Enzyme Active Site

The Active Site

• The active site is the place in the enzyme structure where the reaction occurs.
• Active sites are usually clefts or crevices in the protein where the substrate binds by multiple weak bonds.
• There are two theories that describe the substrate binding to an enzyme's active site: the Lock and Key Theory and the Induced Fit Theory.
• The Lock and Key Theory states that the active site is highly specific, and only molecules with a complementary shape can bind.
• The Induced Fit Theory states that the binding of the substrate often results in changes in the shape of the enzyme to enhance binding.

How Enzymes Work

• Enzymes work by lowering the activation energy needed for a reaction to occur.
• Enzymes employ multiple mechanisms to facilitate catalysis, including:
  • Covalent catalysis: formation of a transient covalent bond between a substrate and a residue in the enzyme active site or with a cofactor.
  • Metal ion catalysis: a metal ion in the active site participates in catalysis by coordinating charge stabilization.
  • Catalysis by proximity or strain: an enzyme can accelerate a reaction between two species simply by holding the two reactants close together in an appropriate orientation.
  • Acid-base catalysis: involves conformational change due to change in pH, so some ionic bond is broken or formed.

Enzyme Nomenclature

• Enzymes are named by adding the suffix "ase" to the name of the substrate.
• Systematic Name: IUB System, consists of two parts: the name of the substrate and the type of reaction (ending in -ase).

Enzyme Classification

• Enzymes are classified into six different groups according to the reaction being catalyzed.
• Each enzyme has a unique EC number that identifies it.

The Michaelis-Menten Model

• The Michaelis-Menten Model describes the kinetics of enzyme-catalyzed reactions.
• The model assumes that an enzyme, E, combines reversibly with a substrate, S, to form an enzyme-substrate intermediate, ES.
• The relationship between [S] and V0 has a hyperbolic shape, which can be expressed algebraically by the Michaelis-Menten equation.

The Lineweaver-Burk Plot

• The Lineweaver-Burk plot is a graphical representation of the Michaelis-Menten equation.
• The plot is a straight line with a slope of Km/Vmax and a y-intercept of 1/Vmax.
• The Lineweaver-Burk plot is useful for determining the kinetic parameters Km and Vmax.

Factors Affecting Enzyme Activity

• Substrate concentration: increasing substrate concentration increases the rate of reaction, but only up to a certain point.
• Enzyme concentration: the rate of reaction is directly proportional to the enzyme concentration.
• Temperature: affects the rate of reaction, with an optimal temperature for enzyme activity.
• pH: affects the rate of reaction, with an optimal pH for enzyme activity.
• Activators and inhibitors: can increase or decrease the rate of reaction, respectively.

Inhibition of Enzyme Activity

• Inhibition can be reversible or irreversible.
• Reversible inhibition can be competitive or non-competitive.
• Competitive inhibitors compete with the substrate for binding at the active site.
• Non-competitive inhibitors bind at a site other than the active site.

Isozymes

• Isozymes are enzymes that differ in amino acid sequence but catalyze the same chemical reaction.