Lecture 14 (10/18/17) Reading: Ch6; 190-191, 194-195, 197-198 Problems: Ch6 (text); 7, 24 Ch6 (study guide-facts); 4, 13 NEXT Reading: Ch6; 198-203 Ch6; Box 6-1 Problems: Ch6 (text); 8, 9, 10, 11, 12, 13, 14, 15, 16 Ch6 (study guide-facts); 8, 10, 12, 16, 17, 18, 19, 20, 21 Ch6 (study guide-applying); 1 ENZYMES: Binding & Catalysis A. Catalysis 1. Transition State Theory a. Energetics (thermodynamics) vs. kinetics b. Lower activation energy; negative DDG 2. Catalytic strategies a. binding the transition state (What an enzyme must do) i. Position (proximity) ii. Polarization iii. Strain iv. desolvation b. Example of carbonic anhydrase c. Example of stickase d. Energetic concerns 3. Mechanistic strategies a. How an enzyme does it b. Acid-base catalysis c. Covalent catalysis d. Metal-ion catalysis B. Kinetics-review Lecture 14 (10/18/17) 1
How do enzymes achieve these HUGE rate enhancements? Let s review what governs the rates of chemical reactions: the transition state energy Reaction rate DG (activation energy) OK, what does a similar plot look like using an enzyme? Reaction Coordinate Diagram + DG CAN change this! DG CANNOT change this! The Equilibrium Constant will NEVER be changed by an enzyme How do enzymes achieve these HUGE rate enhancements? Let s review what governs the rates of chemical reactions: the transition state energy Reaction rate DG (activation energy) OK, what does a similar plot look like using an enzyme? Reaction Coordinate Diagram + DG CAN change this! DG CANNOT change this! The Equilibrium Constant will NEVER be changed by an enzyme 2
Can Decrease ΔG DDG DDG = DG cat DG uncat There is always a difference in activation energies that yield a negative DDG. This is the amount of energy that must be supplied somehow to the reaction by the enzyme *Catalytic Strategies versus WHAT must do to lower Activation Energies? -nearly all enzymes do these HOW do lower Activation Energies? - enzymes may use none, one, or more of these *Textbook uses this term a bit incorrectly. What they term Catalytic strategies are really those that answer HOW enzymes decrease the activation energy. The HOW-to strategies are really Mechanistic strategies. 3
Catalytic Strategies Position Effects: bind substrates where they need to be for reaction (rather than depending on random collisions) Polarization of bonds: make substrates more reactive by polarizing bonds (make better nucleophiles, electrophile, or leaving groups) (Electrostatics) Strain of bonds: bind substrates in such a way that they look like products (put strain on bonds that are to be broken (sessile)) De-solvation: assist in removal of water shell around substrates or adding to products upon release (S & P are usually in direct contact with residues at the active site (no water)) (Geometry) Catalytic Strategies EXAMPLE: Carbonic Anhydrase CO 2 + H 2 O H 2 CO 3 H + + HCO 3 Carbonic Bicarbonate Acid Named for the reverse reaction, the dehydration of Carbonic Acid to get water and carbon dioxide Mostly b-structure It needs a Zn 2+ metal cofactor Held in the active site by 3 His residues Fourth ligand is a water molecule 4
10/18/17 Catalytic Strategies EXAMPLE: Carbonic Anhydrase CO2 + H2O H2CO3 H+ + HCO3 Carbonic Acid Bicarbonate Other important residues in the active site are: His-64 Thr-199 Glu-106 Glu-117, Gln-92, 244C=O H2O Zn2+ Catalytic Strategies Reaction Mechanism H+ + CO2 + H2O H2CO3 H+ + HCO3 His-64 His-64 2a H+ His-64 Thr-199 5
Catalytic Strategies CO 2 + H 2 O H 2 CO 3 H + + HCO 3 Position Effects Polarization of bonds Strain of bonds Desolvation His-64 H + + Let s consider how these strategies help pay for lowering the activation energy: Entropy? Position & Strain (but make it more costly) His-64 H + His-64 Enthalpy? Polarization & Desolvation (by binding tightly to substrates as they go through the TS, they pay for the loss from entropy AND lower the un-catalyzed activation energy) 2a Thr-199 Catalytic Strategies CO 2 + H 2 O H 2 CO 3 H + + HCO 3 Transition State Binding H + + His-64 His-64 H + His-64 2a Thr-199 6
Catalytic Strategies CO 2 + H 2 O H 2 CO 3 H + + HCO 3 Transition State Binding Thr-199 What is another example of binding the TS? Illustration of TS Stabilization Idea: Imaginary Stickase DDG DDG DDG = DG M (in textbook) 7
Illustration of TS Stabilization Idea: Imaginary Stickase HOW do lower Activation Energies? - enzymes use may use none, one, or more of these There are THREE major strategies used by enzymes: acid-base catalysis: give and take protons covalent catalysis: change reaction paths metal ion catalysis: use redox cofactors, pk a shifters 8
General Acid-Base Catalysis EXAMPLES: Carbonic Anhydrase Proteases Phosphoglyceromutase Proline Racemase General Acid-Base Catalysis EXAMPLES: Carbonic Anhydrase Proteases Phosphoglyceromutase Proline Racemase 9
General Acid-Base Catalysis Amino Acids Recall, pk a values can shift by orders of magnitude in the microenvironment of the active site Covalent Catalysis A transient covalent bond between the enzyme and the substrate Changes the reaction pathway un-catalyzed: H2O A B A + B catalyzed (X = catalyst): H2O A B + X: A X + B A Requires a nucleophile on the enzyme can be a reactive hydroxyl, thiolate, amine, or carboxylate Which Amino Acids? Ser, Cys, Lys, Asp, Glu + X: + B EXAMPLES: Carbonic Anhydrase Proteases Aminotransferase Aldolase 10
Metal Ion Catalysis Involves a metal ion bound to the enzyme Interacts with substrate to facilitate binding stabilizes negative charges Participates in oxidation reactions EXAMPLES: Carbonic Anhydrase Carboxylpeptidase A Cytochrome oxidase acid-base catalysis: covalent catalysis: metal ion catalysis: His-64 H + + His-64 2a H + His-64 Thr-199 What about our enzyme, carbonic anhydrase? 11
Enzyme Kinetics What Is Enzyme Kinetics? Kinetics is the study of the rate at which compounds react. The rate of enzymatic reaction is affected by: enzyme substrate effectors Temperature Reaction conditions (salts, buffers, ph) Enzyme Kinetics Why Study Enzyme Kinetics? Quantitative description of biocatalysis Determine the order of binding of substrates Elucidate acid-base catalysis Understand catalytic mechanism Find effective inhibitors (drugs) Understand regulation of activity 12
Enzyme Kinetics Review of Chemical Kinetics k 1 Consider a simple reaction: A B [B] k Thermodynamics tells us: K eq = 1 and K eq = [A] k -1 Kinetics tells us: The rate of a chemical reaction (v) is proportional to the concentration of the specie(s) participating in the rate limiting step. v [A] Furthermore, the reaction rate (v) is determined by measuring how much A disappears as a function of time or how much B appears as a function of time. v B Suppose that we can readily measure the disappearance of A. The velocity of the reaction is given by solving the differential equation above to get the formula below, where k 1 is a proportionality constant. v 1 When the velocity of a reaction is directly proportional to a single reactant concentration, the reaction is called a first-order reaction and the proportionality constant has the units s -1. k -1 making product making reactant Review of Chemical Kinetics Enzyme Kinetics When the velocity of a reaction is directly proportional to the concentrations of two reactants, the reaction is called a second-order reaction and the proportionality constant has the units M -1 s -1. Many important biochemical reactions are biomolecular or second-order reactions. The rate equations for these reactions are: or v 1 2 and v 1 [B] During an enzyme catalyzed reaction when the enzyme binds to substrate, it s a pseudo secondorder reaction.. 13