ENZYMES

DEFINITION

a substance that acts as a catalyst in living organisms, regulating the rate at which chemical reactions proceed

without itself being altered in the process

are proteins that direct and accelerate thousands of biochemical reactions in such processes as digestion, energy

capture, and biosynthesis.

ENZYME STRUCTURE Primary structureEnzymes are made up of α amino acids which are

linked together via amide (peptide) bonds in a linear chain. This is the primary structure. The resulting amino acid chain is called a polypeptide or protein. The specific order of amino acids in the protein is encoded by the DNA sequence of the corresponding gene.

Secondary structure Because the hydrogen in the amide group

(NH2) and the oxygen in the carboxyl group (COOH) of each amino acid can hydrogen bond with each other, this means that the amino acids in the same chain can interact with each other. As a result, the protein chain can fold up on itself, and it can fold up in two ways, resulting in two secondary structures: it can either wrap round forming the α-helix, or it can fold on top of itself forming the β-sheet.

Tertiary structure As a consequence of the folding-up of the

2D linear chain in the secondary structure, the protein can fold up further and in doing so gains a three-dimensional structure. This is its tertiary structure.

Quaternary structure Is the three-dimensional structure of a

multi-subunit protein and how the subunits fit together. In this context, the quaternary structure is stabilized by the same non-covalent interactions and disulfide bonds as the tertiary structure. Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers.

Enzymes are proteins

They have a globular shape

A complex 3-D structure

GENERAL CHARACTERISTICS OF ENZYMES

1. Catalytic Efficiency2. Specificity a. Absolute Specificity

b. Relative Specificityc. Stereochemical Specificity

3. Regulation

1. Catalytic Efficiency

Catalysts increase the rate of chemical reactions but are not used up in the

process

Enzymes are not permanently modified and may be used again and again

CO₂ + H₂O H₂CO₃carbonic anhydrase

2. Specificity

unlike other catalysts, enzymes are often quite specific in the type of reaction they catalyze and even the particular substance that will be involved in the reaction

*UREASE catalyzes only the hydrolysis of a single amide, UREA

H₂N – C – NH₂ + H₂O CO₂ + 2NH₃

Ourease

a. Absolute specificity – The characteristic of an enzyme that is acts on one and only substance

b. Relative specificity – The characteristic of an enzyme that it acts on several structurally related substances examples: proteases splits up proteins

phosphotases hydrolyze phosphate esters

c. Stereochemical specificity – The characteristic of an enzyme that is able to distinguish between stereoisomers

example: D-amino acids will not catalyze the reaction of L-amino acids

3. Regulation

Enzymes catalystic behavior can be regulated

Yes! There are each living cell contains thousands of different molecules that could react with each in unlimited number of ways, only a relatively small number of these possible reactions take place because of the enzymes present.

The cell controls the roles of these reactions and the amount of any given product formed by regulating the action of the enzymes

HOW DO ENZYMES WORK?

They increase the rate of reaction by lowering the energy of activation

product

enzyme

substrate

active site

ACTIVE SITE is the location on an enzyme where a substrate is bound and

catalysis occurs

ENZYMATIC REACTION STEPS

1. Substrate approaches active site2. Enzyme-substrate complex forms3. Substrate transformed into

products4. Products released5. Enzyme recycled

1

2

3

ENZYME COFACTORS

COFACTOR (inorganic ion)A nonprotein molecule or ion required by an

enzyme for catalytic activity

COENZYMEAn organic molecule required by an enzyme

for catalytic activity

APOENZYMEA catalytically inactive protein formed by

removal of the cofactor from an active enzyme

Take note:The combination of an apoenzyme and a

cofactor produces an active enzyme:

apoenzyme + cofactor (coenzyme or inorganic ion) active enzyme

*Inorganic ion are metal ions such as magnesium, zinc, and iron.

Examples to help remove your confusion:

1. The enzyme carbonic anhydrase functions only when zinc is present. Rennin needs calcium to curdle milk

2. The coenzyme nicotinamide adenine dinucleotide (NAD⁺), which is necessary part of some enzyme-catalyzed oxidation-reduction reactions, is formed from the vitamin precursor nicotinamide.

Like other cofactors, NAD⁺ is written separately from the enzyme so that the change in its structure may be shown and to emphasize that the enzyme and cofactor are easily separated.

CH₃ – CH – COO⁻ + NAD⁺ CH₃ – C – COO⁻ + NADH + H⁺

OH

O

pyruvate

lactate

lactate dehydrogenase

THE MECHANISM OF ENZYME ACTION

There are, so far, two theories that explain enzymatic actions.

LOCK-AND-KEY THEORYA theory of enzyme specificity proposing that

a substrate has a shape fitting that of the enzyme’s active site, as a key fits a lock.

INDUCED FIT THEORYA theory of enzyme action proposing that the

conformation of an enzyme changes to accommodate an incoming substrate.

LOCK AND KEY MODEL

- The active site has a rigid shape.

-Only substrates with the matching shape can fit

-The substrate is a key that fits the lock of the active site

This explains enzyme specificity and the loss of activity when enzymes denature.

INDUCED FIT MODEL-The active site is flexible, not rigid- The shapes of the enzyme, active site, and

substrate adjust to maximize the fit, which improves catalysis

- There is a greater range of substrate specificity

This explains the enzymes that can react with a range of substrates of similar types

ENZYME VOCABULARY

• Enzyme– helper protein molecule

• Substrate– molecule that enzymes work on

• Products– what the enzyme helps produce

from the reaction• Active site

– part of enzyme that substrate molecule fits into

WHAT AFFECTS ENZYME ACTIVITY?

• Substrate Concentration• Enzyme Concentration• pH• Temperature• Cofactors

– Influence the rate of reaction

• Inhibitors– Presence can interfere with a

reaction can be reversible or irreversible

substrate concentration

Initially, the rate is responsive to increase in substrate concentration. However, at a certain concentration, the rate levels out

and remains constant. This maximum rate occurs because the enzymes is saturated with substrate and cannot work any faster under the conditions

imposed.

enzyme concentration

The rate of a reaction is directly proportional to the concentration of the

enzyme – that is, if the enzyme concentration is doubled, the rate of conversion of substrate to product is

doubled.

pHIt must be regarded that enzymes has different

optimum pH value. That means, they react differently and accordingly to the

environment’s pH.

This variation in enzyme activity with changing pH may be due to the influence of pH on acidic

and basic side chains within the active site.

Most enzymes are denatured by pH extremes.Many enzymes have an optimum pH near 7, the

pH of most biological fluids.

Examples of Optimum pH for Enzyme Activity

temperature

There is a temperature limit beyond which the enzyme becomes vulnerable to

denaturation.

Every enzyme-catalyzed reaction has an optimum temperature, usually in the range 25⁰C-40⁰C. Above or below that value, the reaction rate will be lower.

ENZYME INHIBITIONEnzyme inhibitor is any substance that

can decrease the rate of an enzyme catalyzed reaction.

Is knowing them important? YES!1. The characteristic function of many poisons and

some medicines is to inhibit one or more enzymes and to decrease the rates of the reactions they catalyze.

2. Some substances normally found in cells inhibit specific enzyme-catalyzed reactions and thereby provide a means for the internal regulation of the

cellular metabolism.

Categories of enzyme inhibitors

1. IRREVERSIBLE INHIBITION2. REVERSIBLE INHIBITION a. COMPETITIVE INHIBITOR

b. NONCOMPETITIVE INHIBITOR

Irreversible inhibition

This forms a covalent bond with a specific functional group of the

enzyme and as a result renders the enzyme inactive.A number of very deadly poisons act as irreversible

inhibitors.

Example: cyanide ion- it interferes with the operation of an iron-containing enzyme called cytochrome oxidase.

But not all enzyme inhibitors act as poisons toward the body.

Therapeutic agents antibiotics that inhibit specific enzymes essential to the life processes of bacteria.

Example: Penicillin, which interferes with transpeptidase, an enzyme that is important in bacterial cell wall construction.

Reversible inhibition

This reversibly binds to an enzyme. An equilibrium is established; therefore, the inhibitor can be removed from the enzyme by

shifting the equilibrium.

A. Competitive inhibitor

It binds to the active site of an enzyme and thus “competes” with substrate molecules for the active

site.

EnzymeSubstrate

B. Noncompetitive inhibitors

It bonds to the enzyme at a site other than the active site and changes the

shape of the active site.

Enzyme

Substrate

active site altered

Allosteric or Feed Back Inhibition

The activity of some enzymes, particularly those involved in metabolic pathways, are controlled by a self-regulating mechanism. Some specific substance, most often the product itself, acts as an inhibitor. Such an inhibitor binds to an enzyme at a specific site and modifies the active site of the enzyme. This prevents the binding of substrate molecule. Such sites on the enzymes are called allosteric sites and such enzymes are called allosteric enzymes.

ENZYME NOMENCLATURE AND CLASSIFICATION

Earliest discovered: ends with –in to indicate the enzyme’s protein

composition *pepsin, trypsin, and chymotrypsin

Now: nomenclature system = Enzyme Commission (EC) system

Enzymes are grouped into six major classes on the basis of the reactions they catalyze.

Unambiguous systematic name that specifies the substrate, functional group acted on, type of reaction catalyzed

All ends in – ase Typical example is the HYDROLYSIS

OF UREA

Hydrolysis of urea

H₂N – C – NH₂ + H₂0 CO₂ + 2NH₃

IEC name: urea amidohydrolaseSubstrate: ureaFunctional group: amideType of reaction: hydrolysis

enzymeO

But do not worry! Enzymes are also assigned with common names

Derived by adding –ase to the name of the substrate or to a combination of the substrate and type of reaction.

urea amidohydrolase

Substrate: urea

Common name: Urea + ase = urease

alcohol dehydrogenase

Substrate: alcohol (ethyl alcohol)

Reaction type: dehydrogenation

Common name: alcohol dehydrogenation + ase = alcohol dehydrogenase

Oxidation and reduction

Enzymes that carry out these reactions are called oxidoreductases. For example, alcohol dehydrogenase converts primary alcohols to aldehydes.

In this reaction, ethanol is converted to acetaldehyde, and the cofactor, NAD, is converted to NADH. In other words, ethanol is oxidized, and NAD is reduced. (The charges don't balance, because NAD has some other charged groups.) Remember that in redox reactions, one substrate is oxidized and one is reduced.

Group transfer reactions

These enzymes, called transferases, move functional groups from one molecule to another. For example, alanine aminotransferase shuffles the alpha‐amino group between alanine and aspartate: 

Other transferases move phosphate groups between ATP and other compounds, sugar residues to form disaccharides, and so on.

 Hydrolysis

These enzymes, termed hydrolases, break single bonds by adding the elements of water. For example, phosphatases break the oxygen‐phosphorus bond of phosphate esters:

Other hydrolases function as digestive enzymes, for example, by breaking the peptide bonds in proteins.

Formation or removal of a double bond with group transfer

The functional groups transferred by these lyase enzymes include amino groups, water, and ammonia. For example, decarboxylases remove CO 2 from alpha‐ or beta‐keto acids:

A. Dehydratases remove water, as in fumarase (fumarate hydratase):

B. Deaminases remove ammonia, for example, in the removal of amino groups from amino acids:

Isomerization of functional groups

In many biochemical reactions, the position of a functional group is changed within a molecule, but the molecule itself contains the same number and kind of atoms that it did in the beginning. In other words, the substrate and product of the reaction are isomers. The isomerases (for example, triose phosphate isomerase, shown following), carry out these rearrangements.

Single bond formation by eliminating the elements of water

Hydrolases break bonds by adding the elements of water; ligases carry out the converse reaction, removing the elements of water from two functional groups to form a single bond. Synthetases are a subclass of ligases that use the hydrolysis of ATP to drive this formation. For example, aminoacyl‐transfer RNA synthetases join amino acids to their respective transfer RNAs in preparation for protein synthesis; the action of glycyl‐tRNA synthetase is illustrated in this figure:

USES OF ENZYME Enzymes are catalysts which speed up

biological processes and reactions and are not really used up in the process but are recyclable. Examples of important body enzymes are:

1.Lactate dehydrogenase[LDH]this controls the conversion of pyruvate to

lactate during glycolysis.It is a reversible reaction.This is important during exercise when lactic acid is produced in excess by glucose breakdown and the krebbs' cycle pathway cannot take the whole load immediately.ATP is produced to support the exercising muscles.

2. NADPH DehydogenaseIn the mitochondria, ATP production

within the Krebs cycle axis electron are transferred to NADP molecules to produce about 32 ATP molecules per atom of glucose combusted.

3.Tyrosine kinase inhibitorIn cytotoxics using immune

modulators like transtuzumab ,this enzyme allow the drugs to inhibit proliferating cells by allowing it to bind the receptor molecules

Digestive enzymes

proteases and peptidases split proteins into small peptides and amino acids.

lipases split fat into three fatty acids and a glycerol molecule.

carbohydrases split carbohydrates such as starch and sugars into simple sugars such as glucose.

nucleases split nucleic acids into nucleotides

REFERENCES

Seager, Spencer L. Slabaugh, Michael R. Organic and Biochemistry for Today, Eight Edition. United States of America. Mary Finch. 2014

Mckee, James. Mckee,Trudy. Biochemistry:The Molecular Basis of Life. Boston. McGraw-Hill. 2003

http://en.wikiversity.org/wiki/Enzyme_structure_and_function http://images.tutorvista.com/content/cellular-

macromolecules/noncompetitive-inhibition-process.jpeg http://images.tutorvista.com/content/cellular-macromolecules/

competitive-inhibition-process.jpeg http://www.tutorvista.com/content/biology/biology-iii/cellular-

macromolecules/enzymes-classification.php http://www.cliffsnotes.com/sciences/biology/biochemistry-i/

enzymes/six-types-of-enzyme-catalysts http://en.wikipedia.org/wiki/Digestive_enzyme