Enzyme Nomenclature

Historically, individual enzymes were identified using the name of the substrate or group upon which they act and then adding the suffix –ase. For example, the enzyme hydrolyzing urea was urease. Later, the type of reaction involved was also identified, as in carbonic anhydrase, D-amino acid oxidase, and succinate dehydrogenase. In addition, some enzymes had been given empirical names such as trypsin, diastase, ptyalin, pepsin, and emulsin.

Because this combination of trivial common names and semisystematic names was found to be inadequate, in 1955 the International Union of Biochemistry (IUB) appointed an Enzyme Commission (EC) to study the problem of enzyme nomenclature. Its subsequent recommendations, with periodic updating, provide a rational and practical basis for identifying all enzymes now known and enzymes that will be discovered in the future (http://www.chem.qmw.ac.uk/iubmb/enzyme/accessed May 6, 2011).¹¹

With the IUB system, a systematic and trivial name is provided for each enzyme. The systematic name describes the nature of the reaction catalyzed and is associated with a unique numeric code. The trivial or practical name, which may be identical to the systematic name but is often a simplification of it, is suitable for everyday use. The unique numeric designation for each enzyme consists of four numbers, separated by periods (e.g., 2.2.8.11), and is prefixed by the letters EC, denoting Enzyme Commission. The first number defines the class to which the enzyme belongs. All enzymes are assigned to one of six classes, characterized by the type of reaction they catalyze: (1) oxidoreductases, (2) transferases, (3) hydrolases, (4) lyases, (5) isomerases, and (6) ligases. The next two numbers indicate the subclass and the sub-subclass to which the enzyme is assigned. For example, these may differentiate the amino-transferring subclass from the phosphate-transferring category, or the ethanol acceptor sub-subclass from that accepting acyl groups. The last number is the specific serial number given to each enzyme within its sub-subclass.

To illustrate how this system is used to name an enzyme, consider the enzyme creatine kinase, which catalyzes the following reaction:

Its system number is

Table 15-1 lists some selected enzymes of clinical interest, identified by trivial, abbreviated, and systematic names and by their code numbers.

Although it is not recommended by the EC, it is a common and convenient practice to use capital letter abbreviations for the names of certain enzymes, such as ALT (formerly GPT) for alanine aminotransferase. Other examples are AST for aspartate aminotransferase, LD for lactate dehydrogenase, and CK for creatine kinase (see Table 15-1).

Enzymes as Proteins

All enzyme molecules possess the primary, secondary, and tertiary structural characteristics of proteins (see Chapter 21). In addition, most enzymes exhibit quaternary structure. The primary structure, the linear sequence of amino acids linked through their α-carboxyl and α-amino groups by peptide bonds, is specific for each type of enzyme molecule. Each polypeptide chain is coiled up into three-dimensional secondary and tertiary structure. Secondary structure refers to the conformation of limited segments of the polypeptide chain, namely α-helices, β-pleated sheets, random coils, and β-turns. The arrangement of secondary structural elements and amino acid side chain interactions that define the three-dimensional structure of the folded protein is referred to as its tertiary structure. In many cases, biological activity, such as the catalytic activity of enzymes, requires two or more folded polypeptide chains (subunits) to associate to form a functional molecule. The arrangement of these subunits defines the quaternary structure. The subunits may be copies of the same polypeptide chain (e.g., the MM isoenzyme of creatine kinase, the H₄ isoenzyme of lactate dehydrogenase), or they may represent distinct polypeptides.

The application of physical methods, such as x-ray crystallography and multidimensional nuclear magnetic resonance (NMR), has provided structural insights upon which enzyme mechanisms have been built. Furthermore, the tools of molecular biology, such as molecular cloning, have enabled the purification and characterization of enzymes that previously were available only in minute amounts. Molecular biology also enables the manipulation of the amino acid sequence of enzymes, and site-directed mutagenesis (substituting one amino acid residue for another) and deletion mutagenesis (eliminating sections of the primary structure) have enabled the identification of chemical groups that participate in ligand binding and in specific chemical steps during catalysis.

In general, no feature of primary structures, such as repetition of particular amino acid sequences, is common to all enzyme molecules. However, considerable homologies of sequence are found between enzymes that appear to share a common evolutionary origin, such as the proteases, trypsin and chymotrypsin, and similarities of sequence are even more marked among the members of a family of isoenzymes. The amino acid sequence in the immediate neighborhood of the active center of the enzyme (discussed later) is often closely similar in enzymes of related function (e.g., the serine proteases are so called because they all have this amino acid in the active center).

Enzyme molecules differ in the proportion of secondary structures—such as α-helices—they contain, although no enzyme molecule so far studied approaches the large proportion of α-helices found in myoglobin and hemoglobin. The tertiary structures of different types of enzyme molecules are as individually characteristic as their primary structures; nevertheless, some common features exist. Enzyme molecules are roughly globular in overall shape, with a preponderance of polar amino acid side chains on the outside of the molecule and nonpolar side chains in the interior. The ionizable residues in contact with the surrounding medium are responsible for many of the properties of the enzyme molecules in solution, such as their migration in an electric field and their solubility. Covalent disulfide bridges may link different parts of the polypeptide chains in some enzyme molecules, but the three-dimensional structure is mainly stabilized by the large number of hydrophobic interactions that are formed between the nonpolar side chains in the interior of the molecule.

The biological activity of a protein molecule depends generally on the integrity of its structure, and any disruption of its structure is accompanied by loss of activity, a process known as denaturation. If the process of denaturation is minimal, it may be reversed with the recovery of enzyme activity upon removal of the denaturing agent. However, prolonged or severe denaturing conditions result in an irreversible loss of activity. Denaturing conditions include elevated temperatures, extremes of pH, and chemical addition. Heat inactivation of most enzymes takes place at an appreciable rate at room temperature and in most cases becomes almost instantaneous above 60 °C. The polymerases are an exception and retain activity at temperatures as high as 90 °C—a property that has been made use of in the polymerase chain reaction (see Chapter 17). Low temperatures are used to preserve enzyme activity, especially in aqueous solutions, such as serum (see Chapter 22). Extremes of pH also cause unfolding of enzyme molecular structures and, except for a few exceptions, should be avoided when enzyme samples are preserved. Addition of chemicals, such as urea and detergents, disrupts hydrogen bonds and hydrophobic interactions so that exposure of enzymes to strong solutions of these reagents results in inactivation.

Specificity and the Active Center

With the exception of enzymes such as proteases, nucleases, and amylases, which act on macromolecular substrates, enzyme molecules are considerably larger than the molecules of their substrates. Consideration of the structure of an enzyme’s active site and its relationship to the structures of the enzyme’s substrate(s) in its ground and transition states is necessary to understand the rate enhancement and specificity of the chemical reactions performed by the enzyme. The active site of an enzyme will vary between enzymes but in general,⁵

Isoenzymes and Other Multiple Forms of Enzymes

An isoenzyme is defined as “one of a group of related enzymes catalyzing the same reaction but having different molecular structures and characterized by varying physical, biochemical, and immunologic properties.” However, the IUB recommends that use of the term isoenzyme be restricted to forms that originate at the level of the genes that encode the structures of the enzyme proteins in question.⁴

Isoenzymes may occur within a single organ or even within a single type of cell. The forms can be distinguished on the basis of differences in various physical properties, such as electrophoretic mobility and resistance to chemical or thermal inactivation. They often have significant quantifiable differences in catalytic properties, but all forms of a particular enzyme retain the ability to catalyze its characteristic reaction.

The existence of multiple forms of enzymes in human tissue has important implications in the study of human disease. The presence in different organs of isoenzymes with distinctive properties helps in our understanding of organ-specific patterns of metabolism, but genetically determined variations in enzyme structure between individuals account for such characteristics as differences in sensitivity to drugs and differences in metabolism, which manifest themselves as hereditary metabolic diseases. For diagnostic enzymology, the existence of multiple forms of enzymes, whether due to genetic or nongenetic causes, provides opportunities to increase the diagnostic specificity and sensitivity of enzyme assays in body fluid samples.

Similar to other proteins, enzymes usually elicit the production of antibodies when they are injected into animals of a species other than those in which they originate. Even small structural differences between closely similar molecules, such as the members of a family of isoenzymes, are often sufficient to render them antigenically distinct, allowing antibodies to be produced specific to a single type of molecule. The availability of enzyme-specific antisera opens up a wide range of methods in enzyme analysis, some of which—such as immunoassay—do not depend on the catalytic activity of the enzyme molecules. The availability of immunochemical methods has been particularly important in the analysis of isoenzyme mixtures. Many commercial immunoassays now use monoclonal antibodies to increase specificity.

Enzymes as Catalysts

A catalyst is a substance that modifies and increases the rate of a particular chemical reaction without being consumed or permanently altered; enzymes are protein catalysts of biological origin. Metabolism is a coordinated series of chemical reactions that occur within a living cell to provide energy and accomplish biosynthesis. The process can be regarded as an integrated series of enzymatic reactions, and some diseases as a derangement of the normal pattern of metabolism. Apart from these fundamental considerations, it is the remarkable properties of enzymes that make them such sensitive indicators of pathologic change.

Because of their remarkable catalytic activity, a given number of enzyme molecules convert an enormous number of substrate molecules to products within a short time. This property is used to measure increased amounts of enzymes in the bloodstream, although the amount of enzyme protein released from damaged cells is small compared with the total quantity of nonenzymatic proteins in blood. Thus a change in the quantity of a particular enzyme is recognized by its characteristic effect on a given chemical reaction.

Units for Expressing Enzyme Activity

When enzymes are measured by their catalytic activities, the results of such determinations are expressed in terms of the concentration of the number of activity units present in a convenient volume or mass of specimen. The unit of activity is the measure of the rate at which the reaction proceeds (e.g., the quantity of substrate consumed or product formed in a chosen unit of time). In clinical enzymology, the activity of an enzyme is generally reported in terms of unit of volume, such as activity per 100 mL or per liter of serum or per 1.0 mL of packed erythrocytes. Because the rate of the reaction depends on experimental parameters, such as pH, type of buffer, temperature, nature of substrate, ionic strength, concentration of activators, and other variables, these parameters must be specified in the definition of the unit.

To standardize how enzyme activities are expressed, the EC proposed that the unit of enzyme activity should be defined as the quantity of enzyme that catalyzes the reaction of 1 µmol of substrate per minute, and that this unit should be termed the international unit (U). Catalytic concentration is to be expressed in terms of U/L or kU/L, whichever gives the more convenient numeric value. In this chapter, the symbol U is used to denote the international unit. In those instances in which there is some uncertainty about the exact nature of the substrate, or when difficulty is encountered in calculating the number of micromoles reacting (as with macromolecules such as starch, protein, and complex lipids), the unit is to be expressed in terms of the chemical group or residue measured in the following reaction (e.g., glucose units, amino acid units formed).

The International System of Units (SI)-derived unit for catalytic activity (see Chapter 9) is the katal, defined as moles converted per second. The name katal had been used for this unit for decades but did not become an official SI-derived unit until 1999 with Resolution 12 of the 21st French Conférence Général des Poids et Mesures (CGPM), on the recommendation of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC). Both the International Union of Pure and Applied Chemistry (IUPAC) and the IUB now recommend that enzyme activity be expressed in moles per second, and that the enzyme concentration be expressed in terms of katals per liter (kat/L).⁸ Thus, 1 U = 10⁻⁶ mol/60 s = 16.7 × 10⁻⁹ mol/s, or 1.0 nkat/L = 0.06 U/L.

The Enzyme–Substrate Complex

Enzymes act through the formation of an enzyme–substrate (ES) complex, in which a molecule of substrate is bound to the active center of the enzyme molecule. The binding process transforms the substrate molecule to its activated state. The energy required for this transformation is provided by the free energy of binding of S to E. Therefore, activation takes place without the addition of external energy, so that the energy barrier to the reaction is lowered and the breakdown to products is accelerated (Figure 15-3). The ES complex breaks down to give the reaction products (P) and free enzyme (E):

(1)

All reactions catalyzed by enzymes are in theory reversible. However, in practice, the reaction is usually found to be more rapid in one direction than in the other, so that an equilibrium is reached in which the product of the forward or the backward reaction predominates, sometimes so markedly that the reaction is virtually irreversible.

If the product of the reaction in one direction is removed as it is formed (e.g., because it is the substrate of a second enzyme present in the reaction mixture), the equilibrium of the first enzymatic process will be displaced so that the reaction will proceed to completion in that direction. Reaction sequences in which the product of one enzyme-catalyzed reaction becomes the substrate of the next enzyme and so on, often through many stages, are characteristic of biological processes. In the laboratory also, several enzymatic reactions may be linked together to provide a means of measuring the activity of the first enzyme or the concentration of the initial substrate in the chain. For example, the activity of CK is usually measured by a series of linked reactions, and the concentration of glucose is determined by consecutive reactions catalyzed by hexokinase and glucose-6-phosphate dehydrogenase.

When a secondary enzyme-catalyzed reaction, known as an indicator reaction, is used to determine the activity of a different enzyme, the primary reaction catalyzed by the enzyme to be determined must be the rate-limiting step. Conditions are chosen to ensure that the rate of reaction catalyzed by the indicator enzyme is directly proportional to the rate of product formation in the first reaction.

Factors Governing the Rate of Enzyme-Catalyzed Reactions

Factors that affect the rate of enzyme-catalyzed reactions include enzyme and substrate concentration, pH, temperature, and the presence of inhibitors, activators, coenzymes, and prosthetic groups.

Stay updated, free articles. Join our Telegram channel

Join