Activation Centre

Enzymes are considered biological molecules that act as catalysts to speed up various processes. They are protein sources formed by chains of amino acids in various combinations. Enzymes are highly specific in reactivity. There are many enzymes in the human body that catalyse various metabolic reactions occurring inside the body. Enzymes work in the mild conditions of temperature, pH, and pressure of the cells. They are highly efficient and specific.

Enzymes are classified into the following six types based on the type of reaction they catalyse:

1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Ligases
6. Isomerases

What are Enzymes?

Enzymes are usually globular proteins that are three-dimensional and produced by ribosomes and RNA (Ribo Nucleic Acids) of the cell. All enzymes have specific activation centres on their surface, which works for a particular substrate. The substrate is the reacting species of a reaction that changes to form products. Every substrate and product has a certain energy. Some can have low energy, and some can have high energy. The reacting particles need to cross the energy barrier called activation energy for the substrate to turn into products. This activation energy for all the substrate molecules may not be equal and results in fewer products and relatively takes longer to complete. 

To increase the rate of conversion of substrate to products, a small number of enzymes are used that are suitable for that particular reaction. This enhances the speed of the reaction by reducing the activation energy for the reaction.

Example 1: Saliva in the mouth produces saliva enzymes to enhance the digestion of food in the mouth.

Example 2: Formation of Ammonia

N₂ + 3H₂ → 2NH₃

This reaction takes a relatively long time to complete, so to speed up the process, an Iron (Fe) metal catalyst is used. In the same reaction, Molybdenum is used as a promoter.

Activation Centres of Enzymes

Enzymes have an activation centre of specific shapes as they have tertiary structures. A small change in the size or shape of the activation centre can change the activity of enzymes. Activation centres of enzymes can be further classified into the binding site and catalytic site.

Binding site: This site chooses the substrate and binds it to the activation centre.

Catalytic site: This site performs the catalytic function of an enzyme.

Cofactors are the non-protein molecules that perform or catalyse reactions that are not carried out by the 20 amino acids present in our body. Cofactors can be organic or inorganic.

Cofactors bind to the protein and make it active, whereas proteins without a cofactor protein are inactive.

Enzymes can be intracellular and extracellular. Intracellular enzymes are those that are produced in the body and retained for the functioning of the cell. Extracellular enzymes are those that are produced in the cell and sent outside of the cell to work externally.

Enzyme-Substrate Complex

When an enzyme (E) binds to its substrate(S), an enzyme-substrate complex (ES) is formed. This enzyme-substrate complex (ES) modifies the activation energy of the reaction by lowering it. Due to the reduction of activation energy, the ES complex promotes the rapid formation of products. 

An enzyme makes the substrates available in an optimal orientation; thereby, increasing the rate of the chemical reactions. 

The activation centre or catalytic site:

1. The activation centre (site) or catalytic site is the specific site present in the enzyme where the substrate binds.
2. The structure of the enzyme and the substrate are complementary to each other to fit each other reciprocally. This reciprocally fitting of the enzyme and the substrate is termed an induced fit.
3. Generally, the activation centre is a groove of the enzyme that can be present in a deep tunnel within the enzyme.
4. In the primary structure of the protein (present in the enzyme), an amino acid residue (present in the activation centre) can be very far. After folding, it forms a tertiary structure, and these amino acid residues come closer to each other.
5. After binding, the substrate with the activation centre undergoes conformational changes.
6. The substrate binding to the activation centre is very specific. The amino acids that are present in the activation centre are highly conserved and unable to fit into the other species.
7. The functional group of the enzyme is the site of the activation centre where the substrate can bind and form the transition state.
8. Molecules with a similar structure to the transition state are highly effective enzyme inhibitors.
9. The activation centre of an enzyme is able to work under an ideal environment like a less acidic or nonpolar condition.
10. The reaction rate can be increased after increasing the temperature, but very great changes in temperature and pH can denature an enzyme, and it cannot catalyse the reaction.
11. The methods used to analyse the activation centres are:

• Affinity labels
• X-ray diffraction analysis
• Site-directed mutagenesis

12. The enzyme comes back to its original form after the completion of the reaction. Hence, the enzymes do not change after the reactions.
13. After the completion of the reaction, an enzyme releases its products (substrates).

Activation by cofactors:

Most of the enzymes get activated by cofactors.

Example 1: DNA-Polymerase, which is a holoenzyme, uses Magnesium ion as a cofactor.

Example 2: Horse liver dehydrogenase uses Zinc ion as a cofactor.

Enzymes act in a highly specific manner. They have different degrees of specificity in terms of:

• Bonding specificity
• Group specificity
• Absolute specificity
• Optical or stereospecificity
• Dual specificity

Working of Enzymes:  

Enzyme-catalysed reactions occur in two steps.

1. An enzyme (E) and the substrate (S) come close to each other after colliding to form an intermediate compound known as the enzyme-substrate (E–S) complex. 

2. The enzyme catalyses the formation of product (P) after the formation of the E–S complex, which is released from the enzyme surface:

S + E → E–SE–S → P + E

Induced Fit model: 

According to this model, after binding, both enzyme and substrate undergo dynamic conformational changes. The enzyme increases the rate of the reaction by twisting the substrate into its transition state.

Conclusion

Enzymes have specific sites called active sites or catalytic sites, or activation centres. Activation centres are the points or regions on enzymes where the substrate attaches to the enzyme. When activated by certain substances, the enzymes get activated and show complete efficiency during a chemical reaction forming the products. The activation centre of an enzyme can work under an ideal environment like a less acidic or nonpolar condition.