What are Enzymes? An Introduction

• Enzymes are the biological macromolecules which speed up the rate of biochemical reactions without undergoing any change. They are also called as biological catalysts.
• An enzyme is a highly selective catalyst that greatly accelerates both the rate and specificity of metabolic reactions.

Properties of Enzymes

• Nearly all enzymes are proteins, although a few catalytically active RNA molecules have been identified.
• Enzyme catalyzed reactions usually take place under relatively mild conditions (temperatures well below 100^oC, atmospheric pressure and neutral pH) as compared with the corresponding chemical reactions.
• Enzymes are catalysts that increase the rate of a chemical reaction without being changed themselves in the process.
• Enzymes are highly specific with respect to the substrates on which they act and the products that they form.
• Enzyme activity can be regulated, varying in response to the concentration of substrates or other molecules.
• They function under strict conditions of temperature and pH in the body.

Coenzymes and prosthetic groups

• Many enzymes require the presence of small, non-protein units or cofactors to carry out their particular reaction.
• Cofactors may be either one or more inorganic ions, such as Zn²⁺ or Fe²⁺ or a complex organic molecule called a coenzyme.
• A metal or coenzyme that is covalently attached to the enzyme is called a prostheticgroup (heme in hemoglobin).
• Some coenzymes, such as NAD⁺, are bound and released by the enzyme during its catalytic cycle and in effect function as co-substrates. Many coenzymes are derived from vitamin precursors.

Holo enzymes and Apo enzymes

A complete catalytically-active enzyme together with its coenzyme or metal ion is called a holoenzyme.

The protein part of the enzyme on its own without its cofactor is termed an apoenzyme.

Isoenzymes

• Isoenzymes are different forms of an enzyme which catalyze the same reaction, but which exhibit different physical or kinetic properties, such as isoelectric point, pH optimum, substrate affinity or effect of inhibitors.
• Different isoenzyme forms of a given enzyme are usually derived from different genes and often occur in different tissues of the body.
• An example of an enzyme which has different isoenzyme forms is lactate dehydrogenase (LDH) which catalyzes the reversible conversion of pyruvate into lactate in the presence of the coenzyme NADH.
• LDH is a tetramer of two different types of subunits, called H and M, which have small differences in amino acid sequence. The two subunits can combine randomly with each other, forming five isoenzymes that have the compositions H₄, H₃M, H₂M₂, HM₃ and M₄. The five isoenzymes can be resolved electrophoretically.

Active site of Enzymes

• The active site of an enzyme is the region that binds the substrate and converts it into product.
• It is usually a relatively small part of the whole enzyme molecule and is a three-dimensional entity formed by amino acid residues that can lie far apart in the linear polypeptide chain.
• The active site is often a cleft or crevice on the surface of the enzyme that forms a predominantly nonpolar environment which enhances the binding of the substrate.
• The substrate(s) is bound in the active site by multiple weak forces (electrostatic interactions, hydrogen bonds, van der Waals bonds, hydrophobic interactions; and in some cases by reversible covalent bonds.

Substrate Specificity of Enzymes

• The properties and spatial arrangement of the amino acid residues forming the active site of an enzyme will determine which molecules can bind and be substrates for that enzyme.
• Substrate specificity is often determined by changes in relatively few amino acids in the active site.
• This is clearly seen in the three digestive enzymes trypsin, chymotrypsin and elastase.

Mechanism of Action of Enzymes

• The substrate(s) is bound in the active site by multiple weak forces which result into the enzyme-substrate complex.
• Once bound active residues within the active site of the enzyme act on the substrate molecule to transform it first into the transition state complex and then into product, which is released.
• The enzyme is now free to bind another molecule of substrate and begin its catalytic cycle again.

The Substrate-Enzyme Binding

Originally two models were proposed to explain how an enzyme binds its substrate.

The Lock and Key Model

• In the lock-and-key model proposed was proposed by Emil Fischer in 1894.
• According to the model, the shape of the substrate and the active site of the enzyme are thought to fit together like a key into its lock.
• The two shapes are considered as rigid and fixed, and perfectly complement each other when brought together in the right alignment.

The Induced Fit Model

• In the induced-fit model was proposed by Daniel E. Koshland, Jr., in 1958.
• It states that the binding of substrate induces a conformational change in the active site of the enzyme.
• In addition, the enzyme may distort the substrate, forcing it into a conformation similar to that of the transition state.
• For example, the binding of glucose to hexokinase induces a conformational change in the structure of the enzyme such that the active site assumes a shape that is complementary to the substrate (glucose) only after it has bound to the enzyme.

The reality is that different enzymes show features of both models, with some complementarity and some conformational change.

Nomenclature of Enzymes

• Many enzymes are named by adding the suffix ‘-ase’ to the name of their substrate.

Example. Urease is the enzyme that catalyzes the hydrolysis of urea, and fructose-1,6-bisphosphatase hydrolyzes fructose-1,6-bisphosphate.

• However, other enzymes, such as trypsin and chymotrypsin, have names that do not denote their substrate.
• Some enzymes have several alternative names.
• To rationalize enzyme names, a system of enzyme nomenclature has been internationally agreed.
• This system places all enzymes into one of six major classes based on the type of reaction catalyzed. Each enzyme is then uniquely identified with a four-digit classification number.

Example: Trypsin has the Enzyme Commission (EC) number 3.4.21.4, where

1. the first number (3) denotes that it is a hydrolase
2. the second number (4) that it is a protease that hydrolyzes peptide bonds
3. the third number (21) that it is a serine protease with a critical serine
4. residue at the active site, and
5. the fourth number (4) indicates that it was the fourth enzyme to be assigned to this class.

• For comparison, chymotrypsin has the EC number 3.4.21.1, and elastase 3.4.21.36.

Classification of Enzymes

1. Oxidoreductases

• Catalyze oxidation-reduction reactions where electrons are transferred.
• These electrons are usually in the form of hydride ions or hydrogen atoms.
• The most common name used is a dehydrogenase and sometimes reductase is used.
• An oxidase is referred to when the oxygen atom is the acceptor.

2. Transferases

• Catalyze group transfer reactions.
• The transfer occurs from one molecule that will be the donor to another molecule that will be the acceptor.
• Most of the time, the donor is a cofactor that is charged with the group about to be transferred.
• Example: Hexokinase used in glycolysis.

3. Hydrolases 

• Catalyze reactions that involve hydrolysis.
• It usually involves the transfer of functional groups to water.
• When the hydrolase acts on amide, glycosyl, peptide, ester, or other bonds, they not only catalyze the hydrolytic removal of a group from the substrate but also a transfer of the group to an acceptor compound
• For example: Chymotrypsin.

4. Lyases

• Catalyze reactions where functional groups are added to break double bonds in molecules or the reverse where double bonds are formed by the removal of functional groups.
• For example: Fructose bisphosphate aldolase used in converting fructose 1,6-bisphospate to G3P and DHAP by cutting C-C bond.

5. Isomerases

• Catalyze reactions that transfer functional groups within a molecule so that isomeric forms are produced.
• These enzymes allow for structural or geometric changes within a compound.
• For example: phosphoglucose isomerase for converting glucose 6-phosphate to fructose 6-phosphate. Moving chemical group inside same substrate.

6. Ligases

• They are involved in catalysis where two substrates are ligated and the formation of carbon-carbon, carbon-sulfide, carbon-nitrogen, and carbon-oxygen bonds due to condensation reactions.
• These reactions are coupled to the cleavage of ATP.

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Significance of Enzymes

1. In the absence of an enzyme, biochemical reactions hardly proceed at all, whereas in its presence the rate can be increased up to 10⁷-fold. Thus, they are crucial for normal metabolism of living systems.
2. Besides in the body, extracted and purified enzymes have many applications.

• Medical applications of enzymes include:

1. To treat enzyme related disorders.
2. To assist in metabolism
3. To assist in drug delivery.
4. To diagnose & detect diseases.
5. In manufacture of medicines.

• Industrial applications of enzymes include:

1. Amylase, lactases, cellulases are enzymes used to break complex sugars into simple sugars.
2. Pectinase like enzymes which act on hard pectin is used in fruit juice manufacture.
3. Lipase enzymes act on lipids to break them in fatty acids and glycerol. Lipases are used to remove stains of grease, oils, butter.
4. Enzymes are used in detergents and washing soaps.
5. Protease enzymes are used to remove stains of protein nature like blood, sweat etc.

References

1. Suzanne J. Baron and Christoph I. Lee (2013).Biochemistry & Genetics. Second Edition. Mc Graw Hill: New York.
2. David Hames and Nigel Hooper (2005). Biochemistry. Third ed. Taylor & Francis Group: New York.
3. https://en.wikibooks.org/wiki/Structural_Biochemistry/Specific_Enzymes_and_Catalytic_Mechanisms/Enzyme_Classification