Enzyme Catalysis in Chemical and Biological Reactions

An enzyme is a substance which fastens a chemical reaction. A substrate is attracted towards the active site of the enzyme which leads to the catalysis of a chemical reaction and formation of products. This attraction may be electrostatic or hydrophobic (non-covalent interactions which are physical in nature rather than being chemical). The combination formed by an enzyme and its substrates is called the enzyme-substrate complex. When a reaction involves two substrates and one enzyme, a ternary complex is formed while in case of one substrate and one enzyme, a binary complex is formed.

As an example, assume two substrates (S1 and S2) bind to the active site of the enzyme during step 1 and react to form products (P1 and P2) during step 2. The products dissociate from the enzyme surface in step 3, releasing the enzyme. The enzyme, unchanged by the reaction, is able to react with additional substrate molecules in this manner many times per second to form products. The step of the chemical reaction during which the actual chemical transformation takes place is of the utmost importance to the scientists but is very poorly understood. In general, there are two types of enzymatic mechanisms, one in which a covalent intermediate forms and one in which none forms.

In the mechanism by which a covalent intermediate—i.e., an intermediate with a chemical bond between substrate and enzyme—forms, one substrate, B―X, for example, reacts with the group N on the enzyme surface to form an enzyme-B intermediate compound. The intermediate compound then reacts with the second substrate, Y, to form the products B―Y and X.

Many enzymes catalyze reactions by this type of mechanism. Acetylcholinesterase is a very common example whose enzyme mechanism has been studied thoroughly. The two compounds which act as a substrate for acetylcholinesterase are acetylcholine (i.e., B―X) and water (Y). After acetylcholine (B―X) binds to the enzyme surface, a chemical bond forms between the acetyl moiety (B) of acetylcholine and the group N (part of the amino acid serine) on the enzyme surface. The result of the formation of this bond called an acyl–serine bond is one product, choline (X), and the enzyme-B intermediate compound (an acetyl–enzyme complex). The water molecule (Y) then reacts with the acyl–serine bond to form the second product, acetic acid (B―Y), which dissociates from the enzyme. Acetylcholinesterase is regenerated and is again able to react with another molecule of acetylcholine. This kind of reaction, involving the formation of an intermediate compound on the enzyme surface, is generally called a double displacement reaction.

Sucrose phosphorylase acts in a similar way. The substrate for sucrose phosphorylase is sucrose or glucosyl-fructose (B―X), and the group N on the enzyme surface is a chemical group called a carboxyl group (COOH). The enzyme-B intermediate, a glucosyl–carboxyl compound, reacts with phosphate (Y) to form glucosyl-phosphate (B―Y). The other product (X) is fructose.

In reactions involving double displacement, the covalent intermediate formed upon enzyme-substrate interaction increases the speed of reaction. Because the enzyme is unaltered at the end of the reaction, it functions as a true catalyst, even though it is temporarily altered during the enzymatic process.

The formation of the covalent intermediate is not necessary for all enzyme-catalytic reactions. One substrate (Y) reacts directly with the second substrate (X―B), in a so-called single displacement reaction. The B moiety, which is transformed in the chemical reaction, is involved in only one reaction and does not form a bond with a group on the enzyme surface. The enzyme maltose phosphorylase, for example, directly affects the bonds of the substrates (B―X and X), which, in this case, are maltose (glucosylglucose) and phosphate, to form the products, glucose (X) and glucosylphosphate (B―Y).

Covalent intermediates between the part of a substrate and an enzyme occur in many enzymatic reactions and various amino acids—serine, cysteine, lysine, and glutamic acid—are involved.

A lot many studies have been conducted on exploring the mechanisms behind the enzyme catalysis. There have been given many theories to explain the interaction between the substrate and the enzyme. Two majorly accepted theories amongst these studies are mentioned below:

• Lock and Key Model: In this model, the substrate is described as fitting into the active site in the same manner as a key fits into a lock.

• Induced Fit Model: In the model, the enzyme has been considered as a flexible active site that changes its shape in order to accommodate the substrate and facilitate the reaction.

The catalytic action of enzymes, in chemistry, has been explained by a lot of mechanisms depending on the type of reaction they are involved in. They may be of the following types:

1. Acid-base catalysis: General acid catalysis involves partial proton transfer from a donor that lowers the free energy of the transition state while the base catalysis involves partial proton abstraction from a free energy lowering acceptor for the transition state.

2. The biochemical reactions susceptible to acid-base catalysis include peptide and ester hydrolysis, tautomerization, the reaction of phosphate groups and addition to carbonyl groups. These reactions typically involve Asp, Glu, His, Cys, Tyr and Lys residues. Many enzymes utilize a concerted acid-base mechanism (i.e., both acid and base catalysis).

3. Covalent Catalysis: Covalent catalysis leads to rapid progression of reactions by forming covalent bonds between enzyme and substrate. There are three stages involved in the covalent catalysis which are – nucleophilic reaction between enzyme and substrate, electrophilic withdrawal of electrons from the substrate and elimination reaction.

4. Metal Ion Catalysis: Metal Ion Catalysis enhances the reaction in three manners – binding to and orienting substrates for reaction, mediating redox reaction through changes in oxidation state and electrostatic stabilization or shielding of negative charges. There are two types of metal ion-dependent enzymes – metalloenzymes that contain tightly bound transition metal ions (e.g., Fe²⁺, Fe³⁺, Cu²⁺, Zn²⁺, Mn²⁺ and Co³⁺) and metal-activated enzymes that loosely bind metal ions (e.g., alkali or alkaline metals including Na⁺, K⁺, Mg²⁺ and Ca²⁺). Metals can act as superacids with a similar role to protons in acid catalyzed reactions and are even more effective than protons because of their high pH and high charge. Metals shield or reduce the effective charge present on the highly anionic substrates and hence facilitate the approach of nucleophile towards the substrate during a reaction.

5. Electrostatic Catalysis: Electrostatic catalysis occurs in enzymes that seem to arrange active site charge distributions to stabilize the transition states of catalyzed reactions. In this type of catalysis, substrate binding generally excludes water from an enzyme active site generating a low dielectric constant within the active site. The electrostatic interactions involved in this catalysis are very strong and the pKa values can vary by several pH units due to the proximity of charged groups. In another form of electrostatic catalysis, charge distribution of the substrates is used by the enzymes for direct them towards their active sites. Other enzymes may have reaction rates greater than the apparent diffusion controlled unit also known as the substrate channeling.

6. Proximity and Orientation Effects: Substrate binding in this type of enzyme catalysis has additional effects that enhancing the reaction rates. In this type of catalytic reactions, the reactants must come together with the proper spatial arrangement and relationship with respect to the enzyme in order for a reaction to occur. Proximity effects are more readily observed by comparing equivalent intermolecular and intramolecular reactions. The intramolecular reactions are typically 10-100 folds more rapid. Orientation effects are more significant to the reaction mechanism, though they are difficult to quantify. This theory suggests that the molecules are maximally reactive when their orbitals are aligned so the electronic energy of the transition state is minimized. This is also termed as stereoelectronic assistance.

7. Preferential Transition State Binding: According to this mechanism of enzyme catalysis, the enzymes bind to the transition state with higher affinity than the substrate or the product. This theory is an explanation for the release of products into the final solution. Besides, it explains the difference between good and bad competitive inhibitors with respect to the proximity and orientation effects accounting for the enhanced rate of reactions. This theory further states that the enzymes mechanically strain substrates towards transition states. This is also known as the rack mechanism. In these types of reactions, the rate enhancement can be expressed in terms of enzyme affinity for the transition state as compared relatively to the substrate. It also explains the reason why the good as well as the bad substrates have typically similar Km values but different kcat values. According to this theory, a good substrate does not need to bind tightly to the enzyme but must bind tightly to the transition state when activated during the reaction.