into two or more stable globular units is called domains. Different domains often play distinct functions, such as binding molecules or interaction with other proteins. A molecule bound reversibly by a protein is called ligand. The site on the protein that binds the ligand is called the binding site. When a protein binds a ligand, the 3D structure of protein is often caused by a conformational change to permit a tighter binding to the ligand. This kind of binding with structural adaption between protein and ligand is called induced fit mechanism. Enzymes have catalytic function that binds and chemically rapidly transforms other molecules. For enzyme‐catalyzed reaction, the molecule bound and acted by the enzyme is called substrate; the binding site is called the active site or catalytic site.
Enzyme is an efficient catalyst and is responsible for thousands integrated chemical reactions of the biological process occurred in the living system. Just like the usual inorganic catalyst, enzymes catalyze a reaction by lowering the transition state energy (the activation energy) of the activated complex and by raising the ground state energy. On the other hand, the catalysis of enzymes, not like simple inorganic catalysts, proceeds by forming several transition states and each with low activation energy instead of one activated complex of greater activation energy. The rate of enzyme‐catalyzed reaction for a simple one enzyme, one substrate and one product system with the following mechanism was studied by Michaelis and Menten in 1913 (Scheme 1.2). In this mechanism, enzyme (E) binds the substrate (S) to form an enzyme–substrate (ES) complex and subsequently the ES breaks down to the product (P).
Scheme 1.2 The proposed enzyme reaction mechanism by Michaelis and Menten.
According to this mechanism, the enzyme‐catalyzed reaction rate equation called Michaelis–Menten equation (Eq. 1.1) was derived by Michaelis and Menten with the second step as the rate‐limiting step and derived by Briggs and Haldane using steady‐state assumption. The term V 0 is the initial rate, V max is the maximum reaction rate, [S] is the substrate concentration, and Km is the Michaelis constant.
For a more common case, enzyme product complexes (EP) release, EP → E + P, is the rate‐limiting step, which is described as the reaction Scheme 1.3.
Therefore, a more general rate constant called the turnover number, k cat, is defined to describe the limiting rate of any enzyme‐catalyzed reaction at saturation, that is, V max = k cat[E t]. In this situation, the Michaelis–Menten equation becomes Eq. 1.2
The turnover numbers of several enzymes are given in Table 1.1.
Scheme 1.3 A generalized enzyme‐catalyzed reaction.
Table 1.1 Turnover numbers for some enzymes.
| Enzyme | Turnover number kcat (s−1) |
|---|---|
| Catalase | 40 000 000 |
| Carbonic anhydrase | 400 000 |
| Acetylcholinesterase | 140 000 |
| β‐Lactamase | 2000 |
| Fumarase | 800 |
| β‐Galactosidase | 208 |
| Phosphoglucomutase | 21 |
| Tryptophan synthetase | 2 |
| RecA protein (an ATPase) | 0.4 |
1.3 Cofactors and Coenzymes
Enzymes have protein nature and molecular weights ranging from about 12 000 to over 1 million. The large molecule of enzymes is flexible for binding natural and unnatural substrates at their active site. The active site contains moieties consisted with amino acid residues. Although the activity of some enzymes requires no chemical groups other than their amino acid residues, others require an additional chemical component called cofactor. A cofactor, also called a coenzyme, is either one or more inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+ (Table 1.2) [9], or an organic or metallo‐organic molecule. Coenzyme are often derived from vitamins and organic nutrients required in small amounts in the diet (Table 1.3) [9]. The cofactor binds to the active site, in some cases covalently and in others noncovalently, which serves as transient carriers of redox equivalents, such as NAD(P)H or chemical energy (ATP) and is essential for the catalytic action of those enzymes that require cofactors.
Table 1.2 Some inorganic metal ions as cofactor of enzymes.
Source: Based on Nelson and Cox [9].
| Fe2+ or Fe3+ | Cytochrome oxidase, catalase, peroxidase |
| K+ | Pyruvate kinase |
| Mg2+ | Hexokinase, pyruvate kinase, enolase |
| Mn2+ | Arginase, ribonucleotide reductase |
| Ni2+ | Urease |
| Zn2+ | Carbonic anhydrase, alcohol dehydrogenase, carboxypeptidases A and B |
Table 1.3 Some coenzymes as transient carriers of specific atoms or functional groups.
Source: Based on Nelson and Cox [9].
| Coenzyme |
Chemical groups transferred
|
