Study Unit 8: Energy, Enzymes and Metabolism Notes

Energy, Enzymes, and Metabolism

Lecture 1: Introduction to Metabolism and Thermodynamics

• Metabolism Definition: The sum total of all chemical reactions occurring in a biological system.
• Functions of Metabolism:
  • Obtaining chemical energy from nutrient degradation or solar energy capture.
  • Converting nutrients into building block precursors for macromolecules.
  • Assembling building blocks into proteins, nucleic acids, lipids, and polysaccharides.
  • Forming and degrading biomolecules for specialized cell functions.
• Anabolism: Building molecules from smaller units, requiring energy input (ATP).
• Catabolism: Breaking down molecules into smaller units, producing energy (ATP).
• Forms of Energy:
  • Potential Energy: Stored energy (e.g., in chemical bonds).
  • Kinetic Energy: Energy of motion.
• Energy Transformation: Living organisms can transform energy from one form to another.
  • Sunlight energy is stored as potential energy in covalent bonds of sugars.
  • Breaking bonds requires energy, which can be used to form new bonds.
• Laws of Thermodynamics:
  • 1st Law: Energy is neither created nor destroyed; it can only be transformed.
  • 2nd Law: Disorder (entropy) tends to increase in a closed system.
• Gibbs Free Energy (G):
  • G = H - TS
    • G: Gibbs free energy (usable energy).
    • H: Enthalpy (total energy contained in chemical bonds).
    • T: Absolute temperature (in Kelvin, K = °C + 273).
    • S: Entropy (disorderliness, unavailable energy).
  • Total energy (H) = usable energy (G) + unusable energy (TS).
    • H = G + TS
• Change in Free Energy (ΔG):
  • \Delta G = \Delta H - T\Delta S
    • ΔG: Change in free energy.
    • ΔH: Change in enthalpy.
    • ΔS: Change in entropy.
    • T: Absolute temperature.
• Reaction Spontaneity based on ΔG:
  • Negative ΔG (-ΔG): Energy is released; the reaction is favorable and spontaneous.
  • Positive ΔG (+ΔG): Energy is required; the reaction is unfavorable and non-spontaneous.
  • ΔG = 0: Free energy is not available; the reaction is at equilibrium.

Lecture 2: Exergonic and Endergonic Reactions, ATP

• Exergonic Reactions:
  • Reactants have more free energy than products.
  • ΔH < 0, ΔS > 0.
  • -ΔG, reaction can occur spontaneously (forward direction →).
• Endergonic Reactions:
  • Products have more free energy than reactants.
  • ΔH > 0, ΔS < 0.
  • +ΔG, reaction cannot occur spontaneously (reverse direction ←).
• Equilibrium Reactions:
  • Chemical reactions are reversible in principle.
  • Chemical Equilibrium: The point at which forward and reverse reaction rates are equal.
  • Equilibrium Constant (Keq):
    • For the reaction aA + bB ↔ cC + dD:
      • Keq = \frac{[C]^c[D]^d}{[A]^a[B]^b}
    • Keq > 1: Equilibrium favors products (far to the right); ΔG is negative.
    • Keq = 1: Reaction is at equilibrium; ΔG is zero.
    • Keq < 1: Equilibrium favors reactants (far to the left); ΔG is positive.
• ATP (Adenosine Triphosphate): The energy currency of the cell.
  • Cells use energy stored in chemical bonds, like ATP, as needed.
  • Converting ATP's chemical energy fuels cellular reactions.
• ATP Hydrolysis:
  • Exergonic reaction (spontaneous) releases energy (−ΔG).
  • Phosphate groups in ATP are negatively charged at physiological pH and repel each other.
  • ADP has lower potential energy than ATP because it has two phosphate groups instead of three.
• Coupling Reactions: Formation and hydrolysis of ATP couple endergonic and exergonic reactions.
  • Exergonic reactions (e.g., cell respiration, catabolism) provide energy for ATP synthesis from ADP and Pi.
  • Endergonic reactions (e.g., active transport, cell movements, anabolism) are powered by ATP hydrolysis to ADP and Pi.
• Importance of Coupling:
  • Thermodynamically unfavorable (endergonic) reactions can be driven forward by coupling them to thermodynamically favorable (highly exergonic) reactions through a common intermediate.

Lecture 3: Enzymes and Catalysis

• Activation Energy (Ea):
  • The energy required to start a reaction; an energy barrier.
  • Reactants in a reactive mode are in the transition state.
  • The rate of exergonic reactions depends on activation energy.
• Ways to Increase Reaction Rate:
  • Increasing the energy of reacting molecules (e.g., heating reactants).
  • Lowering activation energy: catalysis (enzyme catalysis).
• Catalysts and Activation Energy:
  • Lowering the activation energy increases the reaction rate but does not change the free energy of the reaction.
  • The higher the activation energy, the slower the reaction rate.
• Enzymes: Biological catalysts
  • Mostly proteins, except for ribozymes (catalytic RNAs).
  • Highly specific for their substrates.
  • Affect reaction kinetics, not thermodynamics.
  • Not changed or consumed in the reaction; needed in small amounts.
  • Localized in cytoplasm, cell membranes, and organelles.
• Enzyme Structure:
  • Active Site: Crevice or pocket on the enzyme's surface where the substrate (S) binds, forming the enzyme-substrate (ES) complex.
• Enzyme Catalysis Mechanisms:
  • Substrate orientation.
  • Inducing strain.
  • Adding chemical groups.
• Factors Affecting Enzyme Reaction Rate:
  • Temperature, pH, substrate concentration ([Substrate]), cofactor concentration ([Cofactor]), inhibitors, and activators.

Lecture 4: Factors Affecting Enzyme Activity and Regulation

• Substrate Concentration: Reaction rate levels off when the enzyme becomes saturated because there is usually less enzyme than substrate.

• Temperature and pH:

  • Enzymes are sensitive to temperature and pH changes.
  • Have optimum activity in their natural environment.

• Cofactors:

  • Additional small molecules aid catalytic activity.
  • Inorganic molecules (e.g., metal ions like Mg^{2+}).
  • Small organic molecules (coenzymes, e.g., vitamin Bs).
  • Bind to the active site and participate in catalysis but are not substrates.

• Enzyme Activity Modulators:

  • Inhibitor: Substance that binds to an enzyme and decreases its activity.
  • Activator: Substance that binds to an enzyme and increases its activity.

• Enzyme Inhibition:

  • Competitive: Inhibitor binds to the active site, preventing substrate binding.
  • Noncompetitive: Inhibitor binds to a site other than the active site, changing the enzyme structure so normal substrate binding cannot occur.

• Metabolic Pathways:

  • Biochemical reactions are organized into interconnected metabolic pathways.
  • Enzymes help organize and regulate metabolic pathways.
  • Feedback Inhibition (Negative Feedback):
  • The product of a pathway controls its own synthesis rate by inhibiting an early step, usually the first committed step.
  • Important for energy conservation in the cell.

• Regulation of Biochemical Pathways:

  • The first reaction is often catalyzed by an enzyme that can be allosterically inhibited by the end product.

• Types of Feedback Inhibition:

  • Concerted feedback inhibition.