What are Enzymes and how do they work
Enzymes are biological catalysts of a protein nature, without which life could not exist. Only a small group of enzymes are made up of RNA molecules, called ribozymes, which come into play in some processes such as protein synthesis and splicing of messenger RNA in eukaryotic cells.
Enzymes preside over the many metabolic reactions of a living organism, regulating the exchange of energy with the external environment.
Due to enzymes, it is possible to digest food, recover energy in the bonds of biomolecules in the form of ATP, usable for all endergonic processes, which are also catalyzed by enzymes such as the biosynthesis of macromolecules from simpler organic substances.
The enzymes can accelerate the reactions by a factor between 105 and 107, showing a catalytic power and specificity often far superior to inorganic and synthetic catalysts. The central role played by enzymes for the survival of living organisms explains why many genetic diseases that alter the functionality of many enzymes give rise to pathological conditions, even quite serious ones. The evaluation of the number of certain enzymes in the blood and other tissues is a useful diagnostic tool, for example, liver and cardiac dysfunctions. Furthermore, the action of many drugs is based on the interaction with enzymes, modulating their activity in various ways.
Nomenclature of enzymes
The name of the enzymes derives from the substrate or phrase that describes its activity, adding the suffix -asi. In some cases, the names of the enzymes are based on a given function, before the specific catalyzed reaction was discovered, such as for the digestive enzymes pepsin and trypsin or lysozyme. Often many enzymes are indicated by multiple names, which can be confusing.
To overcome possible ambiguities, the international system of nomenclature and classification of enzymes provides six classes, in turn, divided into subclasses.
Each enzyme is indicated by a systematic name that describes the catalyzed reaction and by a series of four numbers, the first of which indicates the class, the second the subclass.
The structure of enzymes
Enzymes are large proteins, often with a quaternary structure, capable of specifically binding one or more reacting substances, called substrates, catalyzing their conversion into others.
In some cases, the enzymes carry out the catalysis autonomously; they require the intervention of cofactors, additional non-protein components.
The cofactors can be metal ions, such as Fe2 +, Mg2 +, Mn2 +, or Zn2 +, or complex organic molecules called coenzymes, such as NAD, FAD, biotin, coenzyme A and many others.
If metal ions or a coenzyme are stably covalently linked to enzymes, they are called prosthetic groups.
The set of the protein component and cofactors of an enzyme is called a holoenzyme. The only protein part is called apoenzyme or apoprotein.
The binding of substrates to enzymes
The bonding of the substrates takes place in pockets of the enzymes called active sites, where the amino acid residues present to ensure the specificity of the bond with the substrates and the catalysis mechanisms necessary to make the reaction take place. Weak interactions mainly ensure specificity.
The interaction between the substrate and the active site has been classically described with the key-lock model, proposed by Fisher in 1894.
However, if the active site perfectly adapted to the substrate, from an energy point of view, the transformation into a different compound would not be more advantageous, because it would compromise the stability of the enzyme-substrate interaction.
The catalytic action of the enzymes
As catalysts, enzymes intervene in reactions without being consumed, lowering their activation energy, often remarkably high considering that most biomolecules are stable in the cellular environment, and conversion to other compounds would be non-spontaneous or even unlikely.
Activation energy is an energy barrier between reagents and products that prevents the reaction from proceeding in a period compatible with the needs and survival of the cell and a living organism.
An enzyme can lower the activation energy by creating a favorable environment that makes the reaction energetically favored and achievable in a short time, in the order of milliseconds.
The mechanisms by which the enzyme favors the lowering of the activation energy are basically three. It reduces the random movements of the reacting molecules that are immobilized on the surface of the enzyme to favor their correct orientation for the purpose of the reaction.
Secondly, the interaction with the enzyme removes the substrate from the solvation halo created by the water molecules, which, due to hydrogen bonds, stabilizes most of the biological molecules in the cells.
Thirdly, the enzyme adopts catalysis mechanisms that make the breakage and formation of chemical bonds energetically possible, processes necessary in the course of a reaction to generate new substances from one or more initial reagents.
The catalysis mechanisms are the strategies implemented by the enzymes in the breaking and bonding processes that take place during the reaction.
Among the best-characterized mechanisms are:
• Acid-base catalysis;
• Covalent catalysis;
• Catalysis by metal ions.
Acid-base catalysis consists in the transfer of H + from the amino acid residues of the active site of the enzyme or vice versa, creating intermediates whose transformation into products occurs more easily.
Covalent catalysis presupposes the formation of a transient covalent bond between the substrate and the protein component of the enzyme or its coenzyme.
Some enzymes have metal ions as a cofactor, whose positive charges generally have the function of orienting the substrate and stabilizing any charges.
Most enzymes show a hyperbolic relationship between the substrate concentration and the speed of the catalyzed reaction, mathematically described by the Michaelis-Menten equation.
The achievement of the maximum speed is due to the saturation of the active sites of the enzyme molecules. Only by increasing the amount of enzyme is it possible to obtain a further increase in speed, also in this case destined to reach a maximum value when there are no more active sites available to bind the substrate molecules.
The Michaelis-Menten equation includes the constant Km (Michaelis constant), specific for each catalyzed reaction. It represents the concentration of substrate at which half of the maximum speed is reached and can be considered a measure of the affinity of the enzyme for the substrate.