Biological Chemistry - Berezov T. T., Korovkin B. F. 1998

Enzymes
A Brief History of the Development of Enzymology
Structure of Enzymes

Both simple and complex Enzymes exist in nature. The former consist entirely of polypeptide chains and, upon Hydrolysis, break down exclusively into Amino Acids. Examples of such enzymes (simple Proteins) include hydrolytic enzymes, notably Pepsin, Trypsin, Papain, urease, Lysozyme, Ribonuclease, and phosphatase, among others. The majority of natural enzymes belong to the Class of complex proteins containing, In addition to polypeptide chains, a non-protein component (cofactor), the presence of which is absolutely essential for catalytic activity. Cofactors can vary in chemical nature and in the strength of their binding to the polypeptide chain. If the dissociation constant of a complex enzyme is so small that all polypeptide chains in solution remain bound to their cofactors and do not dissociate during Isolation and Purification, such an enzyme is termed a holoenzyme (holoenzyme), and the cofactor is called a prosthetic group, which is considered an integral part of the enzyme molecule. The polypeptide portion of the enzyme is commonly referred to as the apoenzyme.

Other names for the components of complex enzymes are still used in the literature, specifically "protein-enzyme", "protein component" (apoenzyme), "coenzyme" (coenzyme), and "prosthetic group". The term coenzyme often refers to an accessory group that is easily detached from the apoenzyme upon dissociation. It is suggested that the prosthetic group may be linked to the protein via covalent and non-covalent bonds. For instance, in the acetyl-CoA carboxylase molecule, the biotin cofactor is covalently bound to the apoenzyme through an amide bond (see Chapter 7). On the other hand, the chemical bonds between cofactors and peptide chains can be relatively weak (e.g., Hydrogen Bonds, Electrostatic Interactions, etc.). In such cases, complete dissociation of both parts is observed during enzyme isolation, and the isolated protein component remains devoid of enzymatic activity until the missing cofactor is added externally. It is precisely to such isolated low-molecular-weight organic substances that the term "coenzyme" applies, with typical representatives being Vitamins B₁, B₂, B₆, and PP, which contain Coenzymes. It is also known that both prosthetic groups and coenzymes are actively involved in Chemical Reactions, functioning as intermediate carriers of electrons, hydrogen atoms, or various functional groups (e.g., amino, acetyl, carboxyl). In such cases, the coenzyme is regarded as a second substrate, or cosubstrate.

The Role of a coenzyme (Co) as a carrier of, for example, hydrogen atoms can be represented as a scheme, where SH is the substrate, CoE is the holoenzyme, and A is the proton acceptor:

The substrate undergoes oxidation by releasing electrons and protons, whereas the CoE undergoes reduction by accepting electrons and protons. In the subsequent half-reaction, the reduced CoEH can transfer electrons and protons to another intermediate electron and proton carrier or to the terminal acceptor (see Chapter 9).

Coenzyme, cofactor, and prosthetic group are ambiguous biochemical jargon. Terminological debates persist because the Structure/97.html">Definitions of "coenzyme," "cofactor," and "prosthetic group" are frequently viewed through the prism of their role in Enzymatic Catalysis. One must reckon, however, with the undeniable fact that in many cases non-protein organic molecules, like Metal Ions, are strictly required by the protein component to perform a specific biological function unrelated to biocatalysis. Undoubtedly, the type and Nature of the bond between the non-protein component and the protein molecule are also significant. Therefore, it is evident that a cofactor can be any factor strictly required for a protein to fulfill its catalytic or any other biological role. Conversely, a coenzyme can be any non-protein factor directly involved in an enzymatic catalysis reaction. A cofactor that does not directly participate in the catalytic act is not a coenzyme. At the same time, a prosthetic group (a covalently bound non-protein component necessary for a specific function) can be called a coenzyme if it directly participates in the enzymatic reaction. A prosthetic group that is not involved in the catalytic act but is functionally essential for both an enzyme and a non-catalytic protein can be termed a cofactor. Finally, Cofactors and Coenzymes that are loosely bound (or weakly bound) to an enzyme or protein are nevertheless not classified as prosthetic groups.

Many divalent metals (Mg²⁺, Mn²⁺, Ca²⁺), as will be shown below, also function as cofactors, although they belong neither to coenzymes nor to prosthetic groups. Examples are known where metal ions are tightly bound to the protein molecule, functioning as a prosthetic group. In particular, the purified enzyme catalyzing The oxidation of ascorbic acid (Vitamin C) to dehydroascorbic acid contains 8 copper atoms per molecule; all of them are so firmly bound to the protein molecule that they neither exchange with ion-exchange resins nor are separated by dialysis. Furthermore, electron paramagnetic Resonance studies have demonstrated the participation of copper ions in intermediate electron transfer. Interestingly, free copper ions also possess catalytic activity in the oxidation of ascorbic acid; however, this activity increases many thousands of times when copper ions combine with the apoenzyme into a single complex—the holoenzyme.

Data on the most important coenzymes and prosthetic groups of enzymes, including their names and structures, the Chemical Nature of the vitamin incorporated into them, and The Nature of their biochemical function in METABOLISM, are discussed in detail in Chapters 7 and 9–13.

Evidence has been obtained regarding the cofactor function in ENZYMATIC REACTIONS OF A number of other biologically active compounds that are not classified as vitamins: HS-Glutathione, ATP, Lipoic Acid, nucleoside derivatives (uridine phosphate, cytidine phosphate, phosphoadenosine phosphosulfate), porphyrin-containing substances, and others. This category also includes tRNAs, which, as part of aminoacyl-tRNA synthetase complexes, take an active part in the Transport of Amino acids to the ribosome where Protein Synthesis occurs (see Chapter 14).

One distinctive feature of two-component enzymes should be noted: neither the cofactor alone (including most coenzymes) nor the apoenzyme by itself possesses catalytic activity. Only their assembly into a single entity—proceeding not chaotically, but in accordance with the program of their structural Organization—ensures the rapid progression of the chemical reaction.