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Energy, Catalysis, and Biosynthesis

Oxidation and Reduction in Organic Molecules

• Polar Covalent Bonds:

  • When carbon forms a polar covalent bond, it can acquire partial positive (δ+) and negative charges (δ–), indicating oxidation and reduction, respectively.

  • Example:

    • Carbon in a C-H bond holds more electrons and is reduced (δ–).

    • When a molecule gains an electron (and often a proton) in a reaction, it is reduced (e.g., A + e– + H+ → AH).

• Counting C-H Bonds:

  • Oxidation occurs with fewer C-H bonds; reduction occurs with more C-H bonds.

• Reactions Involving Electrons:

  • Hydrogenation reactions add hydrogen (reduction); dehydrogenation reactions remove hydrogen (oxidation).

Role of Enzymes in Catalysis

• Second Law of Thermodynamics:

  • Enzymes can accelerate favorable reactions but cannot drive unfavorable ones without an energy input.

  • Cells need to build complex molecules from simpler ones, which requires energy input.

• Free Energy and Reactions:

  • Free energy changes determine the spontaneity of reactions:

    • Energetically favorable reactions produce disorder and lead to a loss of free energy.

  • Enzymes lower the activation energy required for reactions, making processes faster and more efficient.

Thermodynamics of Reactions

• Chemical Reactions Direction:

  • Reactions favor those that result in lowering free energy (negative ΔG) and increasing disorder.

• Example Reaction:

  • Combustion of paper releases energy and products (smoke, CO2, H2O) and proceeds in one direction.

  • Dust and gas mixture at higher order cannot spontaneously revert to paper.

Activation Energy and Enzymes

• Activation Energy Requirements:

  • Live organisms don't spontaneously combust; they require energy to overcome activation energy barriers.

  • Enzymes facilitate lower activation energy, accelerating both the forward and reverse reactions equally.

• Reaction Energetics:

  • Two reactions X → Y (unfavorable, ΔG > 0) and Y → Z (favorable, ΔG < 0) can be coupled due to the overall negative ΔG of the sequence.

Equilibrium and Free Energy

• Chemical Equilibrium:

  • At equilibrium, the forward and reverse reactions occur at equal rates, resulting in a ΔG of 0.

  • Living cells avoid equilibrium by constantly exchanging materials and rerouting metabolic pathways.

• Standard Free Energy Change (ΔG°):

  • Measures energy changes under standard conditions, independent of concentration. Helps predict reaction spontaneity and how far from equilibrium a reaction can be.

Coupled Reactions and Energy Management

• Linking Energetically Unfavorable Reactions:

  • Reactions can be driven by coupling an unfavorable reaction with a highly favorable one, allowing biological processes to proceed efficiently.

• Example of Coupled Reactions:

  • A reaction pathway converting substrates into products can utilize the favorable ΔG of one reaction to drive another unfavorable reaction.

Enzyme Performance Metrics

• Michaelis Constant (KM):

  • The concentration of substrate at which an enzyme operates at half its maximum rate (Vmax).

  • A low KM indicates tight substrate binding, while a high KM indicates weak binding.

• Competitive Inhibition:

  • An inhibitor mimics substrate binding, blocking the active site but can be overcome by increasing substrate concentration.

Understanding Enzyme Efficiency

• Enzyme Kinetics:

  • Max velocity (Vmax) and KM are vital for understanding how enzymes perform under various conditions.

  • The efficiency of an enzyme can be measured by observing how quickly it converts substrates into products under different substrate concentrations.