TCA Cycle

Flashcards covering PDH, TCA cycle, regulation, energy yield, anaplerosis, nitrogen metabolism, and related diseases.

What is the main function of the pyruvate dehydrogenase (PDH) complex?

It converts pyruvate to acetyl-CoA, linking glycolysis to the TCA cycle.

Is PDH part of the TCA cycle itself?

No; PDH is not part of the TCA cycle but provides acetyl-CoA for it.

Name the three catalytic components of the PDH complex.

E1 (pyruvate dehydrogenase), E2 (dihydrolipoamide acetyltransferase), E3 (dihydrolipoamide dehydrogenase).

What are the substrates of the PDH reaction?

Pyruvate, NAD+, and CoA.

What are the products of the PDH reaction?

Acetyl-CoA, CO2, and NADH.

Which cofactor is used by E1 of PDH?

Thiamine pyrophosphate (TPP).

What cofactors are used by E2 and E3 in PDH?

E2 uses lipoic acid and CoA; E3 uses FAD and NAD+.

Which vitamin is thiamine classified as?

Vitamin B1.

List the five PDH cofactors in order.

TPP, lipoic acid, CoA, FAD, NAD+.

How is PDH activity regulated by phosphorylation?

PDH kinase inhibits E1; PDH phosphatase activates E1.

What activates PDH kinase?

ATP, acetyl-CoA, and NADH (high-energy signals).

What effect does pyruvate have on PDH kinase?

Pyruvate inhibits PDH kinase, activating PDH.

How does Ca2+ influence PDH regulation in skeletal muscle?

Ca2+ activates PDH phosphatase, which activates PDH.

Where does PDH occur in the cell?

In mitochondria.

What happens to pyruvate if PDH is inhibited?

It is shunted to lactate via LDH, causing lactic acidosis.

What are the consequences of PDH deficiency?

Congenital lactic acidosis with brain being particularly sensitive.

How is PDH deficiency inherited?

E1 is an X-linked gene; brain sensitivity makes the phenotype resemble X-linked dominant.

Is there a proven treatment for PDH deficiency?

No proven treatment.

How does arsenic poisoning affect PDH?

Arsenite inhibits lipoic acid–dependent enzymes (including PDH) by forming a stable complex with lipoic acid.

Where is the TCA cycle located?

In the mitochondria.

What are alternate names for the TCA cycle?

Tricarboxylic acid cycle and Krebs cycle.

What is the primary function of the TCA cycle?

To transfer energy from acetyl-CoA to NADH, FADH2, and GTP, and to provide biosynthetic precursors.

How does acetyl-CoA enter the TCA cycle?

Acetyl-CoA condenses with oxaloacetate to form citrate.

How many CO2 are released per acetyl-CoA during Part I of the cycle?

Two CO2.

How many NADH are produced in Part I of the cycle?

Two NADH.

What happens in Part II of the cycle?

Regenerate oxaloacetate; produce NADH and FADH2.

Which enzyme catalyzes the condensation of acetyl-CoA and oxaloacetate?

Citrate synthase.

Which substrate binds citrate synthase to promote acetyl-CoA binding?

Oxaloacetate binds to citrate synthase to create a site for acetyl-CoA.

What inhibits citrate synthase?

Citrate, NADH, and succinyl-CoA.

Which enzyme converts citrate to isocitrate?

Aconitase.

Which compound inhibits aconitase?

Fluoroacetate.

What is the first NADH-producing step in the TCA cycle?

Isocitrate dehydrogenase (Step 3).

What activates isocitrate dehydrogenase?

ADP and Ca2+.

What inhibits isocitrate dehydrogenase?

ATP and NADH.

Which enzyme catalyzes the oxidation of α-ketoglutarate?

α-Ketoglutarate dehydrogenase.

What coenzymes are shared with PDH for α-ketoglutarate dehydrogenase?

Thiamine (B1), lipoic acid, CoA, FAD, NAD.

What inhibits α-ketoglutarate dehydrogenase?

ATP, NADH, and succinyl-CoA.

What activates α-ketoglutarate dehydrogenase?

Ca2+ (muscle contraction).

What does succinyl-CoA synthetase produce?

GTP (which is converted to ATP).

What type of phosphorylation occurs at the succinyl-CoA synthetase step?

Substrate-level phosphorylation.

Which enzyme is Complex II of the ETC?

Succinate dehydrogenase.

What does succinate dehydrogenase produce?

FADH2.

Which enzyme hydrates fumarate?

Fumarase.

What does malate dehydrogenase produce?

NADH.

What is produced per acetyl-CoA in the TCA cycle in energy terms?

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

What is the total ATP yield per acetyl-CoA if NADH=3 ATP and FADH2=2 ATP?

12 ATP.

What is the typical total ATP yield per glucose via TCA and oxidative phosphorylation (with the standard shuttle assumptions)?

About 36–38 ATP per glucose (variable with shuttle).

Which shuttle yields fewer ATP in brain and skeletal muscle?

Glycerol phosphate shuttle.

Which shuttle yields more ATP?

Malate–aspartate shuttle (higher ATP yield per NADH).

Which intermediate is a key gluconeogenic precursor in TCA?

Oxaloacetate.

Which enzyme replenishes oxaloacetate from pyruvate in anaplerotic reactions?

Pyruvate carboxylase.

What cofactors does pyruvate carboxylase require?

Biotin, ATP, Mg2+.

What activates pyruvate carboxylase?

Acetyl-CoA.

Besides PDH, what other PDH-like enzyme participates in anaplerosis?

Pyruvate carboxylase (anaplerotic) and amino acids (alanine, serine).

Which amino acids provide anaplerotic inputs?

Alanine and serine (and other amino acids via various routes).

What genetic diseases are linked to TCA cycle and related pathways?

Leigh syndrome; PDH deficiency; PC deficiency; Beriberi and Wernicke–Korsakoff (thiamine deficiency).

Which diseases are associated with thiamine deficiency?

Beriberi disease and Wernicke–Korsakoff syndrome.

Which vitamins are involved as cofactors for PDH and α-ketoglutarate dehydrogenase?

Thiamine (Vitamin B1).

What is Leigh syndrome in context of metabolism?

A subacute necrotizing encephalomyelopathy that can be caused by PDH or PC defects among others.

What happens to pyruvate in PDH deficiency?

Pyruvate is shunted to lactate, causing lactic acidosis.

Which type of inheritance is noted for PDH deficiency due to brain sensitivity?

X-linked (often described as X-linked dominant due to brain sensitivity).

What is a key neurological symptom associated with lactic acidosis from PDH deficiency?

Neurological damage from lactic acidemia.

Which vitamin is deficient in Beriberi and Wernicke–Korsakoff syndromes?

Thiamine (Vitamin B1).

What is the urea cycle’s primary purpose?

To dispose of excess nitrogen as urea.

Where does the urea cycle primarily occur?

In the liver.

What is the first substrate formed in the urea cycle?

Carbamoyl phosphate is formed from NH4+ and CO2 by CPS I.

Which intermediate enters the urea cycle from the TCA cycle via aspartate?

Aspartate (from oxaloacetate via transamination).

List the urea cycle intermediates in order.

Ornithine → Citrulline → Argininosuccinate → Arginine → Urea.

Which enzyme forms citrulline from ornithine?

Ornithine transcarbamylase.

What connects TCA intermediates to nucleotide biosynthesis?

TCA intermediates provide precursors for purines and pyrimidines; oxaloacetate and α-ketoglutarate intermediates contribute to amino acid and nucleotide synthesis.

What is anaplerosis?

Replenishment of TCA cycle intermediates.

Which enzyme is the primary anaplerotic enzyme replenishing oxaloacetate from pyruvate?

Pyruvate carboxylase.

Which cofactor is used by pyruvate carboxylase as a biotin-dependent enzyme?

Biotin.

Which two amino acids are mentioned as replenishing TCA intermediates via degradation?

Alanine and serine.

What is the role of the glycerol phosphate shuttle in energy metabolism?

Transports cytosolic NADH into mitochondria, yielding less ATP per NADH.

Which tissue uses the glycerol phosphate shuttle predominantly?

Brain and skeletal muscle.

Which intermediate is a precursor to heme and porphyrins?

Succinyl-CoA.

Which intermediate feeds purine and pyrimidine synthesis?

Glutamate and related intermediates; TCA links provide carbon skeletons for nucleotide biosynthesis.

Which two key TCA enzymes are most important regulators of flux?

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

What regulates flux through the TCA cycle at the whole-cell level?

Regulation at rate-limiting steps, feedback inhibition, compartmentation, and hormonal regulation.

What molecule directly inhibits citrate synthase as part of feedback?

Citrate (product) and high-energy signals (NADH, ATP).

Which TCA enzyme is inhibited by fluoroacetate?

Aconitase.

Which step in the TCA releases CO2 and yields the first NADH?

Isocitrate dehydrogenase (Step 3).

Which step in the TCA releases CO2 and yields the second NADH?

α-Ketoglutarate dehydrogenase (Step 4).

Which enzyme produces the third NADH in the cycle?

Malate dehydrogenase (Step 8).

Which enzyme produces the FADH2 in the cycle?

Succinate dehydrogenase (Step 6).

Which step in the cycle forms citrate from acetyl-CoA and oxaloacetate?

Citrate synthase (Step 1).

At which step is NADH produced for the first time in the cycle?

Step 3 (isocitrate dehydrogenase).

Which step is the site of substrate-level phosphorylation in the cycle?

Step 5 (succinyl-CoA synthetase) producing GTP.

What is the overall energy yield per acetyl-CoA when using the 3 NADH, 1 FADH2, and 1 GTP assumption?

12 ATP.

What is the common energy yield per glucose under aerobic metabolism?

Typically about 36–38 ATP per glucose (dependent on shuttle).

What is the fate of NADH produced by PDH and the TCA in the cell?

They donate electrons to the electron transport chain to generate ATP.

Which step of the PDH uses a 3-carbon substrate and yields a 2-carbon product?

PDH converts 3C pyruvate to 2C acetyl-CoA, releasing CO2.

Which enzyme complex contains E1, E2, and E3?

The pyruvate dehydrogenase complex (PDH).

What is the role of oxaloacetate besides entering the cycle?

Oxaloacetate is a gluconeogenic precursor and a substrate for citrate synthesis.

Where do oxidative decarboxylations occur in the TCA cycle?

During Step 3 (isocitrate → α-ketoglutarate) and Step 4 (α-ketoglutarate → succinyl-CoA).

What is the first committed step of the TCA cycle?

Citrate synthase reaction (condensation of acetyl-CoA with oxaloacetate).

Which amino acid can donate an amino group to oxaloacetate to form aspartate?

Aspartate (via transamination of oxaloacetate).

Which two major biosynthetic pathways depend on TCA cycle intermediates for carbon skeletons?

Nucleotide biosynthesis (purines/pyrimidines) and amino acid synthesis.

Which disease is commonly linked to thiamine deficiency and PDH impairment?

Beriberi and Wernicke–Korsakoff syndrome.