20.2 Thermodynamics of biological systems

Biological systems defy thermodynamic equilibrium, constantly exchanging energy and matter with their surroundings. They maintain order through energy input, coupled reactions, and compartmentalization. ATP, the cell's energy currency, drives these processes by powering unfavorable reactions.

Free energy determines reaction spontaneity in biochemical systems. Proteins and other biomolecules achieve stability by minimizing free energy through a balance of enthalpic and entropic contributions. Understanding these principles is crucial for grasping how living organisms maintain their complex structures and functions.

Thermodynamic Properties and Energy in Biological Systems

Thermodynamics in biological systems

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• Biological systems operate far from thermodynamic equilibrium
  • Constantly exchange energy and matter with their surroundings (nutrients, waste products)
  • Maintain a stable internal environment (homeostasis) despite external fluctuations (temperature, pH)
• High degree of organization and complexity compared to non-living systems
  • Requires continuous input of energy to maintain order and function (ATP, glucose)
  • Defies the natural tendency towards increasing entropy as described by the Second Law of Thermodynamics
• Coupled reactions and energy transformations are prevalent in metabolic pathways
  • Exergonic reactions (energy-releasing) drive endergonic reactions (energy-requiring)
  • Energy released from one process (ATP hydrolysis) is used to power another (muscle contraction)
• Compartmentalization and selective permeability of biological membranes
  • Allows for the creation and maintenance of concentration gradients (ions, neurotransmitters)
  • Essential for energy storage and utilization in organelles (mitochondria, chloroplasts)

ATP as energy currency

• ATP (Adenosine Triphosphate) is the primary energy carrier in cells
  • Consists of adenosine, ribose, and three phosphate groups
  • Hydrolysis of ATP to ADP + Pi releases energy ($\Delta G = -30.5$ kJ/mol) under standard conditions
• ATP coupling to endergonic reactions drives thermodynamically unfavorable processes
  • Energy released from ATP hydrolysis enables:
    1. Muscle contraction via actin-myosin interactions
    2. Active transport of molecules against concentration gradients (sodium-potassium pump)
    3. Biosynthesis of complex molecules (proteins, nucleic acids)
• ATP regeneration occurs through substrate-level and oxidative phosphorylation
  • Glycolysis and the citric acid cycle generate ATP through substrate-level phosphorylation (direct transfer of phosphate)
  • Electron transport chain and chemiosmosis produce ATP via oxidative phosphorylation (proton gradient-driven)
• ATP maintains a non-equilibrium state in cells crucial for life processes
  • High ATP/ADP ratio drives reactions away from equilibrium
  • Allows for the regulation and control of metabolic pathways (allosteric enzymes, feedback inhibition)

Free Energy and Biomolecular Stability

Free energy in biochemical reactions

• Gibbs free energy ($G$) is a thermodynamic potential that determines reaction spontaneity
  • Defined as $G = H - TS$, where $H$ is enthalpy, $T$ is temperature, and $S$ is entropy
  • Change in free energy ($\Delta G$) predicts the direction of a reaction at constant temperature and pressure
• Spontaneous reactions have a negative $\Delta G$ and proceed without external input
  • Products have lower free energy than reactants (exergonic)
  • Reaction proceeds in the forward direction (glucose oxidation, ATP hydrolysis)
• Equilibrium is reached when $\Delta G = 0$ and no net change occurs
  • Forward and reverse reactions occur at equal rates
  • No net change in reactant and product concentrations (enzymatic reactions at steady state)
• Free energy changes depend on concentration of reactants and products
  • Standard free energy change ($\Delta G^{\circ}$) refers to reactions at 1 M concentrations
  • Actual free energy change ($\Delta G$) varies with reactant and product concentrations according to the equation: $\Delta G = \Delta G^{\circ} + RT \ln Q$

Thermodynamics of biomolecule stability

• Protein folding is driven by the minimization of free energy to the most stable native state
  • Native state is the most thermodynamically stable conformation
  • Balances the contributions of enthalpy (favorable interactions) and entropy (disorder)
• Enthalpic contributions to protein stability arise from favorable interactions
  • Formation of hydrogen bonds, van der Waals interactions, and electrostatic interactions
  • Favorable interactions between amino acid residues and with the solvent (hydrophilic residues on surface)
• Entropic contributions to protein stability are primarily due to the hydrophobic effect
  • Hydrophobic effect: burial of nonpolar residues in the protein core to minimize solvent exposure
  • Reduction of solvent-exposed surface area minimizes entropic cost of solvation (ordered water molecules)
• Protein denaturation occurs when the native state is destabilized by external factors
  • Caused by changes in temperature (heat), pH (acids, bases), or the presence of denaturants (urea, guanidinium chloride)
  • Results in the loss of tertiary and secondary structure, exposing buried hydrophobic residues
• Similar thermodynamic principles apply to the stability of other biomolecules
  • Nucleic acid secondary structures (DNA double helix, RNA hairpins) stabilized by base pairing and stacking interactions
  • Lipid bilayer formation and stability in biological membranes driven by hydrophobic interactions of fatty acid tails