Transition State

Enzyme Catalysis Learning Goals: 1. A catalyst participates in a chemical reaction and enhances the rate but has no effect on the free energy of the reaction. 2. Understand the difference between thermodynamic and kinetic favorability of a chemical reaction. 3. Understand the characteristics of the six recognized classes of enzymes. 4. Enzymes catalyze their reactions by stabilizing the transition state. Stabilization is accomplished principally by binding the transition state tighter than either the original substrate or resulting product. 5. Other contributions to transition state stabilization depend on proximity effects. 6. Understand the factors contributing to the catalytic efficiency of representative enzymes. I.

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IV.

The theory of catalysis a. Catalysts act by increasing the rate of the reaction without being consumed. The rate constant is increased by stabilizing the transition state of the reaction. Catalysts do NOT affect the thermodynamic stability of the product or the equilibrium constant of the reaction. The system of enzyme classification a. Six major classes i. Oxidoreductases ii. Transferases iii. Hydrolases iv. Lyases v. Isomerases vi. Ligases Transition state stabilization a. Non-catalyzed reaction in aqueous solution i. Water molecules sound charged/polar functional groups  hydration spheres. ii. Encounter complex iii. Collide with sufficient energy to exceed the activation energy of the reaction in the correct orientation; water molecules moved away b. Catalyzed reaction i. Binding of the substrate into the active site (substrate specificity, hyperbolic kinetics) ii. Proximity effects (increasing the effective concentration of reactants within the active site)  intramolecular reactions between groups are faster than intermolecular reactions iii. Enzyme tightly binds transition state (has extra constituent)  transition state analogs (inhibitors) iv. Amino acids with reactive side chains that participate in enzyme catalysis: Glu, Asp, Lys, Arg, Cys, His, Ser, Tyr Other factors contributing to the catalytic efficiency of enzymes a. Microenvironment i. Hydrophobic: if the active site is lined with hydrophobic amino acids or undergoes a conformational change following binding of the substrate, solvent molecules will be excluded and functional groups will be desolvated  more reactive functional groups ii. Charged/polar amino acid side chains near a reactive functional group can alter the pKa or reactivity. iii. Example: Carboxypeptidase b. Acid-base catalysis i. Abstraction/donation of H+ ii. Example: Histidine c. Conformational change  induced fit i. Some of the energy of activation involved in forming the transition state conformation of the substrate is compensated by a favorable binding energy. ii. Example: Lysozyme d. Covalent catalysis i. A covalent enzyme-substrate intermediate is formed during the course of the reaction ii. Example: serine protease (family of enzymes with catalytic triad; unique substrate specificitydifferences in the binding pocket that interacts with second-to-last aa)