Lecture Notes on Trophism and Thermodynamics

Trophism in Organisms

• Definition: Trophism refers to how organisms acquire nutrients.
• Categories:
  • Autotrophs: Self-feeders that use inorganic light or chemical energy.
    • Phototrophs: Use light energy (e.g., cyanobacteria).
    • Chemoautotrophs: Use chemical energy (e.g., Thio margarita "sulfur pearls").
  • Heterotrophs: Obtain energy from organic chemicals in the environment.

Thermodynamics in Biological Sciences

• Energy: Capacity to do work, involves moving or changing something against an opposing force (e.g., gravity, friction).
• First Law of Thermodynamics: Energy is transferred or transformed, not created or destroyed.
• Second Law of Thermodynamics: Energy moves from an ordered to a disordered state (entropy).

Gibbs Free Energy

• Concept: Combines the first two laws to understand energy in systems.
  • Delta G (ΔG): Change in free energy, available for work.
  • Delta H (ΔH): Change in enthalpy (heat loss).
  • Delta S (ΔS): Change in entropy (disorder).
• Spontaneity:
  • Negative ΔG: Spontaneous, favorable, exergonic (energy-releasing).
  • Positive ΔG: Non-spontaneous, unfavorable, endergonic (energy-requiring).

Coupled Reactions

• Mechanism: Cells use coupled reactions to accomplish work.
  • Shared Intermediate: Product of one reaction serves as reactant in the next.
  • Overall Negative ΔG: Ensures spontaneity of coupled reactions.

Catalysts in Biological Reactions

• Function: Speed up reactions by lowering activation energy without changing energetics.
• Enzymes: Protein catalysts, e.g., endoenzymes (inside cell), exoenzymes (outside cell).
• Mechanism: Bind and position substrates, lowering the energy hill (activation energy).

Enzyme Models

• Induced Fit Model: Active site adapts to fit substrates; correct substrates induce weak, reversible bond interactions.
• Types of Bonds: Hydrogen bonds, ionic bonds, van der Waals interactions.

Enzyme Helpers

• Coenzymes and Cofactors: Essential for some enzymes' function (e.g., NADH, iron ions).
• Catalytic Efficiency: Enzymes can increase reaction rate significantly.

Graphing Catalyst Impact

• Transition State and Activation Energy:
  • Energy Hill: Visual representation of activation energy.
  • Catalyst Effect: Lowers the hill (activation energy) without changing overall ΔG.

Conclusion

• Understanding of thermodynamics and catalysis is crucial for appreciating metabolic pathways and reactions in cells.