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4.5.3. General Mechanism of Enzyme Catalysis

General Mechanism of Enzyme Catalysis

All chemical reactions need an activation energy to be able to break the bonds of some initial substances, called reactants or substrates (S), to transform them into final substances or products (P).

he enzymes, like other catalysts, accelerate the rate of chemical reactions reducing the activation energy. Thus, a greater number of molecules react and the reaction accelerates.

The transformation from reactant to product is not direct, but there is an intermediate step in which the reactant is activated, and its bonds are weakened. To reach this activated complex, activation energy is necessary.

The reaction rate is the amount of product that is formed per unit of time in a chemical reaction.

The activation energy is the energy to be supplied to the reactants for the reaction to occur.

Catálisis enzimática

By Gonn [Public domain], via Wikimedia Commons

The enzymes are responsible for lowering the activation energy to easily reach the activated complex and allow the reaction to take place. Without the presence of the enzyme it would not be possible to reach the transition state.

This activation energy is necessary in both endothermic and exothermic reactions to reach the activated complex, although, globally, some require energy and others release it.

In spontaneous reactions, the activation energy is so low that it is obtained from the kinetic energy of the molecules or even from the light that falls on the reaction site. In non-spontaneous reactions, it is necessary to apply heat in order to reach that activation energy, which is much higher.

The enzymes can act in two ways:

  • Fixing to the substrate by means of strong bonds (covalent) , to weaken their bonds and that it is not necessary as much energy to break them.
  • By attracting substrates to the enzyme to increase the chance of encounter and facilitate the reaction.

The enzymes, after the reaction, free the products to be able to bind to other substrates. Enzymes often form multienzyme complexes , so that the product of one enzyme is the substrate for the next, so a high concentration of the substrate is not required.

In a biochemical reaction catalyzed by an enzyme, the binding of the substrate to the enzyme always occurs, forming the enzyme-substrate complex , essential for the chemical reaction to be carried out. It can be represented by the equation:

E + S → ES → E + P

Where E represents the enzyme, S to the substrate P to the product of the reaction, and ES is the intermediate enzyme-substrate complex.

Some enzymes are not operational until they are activated by other enzymes or ions, such as pepsinogen , which are transformed by HCl into pepsin. These enzymes are called zymogens or proenzymes .

In short, the enzyme catalyzes a reaction by binding with the substrate that can be summarized in three stages:

1.- The substrate binds to the apoenzyme (protein part) forming the enzyme-substrate complex (ES). There is a high degree of specificity, so that a specific enzyme is required for each type of substrate and reaction. Each enzyme can catalyze only one type of reaction, acting on a single substrate or a very small group of substrates.

Enzyme specificity is due to the shape of the active center of the apoenzyme where the substrate is attached. Before it was compared with the coupling that exists between a key and its lock (key-lock theory), in which all the projections and recesses have to coincide exactly. Currently, the “induced fit or coupling” seems more successful, where the active center can adapt to the substrate, something similar to what happens with a glove and a hand. The hand (the substrate) makes the glove (the active center) adapt as it enters it.

Animation: Induced fit.

The binding of the enzyme to the substrate is reversible, since a part of the substrate enzyme complex (ES) dissociates and, precisely due to this reversibility, this first stage is slower.

E + S ↔ ES

The radicals of the amino acids of the active center bind to the substrate weakening their bonds, which makes it easier to reach the transition state.

2.- Once the enzyme-substrate complex is formed , the cofactor carries out the reaction and the final product (P) is obtained. This stage is very fast and irreversible.

ES → E + P

If there are no cofactors, the catalytic action is carried out by some amino acids from the active center itself .

3.- The product is released from the active center and the apoenzyme is free to reattach to new substrate molecules. The coenzyme can be released intact or released by being modified.

Fundamental insights on the mechanism of enzymatic catalysis

The enzymes are biocatalysts that lower the activation energy necessary for breaking the links reagents or substrates  to be transformed into the final products or substances.

Enzymes increase the rate of reaction.

The enzyme needs a certain activation energy to bind at the active center to the substrate and form the intermediate enzyme-substrate complex. Then the cofactor (or some amino acids of the active center) carries out the reaction and the final product that is released is obtained, leaving the enzyme free to act again, since it is not spent.