Chemical Basis of Enzyme Specificity

Chemical Basis of Enzyme Specificity S binds to E at a site called the “active site” to form a complex, called ES complex The E active site and the S are complimentary to each other chemically and structurally Absolute versus General Specificity Absolute specificity is a property of an enzyme in which it catalyzes only one reaction Carbonic Anhydrase H2 CO3 º º H2 O + CO2 Catalase H2 O2 º º 2 H2 O + O2 General specificity is a property of an enzyme in which it catalyzes only one type of reaction O O N CH C N CH C + HOH H R1 H R2 Chymotrypsin O N CH COH + H R1 H O N CH C H R2 Chemical and Structural Complimentarity ….. H -O -(s er) - Hexokinase or Glucokinase Draw aa side chains that might be likely to interact with these two substrates s)-(l y N + ….. H 3 ATP + glucose à à ADP + glucose-6-phosphate 1 “Imaginary Enzyme” Fig 08 -05.GIF “Driving Force for Catalysis” Weak bonding interactions (binding) between the E and the S provide the “driving force” for enzyme catalysis 1. Chemical Basis of Enzyme Catalysis How do enzymes lower ∆ G‡? 1. Proximity and Orientation: S binds to E at a site called the “active site” to form a complex, called ES complex simple binding “induced fit” Substrate is chemically and structurally complimentary to enzyme active site 2 1. Chemical Basis of Enzyme Catalysis: Models How do enzymes lower ∆ G‡? 1. Proximity and Orientation: Model Systems Fig 08 -07a-c.GIF 2. Chemical Basis of Enzyme Catalysis: Nucleophiles 2. Functional Group Catalysis: The E active site has functional groups that can act as the following: Nucleophiles 2. Chemical Basis of Enzyme Catalysis: General Acid Catalysis 2. Functional Group Catalysis: The E active site has functional groups that can act as the following: General acid/base catalysts 3 2. Chemical Basis of Enzyme Catalysis: Counter Ion Stabilization 2. Functional Group Catalysis: The E active site has functional groups that can act as the following: Counter ion for electrostatic stabilization (common lys, arg, glu, asp) Devlin F04_53A.PCT 2. Chemical Basis of Enzyme Catalysis: Counter Ion Stabilization 2. Functional Group Catalysis: The E active site has functional groups that can act as the following: Counter ion for electrostatic stabilization (common lys, arg, glu, asp) Devlin F04_53B.PCT 2. Chemical Basis of Enzyme Catalysis: H-bonding stabilization 2. Functional Group Catalysis: The E active site has functional groups that can act as the following: H-bonding donors or acceptors for stabilization of transition state: (common: backbone groups, ser, his, lys, arg, glu, asp) 4 3. Chemical Basis of Enzyme Catalysis: Strain Introduction of strain into S: bond angle and bond length distortion Devlin F04_53A.PCT 4. Chemical Basis of Enzyme Catalysis: Ox-Red Enzymes have prosthetic groups that can act as oxidizing agents and reducing agents (some prosthetic groups are actually substrates) ENZYMES: INORGANIC COFACTORS 5 ENZYMES: ORGANIC COFACTORS 4. Chemical Basis of Enzyme Catalysis: Example 1: Ox -Red CuZnSuperoxide Dismutase Dimer of 31,500 g/mole 2 Cu +2 and 2 Zn +2 per Monomer dimer Predominantly ββ -sheet D1 2 2 O H11 8 H H H44 N O H N N N N N Cu +2 N N D81 O N H4 6 H Enzyme Active Site H6 9 Z n+2 N Cu +2 à à + O 2- Cu+ + O2 O H61 N N H H78 Cu + + O2- + 2 H + à à Cu+2 + H2 O2 4. Chemical Basis of Enzyme Catalysis: Example 1: Ox -Red NI COTINAMI DE ADENINE DINUCLE OTIDE ( B3 ni acin( amid e)) H O H C H O C NH2 NH2 O - O P N O N O R **NADH OH O N N O P O ( red uced for m) N N - " b usin ess en d " n icot inam ide r ing ( B3 ) OH NH2 O O OH **NAD (ox idized for m) OH OPi (in NADP + ) 6 So What? Do these processes of catalysis explain why an E stabilizes the Transition State? These other processes help S get to the Transition State! Weak forces…..stabilize the Transition State!! “Driving Force for Catalysis” Weak bonding interactions (binding) between the E and the S provide the “driving force” for enzyme catalysis “transition state stabilization necessary” 7