TCA cycle

What are the two major functions of the tricarboxylic acid (TCA) cycle?

1) Generating energy through the oxidation of acetyl-CoA to $CO_2$ (producing ATP/GTP, NADH, and $QH_2$), and 2) generating carbon precursors for biosynthesis.

Where does the TCA cycle take place within the cell?

In the mitochondrial matrix (except for succinate dehydrogenase, which is embedded in the inner mitochondrial membrane).

Why is the TCA cycle dependent on aerobic conditions?

Because $O_2$ serves as the final electron acceptor when carbon from carbohydrates and fats is completely oxidized.

How does the cyclic pathway of the TCA cycle differ structurally from linear pathways like glycolysis?

Unlike linear pathways where intermediates are used up or converted sequentially, a cyclic pathway continuously regenerates its starting component (oxaloacetate) to process incoming substrate.

What are the products generated from one complete turn of the TCA cycle?

3 NADH, 1 $QH_2$, 1 GTP (or ATP), and 2 $CO_2$ molecules.

What type of chemical reaction occurs in Step 1, catalyzed by citrate synthase?

A condensation reaction between acetyl-CoA and oxaloacetate to form citrate, releasing CoA-SH and forming the only C-C bond in the cycle.

Why is the reaction catalyzed by citrate synthase favorable $(\Delta G^{\circ\prime} = -31.5~kJ/mol)$?

The negative free energy change ensures that the cycle moves forward in one direction, though it does not directly synthesize ATP.

What is the purpose of Step 2, catalyzed by aconitase?

An isomerization (rearrangement) via a nonhydrolytic lyase step that converts citrate into isocitrate, moving the hydroxyl group to allow for subsequent oxidation.

What occurs during Step 3, catalyzed by isocitrate dehydrogenase?

The first oxidative decarboxylation step, which is irreversible, releases the first $CO_2$, transfers a hydride ion to $NAD^+$ to form NADH, and yields oxalosuccinate as an unstable intermediate.

What are the mechanistic similarities between Step 4 ($\alpha$-ketoglutarate dehydrogenase complex) and pyruvate dehydrogenase (PDH)?

Both catalyze oxidative decarboxylation coupled to $NAD^+$ reduction, releasing $CO_2$ and forming a high-energy thioester bond with Coenzyme A (producing succinyl-CoA).

Which step of the TCA cycle directly produces high-energy phosphate via substrate-level phosphorylation?

Step 5, catalyzed by succinyl-CoA synthetase, which conserves the energy of succinyl-CoA to produce GTP (or ATP) directly.

Where is succinate dehydrogenase located, and what is its dual role?

It is located in the inner mitochondrial membrane (also known as Complex II of the electron transport chain) and catalyzes the oxidation of succinate to fumarate while reducing FAD to $QH_2$.

What isomer is exclusively formed during Step 7 by the enzyme fumarase?

The trans addition of water to fumarate exclusively produces the L-isomer of malate via hydration.

What is the function of Step 8, catalyzed by malate dehydrogenase?

The oxidation of L-malate coupled to the reduction of $NAD^+$ to NADH, which regenerates oxaloacetate to keep the cycle running.

How many total ATP equivalents are produced from the complete aerobic oxidation of one glucose molecule?

32 ATP molecules (accounting for glycolysis, the PDH complex, the TCA cycle, and oxidative phosphorylation).

How many ATP equivalents are produced under anaerobic conditions from one glucose molecule?

Only 2 ATP molecules, because without oxygen, the TCA cycle and oxidative phosphorylation cannot run, leaving only glycolysis followed by lactate fermentation.

Which three enzymes regulate the TCA cycle through feedback inhibition and feedforward activation?

1) Citrate synthase, 2) Isocitrate dehydrogenase, and 3) $\alpha$-ketoglutarate dehydrogenase complex.

What molecules act as inhibitors versus activators for the regulated TCA enzymes?

High energy markers like ATP and NADH act as inhibitors (feedback), while low energy indicators like ADP act as activators (feedforward).