13: Citric Acid Cycle

• plays central role in metabolism/catabolic reactions (synthesis of ATP)

• important source of carbon skeletons for biosynthetic reactions

TCA cycle

pyruvate dehydrogenase complex performs oxidative decarboxylation

pyruvate —> acetyl-CoA

1. Build high energy bond to be harvested for later

2. Prevent small molecule from leaving matrix and going back to cytosol

Why are thioester bonds created with CoA?

carrier of activated acyl groups: acyl groups form high energy thioester bonds which activates acyl groups

CoA

1. Pyruvate dehydrogenase (E₁)

2. Dihydrolipoyl transacetylase (E₂)

3. Dihydrolipoyl dehydrogenase (E₃)

Pyruvate dehydrogenase complex components

• Each enzyme does different catalytic activity

• Channel product of 1 rxn to become substrate of next rxn —> substrate channeling

Pyruvate dehydrogenase

mitochondrial matrix

Where does TCA cycle take place?

• STEP 1: Acetyl-CoA + OAA —> Citrate (Claisen condensation)

• STEP 3: Isocitrate —> α-ketoglutarate (Oxidative decarboxylation)

• STEP 4: α-ketoglutarate —> Succinyl-CoA (oxidative decarboxylation)

ALL exergonic

Important TCA cycle

• 3 NADH

• 1 FADH₂

• 1 GTP (ATP)

For every turn of the TCA cycle:

• NADH: steps 3, 4, and 8

• FADH₂: step 6

• GTP (ATP): step 5

Which steps produce NADH/FADH₂ and GTP (ATP)

citrate, since OAA (C₄) + Acetyl-CoA (C₂) —> Citrate (C₆)

What is the tricarboxylic acid in the TCA cycle

malonate

competitive inhibitor of succinate dehydrogenase

OAA, # intermediates available

TCA cycle limiting factor

amphibolic

both catabolic and anabolic

central pathway = catabolic, but key intermediate metabolites can be used to make other metabolites = anabolic

How is the TCA cycle amphibolic

Anaplerotic reactions

metabolic "filling-up" processes that replenish citric acid cycle (TCA cycle) intermediates

2

How many CO₂ released per acetyl entry?

Bicarbonate + pyruvate —pyruvate carboxylase—> OAA

Anaplerosis of pyruvate carboxylase

• TCA —> need more ATP

• Gluconeogenesis —> sufficient ATP, can do biosynthesis

• dependent on Acetyl-CoA concentration

  • High acetyl-CoA conc. = TCA full and no need to make more ATP

pyruvate: TCA or gluconeogenesis

• Activators: AMP, CoA, NAD⁺, and Ca²⁺

• Inhibitors: ATP, Acetyl-CoA, NADH

Regulation of pyruvate dehydrogenase complex

• Activators: ADP

• Inhibitors: NADH, succinyl-CoA, citrate, ATP

Regulation of citrate synthase

• phosphorylation inhibits activity

• Glucagon activates kinase and inhibits PDH

• Insulin activates phosphatase and activates PDH

Pyruvate dehydrogenase complex inhibition vs activation