Chapter 6: Enzymes Biochemistry

Six classes of enzymes

1. Oxidoreductases 2. Transferases 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases

Enzymes bind TS

BEST

Competitive inhibition

Inhibitor I competes with substrate for binding; i binds active site; i does not affect catalysis

Nonlinear M-M plot can be used to calculate

Km and Vmax by measuring initial reaction velocities at various substrate concentrations

Kinetics of allosteric regulators differ from M-M kinetics

Km is K0.5

The idea that enzymes bind TS best was proposed by

Linus Pauling

The non-covalent enzyme substrate (ES) complex is known as the

Michaelis complex

James Sumner

Performed purification and crystallization of urease and postulated than enzymes are proteins

simple reaction

S -> P

Uncompetitive

V max and Km decrease

Non-competitive

V max decreased Km unchanged

Competitive

V max unchanged Km increases

Km is equal to

Vo is half maximal

Metal ion cofactors

Zn2+, Cu2+, Fe2+

Delta G also equals the

activation energy

enyzmes lower the

activation energy

Covalent irreversible

activation of zymogens, chymotrypsin and trypsin

The active site of some enzymes contain

amino acid functional groups

Reversible inhibitors

bind to and can dissociate from the enzyme; often structural analogs; often used as drugs in medicine

Others may be named after their source or their

board function

Enzymes are what?

catalysts

Urease

catalyzes the hydrolysis of urea

covalent catalysis

change reaction paths

4. Lyases

cleavage of C-O, C-N, and C-C bonds

Km

constant that is a measure of affinity of E for S

Free energy

delta G

S to P

delta G

Maria Manasseina

discovered cell-free fermentation a generation earlier than Buchner

Eduard Buchner

discovered yeast extract could ferment sugar

catalyzed rxns

enzyme uses binding energy of susbstrate to organize the reactants to a fairly rigid ES complex Entropically OK

Rate of enzymatic reaction is affected by:

enzyme, substrate, and temperature

Transition state

first hump

un-catalyzed unimolecular rxns

flexible reactant -> rigid TS (entropically unfavorable)

6. Ligases

formation of C-C, C-O, C-N bonds

transient covalent bond

formed between the enzyme and substrate

Reversible inhibitors can bind

free enzymes and enzyme-substrate complex

Acid-base catalysis

give and take protons

Most enzymes are

globular proteins

2. Transferases

group transfer reactions

3. Hydrolases

hydrolysis reactions

Protease inhibitors are

important drugs

Indinavir, Retrovir, ETC

inhibitors of HIV protease

Enzyme inhibition types

irreversible reversible

Blood coagulation cascade uses

irreversible covalent modification

Non-covalent is for enzymes composed of

multiple subunits and has multiple binding sites

Glycogen phophorlyase in muscle uses

multiple types of regulation (covalent, allosteric, and phophorlylation, and dephophorylation)

Bind for effectors to allosteric sites trigger conformational changes in E than can result in increase/decrease in its rate of substrate binding in which regulation method

non-covalent

Enzyme activity can be regulated by

non-covalent modification, covalent modification, irreversible, and reversible

the metal participates in

oxidation-reduction

Covalent modifications include:

phosphorylation/dephosphorylation, methylation, acetylation, proteolytic cleavage

Covalent regulation-reversible

phosphoryltation, adenylation, acetylation, myrisotoylation, ubiquitination, ADP-ribosylation, methylation

electrostatic catalysis

preferential interactions with TS

Michaelis and Menten

proposed a model for investigation of enzyme rates, the concept of ES complex is central for M-M kinectics

kinetics is the study of

rate at which components react

Enzymes increase

rate of reaction

Irreversible inhibitors

react with enzyme; one inhibitor can permanently shut off one enzyme molecule; they are often powerful toxins but may also be used as drugs

Enzymes do not affect

reaction equilibrium

Catalysts increased what?

reaction rates

More accurate determinatino of these values is using the

reciprocal (Lineweaver-Burk plot)

Under biologically relevant conditions (pH~7 and 37 degrees C) most un-catalyzed reactions are

slow

Proteolytic cleavage

some enzymes are produced as inactive precursors (zymogens) and cleaved by proteases to produce the active forms= irreversible

The metal ions interact with

substate

Enzymes act by binding

substrates

enzymes bind ts better than

substrates

an enzyme catalyzed reaction takes place within

the active site

S ground state

the first lower part of graph

P ground state

the last lowest part of graph

1. Oxidoeructases

transfer of electrons hydride ions or H atoms

5. Isomerases

transfer of groups within molecules to yield isomeric forms

un-catalyzed bimolecular rxns

two free reactants -> single restricted transition state (entropically unfavorable and delta G (+))

proximity model

un-catalyzed bimolecular rxns un-catalyzed unimolecular rxns catalyzed rxns

Enzymes may be named using the suffix "ase" like

urease

metal ion catalysis

use redox cofactors

Captopril

used to regulate BP

JBS Haldane

wrote a treatise named "Enzymes"; suggested thatn weak bonds between enzymes and their substrates might be used to catalyze a reaction