Enzymes accelerate the rate of reactions by factors of as much as a million or more (Table 6.1). Indeed, most reactions in biological systems do not take place at perceptible rates in the absence of enzymes. Even a reaction as simple as adding water to carbon dioxide is catalyzed by an enzyme—namely, carbonic anhydrase. This reaction facilitates the transport of carbon dioxide from the tissues where it is produced to the lungs where it is exhaled. Carbonic anhydrase is one of the fastest known enzymes. Each enzyme molecule can hydrate 10⁶ molecules of CO₂ per second. This catalyzed reaction is 10⁷ times as fast as the uncatalyzed one. The transfer of CO₂ from the tissues to the blood and then to the lungs would be less complete in the absence of this enzyme.

Enzymes are highly specific both in the reactions that they catalyze and in their choice of reactants, which are called substrates. An enzyme usually catalyzes a single chemical reaction or a set of closely related reactions. Let us consider proteolytic enzymes as an example. The biochemical function of these enzymes is to catalyze proteolysis, the hydrolysis of a peptide bond:

Proteolytic enzymes differ markedly in their degree of substrate specificity. Papain, which is found in papaya plants, is quite undiscriminating: it will cleave any peptide bond with little regard to the identity of the adjacent side chains. This lack of specificity accounts for its use in meat-tenderizing sauces. Trypsin, a digestive enzyme, is quite specific and catalyzes the splitting of peptide bonds only on the carboxyl side of lysine and arginine residues (Figure 6.1A). Thrombin, an enzyme that participates in blood clotting, is even more specific than trypsin. It catalyzes the hydrolysis of Arg–Gly bonds in particular peptide sequences only (Figure 6.1B). The specificity of an enzyme is due to the precise interaction of the substrate with the enzyme. This precision is a result of the intricate three-dimensional structure of the enzyme protein.

More than a thousand enzymes have been identified—a daunting number for a student of biochemistry. Despite this large number, however, there are only six major classes of enzymes, which makes recognizing the function of enzymes much simpler. We will see many members of these classes as we progress in our study of biochemistry.

The classification of all enzymes into these six classes also allowed the development of a standard nomenclature for enzymes. Many enzymes have common names that provide little information about the reactions that they catalyze. Trypsin exemplifies this lack of information. Most other enzymes are named for their substrates and for the reactions that they catalyze, with the suffix “ase” added. Thus, a peptide hydrolase is an enzyme that hydrolyzes peptide bonds, whereas ATP synthase is an enzyme that synthesizes ATP. Common names will be used in this book, but let’s examine the more accurate nomenclature.

The six groups (classes) of enzymes were subdivided and further subdivided so that a four-digit number preceded by the letters EC for Enzyme Commission, the entity that developed the classification system, could precisely identify all enzymes.

Consider trypsin as an example. Trypsin cleaves bonds by the addition of water; consequently, it is a member of group 3: Hydrolyases. Trypsin cleaves only peptide bonds, and hydrolyases that cleave peptide bonds are classified as 3.4. Trypsin employs a serine residue to facilitate hydrolysis and cleaves the protein chain internally (in contrast with the removal of amino acids from the end of the polypeptide chain). Such enzymes are placed in sub-sub-group 21 and identified as 3.4.21. Finally, trypsin cleaves peptide bonds in which the amino acid donating the carboxyl group to the peptide bond is either lysine or arginine. Thus, the number uniquely identifying trypsin is EC 3.4.21.4. Although the common names are used routinely, the classification number is used when the precise identity of the enzyme might be ambiguous.