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Dep. of Chemistry & Biochemistry Prof. Indig. Chemistry 501 Handout 6 Enzymes Chapter 6. Lehninger. Principles of Biochemistry. by Nelson and Cox, 5 th Edition; W.H. Freeman and Company. With exception of a small group of catalytic RNA molecules, all enzymes are proteins

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Dep. of Chemistry & Biochemistry

Prof. Indig

Chemistry 501 Handout 6EnzymesChapter 6

Lehninger. Principles of Biochemistry.

by Nelson and Cox, 5th Edition; W.H. Freeman and Company


With exception of a small group of catalytic RNA molecules, all enzymes are proteins

Largest class of proteins. More than 3000 enzymes known. Enzymes are biological catalysts that accelerate reactions. Enzymes are generally highly specific and react with only one substrate to form one product and can enhance reaction rates by as much as 1017.

Some enzymes requirecofactors/ coenzymesfor activity

Coenzymes act as transient carriers of specific functional groups

A cofactor or coenzymes that is very tightly or even covalently bound to the enzyme protein is called aprosthetic group.

Complete, catalytically active enzyme:holoenzyme

Only protein part (withoutcofactorand/orcoenzyme): apoenzyme or apoprotein


Enzymes are classified by the reactions they catalyze

International Classification System (nomenclature):

(Four-part classification number and asystematic name)

Systematic name: ATP:glucose phosphotransferase

Classification number:

2. --> Transferase (class)

7. --> phosphotransferase (subclass)

1. --> phosphotransferase with a hydroxyl group as acceptor

1. --> D-glucose as the phosphoryl group acceptor

ATP + D-glucose --> ADP + D-glucose-6-phospate



Binding of a substrate to an enzyme at the active site

Representation of a simple

enzymatic reaction

Enzymes affect reaction rates,

not equilibria

E + SESEPE + P

Reaction coordinate diagram for a chemical reaction

Reaction coordinate diagram comparing enzyme-catalyzed

and uncatalyzed reactions






Reaction rate = V = k [S]

If the rate depends only on the

concentration of S (first-order)

From the Transition-State Theory:


Weak interactions between enzyme and substrate are optimized in the transition state

The energy derived from enzyme-substrate

interaction is called binding energy, DGB

Enzyme active sites are complementary not

to the substrate per se, but to the transition

state through which substrates pass as they

are converted into products during an

enzymatic reaction

Complementary shapes of a substrate and its binding site on the enzyme

Role of binding energy in catalysis

An imaginary enzyme (sticase) designed to catalyze breakage of a metal stick


How a catalyst circumvents unfavorable charge

development during cleavage of a amide

Rate enhancements by entropy reduction







Hydrolysis of an amide bond - same reaction as

that catalyzed by chymotrypsin and other proteases


Amino acids in general acid-base catalysis

Covalent and general acid-base catalysis

First step of the reaction



Amino acid side chains and the functional groups of some cofactors can serve as nucleophiles in the

formation of covalent bonds with substrates


Enzyme Kinetics

Effect of substrate concentration on the initial velocity

of an enzyme-catalyzed reaction

Michaelis-Menten kinetics

initial rate measurements

[S] >> [E]

[ES] ~ constant

V0 = K2[ES]

Michaelis constant


Many enzymes catalyze reactions with two or more substrates

Common mechanisms for enzyme-catalyzed bisubstrate reactions


Pre-steady state kinetics can provide evidence for specific reaction steps

Ternary complex is formed

in the reaction

(as indicated by the intersecting lines)

Ping-Pong (double displacement)



Irreversible inhibition

Reaction of chymotrypsin with


irreversibly inhibits the enzyme

Suicide inactivators


mechanism-based inactivators


Examples of Enzymatic Reactions

Chymotrypsin is a protease specific for peptide bonds adjacent to aromatic amino acids

(Trp, Tyr, Phe)

Key active-site amino acid

residues Ser195, His57, and


Aromatic amino

acid side chain

Pocket in which the amino

acid side chain of the

substrate is bound

Three polypeptide chains linked

by disulfide bonds


The chymotrypsin mechanism

involves acylation and

deacylation of a Ser residue


Regulatory Enzymes

Allosteric enzymes undergo conformational changes in response to modulator binding

Conformational change

Subunit interactions in an

allosteric enzyme, and

interactions with inhibitors

and activators


Two views of the regulatory enzyme aspartate transcarbamoylase

This allosteric regulatory enzyme has two stackedcatalytic clusters, each with three

catalytic polypeptide chains (in shades of blueand purple) and three regulatoryclusters, each with two regulatory peptide chains (in redand yellow).

Modulator binding produces large changes in enzyme conformation and activity


Feedback inhibition

Buildup of the end product ultimately

slows the entire pathway

In many pathways a regulatory

step is catalyzed by an

allosteric enzyme

Example of heterotropic

allosteric inhibition


Phosphoryl groups affect the structure and catalytic activity of enzymes

Regulation of muscle glycogen phosphorylase activity by multiple mechanisms


Some enzymes and other proteins are regulated by proteolytic cleavage of a precursor

Activation of zymogens by

proteolytic cleavage