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Principles and Applications ofInorganic, Organic, and Biological

Chemistry

Denniston, Topping, and Caret4th ed

Chapter 20

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Power Point to Accompany

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IntroductionThe proteins which serve as enzymes, Mother

Nature’s catalysts, are globular in nature. Because of their complex molecular structures, they often have exquisite specificity for their substrate molecule and can speed up a reaction by a factor of millions relative to an uncatalyzed reaction. This presentation will describe how enzymes function.

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20.1 Nomenclature and ClassificationOxidoreductases catalyze redox reactions.

Eg. Reductases or oxidases

CH3

COHCOO

-

H+ NAD+

+ NADH + H+

Lactate dehydrogenase

CH3

C OCOO

-

Transferases transfer a group from one molecule to another. Eg. Transaminases catalyze transfer of an amino group, kinases a phosphate group

CHCH2NH2OHOH

OH CHCH2NHOHOH

OH CH3PNMT

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Enzyme Classes, cont.Hydrolases cleave bonds by adding water.

Eg. Phosphatases, peptidases, lipases

Lyases catalyze removal of groups to form double bonds or the reverse. Eg. decarboxylasaes or synthases

O C O CO OOH

HH O H+

carbonicanhydrase

Protein + H2Oamino acidspeptidase

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Enzyme Classes, cont.Isomerases catalyze intramolecular rearrange-

ments. Eg. epimerases or mutases

CHCOO

-

OHCH2O PO3

2-

phosphoglyceratemutase

O PO32-

CHCOO

-

CH2OH

Ligases catalyze a reaction in which a C-C, C-S, C-O, or C-N bond is made or broken.

DNA strand-3'-OH + O PO

O

O-5'-DNA strand-

-

DNA strand-3'-O-

DNA ligase

PO

O

O-

-5'-DNA strand

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NomenclatureWith some historical exceptions, the name for

an enzyme ends in –ase.

The common name for a hydrolase is derived from the substrate. E. g.

Urea: -a + ase = urease

Lactose: -ose + ase = lactase

Other enzymes may be named for the reaction they catalyze. E. g.

Lactate dehydrogenase, pyruvate decarboxylase

But: catalase, pepsin, chymotrypsin, tripsin

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20.2 Enzymes and Activation Energy

An enzyme speeds a reaction by lowering the activation energy. It does this by changing the reaction pathway.

Reaction progress

Free Energy

Products

Reactants Energy change (H) for the reaction

Activation energy

(Ea) for the reaction

Transition state

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20.3 Substrate ConcentrationRates of uncatalyzed reactions increase as

the concentration increases. Rates of enzyme catalyzed reactions behave

as shown below. The first stage is the formation of an enzyme-substrate complex followed by slow conversion to product. Rate is limited by enzyme availability.

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20.4 Enzyme-Substrate ComplexThe following reversible reactions represent

the steps in an enzyme catalyzed reaction.

The first step involves formation of an enzyme-substrate complex, E-S.

E-S* is the transition and E-P is the enzyme-product complex.

E+S E-SStep I

E-S*Step II

E-PE+PStep IV Step III

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Enzyme-Substrate Complex, cont.The part of the enzyme combining with the

substrate is the active site. Active sites are:

Pockets or clefts in the surface of the enzyme. R groups at active site are called catalytic groups.

Shape of active site is complimentary to the shape of the substrate.

The enzyme attracts and holds the enzyme using weak noncovalent interactions.

Conformation of the active site determines the specificity of the enzyme.

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Enzymes ModelsIn the lock-and-key model, the enzyme is

assumed to be the lock and the substrate the key. The two are made to fit exactly. This model fails to take into account the fact that proteins can and do change their conformations to accommodate a substrate molecule.

The induced-fit model of enzyme action assumes that the enzyme conformation changes to accommodate the substrate molecule.

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Enzymes Models, cont.

Insert Fig 20.3

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20.5 Specificity of the E-S ComplexAbsolute: enzyme reacts with only one

substrate.

Group: enzyme catalyzes reaction involving molecules with the same functional group.

Linkage: enzyme catalyzes the formation or break up of only certain bonds.

Stereochemical: enzyme recognizes only one of two enantiomers.

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20.6 Transition State and ProductAs the substrate interacts with the enzyme, its

shape changes and this new shape is less energetically stable. This transition state has features of both substrate and product and falls apart to yield product which dissociates from the enzyme.

1. The enzyme might put “stress” on a bond.2. The enzyme might bring two reactants into

close proximity and proper orientation.3. The enzyme might modify the pH of the

microenvironment, donating or accepting a H+.

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20.7 Cofactors and CoenzymesPolypeptide portion of enzyme (apoenzyme)

and nonprotein prosthetic group (cofactor) make up the active enzyme (holoenzyme).

Cofactors may be metal ions, organic compounds, or organometallic compounds.

A coenzyme, an organic molecule temporarily bound to the enzyme, is required by some enzymes. Most coenzymes carry electrons or small groups.

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Vitamin Coenzyme Process

Thiamine(B1) TPP decarboxylation

Riboflavin(B2) FMN, FAD carry H atoms

Niacin(B3) NAD(P)+ hydride carrier

Pyradoxine(B6) Pyridoxal P amino group transfer

Folic acid tetrahydrofolate one-carbon transfer

Vit A retinal vision, growth

Biotin biocytin CO2 fixing

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Coenzymes, contNicotinic acid

(niacin) is involved in redox reactions.

O

OH OH

NOPO

O

O

O

OH OH

NOPO

O

C

O

NH2

H

N

N N

NH2

(PO32-)NAD+ (NADP+)

+

nicotinamide

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Coenzymes, cont.The nicotinamide part of NAD+ accepts a

hydride (H plus two electrons) from the alcohol to be oxidized. The alcohol loses a proton to the solvent.

N

C

O

NH2

H

R

+R1C

H

H

OH N

C

O

NH2

H

R

H

+ R1C

H

O

oxred+

+ H+Ox form Red form

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Coenzymes, cont.Flavin

coenzymes also serve in redox reactions

N

N

N

NH

O

O

CH3

CH3

OP OO

O

OPO

OO

OH OH

Adenine

CH2

COHCOHCOHCH2

HHHFMN

Flavinmononucleotide

FAD

Flavinadeninedinucleotide

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Coenzymes, cont,The flavin coenzymes accept electrons in the

flavin ring system.

N

N

N

NH

O

O

CH3

CH3

RN

N

N

NH

O

O

CH3

CH3

R H

H

COO

C

H

H

C

H

H

CO

O_ _

COO

C

H

C

H

CO

O_ _

FAD FADH2

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20.8 Environmental EffectsAn enzyme has an

optimum temperature that is usually close to the temperature at which it normally works, ie.

37 oC for humans. Excessive heat can denature a protein.

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Environmental Effects, cont.Enzymes work best

at the correct physiological pH. Extreme pH changes will denature the enzyme. Pepsin (stomach) and chymotrypsin (small intestine) have different optimum pHs.

pepsinChymo-trypsin

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20.9 Regulating Enzyme ActivitySome methods that organisms use to

regulate enzyme activity are:

1. Produce the enzyme only when the substrate is present.

2. Allosteric enzymes

3. Feedback inhibition

4. Zymogens

5. Protein modification

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Allosteric EnzymesEffector molecules change the activity of an

enzyme by binding at a second site.

Some effectors speed up enzyme action (positive allosterism)

Some effectors slow enzyme action (negative allosterism)

E. g. The third reaction of glycolysis places a second phosphate on fructose-6-phosphate. ATP is a negative effector and AMP is a positive effector of the enzyme phosphofructokinase.

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Allosteric Enzymes

Insert Fig 20.11

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Regulation, cont.With feedback inhibition, a product in a series

of enzyme-catalyzed reactions serves as an inhibitor for a previous allosteric enzyme in the series.

A zymogen is a preenzyme. It is coinverted to its active form, usually by hydrolysis, at the active site in the cell. E. g. Pepsinogen is synthesized and transported to the stomach where it is converted to pepsin.

The most common form of protein modification is addition or removal of a phosphate group.

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20.10 Inhibition of Enzyme ActivityIrreversible inhibitors bind tightly, sometimes

even covalently, to the enzyme and thereby prevent formation of the E-S complex.

Reversible competitive inhibitors often structurally resemble the substrate and bind at the normal active site

Reversible noncompetitive inhibitors usually bind at someplace other than the active site. Binding is weak and thus inhibition is reversible.

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20.11 Proteolytic EnzymesProteolytic enzymes cleave the peptide bond

in proteins.They depend on a hydrophobic pocket.Chymotrypsin cleaves the peptide bond at the

carboxylic end of methionine, tyrosine, tryptophan, and phenylalanine.

C CCH3

HNH3

+O

C CH

NH

OC CH

HNH

OO

Chymotrypsin cleaves here

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Proteolytic Enzymes, cont.Chymostypsin: just seen

Trypsin cleaves on the carboxyl side of basic amino acids.

Elastase cleaves on the carboxyl side of glycine and alanine.

These enzymes have different pockets but the catalytic sites remain unchanged during evolution and the mechanism of proteolytic action is the same for all these serine proteases.

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20.12 Enzymes in MedicineDiagnostic

Heart attack: uses levels of lactate dehydrogenase, creatine phosphate, and serum glutamate-oxaloacetate transaminase

Pancreatitis: elevated amylase and lipaseAnalytical Reagents

Urea converted to ammonia via urease and then blood urea nitrogen (BUN) measured.

Replacement TherapyAdminister genetically engineered -

glucocerebrosidase for Gaucher’s disease.

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THE END

Enzymes