Enzymes

An enzyme is a cellular catalyst; it makes biochemical reactions proceed many times more rapidly than they would if uncatalysed. The participation of an enzyme can increase the rate of a reaction by a factor of millions, or even billions.

Traditionally, all enzymes have been thought of as globular proteins, but around twenty years ago it was demonstrated (surprisingly) that certain RNA molecules also have catalytic properties. These ribozymes however, are very much in the minority, carrying out specific cut-and-splice reactions on RNA molecules, and in the present

Enzyme Enzyme-substrate

Enzyme Enzyme-substrate

Figure 6.2 Enzyme-substrate interaction. An enzyme interacts with its substrate(s) to form an enzyme-substrate complex, leading to the formation of a product. In the example shown, two substrate molecules are held in position by the enzyme and joined together. From Black, JG: Microbiology: Principles and Explorations, 4th edn, John Wiley & Sons Inc., 1999. Reproduced by permission of the publishers

Figure 6.2 Enzyme-substrate interaction. An enzyme interacts with its substrate(s) to form an enzyme-substrate complex, leading to the formation of a product. In the example shown, two substrate molecules are held in position by the enzyme and joined together. From Black, JG: Microbiology: Principles and Explorations, 4th edn, John Wiley & Sons Inc., 1999. Reproduced by permission of the publishers context can be ignored. In this book we shall confine our discussion of enzymes to the protein type.

Like any other catalyst, an enzyme remains unchanged at the end of a reaction. It must, however, at some point during the reaction bind to its substrate (the substance upon which it acts) to form an enzyme-substrate complex (Figure 6.2) by multiple weak forces such as electrostatic forces and hydrogen bonding. Only a small part of the enzyme's three-dimensional structure is involved in this binding; these few amino acids make up the active site, which forms a groove or dent in the enzyme's surface, into which the appropriate part of the substrate molecule fits (Figure 6.3). The amino

binding cleft

Figure 6.3 Catalytic activity occurs at the active site of an enzyme. Four amino acids play an important role in the active site of triose phosphate isomerase; note how they are far apart in the primary sequence, but are brought together by subsequent protein folding binding cleft

Figure 6.3 Catalytic activity occurs at the active site of an enzyme. Four amino acids play an important role in the active site of triose phosphate isomerase; note how they are far apart in the primary sequence, but are brought together by subsequent protein folding

112

MICROBIAL METABOLISM

Table 6.1 Major classes of enzymes

Class

Name

Reaction type

Example

1

Oxidoreductases

Oxidation/reduction (electron

Lactate dehydrogenase

transfer) reactions

2

Transferases

Transfer of functional groups e.g.

Glucokinase

phosphate, amino

3

Hydrolases

Cleavage of bonds with the

Glucose-6-phosphatase

addition of water (hydrolysis)

4

Lyases

Cleavage of C—C, C—O or C—N

Pyruvate decarboxylase

bonds to form a double bond

5

Isomerases

Rearrangement of atoms/groups

Triose-phosphate isomerase

within a molecule

6

Ligases

Joining reactions, using energy

from ATP

acid residues that go to make up the active site may be widely separated in the enzyme's primary structure, but by means of the secondary and tertiary folding of the molecule, they are brought together to give a specific conformation, complementary to that of the substrate. It is this precise formation of the active site that accounts for one of the major characteristics of enzymes, their specificity. You should not think, however, that these few residues making up the active site are the only ones that matter; the enzyme can only fold in this way because the order and arrangement of the other amino acids allows it.

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