Citric Acid Cycle (Krebs) & Pyruvate Dehydrogenase Complex

These flashcards review key concepts, enzymes, regulation, historical discoveries, cofactor chemistry, clinical aspects, and metabolic roles of the Pyruvate Dehydrogenase Complex and the Citric Acid Cycle.

Where does glycolysis occur and does it require oxygen?

In the cytosol; it proceeds anaerobically (no O₂ required).

In which cellular compartment do the Pyruvate Dehydrogenase Complex (PDC) and the Citric Acid Cycle operate?

Inside the mitochondrial matrix (with enzymes of the respiratory chain embedded in the inner membrane).

What determines the overall rate of cellular oxygen consumption during aerobic metabolism?

The combined rates of PDC and TCA-cycle reactions.

Name the three broad stages of aerobic catabolism of glucose.

1) Acetyl-CoA production (glycolysis & PDC), 2) Acetyl-CoA oxidation (TCA cycle), 3) Electron transfer & oxidative phosphorylation.

Which inhibitor revealed the role of succinate dehydrogenase in the TCA cycle during early studies?

Malonate, a competitive inhibitor of succinate oxidation to fumarate.

Who discovered the cyclic pathway of pyruvate oxidation now known as the Krebs cycle, and in what year?

Hans Krebs in 1937.

List the three enzyme components of the Pyruvate Dehydrogenase Complex (E1, E2, E3).

E1: Pyruvate dehydrogenase (TPP-dependent); E2: Dihydrolipoyl transacetylase (lipoic acid & CoA); E3: Dihydrolipoyl dehydrogenase (FAD & NAD⁺).

Give two advantages of organizing enzymes into a multienzyme complex like PDC.

1) Faster reaction rate due to substrate channeling; 2) Reduced side reactions and coordinated regulation.

Which coenzyme carries the reactive thiol group that forms acetyl-CoA?

Coenzyme A (CoA-SH), derived partly from pantothenic acid.

What is the immediate product formed on E2 after E1 decarboxylates pyruvate?

Acetyl-dihydrolipoamide (acetylated lipoic acid arm).

How is the activity of PDC turned OFF and ON?

OFF by phosphorylation of E1 by PDH kinase; ON by dephosphorylation via PDH phosphatase.

Name one activator and one inhibitor of PDH kinase.

Activator: NADH (or Acetyl-CoA); Inhibitor: ADP (or pyruvate).

Which ion and which hormone activate PDH phosphatase?

Ca²⁺ and insulin.

Why does thiamine (vitamin B₁) deficiency cause severe neurological symptoms (beriberi)?

Because thiamine is required to form TPP, an essential cofactor for PDC; without it, aerobic glucose oxidation in the brain is impaired.

How do arsenite and related arsenic compounds inactivate PDC?

They covalently bind to the–SH groups of reduced lipoic acid on E2, blocking its function.

List the eight enzymes of the citric acid cycle in order starting with citrate synthase.

1) Citrate synthase, 2) Aconitase, 3) Isocitrate dehydrogenase, 4) α-Ketoglutarate dehydrogenase, 5) Succinyl-CoA synthetase, 6) Succinate dehydrogenase, 7) Fumarase, 8) Malate dehydrogenase.

Which TCA enzyme operates via an induced-fit mechanism initiated by oxaloacetate binding?

Citrate synthase.

What unique feature distinguishes aconitase catalysis?

It performs dehydration followed by rehydration to isomerize citrate to isocitrate via cis-aconitate.

Isocitrate dehydrogenase exists in two isoforms. What electron acceptors do they use?

One uses NAD⁺; the other uses NADP⁺.

Which TCA enzyme complex is mechanistically analogous to PDC?

α-Ketoglutarate dehydrogenase complex (with E1, E2, E3 components).

How is GTP (or ATP) generated in the citric acid cycle?

By substrate-level phosphorylation catalyzed by succinyl-CoA synthetase using the energy of thioester hydrolysis.

Which TCA enzyme is embedded in the inner mitochondrial membrane and has FAD as its prosthetic group?

Succinate dehydrogenase.

Why does malonate inhibit succinate dehydrogenase?

It is a structural analog of succinate and competes for the enzyme’s active site.

What reaction does fumarase catalyze, and what stereospecificity does it display?

Hydration of fumarate to L-malate; it does not act on the cis isomer (maleate).

Which step of the TCA cycle has a highly endergonic standard ΔG°’, yet proceeds forward in vivo due to product removal?

Oxidation of malate to oxaloacetate by malate dehydrogenase.

Per acetyl-CoA oxidized in the TCA cycle, what reduced cofactors and high-energy nucleotides are produced?

3 NADH, 1 FADH₂, and 1 GTP (which equals 1 ATP).

Approximately what percentage efficiency do cells achieve in converting glucose oxidation energy into ATP under physiological conditions?

Roughly 65 % efficiency.

Which TCA intermediate is missing in certain anaerobic bacteria, causing them to use an incomplete cycle?

α-Ketoglutarate dehydrogenase (thus they cannot convert α-ketoglutarate to succinyl-CoA).

Define 'amphibolic' in the context of the citric acid cycle.

The cycle functions in both catabolism (energy production) and anabolism (providing precursors for biosynthesis).

What term describes reactions that replenish TCA intermediates removed for biosynthesis?

Anaplerotic reactions.

Name the two unique enzymes of the glyoxylate cycle that bypass the CO₂-releasing steps of the TCA cycle.

Isocitrate lyase and malate synthase.

Why is the glyoxylate cycle important for germinating oil-rich seeds?

It allows conversion of acetyl-CoA from fatty acid β-oxidation into succinate, which can enter gluconeogenesis to produce sugars needed for growth.

Which three TCA enzymes are considered primary rate-controlling points?

Citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase.

How do high NADH/NAD⁺ ratios generally affect the TCA cycle?

They inhibit several dehydrogenases, slowing the cycle.

Explain how product inhibition regulates citrate synthase.

Citrate, the product, competes with oxaloacetate for binding, reducing enzyme activity when citrate accumulates.

Which cellular signal directly activates mitochondrial isocitrate dehydrogenase via allosteric binding?

ADP (or AMP), indicating low energy status.

What is substrate channeling, and where is it exemplified in central metabolism?

Direct transfer of intermediates between active sites without diffusion; exemplified in the PDC and α-ketoglutarate dehydrogenase complexes.

Which human diseases or historical deaths were linked to chronic arsenic exposure via Fowler’s solution?

Charles Darwin’s prolonged illness/death and speculation regarding Napoleon Bonaparte.

Describe the biochemical basis of beriberi’s neurological symptoms.

Thiamine deficiency limits PDC activity, hindering ATP production in neurons that rely heavily on aerobic glucose oxidation.

Which TCA intermediate serves as the primary precursor for heme biosynthesis?

Succinyl-CoA.

What is the fate of the two carbons that enter the TCA cycle as acetyl-CoA during one turn of the cycle?

They are oxidized to two CO₂ molecules, but the specific acetyl carbons usually appear as CO₂ in later cycles.

How does calcium (Ca²⁺) coordinate muscle contraction with energy supply through the TCA cycle?

Ca²⁺ activates PDH phosphatase and directly stimulates isocitrate dehydrogenase and α-ketoglutarate dehydrogenase, increasing NADH production for ATP synthesis.

Which TCA cycle step constitutes substrate-level phosphorylation, producing a nucleoside triphosphate without the electron-transport chain?

Conversion of succinyl-CoA to succinate by succinyl-CoA synthetase.

Why does removal of oxaloacetate for gluconeogenesis slow the TCA cycle, and how do cells compensate?

Oxaloacetate is required to condense with acetyl-CoA; cells replenish it via anaplerotic reactions such as pyruvate carboxylase.

Which small molecule is an allosteric inhibitor of both isocitrate dehydrogenase and α-ketoglutarate dehydrogenase, linking TCA flux to the energy state?

ATP (or high NADH).