Enzyme Structure

Basic concepts of enzymology

The branch of biochemistry that studies these remarkable molecules is called enzymology. The main task of enzymes is enzymatic catalysis, meaning the multifold acceleration of chemical reactions in the body.

To understand the mechanisms of action, it is necessary to know key terms:

• Substrate — the substance upon which the enzyme directly acts.
• Specificity — the strict selectivity of an enzyme's action regarding its substrate.
• Active site — a specific region of the enzyme molecule. It is precisely here that substrate binding and its subsequent chemical transformation take place.

During catalysis, the enzyme and substrate temporarily combine to form an intermediate compound — the enzyme-substrate complex.

Simple and conjugated enzymes

Abruptly all enzymes are proteins, yet their structural organization varies. Two main groups are distinguished:

1. Simple enzymes. Built exclusively from amino acids. They require no additional chemical groups to exhibit catalytic activity.
2. Conjugated enzymes. Consist of two mandatory components: protein and non-protein parts.

The protein part of a conjugated enzyme is called the apoenzyme. It is important to remember: in the absence of its non-protein partner, the apoenzyme is completely inactive.

The non-protein part bears the general name cofactor. Only upon the union of the apoenzyme and cofactor is a holoenzyme formed — the complete, catalytically active complex ready to carry out the reaction.

Diversity of cofactors

Cofactors are extremely diverse in their chemical nature. They are generally divided into two major categories:

• Inorganic. This group includes various metal ions.
• Organic. An extensive group of substances including vitamins and their derivatives (most common), nucleosides and nucleotides, heme, peptides, and even transfer RNAs (tRNAs).

Organic substances located in the active site that take direct part in the act of catalysis are called coenzymes.

Types of coenzyme-protein binding

Depending on how tightly the non-protein part is attached to the apoenzyme, two types of interaction are distinguished:

• Temporary (loose) bond. The coenzyme attaches to the protein molecule exclusively at the time of the chemical reaction.
• Strong (covalent) bond. The non-protein component is permanently and very firmly bound to the apoenzyme. In this case, the coenzyme receives a special designation — the prosthetic group.

Examples of enzymes and their classes

According to the international classification, enzymes are divided into major classes depending on the type of catalyzed reaction. Let us examine a few practical examples:

• Succinate dehydrogenase — a typical representative of the oxidoreductase class.
• Pyruvate carboxylase — belongs to the ligase class.
• DNase — is an enzyme from the hydrolase class.

Class and exam questions

What else to study on this topic

• Enzymatic catalysis kinetics: maximum reaction velocity ($V_{max}$) and Michaelis constant ($K_m$)
• Units of enzyme activity measurement (katals, international units — IU)
• Calculation of specific enzyme activity (number of activity units per 1 mg of protein)
• Detailed characteristics of the six main enzyme classes (oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases)

Other topics in the "Enzymology" section

Prepared by WhiteCoat Pro faculty in accordance with the medical school curriculum. For educational purposes only.