Biosynthetic enzymes are often highly specific, in contrast to degradative enzymes, which often show wide specificity.

L-isomer of aspartate. Aspartase can also catalyze the reverse reaction, but it will add only NH3 to fumarate and will not use maleate, the cw-isomer of fumarate.

Other enzymes have much broader substrate specificity. Broad specificity is shown by many degradative enzymes; for example, alkaline phosphatase, which removes phosphates from a wide range of molecules, or carboxypeptidase, which snips the C-terminal amino acid off many polypeptide chains. Most enzymes have intermediate specificity. For example, alcohol dehydrogenase from E. coli will act on C3 and C4 alcohols as well as its natural substrate, ethanol. Again, b-galactosidase uses several compounds in which galactose is linked to another chemical group, such as lactose, ONPG and X-gal (see below, Fig. 7.36).

Differences in specificity between similar enzymes are largely determined by the nature of the active site. The active site pocket can vary in size and shape and in the chemical nature of the amino acids comprising it. For example, the three digestive enzymes trypsin, chymotrypsin and elastase all split polypeptide chains by the same catalytic mechanism (Fig 7.31). However, the active site of trypsin has a negative charge at the bottom, so trypsin cuts after positively charged residues (e.g., Lys or Arg). In chymotrypsin, the active site pocket is lined by hydrophobic groups and so this enzyme cuts after hydrophobic residues (e.g., Phe or Val). In elastase, the active site pocket is very small and so elastase cuts after residues with small side chains (e.g., Ala).

L-isomer That one of a pair of optical isomers that rotates light in an anticlockwise direction

Enzymes Are Named and Classified According to the Substrate 181

FIGURE 7.32 Lock and Key Versus Induced Fit

A) The lock and key model says that the active site and the substrate must fit perfectly. B) The induced fit model proposes that the conformation of the active site will change upon binding to the substrate.

Lock and Key and Induced Fit Models Describe Substrate Binding

Two different models have been proposed to explain the binding of substrate in the active site of enzymes. In the lock and key model, the active site of the enzyme fits the substrate precisely. In contrast, the induced fit model proposes that the binding of the substrate induces a change in enzyme conformation so that the two fit together better (Fig. 7.32).

Enzymes may be found that operate by both mechanisms. For example, the enzyme chymotrypsin degrades proteins in the digestive tract. Almost no detectable structural change occurs when chymotrypsin binds its substrate. Carboxypeptidase also degrades proteins, but by snipping amino acids off from the carboxyl end. When carboxypeptidase binds substrate, this causes a tyrosine (at position 248) to move 12 Angstroms to a position where it is in physical contact with the substrate and can now play a direct catalytic role.

Enzymes Are Named and Classified According to the Substrate

Nowadays enzyme names end in "ase." Some enzymes, such as trypsin or lysozyme, were named before this convention was introduced and so have irregular names. Some major categories of enzymes of interest in molecular biology are listed in Table 7.03.

induced fit When the binding of the substrate induces a change in enzyme conformation so that the two fit together better lock and key model Model of enzyme action in which the active site of an enzyme fits the substrate precisely

Enzymes Are Named and Classified According to the Substrate 181

Chymotrypsin Active Site

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