Enzymes Nomenclature

7/27/2019 Enzymes Nomenclature

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19.1 Nomenclature and

Classification

Enzymes are often classified by placing themin categories according to the reactions thatthey catalyze:

1. Oxidoreductase

2. Transferase

3. Hydrolase

4. Lyase5. Isomerase

6. Ligase


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Classification of Enzymes

Oxidoreductases catalyze redox reactions

Reductases

Oxidases

Transferases transfer a group from one

molecule to another

Transaminases catalyze transfer of an amino group

Kinases transfer a phosphate group

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Hydrolases cleave bonds by adding waterPhosphatases

Peptidases

Lipases

Lyases catalyze removal of groups to form

double bonds or the reverse break double

bondsDecarboxylases

Synthases19.1

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Isomerases catalyze intramolecularrearrangements

Epimerases

Mutases

Ligases catalyze a reaction in which a C-C,

C-S, C-O, or C-N bond is made or broken

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Nomenclature of Enzymes In most cases, enzyme names end inase

The common name for a hydrolase is derivedfrom the substrate Urea: remove -a, replace with -ase = urease

Lactose: remove -ose, replace with -ase = lactase

Other enzymes are named for the substrate andthe reaction catalyzed Lactate dehydrogenase

Pyruvate decarboxylase

Some names are historical - no direct

relationship to substrate or reaction type Catalase

Pepsin

Chymotrypsin

Trypsin

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19.2 The Effect of Enzymes on the

Activation Energy of a Reaction

An enzyme speeds a reaction by lowering the activationenergy, changing the reaction pathway This provides a lower energy route for conversion of substrate to

product

Every chemical reaction is characterized by an equilibriumconstant, Keq, which is a reflection of the difference inenergy between reactants, aA, and products, bB


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Diagram of Energy Difference

Between Reactants and Products

The uncatalyzed reaction has a large activationenergy,Ea, seen at left

In the catalyzed reaction, the activation energyhas been lowered significantly increasing the

rate of the reaction19.2

EffectofEnzyme

son

Act

ivation

Energy


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19.3 The Effect of SubstrateConcentration on Enzyme-

Catalyzed Reactions Rates of uncatalyzed reactions increase as the substrateconcentration increases

Rates of enzyme-catalyzed reactions show two stages The first stage is the formation of an enzyme-substrate complex

This is followed by slow conversion to product

Rate is limited by enzyme availability

Uncatalyzed Enzyme-CatalyzedReaction Reaction


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19.4 The Enzyme-Substrate

Complex These reversible reaction steps represent the steps in an

enzyme catalyzed reaction

The first step involves formation of an enzyme-substratecomplex, E-S

E-S* is the transition state

E-P is the enzyme-product complex


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Enzyme-Substrate Complex

Details The part of the enzyme combining with the

substrate is the active site

Active sites characteristics include:

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 ofthe substrate

The enzyme attracts and holds the enzyme using weaknoncovalent interactions

Conformation of the active site determines thespecificity of the enzyme

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TheEnzym

e-Substrate

Comp

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Lock and Key Enzyme Model

In the lock-and-key model, the enzyme isassumed to be the lock and the substrate the key

The enzyme and substrate are made to fit exactly

This model fails to take into account proteins

conformational changes to accommodate a substrate

molecule

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TheEnzym

e-Substrate

Comp

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Induced Fit Enzyme Model

The induced-fit model of enzyme action assumes

that the enzyme active site is more a flexible

pocket whose conformation changes to

accommodate the substrate molecule

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TheEnzym

e-Substrate

Comp

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Classes of Enzyme Specificity

1. Absolute: enzyme reacts with only one

substrate

2. Group: enzyme catalyzes reaction involving

any molecules with the same functional group3. Linkage: enzyme catalyzes the formation or

break up of only certain category or type of

bond

4. Stereochemical: enzyme recognizes only one

of two enantiomers19.5

Specificityoft

he

E

nzyme-SubstrateCom

plex


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19.6 The Transition State and

Product Formation

How does the enzyme promote a faster chemical

reaction?

As 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


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Possible Types of Transition

State Changes1. The enzyme might put stress on a bond

facilitating bond breakage

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TheTran

sitionS

tate

andProductFormation


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State Changes

2. The enzyme might bring two reactants into

close proximity and maintain proper

orientation

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TheTran

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tate

andProductFormation


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State Changes

3. The enzyme might modify the pH of the

microenvironment, donating oraccepting a H+

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TheTran

sitionS

tate

andProductFormation


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19.7 Cofactors and Coenzymes

Active enzyme / Holoenzyme: Polypeptide portion of enzyme (apoenzyme)

Nonprotein prosthetic group (cofactor)

Cofactors are bound to the enzyme for it to maintain

the correct configuration of the active site Metal ions Organic compounds

Organometallic compounds


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Coenzymes

A coenzyme isrequired by someenzymes

An organic moleculebound to the enzymeby weak interactions /Hydrogen bonds

Most coenzymes carryelectrons or small

groups Many have modified

vitamins in theirstructure

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Cofac

torsand

Coenzy

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Water-Soluble Vitamins and

Their Coenzymes

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torsand

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Nicotinamide Adenine Dinucleotidein Oxidized and Reduced Forms

19.7Cofac

torsand

Coenzy

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NAD+ to NADH Mechanism

The nicotinamide part of NAD+ accepts a hydride

ion (H plus two electrons) from the alcohol to be

oxidized

The alcohol loses a proton (H+ ) to the solvent

N

C

O

NH2

H

R

+

R1C

H

H

OHN

C

O

NH2

H

R

H

+ R1C

H

O

ox

red+

Oxidized form Reduced form

+H+

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torsand

Coenzy

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Two Other Adenine

Dinucleotide Coenzymes

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torsand

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19.8 Environmental Effects The environment surrounding

an enzyme can have a directeffect on enzyme function

Enzymes work best within aparticular range of pH

Extreme pH changes willdenature the enzyme,destroying its catalytic ability

Pepsin (stomach)

Chymotrypsin (small intestine)

have different optimum pHsTop panel at right - a

representative pH rangeBottom panel at rightspecific

examples of pH ranges for 2

enzymes


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Temperature Effects

An enzyme has an optimumtemperature associated withmaximal function

The rate of an uncatalyzedreaction will increase

proportionally withtemperature increase

Optimum temperature isusually close to thetemperature at which the

enzyme typically exists 37oC for humans

Excessive heat can denature aenzyme making it completely

nonfunctional1

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EnvironmentalEffects


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19.9 Regulation of Enzyme Activity

One of the major ways that enzymes differ fromnonbiological catalysts is in the regulation ofbiological catalysts by cells

Some methods that organisms use to regulateenzyme activity are:

1. Produce the enzyme only when the substrateis presentcommon in bacteria

2. Allosteric enzymes3. Feedback inhibition

4. Zymogens

5. Protein modification


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Allosteric Enzymes

Effector molecules change the activity of anenzyme by binding at a second site

Some effectors speed up enzyme action (positiveallosterism)

Some effectors slow enzyme action (negative allosterism)

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Allosteric Enzymes in Metabolism

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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Feedback Inhibition

Allosteric enzymes are the basis for feedbackinhibition

With feedback inhibition, a product late in aseries of enzyme-catalyzed reactions serves as

an inhibitor for a previous allosteric enzymeearlier in the series

In this example, product F serves to inhibit theactivity of enzyme E1 Product F acts as a negative allosteric effector on

one of the early enzymes in the pathway

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Proenzymes

A proenzyme, an enzyme made in aninactive form

It is converted to its active form

By proteolysis (hydrolysis of the enzyme)When needed at the active site in the cell

Pepsinogen is synthesized and transported to the

stomach where it is converted to pepsin

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Proenzymes of the Digestive

Tract

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Protein Modification

In protein modification a chemical group iscovalently added to or removed from the

protein

Covalent modification either activates or turns off

the enzyme The most common form ofprotein modification

is addition or removal of a phosphate group

This group is located at the R group (with a free

OH) of: Serine

Threonine

Tyrosine

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19.10 Inhibition of Enzyme Activity

Chemicals can bind to enzymes and eliminate ordrastically reduce catalytic activity

Classify enzyme inhibitors on the basis of

reversibility and competition

Irreversible inhibitors bind tightly 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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Irreversible Inhibitors

Irreversible enzyme inhibitors bind very tightlyto the enzyme

Binding of the inhibitor to one of the R groups of a

amino acid in the active site

This binding may block the active site binding groups so

that the enzyme-substrate complex cannot form

Alternatively, an inhibitor may interfere with the catalytic

group of the active site eliminating catalysis

Irreversible inhibitors include: Arsenic

Snake venom

Nerve gas

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Reversible, Competitive Inhibitors

Reversible, competitive enzyme inhibitors arealso calledstructural analogs

Molecules that resemble the structure and chargedistribution of a natural substance for an enzyme

Resemblance permits the inhibitor to occupy theenzyme active site

Once inhibitor is at the active site, no reaction canoccur and the enzyme activity is inhibited

Inhibition is competitive because the inhibitorand the substrate compete for binding to theactive site

Degree of inhibition depends on the relativeconcentrations of enzyme and inhibitor

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R ibl C i i


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Reversible, Competitive

Inhibitors

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R ibl N titi


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Reversible, Noncompetitive

Inhibitors

Reversible, noncompetitive enzymeinhibitors bind to R groups of aminoacids or to the metal ion cofactors

This binding is weak

Enzyme activity is restored when theinhibitor dissociates from the enzyme-inhibitor complex

These inhibitors: Do not bind to the active site

Do modify the shape of the active site oncebound elsewhere in the structure

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19.11 Proteolytic Enzymes

Proteolytic enzymes cleave the peptide bond in

proteins These enzymes break the peptide bonds that maintain the

primary protein structure

These enzymes specificity depend on a

hydrophobic pocket A cluster of hydrophobic amino acids brought togetherby the 3-D folding of the protein chain

Chymotrypsin cleaves the peptide bond at thecarboxylic end of:

Methionine Tyrosine

Tryptophan

Phenylalanine

S ifi i f h P l i


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Specificity of the Proteolytic

Enzyme, Chymotrypsin

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P t l ti E


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Proteolytic Enzymes

and Evolution

Pancreatic serine proteases are a category of

enzymes which all hydrolyze peptide bonds Appear to have arisen through divergent evolution

from a common ancestor

Similar primary structures Similar tertiary structures Different specificities

Each enzyme has a different pocket to fit the

specificity for the side chains of their substratesDifferent keys fit different locks

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Proteolytic Enzymes and Evolution

Chymotrypsin: cleaves peptide bonds on the carbonyl side ofaromatic amino acids and large, hydrophobic amino acids

Trypsin: cleaves on the carbonyl side of basic amino acids

Elastase: cleaves on the carbonyl side of Gly and Ala

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19.12 Uses of Enzymes in Medicine Diagnosticenzyme levels altered with disease

Heart attack: Lactate dehydrogenase

Creatine phosphate

Serum glutamate-oxaloacetate transaminase (SGOT)

Pancreatitis: Amylase

Lipase

Analytical reagentsenzyme used to measure anothersubstance

Urea converted to NH3 via urease Blood urea nitrogen (BUN) measured

Replacement therapy Administer genetically engineered b-glucocerebrosidase for

Gauchers disease

Documents

Enzymes Nomenclature