds to enter the TCA cycle, which will be covered in Lectures 10-12.

Process: Acetyl group is transferred to Coenzyme A to yield acetyl-CoA.
Function: The two-carbon acetyl unit is utilized in the TCA cycle, generating high-energy electrons necessary for ATP synthesis and producing two molecules of CO2.

Description: The citric acid cycle is a series of chemical reactions used by all aerobic organisms to release stored energy.
Schematic Representation:
- Initial Input: 2C (from acetyl CoA) + 4C (from oxaloacetate) = 6C (citrate).
- Cycle progression: 6C -> 4C (after 2C is released as CO2) with high-energy electrons captured by NAD+ and FAD, and 1 ATP produced.

Importance: Many compounds are processed into acetyl-CoA, showing the TCA cycle's central role in metabolism.

Function: Converts pyruvate into acetyl-CoA through oxidative decarboxylation.
Significance: Irreversible link between glycolysis and the citric acid cycle.
Reaction Type: The oxidative decarboxylation involves removing a carboxyl group from pyruvate, resulting in CO2 and the reduction of NAD+ to NADH (3C to 1C + 2C).

Note: Pyruvate crosses the mitochondrial outer membrane easily but requires active transport into the inner membrane via the mitochondrial pyruvate carrier (MPC), consuming energy.
Genetic Note: Two genes are responsible for MPC in humans; mutations can lead to mitochondrial pyruvate carrier deficiency (MPYCD).
Clinical Presentation:
- Symptoms might include lactic acidosis, low muscle strength, cardiomegaly, hepatomegaly, hypoglycemia, neurological problems, and facial dysmorphia.

Composition: The PDH complex consists of three different enzymes, which carry out three distinct functions—decarboxylation, oxidation, and acetyl transfer.
Enzymes Involved:
- Pyruvate dehydrogenase (E1)
- Dihydrolipoyl transacetylase (E2)
- Dihydrolipoyl dehydrogenase (E3)
- Functional Types: E1 and E2 perform the reactions, while E3 regenerates the system using five coenzymes.

Decarboxylation by E1: Pyruvate is combined with thiamine pyrophosphate (TPP), leading to the release of CO2.
Oxidation by E1: The hydroxyethyl group is then oxidized to an acetyl group and transferred to the coenzyme lipoamide, resulting in the reduced form of lipoamide.
Acetyl CoA Formation by E2: The acetyl group is transferred to CoA, forming acetyl-CoA, while lipoamide remains reduced.
Regeneration by E3: The oxidized lipoamide is regenerated through oxidative reduction, enabling PDH complex to function repeatedly.

Chemical Reaction:
$ext{Pyruvate} + ext{CoA-SH} + ext{NAD}^+ <br>ightarrow ext{NADH} + ext{CO}_2 + ext{Acetyl-CoA}$
Note: This reaction occurs twice per glucose, leading to the formation of 2 NADH by the time glucose is fully processed.

Definition: The transfer of intermediate products directly from one enzyme to another without their release into the surrounding solution, enhancing efficiency of reactions in the complex.

Context: The conversion of pyruvate to acetyl CoA is irreversible and critical; thus, its regulation is crucial for energy balance.
Conditions for PDH Activity:
- Turned off at high ATP/ADP and NADH/NAD+ ratio.
- Turned on at low ATP/ADP ratio when energy is demanded.

PDH kinase: Inhibits PDH through phosphorylation, activated by PDH products (ATP, NADH, acetyl-CoA).
PDH phosphatase: Reverses the inhibition mediated by PDH kinase, restoring PDH activity.

Beriberi: Thiamine deficiency causes insufficient pyruvate dehydrogenase activity, leading to neuromuscular symptoms including weakness, pain, and confusion.
Neurological Disorders: Inhibition of PDH complex activity by environmental toxins (e.g., mercury, arsenate) leading to neurological effects, historically known as "mad as a hatter" due to mercury exposure in felting processes.

Main Role: The TCA cycle carries out the oxidation of the acetyl fragment from acetyl-CoA to CO2, capturing high-energy electrons in the form of NADH and FADH2 for ATP production.
Stages:
- Stage 1: Introduction of two carbons into the cycle via acetyl group and formation of citrate.
- Stage 2: Regeneration of oxaloacetate and generation of CO2 and high-energy electrons for ATP synthesis.

For each "turn" of the cycle, the outputs are:
- 2 CO2
- 3 NADH
- 1 FADH2
- 1 GTP or ATP

Shared by Hans Adolf Krebs (for the discovery of the citric acid cycle) and Fritz Albert Lipmann (for discovering co-enzyme A).

Citrate Synthase: Forms citrate from acetyl-CoA and oxaloacetate; CoA is regenerated.
Aconitase: Converts citrate to isocitrate; an endergonic process followed by high flux.
Isocitrate Dehydrogenase: Catalyzes oxidative decarboxylation forming α-ketoglutarate and CO2, capturing NADH.
α-Ketoglutarate Dehydrogenase: Similar to PDH, catalyzes oxidative decarboxylation to succinyl-CoA, yielding NADH.
Succinyl-CoA Synthetase: Catalyzes substrate-level phosphorylation turning succinyl-CoA into succinate, driving ATP synthesis.
Succinate Dehydrogenase: Oxidizes succinate to fumarate, generating FADH2.
Fumarase: Hydrates fumarate into malate.
Malate Dehydrogenase: Oxidizes malate back to oxaloacetate, producing NADH in the end.

The two carbons entering as the acetyl group are different from those that exit as CO2.
ATP yield varies, commonly cited as 30-32 ATP per glucose when considering oxidative processes following the cycle.

Key enzymes regulated by energy charge: isocitrate dehydrogenase and α-ketoglutarate dehydrogenase; ATP and NADH act as negative regulators.
Anaplerotic Reactions: Necessary to replenish TCA cycle intermediates consumed for other biosynthetic processes.
- Pyruvate Carboxylase: Synthesizes oxaloacetate to maintain cycle continuity.

The TCA cycle serves as a hub for both catabolic and anabolic processes and it is crucial for energy production in aerobic organisms. Energetic output must maintain the cycle's function, and any disruption has clinical ramifications.