Rodney Boyer

Concepts in Biochemistry
Third Edition

Chapter 5:
Enzymes I: Kinetics, Mechanism, and Inhibition

Copyright 2006 by John Wiley & Sons, Inc.

Enzymes
Biological catalyst Protein in nature Reaction specific Nomenclature: often suffix ase (urease, amylase) Ribozymes also biological catalyst; RNA Provide an alternative pathway that will lower the activation energy of reaction

Enzymes and cofactors

Some enzymes are active in their native state (protein enzyme is active) Some enzymes require another chemical entity for activity called cofactor Protein + cofactor = holoenzyme (active) Protein component = apoenzyme (inactive) Cofactors metals (Zn,Cu, Mn, Ca, Mg) - organic molecules (coenzymes: NAD, FAD, Biotin, pyridoxal phosphate refer to Table 6.1) Prosthetic group cofactor covalently bonded to the protein

 In an enzyme-catalyzed reaction
Substrate, S: a reactant Active site: the small portion of the enzyme surface where the substrate(s) becomes bound by noncovalent forces, e.g., hydrogen bonding, electrostatic attractions, van der Waals attractions

Two models of the formation of ES

Lock-and-key model: substrate binds to that portion of the enzyme with a complementary shape
Induced fit model: binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit

Factors affecting rate of enzymecatalyzed reactions

Temperature pH Enzyme concentration Substrate concentration

Point at which the rate of reaction does not change, enzyme is saturated, maximum rate of reaction is reached

Michaelis-Menten Equation

Vmax [S] V= KM + [S]

(an equation for a hyperbola)

Vmax = K2[E]total
K2 or Kcat = turn over number

Transform hyperbolic equation to a linear equation

V init = V max [S] KM + [S] Michaelis-Menten equation

1 V 1 V

KM + [S] Vmax [S] KM Vmax [S] +

KM Vmax [S] 1

[S ] Vmax [S]

Vmax

Enzyme inhibition
Inhibitors Types of E inhibition Irreversible Reversible Competitive Non competitive (pure and mixed) Uncompetitive

Mixed non competitive inhibitor affects the binding of the substrate