17 tca cycle

Where do glycolysis, PDC, the TCA cycle, and oxidative phosphorylation occur?

Glycolysis: cytosol. PDC: mitochondrial matrix. Most TCA reactions: matrix. Electron transport and oxidative phosphorylation: inner mitochondrial membrane.

Which TCA enzyme is an exception to the usual mitochondrial-matrix location?

Succinate dehydrogenase (Step 6) is located in the inner mitochondrial membrane.

Why are PDC and TCA described as aerobic processes even though oxygen is not consumed directly in each TCA reaction?

They produce NADH/FADH₂ that normally must be reoxidized by mitochondrial electron transport, which ultimately uses O₂ as the terminal electron acceptor.

What must happen to pyruvate after cytosolic glycolysis before it can enter the TCA cycle?

Pyruvate must enter the mitochondrion and reach the matrix, where PDC converts it into acetyl-CoA.

How are PDC/TCA and the electron transport chain connected across mitochondrial compartments?

PDC and the TCA cycle in the matrix produce reduced electron carriers (NADH, FADH₂). Their electrons are transferred to the ETC at the inner mitochondrial membrane.

Write the overall pyruvate dehydrogenase complex (PDC) reaction.

Pyruvate + CoA-SH + NAD⁺ → acetyl-CoA + CO₂ + NADH + H⁺.

Why is the PDC reaction called oxidative decarboxylation?

One carbon from pyruvate leaves as CO₂ (decarboxylation), and electrons are transferred to NAD⁺ to produce NADH (oxidation).

Trace the carbon atoms from pyruvate to acetyl-CoA.

Pyruvate contains 3 carbons. One exits as CO₂; the remaining 2 form the acetyl group carried by coenzyme A.

How many times does PDC run per glucose, and what does it produce before the TCA cycle?

Twice, because glycolysis makes 2 pyruvate per glucose. PDC therefore produces 2 acetyl-CoA, 2 NADH and 2 CO₂.

Name the five cofactors/coenzymes used by PDC.

TPP (thiamine pyrophosphate), lipoate, coenzyme A, FAD, and NAD⁺. The complex contains three enzyme components (E1, E2, E3).

Match the PDC cofactors to their main chemical jobs.

TPP: carries a 2-carbon fragment. Lipoate: carries acyl groups and electrons. CoA: carries the acetyl group. FAD and NAD⁺: electron carriers; NADH is released as an overall product.

Which high-energy or product signals inhibit PDC?

High ATP, high NADH and high acetyl-CoA signal that sufficient energy/products are available and inhibit PDC.

Which molecules favor increased PDC activity when energy is needed?

ADP and pyruvate promote PDC activity (the slide highlights these as activating signals).

A cell has high ATP, NADH, and acetyl-CoA. Predict what happens to conversion of pyruvate to acetyl-CoA.

PDC activity decreases. There is little need to make more acetyl-CoA or reduced electron carriers when energy/products are abundant.

What does phosphorylation do to the regulated E1 component of PDC?

PDH kinase phosphorylates E1/PDH and INACTIVATES the complex.

How is inactive, phosphorylated PDC reactivated?

PDH phosphatase removes the phosphate, converting PDC back into its active form.

Write all eight TCA intermediates in the correct order, starting with oxaloacetate + acetyl-CoA.

Oxaloacetate + acetyl-CoA → citrate → isocitrate → α-ketoglutarate → succinyl-CoA → succinate → fumarate → malate → oxaloacetate.

TCA Step 1 — What does citrate synthase do? Include substrates and structural change.

Acetyl-CoA (2 C) + oxaloacetate (4 C) + H₂O → citrate (6 C) + CoA-SH. A new C–C bond forms; thioester hydrolysis helps drive this irreversible reaction.

TCA Step 2 — How does aconitase convert citrate into isocitrate?

It removes H₂O to form cis-aconitate, then adds H₂O back stereospecifically. This relocates the hydroxyl group; no NADH, FADH₂, ATP, or CO₂ is produced.

TCA Step 3 — What is the isocitrate dehydrogenase reaction?

Isocitrate (6 C) + NAD⁺ → α-ketoglutarate (5 C) + CO₂ + NADH + H⁺. Oxidation occurs before decarboxylation; this step is irreversible.

TCA Step 4 — What does α-ketoglutarate dehydrogenase produce?

α-Ketoglutarate (5 C) + CoA-SH + NAD⁺ → succinyl-CoA (4 C) + CO₂ + NADH + H⁺. This irreversible oxidative decarboxylation uses PDC-like chemistry.

TCA Step 5 — What does succinyl-CoA synthetase do?

Succinyl-CoA + GDP + Pi → succinate + CoA-SH + GTP. Thioester energy drives SUBSTRATE-LEVEL PHOSPHORYLATION.

TCA Step 6 — What happens to succinate in the succinate dehydrogenase reaction?

Succinate → fumarate; an alkane is oxidized to an alkene (a C=C double bond is formed). FAD is reduced to FADH₂.

TCA Step 7 — What is the fumarase reaction?

Fumarate + H₂O → L-malate. Water is added across fumarate’s C=C double bond (hydration), creating an –OH group.

TCA Step 8 — How does malate dehydrogenase regenerate oxaloacetate?

L-malate + NAD⁺ ⇌ oxaloacetate + NADH + H⁺. The alcohol is oxidized to a carbonyl (ketone), regenerating OAA.

Draw the carbon-count pattern during one TCA turn.

OAA (4 C) + acetyl (2 C) → citrate (6 C) → isocitrate (6 C) → α-KG (5 C) → succinyl-CoA (4 C) → succinate (4 C) → fumarate (4 C) → malate (4 C) → OAA (4 C).

What changes chemically in the final three TCA steps (succinate → fumarate → malate → OAA)?

Succinate → fumarate: oxidation creates C=C and FADH₂. Fumarate → malate: hydration adds H and OH. Malate → OAA: alcohol oxidation creates C=O and NADH.

Why does malate → oxaloacetate proceed in cells despite being thermodynamically unfavorable by itself?

Oxaloacetate is kept at very low concentration because citrate synthase consumes it; this helps pull malate dehydrogenase forward.

Which two TCA steps release CO₂, and what kind of reaction do they share?

Steps 3 and 4: isocitrate dehydrogenase and α-ketoglutarate dehydrogenase. Both are oxidative decarboxylations.

What are the products of ONE turn of the TCA cycle (one acetyl-CoA)?

3 NADH + 1 FADH₂ + 1 GTP (ATP equivalent) + 2 CO₂. Oxaloacetate is regenerated, not consumed overall.

What are the TCA products from ONE glucose, excluding PDC and glycolysis?

Because TCA turns twice per glucose: 6 NADH + 2 FADH₂ + 2 GTP + 4 CO₂.

Combine PDC and TCA for one glucose. How many NADH, FADH₂, GTP and CO₂ form (before ETC)?

PDC (2 pyruvate): 2 NADH, 0 FADH₂, 0 GTP, 2 CO₂. TCA (2 turns): 6 NADH, 2 FADH₂, 2 GTP, 4 CO₂. TOTAL: 8 NADH, 2 FADH₂, 2 GTP, 6 CO₂.

If TWO acetyl-CoA molecules enter TCA, how many reduced electron carriers result?

6 NADH and 2 FADH₂. Each acetyl-CoA gives 3 NADH and 1 FADH₂.

Practice-final application: Glycerol enters glycolysis as one GAP after costing 1 ATP. It is completely oxidized, but there is NO ETC. What are total NADH, FADH₂ and ATP/GTP?

From GAP to pyruvate: 1 NADH + 2 ATP. PDC: 1 NADH. One TCA turn: 3 NADH + 1 FADH₂ + 1 GTP. Subtract 1 ATP for entry. TOTAL: 5 NADH, 1 FADH₂, and 2 net ATP/GTP equivalents. Do NOT count ETC ATP.

Name the major regulated reactions linking pyruvate oxidation with the TCA cycle.

PDC (before TCA), citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase.

Which metabolites generally signal TCA inhibition versus activation?

High ATP and NADH inhibit. ADP/AMP and oxidized electron carriers (NAD⁺) favor flux. Product buildup also inhibits key steps.

Which enzyme catalyzes the rate-limiting step of the TCA cycle according to Dr. Radi’s slides?

Citrate synthase. It catalyzes the irreversible condensation of oxaloacetate and acetyl-CoA to make citrate.

Exam application: Why might a buildup of NADH slow several TCA reactions simultaneously?

NADH signals a reduced, energy-rich state and is a product of major oxidative steps. Its buildup inhibits regulated dehydrogenases, slowing further oxidation.

What does it mean that the TCA cycle is amphibolic?

It has CATABOLIC functions (oxidizing fuel carbon for energy) and ANABOLIC functions (supplying intermediates for biosynthesis).

Give one example of how a TCA intermediate is used to make another molecule.

Examples from the slide: citrate → fatty acids/sterols; α-ketoglutarate → amino acids; succinyl-CoA → porphyrins/heme; oxaloacetate → aspartate or gluconeogenic glucose.

How do nutrients other than glucose feed carbon into the TCA cycle?

Carbohydrates supply pyruvate and related intermediates; fatty acids supply acetyl-CoA; amino-acid carbon skeletons enter at acetyl-CoA or cycle intermediates.

What is an anaplerotic reaction, and why does TCA need it?

An anaplerotic reaction replenishes TCA intermediates removed for biosynthesis, maintaining cycle operation.

Which enzyme replenishes oxaloacetate from pyruvate, and what does the reaction require?

Pyruvate carboxylase: pyruvate + HCO₃⁻ + ATP → oxaloacetate + ADP + Pi. It uses biotin as a CO₂-carrier cofactor (also covered in Lecture 15).

High acetyl-CoA levels favor pyruvate entering which reaction, and why?

Pyruvate carboxylase is activated, forming more oxaloacetate to replenish TCA intermediates and help use the available acetyl-CoA.

From which major fuel types can cells obtain acetyl-CoA?

Carbohydrates (glucose → pyruvate → PDC), fatty acids (β-oxidation), and some amino-acid carbon skeletons.

Why is acetyl-CoA called a metabolic crossroads?

It carries activated two-carbon units into the TCA cycle and connects carbohydrate, fatty-acid, and amino-acid metabolism.

Compare the energy-producing and biosynthetic fates of acetyl-CoA.

Energy: its acetyl group enters TCA, creating NADH/FADH₂ and GTP. Biosynthesis: acetyl-CoA carbon is used to build fatty acids, sterols/cholesterol and other molecules.

Suppose TCA intermediates are drained into biosynthesis while acetyl-CoA remains abundant. What must occur for continued oxidation?

Anaplerotic reactions must replenish intermediates such as oxaloacetate; otherwise acetyl-CoA cannot continue condensing with OAA at the normal rate.