overview of citric acid cycle

The citric acid cycle, also known as the Krebs cycle, is a metabolic pathway that involves the incorporation and loss of carbon atoms throughout its various stages.
Up to the central step discussed, two carbons from acetyl CoA are introduced, culminating in the release of two carbon atoms as carbon dioxide (CO₂).
The ultimate aim is to convert the remaining four-carbon molecule, succinyl CoA, back to oxaloacetate, thus regenerating the original starting substrate.

The initial step in this process involves the conversion of succinyl CoA to succinate.
This transformation utilizes the hydrolysis of a thioester bond within coenzyme A (CoA), which generates a high-energy compound, GTP.
GTP is functionally similar to ATP, acting as an energy currency for the cell.
The Gibbs free energy change (ΔG) for this reaction is approximately zero, indicating it is freely reversible.
- This reversibility is attributed to the hydrolysis of the thioester which drives the overall reaction forward.

In this mechanism:
- A phosphate group is first incorporated onto a histidine residue, creating a phosphohistidine intermediate.
- The reaction commences with succinyl CoA, wherein coenzyme A departs as a phosphate attacks the carbonyl carbon of the thioester.
- This mechanism parallels the formation of a high-energy compound, analogous to 1,3-bisphosphoglycerate in glycolysis.

The phosphohistidine intermediate formed is resonance stabilized, reflecting its thermodynamic stability.
GDP (guanosine diphosphate) is then brought in, where it interacts with the phosphohistidine, displacing the phosphate to regenerate the active histidine.

The next reaction in the cycle involves the oxidation of succinate to fumarate.
This transformation involves the oxidation of a carbon-carbon single bond (between two carbon atoms) to a carbon-carbon double bond,
For this specific oxidation, FAD (flavin adenine dinucleotide) is utilized as the electron acceptor rather than NAD⁺ (nicotinamide adenine dinucleotide) because NAD⁺ cannot oxidize such a bond.
The reaction generates the trans-isomer fumarate, while the cis-isomer is not produced due to sterics in the reaction mechanism.

The electrons transferred to FADH₂ (the reduced form of FAD) are then channeled to ubiquinone, an essential electron carrier in the electron transport chain located in the inner mitochondrial membrane.
Notably, succinate dehydrogenase is the only citric acid cycle enzyme found within the inner mitochondrial membrane.
- This highlights its unique functional role different from other enzymes in the cycle.

Malonate acts as an effective inhibitor of succinate dehydrogenase due to its structural similarity, containing two carboxylate groups like succinate.
- However, malonate cannot undergo the necessary oxidation due to the lack of a central carbon atom required to stabilize the structure needed to serve as a substrate.
Malonate inhibits succinate from binding to the active site of the enzyme, thereby preventing product formation from succinate.

The mechanism employed by succinate dehydrogenase involves regenerating a carbocation through hydride oxidation via FAD.
In this process, electrons are transferred, resulting in a charged nitrogen atom within the enzyme.
- This nitrogen may then act as a base, facilitating further reactions to yield a stable carbon-carbon double bond.

To convert fumarate into malate, which is an alcohol, a two-step process is employed:
1. Formation of the carbon-carbon double bond in fumarate.
2. Hydration reaction which yields L-malate.
Fumarase catalyzes this hydration reaction, which can proceed via two mechanisms:
- Carbanion Mechanism: Water is first deprotonated to form a hydroxide ion, which then attacks the double bond, resulting in the formation of product.
- Carbocation Mechanism: The carbon-carbon double bond grabs a proton from the acid at the enzyme's active site, generating a carbocation, followed by water attacking the carbocation to yield the alcohol product.
Only L-malate is produced from this hydration; the D-isomer is not formed.

The final step is the oxidation of L-malate to oxaloacetate carried out by malate dehydrogenase.
NAD⁺ serves as the oxidizing agent in this reaction, removing a hydride along with its electrons, which results in the formation of NADH.
This reaction is notably endergonic, with a positive change in Gibbs free energy (ΔG).
- The only pathway for this reaction to proceed involves rapid utilization of the produced oxaloacetate by citrate synthase to re-initiate the cycle through a highly exergonic step with a ΔG of approximately -30 kJ/mol.

The coordination between these steps allows effective cycling within the citric acid cycle, with essential interdependencies among substrates, products, and enzyme activities, ensuring cellular respiration efficiency and energy production.