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.

• Enzymes: Each step is catalyzed by a specific enzyme (e.g., citrate synthase, isocitrate dehydrogenase).

• Substrates and Products: Key substrates include acetyl-CoA and oxaloacetate; products include CO2, NADH, FADH2, and GTP/ATP.

• Structures: Students should be able to draw the structures of main intermediates (e.g., citrate, α-ketoglutarate, succinate).

Reactions Feeding Into and Out of the TCA Cycle

Several metabolic pathways intersect with the TCA cycle, allowing for the exchange of metabolites between the mitochondrial matrix and the cytosol.

• Phosphoenolpyruvate Transporter: Moves phosphoenolpyruvate (PEP) across the mitochondrial membrane.

• Malate-Aspartate Shuttle: Transfers reducing equivalents (NADH) from the cytosol into the mitochondria.

• Tricarboxylic Acid Transporter: Facilitates the movement of TCA intermediates.

• Glyoxylate Cycle: A variation of the TCA cycle in plants and some microorganisms, allowing net synthesis of glucose from acetyl-CoA.

Thermodynamics of the TCA Cycle

The direction and spontaneity of TCA cycle reactions depend on free energy changes.

• Standard Free Energy (ΔG°') vs. Cellular Free Energy (ΔG): ΔG°' is measured under standard conditions; ΔG reflects actual cellular conditions.

• Equilibrium Constant (K) and Reaction Quotient (Q): The relationship between K and Q determines reaction direction.

Regulation of the TCA Cycle

• Substrate Concentration: Levels of acetyl-CoA, oxaloacetate, and NAD+ affect cycle rate.

• Energy Charge: High ATP/ADP ratio inhibits the cycle; high ADP stimulates it.

• Allosteric Regulation: Key enzymes are regulated by effectors (e.g., NADH inhibits isocitrate dehydrogenase).

• Phosphorylation: Some enzymes are regulated by reversible phosphorylation.

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 oxygen, generating a proton gradient.

• Complexes I-IV: Each complex has a specific role in electron transfer and proton pumping.

• Electron Carriers: NADH, FADH2, ubiquinone (Q), and cytochrome c shuttle electrons between complexes.

• Proton Transfer: Electron flow is coupled to proton movement from the matrix to the intermembrane space.

Oxidative Phosphorylation

• Substrate-Level vs. Oxidative Phosphorylation: Substrate-level phosphorylation generates ATP directly in metabolic reactions; oxidative phosphorylation uses the proton gradient to drive ATP synthesis.

• ATP Synthase (F0F1-ATPase): Enzyme complex that synthesizes ATP as protons flow back into the matrix.

• Regulation: ATP synthesis is regulated by ADP availability and the proton gradient.

• Free Energy Calculations: The energy stored in the proton gradient can be calculated using the Nernst equation.

Lipid Metabolism

Mobilization of Fatty Acids

• Source: Triacylglycerols stored in adipose tissue.

• Digestion and Transport: Fatty acids are released, transported in the blood (bound to albumin), and taken up by tissues.

• Storage and Utilization: Fatty acids are stored as triacylglycerols and mobilized for energy production.

Fatty Acid Activation and Beta-Oxidation

• Acyl-CoA Synthetase: Activates fatty acids by attaching CoA, forming acyl-CoA.

• Beta-Oxidation: Sequential removal of two-carbon units as acetyl-CoA.

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

• Substrates and Products: Fatty acyl-CoA, FADH2, NADH, acetyl-CoA.

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

Fatty Acid Synthesis vs. Degradation

Ketone Bodies

• Formation: Acetyl-CoA is converted into acetoacetate, β-hydroxybutyrate, and acetone during fasting or diabetes.

• Function: Serve as alternative energy sources for brain and muscle.

Regulation of Lipid Metabolism

• Malonyl-CoA: Inhibits carnitine shuttle, preventing fatty acid oxidation during synthesis.

• Carnitine Shuttle: Transports fatty acyl-CoA into mitochondria for 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 and Chlorophylls: Absorb light energy; chlorophyll a is the primary pigment.

• Light Absorption: Excites electrons, initiating electron transfer chains.

Photosystems and Electron Transfer

• Photosystem II (PSII): Absorbs light, splits water, and transfers electrons to plastoquinone.

• Photosystem I (PSI): Receives electrons, further excites them, and reduces NADP+ to NADPH.

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

• Source of Electrons: Water (non-cyclic); recycled electrons (cyclic).

• Ultimate Electron Acceptor: NADP+ (non-cyclic); PSI (cyclic).

• Proton Gradient: Electron flow is coupled to proton pumping, generating a gradient for ATP synthesis.

Organization and Energy Calculations

• Thylakoid Membranes: Photosystems are organized in the thylakoid membranes of chloroplasts.

• Free Energy: Light energy is converted into chemical energy, and the resulting proton gradient can be quantified.

Calvin Cycle (Dark Reactions)

• Three Stages: Carbon fixation, reduction, and regeneration of ribulose-1,5-bisphosphate.

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

Nitrogen and Amino Acid Metabolism

Nitrogen Fixation

• Fundamentals: Conversion of atmospheric N2 to NH3 by nitrogenase enzyme complex.

• Rhizobium/Plant Symbiosis: Bacteria in root nodules fix nitrogen for plants in exchange for nutrients.

Amino Acid Biosynthesis

• Biosynthetic Families: Amino acids are grouped by their metabolic precursors (e.g., α-ketoglutarate, oxaloacetate).

• Transamination: Transfer of amino groups between amino acids and α-keto acids, catalyzed by aminotransferases.

• General Reaction:

• Essential vs. Non-Essential Amino Acids: Essential amino acids cannot be synthesized by humans and must be obtained from the diet.

Amino Acid Degradation

• Ketogenic Amino Acids: Degraded to acetyl-CoA or acetoacetate (e.g., leucine, lysine).

• Glucogenic Amino Acids: Degraded to pyruvate or TCA cycle intermediates (e.g., alanine, glutamine).

• Classification Table:

Nitrogen Transport and the Urea Cycle

• Nitrogen Transport: Nitrogen is transported as glutamine or alanine from tissues to the liver.

• Nitrogen Assimilation: Incorporation of ammonia into amino acids (e.g., glutamate, glutamine).

• Glucose-Alanine Cycle: Transfers amino groups from muscle to liver for urea synthesis.

• Urea Cycle: Converts toxic ammonia to urea for excretion; occurs in hepatocytes, with reactions in both the mitochondrial matrix and cytosol.

• Inputs: Ammonia, CO2, aspartate.

• Outputs: Urea, fumarate.

• Key Intermediates: Carbamoyl phosphate, citrulline, argininosuccinate, arginine, ornithine.