Chemical Composition of Enzyme Molecules

The essence of most enzymes is protein, and only a few enzymes are RNA, so this article only discusses enzymes composed of proteins. These enzymes, like other proteins, are composed of amino acids and have primary, secondary, tertiary, and quaternary structures. Enzymes will also be denatured and lose vitality due to certain physical and chemical factors. Enzymes also have colloidal properties and cannot penetrate semi-permeable membranes.

Enzymes can also be hydrolyzed by proteases. Some people think that proteases cannot act on themselves. In fact, one enzyme molecule can cut another enzyme molecule as long as there is a corresponding enzyme cutting site. For example, when the zymogen of chymotrypsin is activated by trypsin, the direct product is π-chymotrypsin. π-chymotrypsin has high activity, but it will self-cleave to produce α-chymotrypsin which is less active but more stable.

Some enzymes are composed entirely of protein and are simple proteins, such as urease and trypsin. In addition to protein, some enzymes also contain non-protein components, which are binding proteins. The non-protein components are called cofactors, the protein part is called enzyme protein, and the complex is called holoenzyme. Cofactors generally play the role of carrying and transferring electrons or functional groups. Among them, those that are tightly bound to the enzyme protein by covalent bonds are called prosthetic groups, and those that are loosely bound by non-covalent bonds are called coenzymes.

Recently, there is a term "conjugated enzyme" used to refer to holoenzymes. However, there is no such name in biochemistry books, and conjugated enzyme is not available on Wikipedia. Conjugated protein does exist (translated as binding protein or conjugated protein). So this term should be derived by some people, not a professional term. The official name should be holoenzyme, and apoenzyme. Because Conjugated protein is actually just a classification, it is emphasized that such proteins can have cofactors, but it is not guaranteed to have cofactors. The search results on PubMed are all about coupling enzymes to carriers, so don't use them indiscriminately.

In the process of catalysis, the prosthetic group is not separated from the enzyme protein, and only functions as the carrier in the enzyme. For example, the prosthetic group of FAD and FMN in the flavin protein enzyme molecule carries hydrogen, and the biotin prosthetic group of carboxylase carries carboxyl group, etc. Coenzymes are often used as inter-enzyme carriers to connect two enzymatic reactions. For example, NAD+ is reduced to NADH in one reaction, and then oxidized back to NAD+ in another reaction. It acts like a substrate in the reaction and is sometimes called a secondary substrate. Therefore, the systematic naming of dehydrogenase is often like "alcohol: NAD + oxidoreductase".

More than 30% of enzymes require metal elements as cofactors. The metal ions of some enzymes are tightly bound to the enzyme protein and are not easily separated, which are called metalloenzymes; the metal ions of some enzymes are loosely bound and are called metal activating enzymes. The cofactors of metalloenzymes are generally transition metals, such as iron, zinc, copper, and manganese. The cofactors of metal activating enzymes are generally alkali metals or alkaline earth metals, such as potassium, calcium, and magnesium.

An enzyme composed of one peptide chain is called a monomeric enzyme, and an enzyme formed by multiple peptide chains joined by non-covalent bonds is called an oligomerase, which is an oligomeric protein. Sometimes some functionally related enzymes in the organism are organized to form a multi-enzyme system, which in turn catalyzes related reactions. The formation of a multi-enzyme system is a requirement of metabolism, which can reduce the diffusion limit of substrates and products, and improve the speed and efficiency of the overall reaction.

Sometimes there are multiple enzyme activities on a peptide chain, which is called a multi-enzyme fusion. For example, the debranching enzyme in glycogen decomposition has starch-1,6-glucosidase and 4-α-D-glucanotransferase activities on one peptide chain. The AROM multi-enzyme fusion from N. rubrum is a dimer, and each peptide chain contains five enzyme activities, which can catalyze the second to sixth steps of the shikimate pathway. Due to the intermediate product transfer channel, the catalytic efficiency is greatly improved.