7.1 Enzymes Are Powerful and Highly Specific Catalysts

Energetics of Enzyme-Catalyzed Reactions

Enzymes are biological catalysts that accelerate chemical reactions in living organisms. They are highly specific, both in the reactions they catalyze and the substrates they bind.

• Cellular energy and information processing depend on thousands of chemical reactions, which must occur rapidly and with specificity to meet physiological needs and avoid harmful by-products.

• Enzymes speed up chemical reactions without being consumed in the process.

• All enzymes are proteins, except for some catalytic RNA molecules (ribozymes).

Rate Acceleration by Enzymes

Enzymes can accelerate reaction rates by factors up to a billion or more. Most biological reactions occur at imperceptible rates without enzymes.

Enzyme Specificity

• Enzymes are highly specific in both the reactions they catalyze and the substrates they use.

• Specificity arises from the precise interaction between substrate and enzyme, a result of the enzyme’s intricate 3D structure.

• An enzyme typically catalyzes a single chemical reaction or a set of closely related reactions.

Proteases

• Proteases catalyze proteolysis (hydrolysis of peptide bonds). All proteases use water to break chemical bonds.

• Trypsin: Digestive enzyme that cleaves peptide bonds on the carboxyl side of lysine and arginine.

• Thrombin: Blood clotting enzyme that is more specific than trypsin and cleaves Arg-Gly bonds in particular sequences.

Example: Trypsin cleaves on the carboxyl side of arginine and lysine residues, whereas thrombin cleaves Arg-Gly bonds in specific sequences.

Classes of Enzymes

• Oxidoreductases: Oxidation-reduction reactions

• Transferases: Group transfer reactions

• Hydrolases: Hydrolysis (cleavage of bonds by water)

• Lyases: Breaking (elimination) of various chemical bonds by means other than hydrolysis or oxidation, often forming a new double bond or ring structure

• Isomerases: Isomerization (intramolecular group transfer)

• Ligases: Ligation of two substrates (ATP hydrolysis required)

• Translocases: Movement of ions/molecules across membranes

7.2 Many Enzymes Require Cofactors for Activity

Cofactors

Many enzymes require small molecules or ions, called cofactors, for catalytic activity.

• Apoenzyme: Enzyme without its cofactor.

• Holoenzyme: Complete, catalytically active enzyme.

Types of Cofactors

• Coenzymes: Small organic molecules, often vitamin-derived. Can be tightly (prosthetic groups) or loosely (cosubstrates) bound.

• Metals: Inorganic ions essential for activity.

7.3 Gibbs Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes

Gibbs Free Energy

The free energy difference between products and reactants determines whether a reaction can occur spontaneously.

• Spontaneous reactions: Exergonic, release energy ().

• Nonspontaneous reactions: Endergonic, require energy input ().

• At equilibrium, .

Thermodynamic Properties

• Free-energy difference (): Determines spontaneity.

• Activation energy (): Determines reaction rate.

Enzymes and Thermodynamics

• Enzymes do not alter the equilibrium or of a reaction.

• Catalysts, including enzymes, lower the activation energy (), increasing reaction rate.

Standard Free Energy Change and Equilibrium

• is the standard free-energy change, the free-energy change for a reaction under standard conditions (1 M concentration, 25°C, pH 7.0).

• The gas constant in SI units is 8.314 J·mol-1·K-1.

• is the absolute temperature in Kelvin.

For a reaction :

Equilibrium constant () relates to :

7.4 Enzymes Facilitate the Formation of the Transition State

Transition State

• A chemical reaction of substrate S to form product P goes through a transition state (X‡) that has a higher free energy than either S or P.

• The transition state is a fleeting molecular structure that is no longer substrate but not yet product.

• The activation energy () is the energy difference between substrate and transition state.

Enzyme Mechanism

• Enzymes lower , increasing the number of molecules reaching the transition state and thus the reaction rate.

• The first step is formation of the enzyme–substrate (ES) complex at the active site.

Active Sites

• Region where substrates (and cofactors) bind and catalysis occurs.

• Contains amino acid residues (catalytic groups) that participate in bond-making/breaking.

• Promotes transition state formation and lowers activation energy, accelerating reactions in both directions.

Common Features of Active Sites

• Three-dimensional cleft or crevice formed by amino acids from different parts of the sequence.

• Small part of total enzyme volume.

• Unique microenvironment: Water is usually excluded unless a reactant; nonpolar environment enhances binding and catalysis; may contain essential polar residues.

• Substrates bind via multiple weak, reversible interactions: Ionic, hydrogen bonds, van der Waals forces, and hydrophobic effect.

• Specificity depends on shape and arrangement of atoms in the active site.

Models of Enzyme-Substrate Binding

• Induced fit model: Enzyme changes shape upon substrate binding, forming a complementary active site only after binding.

• Lock-and-key model: (Historical) Enzyme active site is complementary to substrate before binding.

Binding Energy

• Free energy released by weak interactions between enzyme and substrate is called binding energy.

• Maximum binding energy (and specificity) occurs when the substrate is in the transition state.

Transition-State Analogs (TSAs)

• Molecules resembling the transition state but not acted on by the enzyme.

• Potent inhibitors, as they bind tightly to the enzyme’s active site.

Example: Pyrazole carboxylic acid is a potent inhibitor of proline racemase because its geometry mimics the transition state of the catalyzed reaction.

Summary Table: Key Concepts in Enzyme Catalysis

Additional info: The notes also include example calculations for under cellular conditions and emphasize the importance of enzyme structure in catalysis and specificity.