Chapter 5: Enzymes: Core Concepts and Kinetics

Exam 2

catalyst

An agent that enhances the rate of a chemical reaction without being permanently affected itself

enzyme

A biological macromolecule that acts as a catalyst for a biochemical reaction

riboenzyme

RNA molecules that display enzymatic activity

properties of enzymes

1. speed: can accelerate rates of reaction by a factor of a billion or more

2. specificity for substrated

substrate

A reactant in a chemical reaction, binds to enzyme

proteases

A class of enzymes that hydrolyze the peptide bonds between amino acids, thus digesting proteins

papain

cleaves any peptide bond, no specificity for sequence/side chains

trypsin

digestive enzyme, only cleaves peptide bonds on C-terminal side of K or R

thrombin

involved in blood clotting, only cleave R-G in specific peptide sequences

classes of enzymes

1. oxidoreductases

2. transferases

3. hydrolases

4. lyases

5. isomerases

6. ligases

7. translocases

oxidoreductases

catalyze oxidative-reduction reactions (transfer of electrons)

transferases

group transfer

hydrolases

hydrolysis reactions (transfer of functional groups to water)

lyases

addition or removal of groups to form double bonds

• cleavage of C-C, C-O or C-N by elimination

• leaves double bonds/rings or addition of groups to double bonds

isomerases

catalyze isomerization (intramolecular group transfer)

ligases

join 2 substrates together at the expense of ATP (or similar molecule) hydrolysis

• formation of bonds (C-C, C-N, C-O, C-S) via condensation reaction coupled to cleavage of ATP

translocases

movement of ions or molecules across membrane, or separation of ions and molecules within a membrane

exergonic

spontaneous, negative delta G

endergonic

non-spontaneous, positive delta G

cofactor

A small molecule on which the catalytic activity of an enzyme may depend

apoenzyme

An enzyme without its cofactor(s)

holoenzyme

A complete and functional enzyme that consists of the protein component forming the main body of the enzyme (the apoenzyme) and any necessary cofactors

metals

category of cofactor (Mg2+, Zn2+, Se)

co-enzymes

category of cofactor, small organic molecules (FAD, NAD, CoA)

prosthetic group

A coenzyme that is tightly bound or covalently linked to an enzyme such that it does not readily dissociate but instead remains continuously associated with an enzyme

• uncharged in overall reaction

• behave like second substrate (bind to enzyme, are changed by it and released by enzyme)

transition state

A chemical species that has the highest free energy and the lowest concentration of those on the pathway from a substrate to a produc

Gibbs free energy of activation

The energy required to form the transition state from the substrate of a reaction when considered from a particular direction

Enzyme-substrate complex (ES complex)

active site

A specific region of an enzyme that binds the enzyme’s substrate and carries out catalysis

induced fit

The modification of the shape of an active site in an enzyme, toward a structure complementary to the transition state, after the substrate has been bound

binding energy

The free energy released in the formation of the noncovalent interactions between enzyme and substrate that facilitate the formation of the transition state

KM (Michaelis constant)

The concentration of substrate at which an enzyme is operating at one-half maximum velocity

Vmax (maximal rate)

The theoretical maximum velocity of an enzyme catalyzed reaction at infinite substrate concentratioAn equation that expresses the initial velocity (V0)of an enzyme-catalyzed reaction in terms of maximum velocity, Vmax, substrate concentration, [S], and the Michaelis–Menten constant, KM

Michaelis-Menten equation

An equation that expresses the initial velocity (V0)of an enzyme-catalyzed reaction in terms of maximum velocity, Vmax, substrate concentration, [S], and the Michaelis–Menten constant, KM

Lineweaver-Burk plot

A plot of 1/V0 versus 1/[S] yields a straight line with a y-intercept of 1/Vmax and a slope of KM/Vmax. Also called a double-reciprocal plot.

elasticity

The responsiveness of the velocity of an enzyme to changes in substrate concentration. Diminishes as substrate concentrations increase significantly above the KM value

turnover number (kcat)

The number of substrate molecules converted into product by an enzyme active site in a unit time when the enzyme is fully saturated with substrate; equal to the kinetic constant k2

kcat/KM (specificity constant)

A single number that directly relates the rate of a reaction to the concentration of the reactant and allows comparison of the efficiency of an enzyme capable of reacting with different substrates

sequential reaction

A reaction having multiple reactants, in which all substrates bind to the enzyme before any product is released. Thus, in a reaction with two substrates, a ternary complex of the enzyme and both substrates forms

sequential reaction (ordered)

the substrates bind the enzyme in a defined sequence

sequential reaction (random)

the order of the addition of substrates and the release of products is arbitrary

Double-displacement reaction (Ping-Pong reaction)

A reaction having multiple substrates in which one or more products are released before all substrates bind the enzyme. The defining feature of these reactions is the formation of a substituted-enzyme intermediate

allosteric enzymec

An enzyme having multiple active sites and/or distinct regulatory sites that control the flux of biochemicals through a metabolic pathway

competitive inhibition

The reduction in the rate of enzyme activity observed when a reversible inhibitor binds only to the free enzyme, not to the substrate-bound enzyme

uncompetitive inhibition

Reversible enzyme inhibition distinguished by the fact that the inhibitor binds only to the enzyme–substrate complex and not to the free enzyme

pure noncompetitive inhibition

The reduction in the rate of enzyme activity observed when a reversible inhibitor binds equally well to both the enzyme–substrate complex and to the free enzyme

mixed noncompetitive inhibition

The reduction in the rate of enzyme activity observed when a reversible inhibitor binds significantly to both the enzyme–substrate complex and to the free enzyme but with different affinities

transition-state analog

A compound resembling the transition state of a catalyzed reaction

group-specific reagent

A reagent that reacts with specific R groups (side chains) of amino acids

affinity label/reactive substrate analog

A substrate analog used to map the active site of an enzyme by binding to the active site and forming a covalent bond with a nearby amino acid

mechanism-based/suicide inhibitor

An inhibitor that binds to an enzyme as a substrate and initiates the normal catalytic mechanism, but via a subsequent mechanism generates a chemically reactive intermediate that inactivates the enzyme irreversibly through covalent modification