Enzyme: Mechanisms

What are the major biochemical properties of enzymes?

• Enzymes are biological catalysts that alter reaction rates without changing the overall ΔG or K_eq and are not consumed by the reaction.

• Substrates often bind with high specificity to the active site of an enzyme, which is a cleft or pocket in the protein structure where the catalyzed reaction takes place.

• Substrate binding to enzymes is often associated with structural changes in the enzyme. These changes maximize the number of weak noncovalent interactions between the substrate and amino acid residues in the enzyme active site.

• Enzyme activity is highly regulated in cells to maximize energy balance between anabolic and catabolic pathways and to alter cell behavior in response to environmental stimuli.

• According to transition state theory, a reactant must first reach an energy level required for chemical transformation before the product can be formed.

• The activation energy (ΔG^‡) is the difference between the ground state energy of the reactant and the transition state energy. Enzymes lower ΔG^‡ by providing a favorable physical and chemical environment in the active site to promote catalysis.

• Cofactors provide additional reactive groups to the enzyme active site that complement the limited chemistry of amino acid side chains. Some cofactors are inorganic ions. Organic cofactors are called coenzymes, many of which are derived from vitamins.

• The IUBMB enzyme classification system provides a standard nomenclature for enzymes. It is based on a hierarchical numbering system beginning with one of seven classes of reactions (redox reactions, transferase reactions, hydrolase reactions, lyase reactions, isomerase reactions, ligase reactions, and translocase reactions).

How do enzymes function as biological catalysts in cells?

• Enzymes lower the activation energy (ΔG^‡) of a reaction in three different ways: (1) by stabilizing the transition state, which lowers the activation barrier; (2) by providing an alternative path for product formation through reaction intermediates; and (3) by orienting the substrates appropriately for the reaction to occur.

• Stabilizing the transition state is one of the key mechanisms of enzyme catalysis and is the molecular basis for tight binding of transition state analogs, which often function as enzyme inhibitors.

• Functional groups in the active site mediate three main types of catalytic reaction mechanisms: (1) acid–base catalysis, (2) covalent catalysis, and (3) metal-ion catalysis.

• Metal ions are important enzyme cofactors and promote catalysis by aiding in substrate orientation, mediating redox reactions, and shielding or stabilizing negative charges through electrostatic interactions.

• Enzymes perform three main types of work in the cell: (1) coenzyme-dependent redox reactions associated with energy conversion; (2) metabolite transformation reactions to interconvert metabolites in anabolic and catabolic pathways; and (3) reversible covalent modification reactions to control cell signaling processes and enzyme activity.

• Enzyme-catalyzed redox reactions in the cell often require coenzymes such as NAD⁺/NADH, NADP⁺/NADPH, FAD/FADH₂, or FMN/FMNH₂. These redox reactions involve the transfer of a pair of electrons or a single electron through a radical intermediate.

• Metabolite transformations in metabolic pathways most often involve isomerization reactions, condensation reactions, or hydrolysis or dehydration reactions.

• One of the most common types of reversible covalent modification reactions in cells is the addition and removal of a phosphoryl group in biomolecules. Enzymes that attach phosphoryl groups are called kinases, whereas enzymes that remove phosphoryl groups are called phosphatases.

What are examples of acid–base, covalent, and metal-ion enzyme catalysis?

• Acid–base and covalent catalysis are common in enzyme mechanisms. Chymotrypsin is an enzyme that uses both acid–base catalysis and covalent catalysis during the cleavage of a peptide bond. In addition, a tetrahedral transition state forms and is stabilized by the oxyanion hole.

• A key feature of serine proteases is the presence in the enzyme active site of three amino acids called the catalytic triad, which consists of a catalytic serine residue plus histidine and aspartate residues that function to convert the serine residue into a highly reactive nucleophile.

• Metal ions can play multiple roles in catalysis. For example, enolase catalyzes the dehydration of 2-phosphoglycerate to form phosphoenolpyruvate in a four-step mechanism that involves both acid–base catalysis and metal-ion catalysis. The metal ions in this reaction are necessary for ionic interactions with the substrate and intermediate.

• HMG-CoA reductase, an enzyme that catalyzes an early step in cholesterol biosynthesis, uses two NADPH coenzymes to achieve catalysis.