chapter 6

Enzymes: Overview

• Enzymes accelerate the rate of reactions within cells spontaneously.
• Enzymes display specificity by binding to specific substrates and producing specific products.
• Enzyme specificity is determined by the protein's structure, allowing it to perform one or a few similar reactions.
• Proteolytic enzymes catalyze proteolysis, which is the hydrolysis of peptide bonds.
• Examples of proteolytic enzymes that exhibit varying degrees of specificity:
  • Papain cleaves almost any peptide bond regardless of involved amino acids.
  • Trypsin cleaves peptides only on the carboxyl side of lysine and arginine.
  • Thrombin cleaves peptide bonds only between arginine and glycine.

Major Enzyme Classes

• Oxidoreductases transfer electrons promoting oxidation-reduction reactions
• Transferases transfer functional groups between molecules.
• Hydrolases cleave molecules by adding water.
• Lyases add atoms or functional groups to a double bond or removes them to form a double bond.
• Isomerases move functional groups within a molecule.
• Ligases join two molecules together, breaking down ATP in the process.

Enzyme Cofactors

• Cofactors are small molecules that must be present for some enzymes to catalyze reactions.
• Apoenzymes are enzymes without their cofactor, while holoenzymes are enzymes with their cofactor.
• There are 2 groups of cofactors:
  • Small organic molecules (coenzymes) are often derived from vitamins.
  • Metals
• Prosthetic groups bind tightly to an enzyme.
• Coenzymes that bind loosely act like cosubstrates, binding and releasing from the enzyme.
• Enzymes that use the same coenzyme carry out similar chemical reactions.

Gibbs Free Energy (G)

• Gibbs free energy is a thermodynamic property measuring the energy available to do work.
• Two key thermodynamic properties needed to understand enzyme function:
  • Free-energy difference (ΔG) between products and reactants, determining reaction spontaneity.
  • Free energy (activation energy) required to initiate reactant conversion into products, influencing the reaction rate.

Free-Energy Difference (ΔG)

• Determines if a reaction occurs spontaneously:
  • A negative ΔG indicates a spontaneous reaction that does not require energy input (exergonic).
  • A positive ΔG means energy must be added for the reaction to occur (endergonic).
  • A ΔG of zero indicates the system is at equilibrium with no net change in reactant or product concentrations.
• ΔG depends solely on the free energy difference between products and reactants, regardless of the reaction path.
• ΔG does not provide information about reaction rate.

Reaction Rate & Equilibrium

• Enzymes alter the reaction rate but not the reaction equilibrium.
• Enzymes allow reactions to reach equilibrium faster.
• Equilibrium depends on the free-energy difference between reactants and products.

Enzymes & Transition State

• The transition state has a higher free energy than the substrate or product.
• The transition state represents the least stable and most seldom-occurring species in a reaction.
• Activation energy is the free energy difference between the transition state and the substrate.
• Enzymes lower activation energy, facilitating the formation of the transition state.
• Activation energy is not part of the final ΔG calculation.
• Energy spent to reach transition state is released when the product forms.

Enzyme-Substrate Complex

• Formation of an enzyme-substrate complex is the initial step in enzymatic catalysis.
• Substrates bind to the active site of the enzyme.
• Active sites:
  • Bind substrates and cofactors, contain amino acids needed to make/break bonds (catalytic groups)
• Enzyme-substrate interaction at the active site accelerates transition state formation.

Active Sites of Enzymes

• The active site is a three-dimensional cleft or crevice, formed by amino acid groups from different parts of the sequence.
• The active site occupies only a small part of the total enzyme volume.
• Cooperative movement of the entire enzyme promotes the correct positioning of catalytic residues at the active site.
• Enzymes typically have a minimum size of at least 100 amino acids.
• Active sites are unique microenvironments, with water excluded unless it is a reactant.
• The environment is mostly nonpolar.
• Substrates bind to enzymes via multiple weak attractions:
  • Electrostatic interactions
  • Hydrogen bonds
  • Van der Waals forces are powered by hydrophobic interactions
• Complementary shapes of the enzyme and substrate strengthen interactions.
• Binding specificity depends on precise arrangements of atoms in the active site.
• The enzyme's active site can be modified upon substrate binding (induced fit).

Binding Energy & Catalysis

• Binding energy refers to the free energy released upon substrate binding to the enzyme and lowers activation energy.
• Free energy releases when a large number of weak interactions form between the substrate and enzyme.
• A full complement of weak interactions forms only when the substrate is in the transition state, which releases maximal binding energy.
• The transition state is unstable and proceeds to either substrate or product formation depending on the energy difference (ΔG) between them.