Bio 98 - Leture 8 Enzymes I

Enzymes 1. Selective catalysis and regulation of metabolic rxnscatalysis - enzymes are unchanged by the reactionenzymes - some require co-factors (small organic molecules &/or metals such as Ca, Zn, Cu or Fe, or heme) 2. Most are proteins; some RNAs can also catalyze rxns 3. Example of extreme catalytic efficiency: “catalase” Reaction: 2 H 2 O 2  2 H 2 O + O 2 CatalystRelative rate None 1 Fe 3+ 1,000 Catalase enzyme (heme) 10 9 (40,000,000/sec)

3D structure of catalasecatalase

Reaction scheme of catalasecatalase Reaction: 2 H 2 O 2  2 H 2 O + O 2 Compound I

Enzymes 4. Another example of extreme catalytic efficiency: “triosephosphate isomerase”triosephosphate isomerase Reaction Free energy profile DHAPDAP

3D structure of triosephosphate isomerase (TIM barrel) The enzyme is so efficient that it is said to be catalytically perfect: It is limited only by the rate the substrate can diffuse into and out of the enzyme’s active site!

3D structure of triosephosphate isomerase (TIM barrel)

Uncatalyzed reaction: 1.  G determines where equilibrium lies. 2.  G ‡ determines the rate at which equilibrium is achieved. transition state free energy (activation energy) overall reaction free energy change G (free energy) Reaction coordinate P S‡S‡ S (transition state) G‡G‡ GG SP

1. Enzymes do not alter the equilibrium or  G. 2. They accelerate reactions by decreasing  G ‡. 3. They accomplish this by stabilizing the transition state(s). Enzyme-catalyzed reaction: G (free energy) Reaction coordinate E+P ES ‡ E+S G‡G‡ GG S ‡ SP E

Models of Enzyme-Substrate Interaction Emil Fischer, 19th century Daniel Koshland, 20th century (sequential model for Hb coop.!)

The “Stickase” Enzyme

Factors Contributing to Rate Enhancement by Enzymes 1. Concentration - effective molarity in the active site.effective molarity 2. Orientation - increases the probability of correct bond or orbital alignment. enzyme A B A B k 1 (first order rate constant) Effective molarity = k 1 [s -1 ] / k 2 [M -1 s -1 ] = k 1 / k 2 [M] k 2 (second order rate constant)

3. Strain - weakening of bonds by distortion - exemplified by “stickase” model 4. Chemical catalysis (a catch-all term) major factor for most enzymes major types: acid-base, covalent, metal ion a given enzyme may use several types of chemical catalysis in its mechanism

Combines with the final slide of the lecture

R2R2 Chymotrypsin is a serine protease that cleaves a peptide at Phe/Tyr/Trp (C) - leaving a COO - on Phe/Tyr/Trp

2 R2R2

R2R2 R2R2

To aid in the understanding of slide 15: Acid-base forms of amino acid side chain