Principles of nomenclature
In biochemistry, several approaches to naming biocatalysts are accepted. The vast majority of such terms have the characteristic "-ase" suffix. There are three main ways names are formed:
- Based on the substrate. In this case, the signature suffix is simply added to the name of the substance upon which the enzyme acts. For example, if the target is urea, the result is urease. Sucrase, lipase (which breaks down lipids), and nuclease (which works with nucleic acids) are named according to the same logical principle.
- By the type of chemical transformation. This is a more informative approach. The name is composed of the substrate name and a description of what specifically happens to it during the reaction. Examples include lactate dehydrogenase, phosphoglucomutase, pyruvate carboxylase, and adenylyl cyclase.
- Trivial nomenclature. There are historically established terms that appeared before the introduction of strict rules. They do not contain the "-ase" suffix and give no hints about either the substrate or the type of reaction taking place. Medical students simply need to memorize them: these are pepsin, trypsin, thrombin, and renin.
International classification (IUBMB)
In 1961, the International Union of Biochemistry and Molecular Biology adopted a strict system by which all enzymes are divided into 6 main classes. The main criterion for distribution is the type of catalyzed reaction. Within each class, there are subclasses and subclasses that refine the details of the process: the chemical group of the substrate, the nature of the donor or acceptor, and the required cofactors.
It is necessary to memorize the classes 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 digits separated by dots (EC number). Let us examine this principle using malate dehydrogenase (its exact systematic name is L-malate:NAD oxidoreductase), which has the code 1.1.1.38.
Each position in the code has its own meaning:
- First digit (1) — indicates belonging to the main class. In our case, these are oxidoreductases.
- Second digit (1) — denotes the specific type of catalyzed reaction within the class (here, it is the oxidation of a hydroxyl group).
- Third digit (1) — reflects the presence of a specific coenzyme required for work (in this example, NAD+ is required).
- Fourth digit (38) — is simply the individual sequence 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 functioning. The following concepts are used to describe their structure:
- Apoenzyme — is exclusively the protein part of the molecule. It is important to remember that by itself, without additional helpers, it is not capable of exhibiting catalytic activity.
- Holoenzyme — is the assembled, fully working complex consisting of the apoenzyme and the coenzyme attached to it. It is this complex that possesses enzymatic activity.
- Prosthetic group — this is what a coenzyme is called if it is bound to the protein part (apoenzyme) by very strong covalent bonds, becoming its inseparable element.
Briefly: answers to topical questions
What subclasses are distinguished within the class of oxidoreductases?
Within the class of oxidoreductases, sources distinguish the following subclasses:
- Dehydrogenases — remove hydrogen from the substrate; coenzymes: NAD⁺, NADP⁺, FAD, FMN.
- Oxidases — transfer hydrogen from the substrate to oxygen.
- Oxygenases — incorporate oxygen into the substrate molecule; among them, monooxygenases and dioxygenases are indicated.
- Peroxidases / hydroxyperoxidases — destroy hydrogen peroxide and organic peroxides.
What exact chemical reaction do lyases catalyze?
Lyases catalyze reactions of non-hydrolytic cleavage or formation of bonds (C–C, C–N, C–O, C–S). They remove certain groups (CO₂, H₂O, NH₂, SH₂, etc.) from substrates without the participation of water, which often leads to the formation of a double bond, or add molecules across a double bond.
What chemical reaction do transferases catalyze?
Transferases catalyze reactions of intermolecular transfer of functional groups from one compound (donor) to another (acceptor). Transferred groups include methyl, methylene, glycosyl, phosphate, amino, and acyl groups.
Which coenzymes are most characteristic of oxidoreductase activity?
Oxidoreductases require coenzymes to function. For dehydrogenases as a subclass of oxidoreductases, the sources name the following electron-acceptor coenzymes:
- NAD⁺ (nicotinamide adenine dinucleotide)
- NADP⁺ (nicotinamide adenine dinucleotide phosphate)
- FAD (flavin adenine dinucleotide)
- FMN (flavin mononucleotide)
Also functioning with oxidoreductases is lipoic acid (lipoamide).
To easily memorize all 6 classes in order, use the mnemonic: Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases.
Class and exam questions
Can an apoenzyme catalyze a reaction on its own?
No, the apoenzyme is only the protein part. Without its coenzyme, it is completely devoid of catalytic activity.
What does the first digit in the EC number mean?
The first digit in the four-digit enzyme code always indicates the number of one of the six main classes to which it belongs.
How does a prosthetic group differ from a regular coenzyme?
A prosthetic group is a coenzyme attached to the protein part (apoenzyme) by powerful covalent bonds.
What does the trivial name of an enzyme indicate?
Trivial names (e.g., pepsin or trypsin) are established historically. They do not contain the "-ase" suffix and do not provide information about the substrate or reaction type.
What else to study on this topic
- Detailed characteristics of the oxidoreductase class
- Transferase subclasses and mechanisms of chemical group transfer
- Principles of hydrolase action and the role of water molecules
- Differences between lyases and isomerases in chemical transformations
- Synthesis reactions catalyzed by ligases
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