5.3 Reaction Mechanisms in Biological Systems

Reaction mechanisms in biological systems are the step-by-step processes that drive chemical changes in living organisms. From enzyme catalysis to metabolic pathways, these mechanisms control how molecules interact and transform within cells.

Understanding reaction mechanisms is crucial for grasping how life functions at a molecular level. Key concepts include elementary steps, rate-determining steps, and steady-state approximations, which help explain the complex dance of molecules in biological processes.

Reaction Mechanisms in Biological Systems

Key steps in reaction mechanisms

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• Elementary steps transform reactants to products in a single chemical event without breaking down into simpler reactions
• Reactants and products mark the starting and ending substances for each step in the mechanism
• Intermediates form temporarily during the reaction but do not appear in the overall balanced equation
• Transition states represent highest energy configurations in each step and determine activation energy required
• Rate constants quantify the speed of each elementary step in the mechanism
• Molecularity indicates number of reactant molecules involved (unimolecular, bimolecular, or termolecular)
• Rate-determining step controls overall reaction rate as the slowest step with highest activation energy

Rate-determining vs non-rate-determining steps

• Rate-determining step (RDS) controls overall reaction rate with highest activation energy and slowest progression
• Non-rate-determining steps progress faster and do not significantly impact overall reaction rate
• Kinetic factors like reactant concentration, temperature, and catalysts influence step rates
• Energy profile diagrams visualize activation energies for different steps in the mechanism
• Pre-equilibrium involves fast reversible step occurring before the RDS
• Steady-state approximation assumes constant concentration of intermediates throughout reaction

Steady-state approximation for rate laws

• Steady-state approximation balances intermediate formation and consumption rates
• Apply by:
  1. Writing all elementary steps
  2. Identifying intermediates
  3. Setting up rate equations
  4. Equating intermediate formation and consumption
  5. Solving for intermediate concentrations
• Derive overall rate law by substituting intermediate concentrations into rate equation
• Michaelis-Menten kinetics applies steady-state approximation to enzyme catalysis
• Rate-determining step method offers simpler alternative for less complex mechanisms
• Assumptions work best for reactions with short-lived intermediates but may not suit all complex systems

Reaction mechanisms in biological systems

• Enzyme-substrate complex forms via lock-and-key or induced fit models
• Active site provides specific catalytic region and substrate binding pocket
• Cofactors and coenzymes enhance enzyme function as non-protein components
• Michaelis-Menten kinetics describe enzyme catalysis: $v = \frac{V_{max}[S]}{K_m + [S]}$
• Enzyme inhibition occurs through competitive, non-competitive, or uncompetitive binding
• Allosteric regulation modifies enzyme activity through effector binding at non-active sites
• Cooperativity changes enzyme affinity with substrate binding, described by Hill equation: $v = \frac{V_{max}[S]^n}{K' + [S]^n}$
• Ping-pong mechanisms involve formation of covalent enzyme-substrate intermediates
• Metabolic pathways link series of enzyme-catalyzed reactions with regulated flux