Most commonly used enzyme names have the suffix “-ase” attached to the substrate of the reaction (for example, glucosidase and urease) or to a description of the action performed (for example, lactate dehydrogenase and adenylyl cyclase). [Note: Some enzymes retain their original trivial names, which give no hint of the associated enzymic reaction, for example, trypsin and pepsin.]
B. Systematic name
In the systematic naming system, enzymes are divided into six major classes (Fig. 5.1), each with numerous subgroups. For a given enzyme, the suffix ase is attached to a fairly complete description of the chemical reaction catalyzed, including the names of all the substrates, for example, lactate:nicotinamide adenine dinucleotide (NAD+) oxidoreductase. [Note: Each enzyme is also assigned a classification number. Lactate:NAD+ oxidoreductase is 1.1.1.27.] The systematic names are unambiguous and informative but are frequently too cumbersome to be of general use.
inorganic phosphate.
Potentially confusing enzyme nomenclature includes synthetase (requires ATP), synthase (no ATP required), phosphatase (uses water to remove a phosphate group), phosphorylase (uses inorganic phosphate to break a bond and generate a phosphorylated product), dehydrogenase (NAD+ or flavin adenine dinucleotide [FAD] is an electron acceptor in a redox reaction), oxidase (oxygen is the acceptor, and oxygen atoms are not incorporated into substrate), and oxygenase (one or both oxygen atoms are incorporated).
III. PROPERTIES
Enzymes are protein catalysts that increase the velocity of a chemical reaction and are not consumed during the reaction. [Note: Some ribonucleic acids (RNA) can catalyze reactions that affect phosphodiester and peptide bonds. RNAs with catalytic activity are called ribozymes (see p. 434) and are much less common than protein catalysts.]
A. Active site
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 (Fig. 5.2). The substrate binds the enzyme noncovalently, 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.
B. Efficiency
Enzyme-catalyzed reactions are highly efficient, proceeding from 103 to 108 times faster than uncatalyzed reactions. The number of substrate molecules converted to product per enzyme molecule per second is called the turnover number, or kcat, and typically is 102–104 s−1 . [Note: kcat is the rate constant for the conversion of ES to E + P (see p. 58).]
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