Recording-2025-02-24T20:22:35.530Z

Key Concepts of Reaction Dynamics

Delta G and Reaction Spontaneity

• Delta G: Represents the change in free energy in a chemical reaction.

  • A negative Delta G indicates a spontaneous reaction (A -> B).

  • If product (B) is more stable than reactant (A), the reaction favors the formation of B.

  • A spontaneous reaction typically sees an increase in the system's entropy.

Temperature and Standard Conditions

• Standard Conditions: For biological reactions, these conditions are generally defined as:

  • 1 atmosphere of pressure,

  • 298 Kelvin (approximately room temperature),

  • 1 molar concentrations of reactants.

Rate Constants and Equilibrium

• Rate Terms Relationship: The rate of a reaction can be expressed involving rate constants for forward and reverse reactions.

• K(eq): Equilibrium constant related to the ratio of the concentrations of products and reactants.

• The relationship between Delta G and the equilibrium constant provides insight on spontaneity:

  • Delta G = Delta G° + RT ln(Q) where Q is the reaction quotient.

  • At equilibrium, Delta G = 0, indicating no net change in concentrations.

Reaction Quotients and Real Concentrations

• The actual concentrations of A and B affect the spontaneity of a reaction:

  • With greater concentration of A, Delta G becomes more negative, favoring A -> B transitions.

  • Understanding the effect of concentrations is critical for predicting reaction dynamics.

Binding and Equilibrium in Biological Systems

Complex Formation

• Formation of Complex AB: When two molecules A and B bind to form a complex (A + B ↔ AB).

• The rate of change of the complex is governed by the forward and reverse rates:

  • d[AB]/dt = k_f[A][B] - k_r[AB]

• At equilibrium, the interaction can be described by the dissociation constant (Kd):

  • Kd = [A][B]/[AB]

Fraction Bound

• The fraction of binding can be defined as:

  • Fraction Bound = [AB]/[B total]

• This ratio provides a practical measure for how effective a drug or inhibitor may be in a biological context.

Energy Transfer in Biological Systems

Role of ATP

• ATP: Acts as an energy currency, allowing the transfer of energy for various cellular processes.

  • Energy is stored in the phosphate bonds of ATP and released upon hydrolysis.

  • Useful for driving endergonic reactions by coupling them to exergonic ATP reactions.

Biological Reactions and Intermediate States

• Metabolism involves breaking down high-energy molecules and capturing energy in a form that can be used for biosynthesis.

• Direct Bartering: Instead of trading specific food molecules for specific reactions, cells convert food energy into ATP, a universal form of energy store for different metabolic pathways.

Electron Transfer Currency

• NADP and NADPH: Involved in redox reactions, transferring electrons in metabolic processes.

  • NADP+ accepts electrons and becomes NADPH, which can donate electrons in biosynthetic reactions.

• Distinction between NAD and NADH vs. NADP and NADPH allows for distinct pathways to be controlled separately in metabolic networks.