Classification and Nomenclature of Enzymes

Principles of Naming

In biochemistry, several approaches are used to name biocatalysts. The absolute majority of such terms feature the characteristic suffix "-ase". There are three main ways names are formed:

1. Based on the substrate. In this case, the standard suffix is simply added to the name of the substance upon which the enzyme acts. For example, if the target is urea, the name is urease. Sucrase, lipase (which breaks down lipids), and nuclease (acting on nucleic acids) are named using the same logical principle.
2. By the nature of the chemical transformation. This is a more informative approach. The name consists of the substrate name combined with a description of what specifically happens to it during the reaction. Examples include lactate dehydrogenase, phosphoglucomutase, pyruvate carboxylase, and adenylyl cyclase.
3. Trivial nomenclature. These are historically established terms that appeared before strict rules were introduced. They do not contain the "-ase" suffix and provide no clues about either the substrate or the type of reaction. Medical students simply need to memorize them: pepsin, trypsin, thrombin, and renin.

International Classification (IUBMB)

In 1961, the International Union of Biochemistry and Molecular Biology adopted a rigorous system dividing all enzymes into 6 main classes. The primary sorting criterion is the type of catalyzed reaction. Within each class, subclasses and sub-subclasses specify details of the process: the chemical group of the substrate, the nature of the donor or acceptor, and required cofactors.

The classes must be memorized in strict sequence:

• 1. Oxidoreductases (this class includes, for example, succinate dehydrogenase).
• 2. Transferases.
• 3. Hydrolases (a prominent representative is DNase).
• 4. Lyases.
• 5. Isomerases.
• 6. Ligases (an example from this class is pyruvate carboxylase).

Code Number (EC Number)

To avoid confusion, each enzyme is assigned a unique international code consisting of four numbers separated by periods (EC number). Let us examine this principle using malate dehydrogenase (whose precise systematic name is L-malate:NAD oxidoreductase), which has the code 1.1.1.38.

Each position in the code has a specific meaning:

• First digit (1) — indicates the main class. In our case, these are oxidoreductases.
• Second digit (1) — designates the specific type of catalyzed reaction within the class (here, oxidation of a hydroxyl group).
• Third digit (1) — reflects the presence of a specific coenzyme required for function (this example requires NAD⁺).
• Fourth digit (38) — is simply the individual serial number of the enzyme within its narrow subgroup.

Structure of Complex Enzymes

Many enzymes require not only a protein framework but also additional non-protein components for full function. The following terms are used to describe their structure:

• Apoenzyme — the protein-only part of the molecule. It is important to remember that by itself, without additional helpers, it is incapable of exhibiting catalytic activity.
• Holoenzyme — the assembled, fully functional complex consisting of the apoenzyme and its attached coenzyme. This form possesses enzymatic activity.
• Prosthetic group — a coenzyme is referred to by this term if it is bound to the protein part (apoenzyme) by very strong covalent bonds, becoming an inseparable element of it.