ENZYMES

Reff: Advances in Food Biochemistry, Ed. Fatih Yildiz, 2010, CRC Press

Introduction Special kinds of protein molecules:

long chain of amino acids bound by peptide bonds

produced by living cells absolutely essential as catalysts in

biochemical reactions. i.e., controlling the metabolic processes, converting nutrients into energy, breaking down food materials, etc

to catalyze the making and breaking of chemical bonds.

increase the rate of reaction without themselves undergoing permanent chemical changes.

Decrease activation energy enzymes are released again after a reaction ceases and can

continue in another reaction This processes cannot go forever limited stabilities and,

slowly, they become inactive

The catalytic ability of enzymes is due to its particular protein structure.

A specific chemical reaction is catalyzed at a small portion of the surface of an enzyme, which is known as the active site.

Some physical and chemical interactions occur at this site to catalyze a certain chemical reaction for a certain enzyme.

Selection of enzyme:• Cost benefi t (adding

value or reducing production cost)

• Availability, consistency, and quality support (reputation of suppliers)

• Activity (specific substrate alteration by pH, ions, temperature, and inhibitors)

• Ability to modify a reaction’s quality (quality measurement and understanding of an enzyme can control its activity more precisely)

Added substances sometimes increase or decrease the rate of an enzyme-catalyzed reaction without interacting with the enzyme itself.

These substances may interact with substrates or with modifiers or effectors that are already present in the system.

An inhibitor is a substance that diminishes the rate of a chemical reaction; the process is called inhibition.

an inhibitor frequently acts by binding to the enzyme an enzyme inhibitor

An activator is a substance, other than the catalyst or one of the substrates, that increases the rate of a catalyzed reaction.

An activator of an enzyme-catalyzed reaction may be called an enzyme activator if it acts by binding to the enzyme

The advantages An enzyme catalyst highly specific; reducing

the number of side reactions and by-products. A great variety of enzymes exist, which can catalyze a very wide range of reactions.

The rate of an enzyme-catalyzed reaction is usually much faster

the rates of reaction are easily controlled by adjustment of incubation conditions

Only require a small amount mild conditions of temperature and pH,

The disadvantages Sensitive or unstable molecules require more care Expensive in some products, enzymes must be inactivated or

removed after processing which adds to the cost of the product

Like other proteins, enzymes may cause allergic responses

usually coated or immobilised on carrier materials to reduce the risk of inhalation, reduce cost

Characteristics of enzymes High activity. Increase rate

by reducing Ea Selectivity. Active sites3D

pocket/cleft fit only to a specific substrates; may be unable to recognize the substrate minor changes

Regiospecificity. An enzyme can detect differences in the spatial arrangement of atoms in a compound specific ring group

Stereospecificity in the choice of substrate or in the formed product optical isomer L or D

Controllability by the amount of substrate & by other factors (temperature, pH, etc.) active site

Environmentally friendly lower by-product produced. Natural substrates natural products

Enzyme Configuration The enzyme: a protein,

and a combination of one or more parts are called “cofactors.”

An extra molecule is covalently attached to the enzyme, it is referred as the “prosthetic group”

The activity depends on a specific protein molecule and other molecules and ions affect the enzyme structure, facilitating their activity as catalysts.

The polypeptide or protein part of the enzyme is called an apoenzyme; originally inactive proenzyme/zymogen, contains extra amino acid

A cofactor is usually a nonprotein substance, which may be organic a coenzyme, often derived from a vitamin;

inorganic metal ion called a metal ion activator, may be bonded through coordinate covalent bonds.

The role of a cofactor is to activate the protein by changing its geometric shape, or by actually participating in the overall reaction.

The whole enzyme contains a specific geometric shape called the active site where the reaction takes place

Models for how enzymes work

LOCK & KEY Only the right key fits (for for

certain substrate): right size and shape, have charges in the correct place, have the right hydrogen-bond donors and acceptors, and have just the right hydrophobic patches

Why the reaction fast, the mechanism?

Change in structure of S to P complementary to?

INDUCES FIT Binding the correct substrate

change enzyme structure catalytic groups into right position to facilitate reaction

Good substrate fancy part of molecule is necessary to induce (not directly participate) the enzyme to change its conformation and become an efficient catalyst

Bad substrates can not to make the specific interactions that cause the conformation change enzyme stays in its inactive conformation.

Example for glucose-OH & H-OH with hexokinase

Explaining bad substrate not good substrate

Proper arrangement to make reaction fast?

NON PRODUCTIVE BINDING

Poor substrates bind the enzyme in the wrong orientation

catalytic groups and specific interactions that accelerate the reaction of the correct substrate come into play in only a very small number of the interactions between the enzyme and a bad substrate.

In contrast to the induced-fit model, this model does not require a change in the conformation of the enzyme

STRAIN & DISTORTION the binding of S to E

pulls/pushes specific chemical bonds make the subsequent chemical reaction easier

If a bond has to be broken, the enzyme grabs onto both sides of the bond and pulls.

If a bond has to be formed, the enzyme grabs onto both sides and pushes.

Nomenclature Originally nondescriptive names:

rennin curding of milk to start cheese-making processpepsin hydrolyzes proteins at acidic pH

adding the suffix -ase to the name of the substrate with which the enzyme functions, or to the reaction that is catalyzed

New system “International Union of Biochemistry and Molecular Biology (IUBMB)” characterized enzyme for which an EC (Enzyme Commission) number has been provided.

EC classes define enzyme function based on the reaction, which is catalyzed by the enzyme six major classes (general type of chemical reaction which they catalyze)

Each main class contains subclasses, subsubclasses, and subsubsubclasses

6 Classes of enzymeOxidoreductases catalyze oxidation–reduction

reactions in which hydrogen or oxygen atoms or electrons are transferred between molecules.

Includes class of dehydrogenases (hydride transfer), oxidases (electron transfer to molecular oxygen), oxygenases (oxygen transfer from molecular oxygen), and peroxidases (electron transfer to peroxide).

E.g. glucose oxidase (EC 1.1.3.4)

Transferases catalyze the transfer of an

atom or group of atoms (e.g., acyl-, alkyl-, and glycosyl-), from one molecular and/or functional groups to another

but excluding such transfers as are classifi ed in the other groups (e.g., oxidoreductases and hydrolases).

E.g. the aspartate aminotransferase (EC 2.6.1.1)

Hydrolases These involve hydrolytic

reactions and their reversal (degradation of H2O to OH− and H+ products).

This is presently the most commonly encountered class of enzymes within the field of enzyme technology

includes the esterases, glycosidases, lipases, and proteases.

An example of the chymosin (EC 3.4.23.4)

Lyases involve elimination reactions

in which a group of atoms is removed from the substrate.

These catalytic reactions require the addition of groups to a double bond or the formation of a double bond (e.g., C=C, C=N, C=O).

This includes the aldolases, decarboxylases, dehydratases, and some pectinases but does not include hydrolases.

An example is the histidine ammonia-lyase (EC 4.3.1.3).

Isomerases catalyze molecular

isomerizations nclude the epimerases,

racemases, and intramolecular transferases.

An example xylose isomerase (EC 5.3.1.5, d-xylose ketol-isomerase; commonly called glucose isomerase) transformation of α-d-glucopyranose to α-d-fructofuranose

Ligases catalyze the condensation

of two molecules together with the cleavage of ATP or another pyrophosphate bond.

also known as synthetases, form a relatively small group of enzymes, which involve the formation of a covalent bond joining two molecules together, coupled with the hydrolysis of a nucleoside triphosphate. An example is the glutathione synthase (EC 6.3.2.3)