Properties of Enzymes

Enzymes are protein catalysts that increase the velocity of a chemical reaction and are not consumed during the reaction. [Note: Some RNAs can act like enzymes, usually catalyzing the cleavage and synthesis of phosphodiester bonds. RNAs with catalytic activity are called ribozymes and are much less commonly encountered than protein catalysts.]

A. Active sites

Enzyme molecules contain a special pocket or cleft called the active site. The active site, formed by folding of the protein, contains amino acid side chains that participate in substrate binding and catalysis (Figure 5.2). The substrate binds the enzyme, forming an enzyme–substrate (ES) complex. Binding is thought to cause a conformational change in the enzyme (induced fit model) that allows catalysis. ES is converted to an enzyme–product (EP) complex that subsequently dissociates to enzyme and product.

Figure 5.2 Schematic representation of an enzyme with one active site binding a substrate molecule.

B. Catalytic efficiency

Enzyme-catalyzed reactions are highly efficient, proceeding from 10³–10⁸ times faster than uncatalyzed reactions. The number of molecules of substrate converted to product per enzyme molecule per second is called the turnover number, or k cat, and typically is 10²–10⁴s^-1.

C. Specificity

Enzymes are highly specific, interacting with one or a few substrates and catalyzing only one type of chemical reaction. The set of enzymes made in a cell determines which reactions occur in that cell.

D. Holoenzymes, apoenzymes, cofactors, and coenzymes

Some enzymes require molecules other than proteins for enzymic activity. The term holoenzyme refers to the active enzyme with its nonprotein component, whereas the enzyme without its nonprotein moiety is termed an apoenzyme and is inactive. If the nonprotein moiety is a metal ion, such as Zn²⁺ or Fe²⁺, it is called a cofactor. If it is a small organic molecule, it is termed a coenzyme. Coenzymes that only transiently associate with the enzyme are called cosubstrates. Cosubstrates dissociate from the enzyme in an altered state (NAD⁺ is an example). If the coenzyme is permanently associated with the enzyme and returned to its original form, it is called a prosthetic group (FAD is an example). Coenzymes commonly are derived from vitamins. For example, NAD⁺ contains niacin, and FAD contains riboflavin (see Chapter 28).

Figure 5.3 The intracellular location of some important biochemical pathways. TCA = tricarboxylic acid; PP = pentose phosphate.

E. Regulation

Enzyme activity can be regulated, that is, increased or decreased, so that the rate of product formation responds to cellular need.

F. Location within the cell