Enzymes, which are protein catalysts, enhance the speed of chemical reactions without being consumed in the process. These catalysts are named based on their function or the substrate they act upon, often using the suffix "-ase." For instance, glucosidase and urease are named after their respective substrates, while lactate dehydrogenase and adenylyl cyclase describe the action they perform. However, some enzymes retain their original trivial names, such as trypsin and pepsin, which do not hint at the associated enzymic reaction.

Alternatively, enzymes can also be named systematically. In this naming system, enzymes are classified into six major classes and numerous subgroups. The systematic name includes a detailed description of the chemical reaction that the enzyme catalyzes, including the names of all the substrates involved. For example, lactate:nicotinamide adenine dinucleotide (NAD+) oxidoreductase is a systematic name. Additionally, each enzyme is assigned a classification number, and lactate:NAD+ oxidoreductase is classified as 1.1.1.27. Although systematic names are informative, they are often too cumbersome for general use.

There are certain enzyme names that can be confusing. For instance, synthetase requires ATP, whereas synthase does not require ATP. Phosphatase uses water to remove a phosphate group, while phosphorylase uses inorganic phosphate to break a bond and generate a phosphorylated product. Dehydrogenase utilizes NAD+ or flavin adenine dinucleotide (FAD) as an electron acceptor in a redox reaction. Oxidase, on the other hand, uses oxygen as the acceptor without incorporating oxygen atoms into the substrate. Finally, oxygenase incorporates one or both oxygen atoms into the substrate.

Enzyme properties include the presence of an active site, which is a specific pocket or cleft within the enzyme molecule. The active site is formed by the folding of the protein and contains amino acid side chains that participate in substrate binding and catalysis. When the substrate binds to the enzyme, an enzyme-substrate (ES) complex is formed. This binding is believed to induce a conformational change in the enzyme, facilitating catalysis. The ES complex is then converted into an enzyme-product (EP) complex, which eventually dissociates into the enzyme and the product.

Enzyme-catalyzed reactions are highly efficient, occurring 103 to 108 times faster than uncatalyzed reactions. The turnover number, or kcat, represents the number of substrate molecules converted to product per enzyme molecule per second and typically ranges from 102 to 104 s−1.

Enzymes exhibit high specificity, interacting with one or a few substrates and catalyzing only one type of chemical reaction. The repertoire of enzymes present in a cell determines the reactions that occur within that cell.

Enzymes can exist in different forms. Holoenzymes are complete and catalytically active enzymes, while apoenzymes are inactive without the necessary cofactors or coenzymes. Cofactors are inorganic ions or small organic molecules that aid in enzyme function, while coenzymes are organic molecules that act as transient carriers of specific functional groups during the reaction.
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