Tricarboxylic Acid (TCA) Cycle

Overview of the TCA Cycle

The Tricarboxylic Acid (TCA) Cycle, also known as the Citric Acid Cycle or Krebs Cycle, is a central metabolic pathway that oxidizes acetyl-CoA to CO2 and generates high-energy electron carriers (NADH, FADH2) for ATP production.

• Location: Mitochondrial matrix

• Main function: Energy production and provision of biosynthetic intermediates

• Inputs: Acetyl-CoA, NAD+, FAD, GDP, Pi, H2O

• Outputs: CO2, NADH, FADH2, GTP (or ATP), CoA-SH

TCA Cycle Reactions and Enzymes

• Key reactions: The cycle consists of eight main steps, each catalyzed by a specific enzyme.

• Substrates and products: Each step transforms a substrate into a product, often with the release of CO2 or reduction of NAD+/FAD.

• Structures: Students should be able to draw the structures of key intermediates (e.g., citrate, isocitrate, α-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, oxaloacetate).

Reactions Feeding Into and Out of the TCA Cycle

• Anaplerotic reactions: Replenish TCA intermediates (e.g., pyruvate carboxylase forms oxaloacetate).

• Cataplerotic reactions: Remove intermediates for biosynthesis (e.g., citrate for fatty acid synthesis).

• Transporters:

  • Phosphoenolpyruvate transporter: Moves PEP across mitochondrial membrane.

  • Malate-aspartate shuttle: Transfers reducing equivalents (NADH) between cytosol and mitochondria.

  • Tricarboxylic acid transporter: Exchanges TCA intermediates across membranes.

Glyoxylate Cycle

The glyoxylate cycle is a variation of the TCA cycle in plants, bacteria, and fungi, allowing net conversion of acetyl-CoA to succinate for gluconeogenesis.

• Key enzymes: Isocitrate lyase and malate synthase

• Bypasses: Decarboxylation steps of TCA, conserving carbon

Thermodynamics: Standard vs. Cellular Free Energies

• Standard free energy change (ΔG°'): Free energy change under standard conditions.

• Cellular free energy change (ΔG): Actual free energy change in the cell, depends on concentrations.

• Relationship:

• K (equilibrium constant) and Q (reaction quotient): Direction of reaction depends on comparison of Q to K.

Regulation of the TCA Cycle

• Substrate availability: Acetyl-CoA, oxaloacetate, NAD+

• Energy charge: ATP/ADP ratio regulates key enzymes

• Allosteric regulation: Enzymes like isocitrate dehydrogenase are activated/inhibited by metabolites

• Phosphorylation: Modifies enzyme activity (e.g., pyruvate dehydrogenase complex)

Electron Transport and Oxidative Phosphorylation

Electron Transport Chain (ETC)

The Electron Transport Chain is a series of protein complexes (I-IV) in the inner mitochondrial membrane that transfer electrons from NADH and FADH2 to O2, generating a proton gradient.

• Complex I: NADH:ubiquinone oxidoreductase

• Complex II: Succinate dehydrogenase

• Complex III: Cytochrome bc1 complex

• Complex IV: Cytochrome c oxidase

• Electron carriers: NADH, FADH2, ubiquinone (Q), cytochrome c

• Proton transfer: Electron flow is coupled to proton pumping, creating an electrochemical gradient

Oxidative Phosphorylation

• Substrate-level phosphorylation: Direct ATP synthesis via enzyme-catalyzed reactions (e.g., in glycolysis, TCA cycle)

• Oxidative phosphorylation: ATP synthesis driven by the proton gradient via ATP synthase (F0F1-ATPase)

• ATP Synthase: Uses proton motive force to convert ADP + Pi to ATP

• Regulation: Controlled by ADP availability and proton gradient

• Free energy calculation: and

Lipid Metabolism

Mobilization of Fatty Acids

• Source: Triacylglycerols in adipose tissue

• Digestion and transport: Lipases hydrolyze triacylglycerols; fatty acids transported in blood bound to albumin

• Storage/utilization: Fatty acids stored as triacylglycerols; mobilized for β-oxidation

Fatty Acid Activation and β-Oxidation

• Acyl-CoA synthetase: Activates fatty acids to acyl-CoA (requires ATP)

• β-oxidation: Sequential removal of two-carbon units as acetyl-CoA

• Enzymes: Acyl-CoA dehydrogenase, enoyl-CoA hydratase, hydroxyacyl-CoA dehydrogenase, thiolase

• Substrates/products: Fatty acyl-CoA → acetyl-CoA, NADH, FADH2

• Carbon oxidation states: Students should be able to determine oxidation states of carbons in intermediates

Fatty Acid Synthesis vs. Degradation

Ketone Bodies

• Produced from: Acetyl-CoA in liver mitochondria during fasting or diabetes

• Main products: Acetoacetate, β-hydroxybutyrate, acetone

Regulation of Lipid Metabolism

• Malonyl-CoA: Inhibits carnitine shuttle, preventing fatty acid entry into mitochondria

• Carnitine shuttle: Transports fatty acyl-CoA into mitochondria for β-oxidation

• Acetyl-CoA Carboxylase (ACC): Key regulatory enzyme in fatty acid synthesis; regulated by phosphorylation and allosteric effectors

Photosynthesis: Light and Dark Reactions

Capture of Light Energy

• Pigments: Chlorophylls and accessory pigments absorb light energy

• Mechanism: Absorbed light excites electrons, initiating electron transfer

Photosystems and Electron Transfer

• Photosystem II (PSII): Oxidizes water, releases O2, transfers electrons to plastoquinone

• Photosystem I (PSI): Transfers electrons to NADP+ to form NADPH

• Cyclic vs. non-cyclic electron flow: Cyclic generates ATP only; non-cyclic produces both ATP and NADPH

• Source of electrons: Water (non-cyclic), recycled electrons (cyclic)

• Ultimate electron acceptor: NADP+ (non-cyclic)

• Proton gradient: Electron flow drives proton pumping, generating ATP via ATP synthase

Organization of Photosystems

• Location: Thylakoid membranes of chloroplasts

• Arrangement: PSII and PSI are spatially separated but functionally linked

Calvin Cycle (Dark Reactions)

• Three stages: Carbon fixation, reduction, regeneration of RuBP

• Rubisco: Catalyzes CO2 fixation; regulated by pH, Mg2+, and activator proteins

Nitrogen and Amino Acid Metabolism

Nitrogen Fixation

• Process: Conversion of atmospheric N2 to NH3 by nitrogenase

• Symbiosis: Rhizobium bacteria fix nitrogen in association with plant roots

Amino Acid Biosynthesis

• Biosynthetic families: Grouped by precursor metabolites (e.g., α-ketoglutarate, oxaloacetate)

• Transamination: Transfer of amino group from amino acid to α-keto acid

  • General reaction:

  • Enzyme: Aminotransferase (requires PLP cofactor)

• Essential vs. non-essential amino acids: Essential must be obtained from diet; non-essential can be synthesized

Amino Acid Degradation

• Ketogenic amino acids: Degraded to acetyl-CoA or acetoacetate (can form ketone bodies)

• Glucogenic amino acids: Degraded to pyruvate or TCA intermediates (can form glucose)

• Classification table:

Nitrogen Transport and the Urea Cycle

• Nitrogen transport: Carried as glutamine or alanine in blood

• Glutamate and glutamine: Central in nitrogen assimilation and transport

• Glucose-alanine cycle: Transfers amino groups from muscle to liver

• Urea cycle: Converts toxic NH3 to urea for excretion

  • Location: Hepatocytes (mitochondrial matrix and cytosol)

  • Inputs: NH3, CO2, aspartate

  • Outputs: Urea, fumarate

  • Key intermediates: Carbamoyl phosphate, citrulline, argininosuccinate, arginine, ornithine

Example: The urea cycle is essential for detoxifying ammonia produced during amino acid catabolism, especially in terrestrial vertebrates.