ENZYMES

1. CELL BIOLOGY - BIOMOLECULES INTRODUCTION

2. CARBOHYDRATES

3. PROTEINS

4. LIPIDS

5. NUCLEIC ACIDS

6. ENZYMES

1. ENZYMES

•Enzymes can be defined as very specific, proteinaceous, biocatalysts.

•They enhance the rate of a biochemical reaction without themselves undergoing any change and without affecting the nature of final product.

•They continue to work as long as the substrate is present and is totally converted into the product.

• Enzymology can be defined as the study of the composition and function of the enzyme.



2. Classification and Nomenclature

The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers; each enzyme is described by a sequence of four numbers preceded by "EC", which stands for "Enzyme Commission".



On the basis of mechanism the first number broadly classifies the enzyme as:

Enzyme Involved in Example

EC 1, Oxidoreductases

Catalyses oxidation/reduction reactions, mostly involving transfer of hydrogen atoms or ions from one molecule to another

Cytochrome oixidase

EC 2, Transferases

transfer a functional group (e.g. a methyl or phosphate group) from one kind of molecule to another

Transpeptidase

EC 3, Hydrolases

Catalyses the hydrolysis of various bonds by addition of water, such as lipases.

lipases

EC 4, Lyases

By means other than hydrolysis and oxidation lyases are capable of cleaving various bonds

Histidine decarboxylase- it splits C-C bond of histidine, forming CO2 and histamine

EC 5, Isomerases

Catalyses isomerization changes within a single molecule

Phoshoglucomutase acts on glucose-6-phosphate to form fructose-6-phosphate

EC 6, Ligases

Ligates two molecules with covalent bonds using the energy supplied from the breakdown of ATP.

DNA ligase is used to repair breaks in DNA molecules



• These sections are subdivided by other features such as the substrate, products, and chemical mechanism.

• An enzyme is fully specified by four numerical designations.

•For example, hexokinase (EC 2.7.1.1) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule containing an alcohol group (EC 2.7.1).



3. Types of Enzymes

•There are two types of enzymes on the basis of structure i.e. simple enzymes and conjugated enzymes.

Simple Enzymes can be defined as enzymes which are composed of only proteins. E.g. Pepsin

Conjugated Enzymes can be defined as enzymes which are composed of protein and non-protein component known as cofactor.Protein content of the conjugated enzyme is known as apoenzyme.

Holoenzyme (Complete conjugated enzyme) = Apoenzyme (Protein part) + Co-factor (Non-protein part)



4. Cofactors

(a) Cofactors (Organic in Nature)

(i) Prosthetic Groups:

• Prosthetic groups help proteins bind other molecules, act as structural elements, and act as charge carriers.

•An example of a prosthetic group is heme in hemoglobin, myoglobin, and cytochrome.

•The iron (Fe) found at the center of the heme prosthetic group allows it to bind and release oxygen in the lung and tissues, respectively.

• Vitamins are also examples of prosthetic groups.

(ii) Coenzymes:

•These are small non-proteinaceous molecules organic in nature which provide a transfer site for a functioning enzyme.

•They are intermediate carriers of an atom or group of atoms, allowing a reaction to occur.

•Many (not all) are vitamins or are derived from vitamins.



(b) Cofactors (Inorganic in Nature)

Metal ions:

•Many enzymes function with a bound metal ion in the active site. Such enzymes are known as metalloenzymes.

•In daily nutrition, this kind of cofactor plays a role as the essential trace elements.

•Example: Mg2+ is used in glycolysis.

•In the first step of glycolysis, glucose is converted to glucose 6-phosphate, before ATP is used to give ADP and one phosphate group as it stabilizes the other two phosphate groups so it is easier to release only one phosphate group



5. Mechanism of Enzyme Action

•There is a potential energy barrier to cross by the reactant molecules to get converted into a product. This potential energy barrier is termed as activation energy.

•All molecules have variable amount of energy and generally only few have enough energy for the reaction.

•The lower the potential energy barrier to reaction, the more reactants have enough energy and, hence, the faster the reaction will occur.

•All enzymes, function by forming a transition state, with the reactants, of lower free energy than would be found in the uncatalyzed reaction.

Graph showing mechanism of enzyme action



6. The Mode of Action of Enzymes - Theories

(a) Lock and Key Model

• Emil Fischer first postulated "The lock and key model" theory in 1894, based on the high specificity of enzymes.

• In lock-and-key model, the enzyme-substrate interaction suggests that the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another.

• Like a key into a lock, only the correct size and shape of the substrate (the key) would fit into the active site (the key hole) of the enzyme (the lock).

(b) The Induced Fit Model

• The Induced Fit model was suggested by Daniel Koshland in 1958, is based on the enzyme-substrate interaction.

• It is the more accepted model for enzyme-substrate complex than the lock-and-key model.

• According to this model the final shape and charge is determined eventually as the active site continues to change until the substrate is completely bound to the active site of the enzyme.

• Unlike the lock-and-key model, the induced fit model shows that enzymes are rather flexible structures.

Lock and Key Model

The Induced Fit Model



7. Factors Affecting the Enzyme Activity

(a)Temperature

•Enzymes being protein in nature are extremely sensitive to thermal fluctuations.

•Each enzyme has its activity optimum at a certain temperature known as the optimal temperature, which ranges between 37 to 400C.

• Initially as temperature increases, the rate of reaction increases, because of increased Kinetic Energy.

•However, the chances of breaking of bonds will be greater and the rate of reaction will eventually decrease.

Graph showing relation between enzyme activity and temperature

(b) pH :

•Enzymes being structurally protein substances contain both acidic carboxylic groups (COOH-) and basic amino groups (NH2).

•So, the enzymes are affected by altering the pH value.

•Each enzyme has a pH value that it works at with maximum efficiency called the optimal pH.

•H+ and OH- Ions are charged and therefore interfere with hydrogen and ionic bonds that hold together an enzyme, since they will be attracted or repelled by the charges created by the bonds.

• This interference causes a change in shape of the enzyme, and especially, its active Site.

Graph showing relation between enzyme activity and pH

(c) Enzyme Concentration:

•As the concentration of the enzyme is increased, the velocity of the reaction proportionately increases.

Graph showing how enzyme concentration affects rate of reaction.

(d) Substrate Concentration

• In a given amount of enzyme, the rate of enzymatic reaction increases as the substrate concentration increases until a limiting rate is reached, after which further increase in the substrate concentration produces no significant change in the reaction rate.

• At this point, the enzyme molecules are saturated with substrate.

•The excess substrate molecules cannot react until the substrate already bound to the enzymes has reacted and been released (or been released without reacting).

Graph showing relation between enzyme activity and substrate concentration



8. Enzyme Inhibition:

•It can be defined as a process which involves the interference by a substance known as inhibitor in the enzyme activity directly or indirectly bringing about a decrease in its catalytic activity.

•The inhibitor can be organic or inorganic in nature.

(a) Competitive Inhibition:

• Competitive inhibition involves a molecule, other than the substrate, binding to the enzyme's active site.

• The molecule (inhibitor) is structurally and chemically like the substrate (hence able to bind to the active site).

• The competitive inhibitor prevents substrate binding by blocking the active site.

• As the inhibitor competes with the substrate, its effects can be reduced by increasing substrate concentration.

• Competitive inhibition is observed when the substrate and the inhibitor compete for the active site on the enzyme.

•In competitive inhibition, chemically the inhibitor molecule remains unchanged by the enzyme.

• Example: a competitive inhibitor of succinic dehydrogenase is malonate and oxaloacetate.

•Addition of lot of succinate reverses the inhibition of succinic dehydrogenase by malonate.

Competitive Inhibition

(b)Non-Competitive Inhibition:

•Non-competitive inhibition involves a molecule binding to a site other than the active site (an allosteric site).

•The binding of the inhibitor to the allosteric site causes a conformational change to the enzyme's active site.

•Because of this change, the active site and substrate no longer share specificity, meaning the substrate cannot bind.

•Here as we know that there is no direct competition between the and the substrate, increasing substrate levels cannot overcome the inhibitor's effect.

Non-competitive inhibition

(c) Allosteric Regulation:

• Allosteric regulation can be defined as the modulation of an enzyme's activity through the binding of an effector molecule (ligand) to a site other than the enzyme's active site known as allosteric site.

•Allosteric binding leads to a conformational change in the enzyme's structure that affects the enzyme's affinity for substrate.

• Example: Inhibition of hexokinase enzyme by glucose-6-phosphate. Allosteric regulation can be of two types i.e. positive (activation) or negative (non-competitive inhibition).

Diagram depicting allosteric inhibition and activation



9. Michaelis Menten Equation

Michaelis and Menten in 1913 proposed the basic theory of enzyme action which mainly introduced a constant known as Km constant (Michaelis Constant).

•It indicates the substrate concentration at which the reaction catalysed by an enzyme attains half of its maximum velocity known as Vmax.

•Km indicates enzyme affinity for its substrate.

•Higher the Km value lower the affinity and vice versa.

•Inversely,1/km depicts the measure of enzyme affinity for its substrate.

•The MM equation explains how the reaction varies relatively with substrate concentration:

•V0 = RATE OF INITIAL REACTION

•Vmax = RELATIVE REAC TION STATE WITH EXCESS SUBSTRATE

•Km = MM CONSTANT

•[S] = SUBSTRATE CONCENTRATION.

Michaelis-Menten Equation Graph