Chapter 6 CHM 341 Fall 2016 Suroviec

Increase likelihood that reactants can interact productively. I. Introduction Biological Catalysts Accelerate biochemical reactions by physically interacting with reactants and products to provide a more favorable pathway for the transformation of one to another. Increase likelihood that reactants can interact productively. CANNOT promote reactions where G>0.

II. General Properties Higher Reaction Rates Milder reaction conditions Greater reaction specificity Capacity for regulation

Normally named by adding “-ase” to the name of enzyme’s substrate A. Nomenclature Normally named by adding “-ase” to the name of enzyme’s substrate Currently most enzymes are named by using a more systematic method International Union of Biochemistry and Molecular Biology

Uses non-covalent forces to bind the substrate into the active site B. Specificity Uses non-covalent forces to bind the substrate into the active site

II. Activation Energy and Reaction Coordinates One understanding of how enzymes catalyzes come from transition state theory Intermediate must be formed These are high energy and unstable

II. Activation Energy and Reaction Coordinates Reactants generally approach using path of LOWEST energy Reaction Coordinate

II. Activation Energy and Reaction Coordinates No longer symmetrical - why? G‡ =

II. Activation Energy and Reaction Coordinates From the Arrehenius equation Reaction rates depend on energy and frequency of collisions

II. Activation Energy and Reaction Coordinates Reactions usually occur in 2 steps 2 transition steps = 2 activation barriers

II. Activation Energy and Reaction Coordinates Catalysts reduce G‡ Provide reaction pathway with transition state whose free energy is lower than that in uncatalyzed reaction

III. Catalytic Mechanisms Cofactors and Coenzymes In an enzyme, functional groups in the active site can perform the same catalytic faction as in chemical reactions such as acid/base reactions, transient covalent bonds and charge-charge interactions. Functional groups cannot do redox reactions or group transfer reactions. For those you need a bound cofactor.

B. Acid-Base Catalysis Acid catalysis is process in which a proton is transferred between the enzyme and the substrate

B. Covalent or Nucleophilic Catalysis Accelerates reaction through transient formation of catalyst – substrate covalent bond Need nucleophilic group on catalyst with electrophilic group on substrate

Mediate redox reactions D. Metal Ion Catalysis Metalloenzymes Fe2+, Cu2+ Mediate redox reactions Promote reactivity of other groups in active sites by electrostatic effects

E. Transition state stabilization Bind the transition state of the reaction it catalyzes with greater affinity than its substrates or products Binding transition state increases its concentration and increases reaction rate

F. Catalysis through Proximity/Orientation Bring reactants close together Binding causes conformational shift

IV. Structure and Function The structure and mechanism can reveal quite a bit about an enzyme’s function

S  P Progress of this reaction can be expressed as a velocity A. Reaction Kinetics S  P Progress of this reaction can be expressed as a velocity

A. Reaction Kinetics When enzyme concentration is help constant the reaction velocity will vary with [A]

V. Michaelis – Menton Eqn. Rate equations describe chemical processes Unimolecular reactions Bimolecular reactions

B. Michaelis Menton Equation is rate equation Simplest cases enzyme binds to substrate before converting to product The reaction of E + P converting back to ES is a step that we assume does NOT happen.

B. Michaelis Menton Equation We can measure n by choosing the experimental conditions We then further choose experimental conditions to simplify the calculations: STEADY STATE

C. Michaelis Constant (Km) and Initial Velocity (n) and Maximal Velocity (Vmax)

KM is unique for each enzyme- substrate pair C. Michaelis Constant (Km) and Initial Velocity (n) and Maximal Velocity (Vmax) Occurs a high substrate concentration when enzyme is saturated At substrate concentration at which [S] = KM So if enzyme has small Km achieves max catalytic efficiency at low [S] KM is unique for each enzyme- substrate pair

C. Michaelis Constant (Km) and Initial Velocity (n) and Maximal Velocity (Vmax) Michaelis Constant is a combination of 3 rate constants that is experimentally determined.

D. kcat catalytic constant = turnover # How fast an enzyme operates after it has selected and bound its substrate. Number of catalytic cycles that each active site undergoes per unit time

E. kcat/KM = measure of efficiency Enzyme effectiveness depends on ability to bind substrates and rapidly convert

F. Analysis: Find Vmax , KM High values of [S] lead to vo asymptotically reaching Vmax Use linear plot Lineweaver-Burk

G. Exceptions to M-M Model 1. Multi-substrate reaction

G. Exceptions to M-M Model 2. Multi-step reactions 3. Non-hyperbolic reaction

Substance that reduces an enzyme’s activity by influencing VI. Inhibition Substance that reduces an enzyme’s activity by influencing Binding of substrate Turnover number Variety of mechanisms Irreversible enzyme inhibitors Inactivators Reversible Diminish enzyme’s activity by interacting reversibly Structurally resemble substrates Affect catalytic activity without interfering with substrate binding A. Competitive Inhibition Compete directly with normal substrate for binding site Resemble substrate Specifically binds to active site Product inhibition

A. Competitive Inhibition Transition state analogs Depends on inhibitor binding selectively with RAPID equilibrium

A. Competitive Inhibition M-M equation for competitive inhibition reaction

1. KI can be measured

B. Transition State Inhibitors Inhibitor binds to ES complex Not to free enzyme

Interact in a way with the enzyme that affects substrate binding C. Mixed Inhibition Interact in a way with the enzyme that affects substrate binding

III. Allosteric Regulation Organism must be able to regulate catalytic activities Metabolic processes Respond to changes in environment Control of enzyme availability Amount of given enzyme in a cell depends on its rate of synthesis and its rate of degradation Control of enzyme activity Catalytic activity controlled through structural alteration Can cause large changes in enzymatic activity

Chymotrypsin