Citric Acid Cycle

Pyruvate dehydrogenase (overall reaction)

Pyruvate → Acetyl-CoA + CO₂ + NADH

Location of PDH complex

Eukaryotes: mitochondrial matrix; Prokaryotes: cytosol

Purpose of PDH complex

Links glycolysis to the TCA cycle by producing acetyl-CoA

PDH E1 enzyme

Pyruvate dehydrogenase; requires TDP (thiamine pyrophosphate)

PDH E2 enzyme

Dihydrolipoamide acetyltransferase; uses lipoamide swinging arm

PDH E3 enzyme

Dihydrolipoamide dehydrogenase; uses FAD and NAD⁺

PDH cosubstrates

CoA and NAD⁺

PDH prosthetic groups

TDP, lipoamide, FAD

Role of lipoamide in PDH

Swinging arm transferring intermediates between enzymes

Energy coupling in PDH

Oxidation of pyruvate to CO₂ coupled to reduction of NAD⁺ → NADH

Coenzyme order in PDH

TDP → lipoamide → CoA → FAD → NAD⁺

Regulation of PDH

Phosphorylation by PDH kinase inactivates E1; dephosphorylation activates

Significance of PDH

Controls entry of pyruvate into aerobic metabolism

Electron flow in PDH

Pyruvate → TDP → lipoamide → FAD → NAD⁺

Location of E2 core in PDH

Pentagonal dodecahedron of 60 E2 subunits (eukaryotes)

TCA cycle purpose

Oxidize acetyl-CoA to CO₂ and produce NADH, FADH₂, and GTP

TCA cycle discovery

Hans Krebs (1930s)

Where CO₂ in TCA comes from

Not from acetyl-CoA directly in first turn; from oxaloacetate

Citrate synthase reaction

Oxaloacetate + Acetyl-CoA → Citrate + CoA-SH

Why citrate synthase is a synthase

Does not require ATP

Aconitase function

Citrate ↔ cis-Aconitate ↔ Isocitrate

Aconitase cofactor

Contains [4Fe-4S] iron-sulfur cluster

Isocitrate dehydrogenase reaction

Isocitrate → α-ketoglutarate + CO₂ + NADH

Steps of isocitrate dehydrogenase

Oxidation → decarboxylation

Isocitrate dehydrogenase regulation

Activated: ADP, Ca²⁺; Inhibited: NADH

α-ketoglutarate dehydrogenase reaction

α-ketoglutarate → Succinyl-CoA + CO₂ + NADH

α-KG dehydrogenase similarity

Structurally similar to PDH; 3-enzyme complex

Succinyl-CoA synthetase reaction

Succinyl-CoA → Succinate + GTP/ATP (substrate-level phosphorylation)

Succinate dehydrogenase reaction

Succinate → Fumarate + FADH₂

Succinate dehydrogenase unique

Part of both TCA and ETC (Complex II)

Succinate dehydrogenase inhibitor

Malonate (competitive inhibitor)

Fumarase reaction

Fumarate + H₂O → Malate (stereospecific)

Malate dehydrogenase reaction

Malate → Oxaloacetate + NADH

Why malate dehydrogenase proceeds forward

Mass action; high malate levels

Pyruvate transport into mitochondria

Pyruvate-H⁺ symport via pyruvate translocase

Citrate export purpose

Fatty acid synthesis (cleaved into Acetyl-CoA in cytosol)

ATP per NADH

~2.5 ATP

ATP per FADH₂ (ubiquinone)

~1.5 ATP

ATP per acetyl-CoA oxidized

~10 ATP

ATP per glucose (glycolysis + TCA)

~32 ATP

PDH regulation summary

Activated by dephosphorylation; inhibited by PDH kinase

Citrate synthase regulation

Inhibited by ATP, NADH (bacteria); activated by α-ketoglutarate

Isocitrate dehydrogenase bacterial regulation

Also regulated by phosphorylation

α-KG dehydrogenase regulation

Activated by Ca²⁺ (lowers Km)

TCA cycle description

Amphibolic (catabolic + anabolic)

Anaplerotic definition

Replenish TCA intermediates

Cataplerotic definition

Remove TCA intermediates for biosynthesis

Examples of anabolic uses of TCA intermediates

Citrate → lipids; α-KG → glutamate; Succinyl-CoA → porphyrins; OAA → aspartate

Glyoxylate cycle purpose

Bypasses CO₂-producing steps to allow net glucose synthesis from acetyl-CoA

Glyoxylate cycle key enzymes

Isocitrate lyase and malate synthase

Organisms with glyoxylate cycle

Bacteria, plants (glyoxysomes), fungi, protists, some animals

Energy yield: PDH + TCA from one pyruvate

~12.5 ATP

Energy yield: PDH + TCA from one glucose

~25 ATP (+glycolysis = ~32 total)

Evolutionary origin of TCA enzymes

Malate DH from LDH; Aconitase & IDH from leucine enzymes