What are enzymes?

Introduction

Enzymes are bio-catalysts that catalyze a biochemical reaction inside a body without being altered in a biochemical reaction. All enzymes are highly specialized proteins, (with exception of RNase) that are made up of a sequence of amino acids that form a polypeptide chain and fold into a stable conformation to catalyze a reaction. If enzymes are not present, then the reaction will not be catalyzed at a noticeable rate.

However, the first enzyme to be discovered was diastase (mixture of amylase) and then followed up by pepsin and invertase enzymes. The term enzyme was first proposed by Wilhelm Kühne in 1877.

Conditions for Enzyme activity

Enzymes work well under specific conditions and have a high degree of substrate specificity. The enzyme can increase reaction rate only when the environment in which they are present has optimum pH, temperature, and an aqueous phase.

Enzymes have a high degree of catalytic power; without enzymes the reaction will not be carried out at a predictable rate. If the enzyme is denatured or not present in its native conformation then the catalytic power is lost. Thus, the structure of the enzyme is essential for its catalytic activity.

Chemical compounds required for Enzyme activity

Some enzymes require chemical groups for their activity. If the chemical group is a small molecule and in-organic in nature it will be called a co-factor for example Na⁺, Cl^–, if the compound is organic or metal-organic it will be called a coenzyme for-example NAD⁺, FAD⁺. When a co-enzyme has a chemical compound tightly and covalently attached to it will form a prosthetic group.

An enzyme (protein part) with its coenzyme or metal ion (non-protein part) present in the catalytically active form will call a Holoenzyme on the contrary when there is only protein part i.e., enzyme, not present in its catalytically active form, it will be called as apoenzyme.

How enzyme work, Mechanism, folding

The catalysis of enzymes is essential for living systems. The reactions without enzymes tend to be slow and can be carried out at a mild temperature and pH inside a cell. But some reactions are unfavorable, and cannot be catalyzed without enzymes like the formation of unstable charged intermediate or the collision of two or more molecules in a precise orientation to react and the formation of a product takes place.

The enzyme evades these problems by providing an environment that is highly favorable for the molecules to react and form a product. However, an enzyme has a specific site (active site/binding site) where a molecule called a substrate and the formation of a product takes place.

When a substrate attaches to the active site different bond formation (like a covalent bond) takes place between the amino acid residues of the enzyme and the substrate molecules. Thus, an enzyme-substrate complex (ES) is formed, which was first proposed by Charles-Adolphe Wurtz in 1880. The enzyme-substrate complex leads to the formation of a product.

Enzyme + substrate → Enzyme substrate complex + Product

Reaction rate and enzyme

An enzyme catalyzes a chemical reaction without affecting the reaction equilibria. The equilibrium between substrate and product represents the free energy as shown in the figure; Here, the free energy of the product is less than the free energy of the substrate, where the transition state shows the intermediate formation in a reaction known as “energy hill”.

The rate of a reaction depends upon physical and chemical parameters:

The energy barrier between the substrate and the product.
Proper orientation of molecules to react and the formation of a product takes place.
Transformations that are required for the reaction to be catalyzed.
Formation of a charged intermediate during the transition state.

However, enzymes are not used up in the reaction and the equilibrium point is unaffected. Thus, the equilibrium reaches much faster.

Steps in a reaction:

Several steps are involved in a chemical reaction like the formation and the decay of a species called reaction intermediate. The formation of reaction intermediate reflects the ES complex where the substrate immediately occupies the binding site of the substrate. If the intermediate is stable then the decay of intermediate will lead to the formation of a product.

On the contrary, if the intermediate is not stable then the decay will lead to the reactants again and the reaction is not catalyzed. Thus, the activation is much higher so no formation of products takes place. Enzymes are also responsible for lowering the activation energy so that the reaction is being catalyzed.

However, activation energy can be determined by the highest point of energy where the energy barrier is overcome and the formation of the product takes place. This step is known as the rate-limiting step.

Enzyme Inhibition

Enzymes catalyze reactions in favorable environments like optimum pH, temperature, etc. There are chemical compounds that attach to the enzyme either on the active site or on the allosteric site (other than the active site) and chemically retard or specifically block the activity of an enzyme. These chemical species are known as inhibitors.

Inhibitors either form covalent bonds with the enzyme or a non-covalent bond to inhibit or retard the activity of the enzyme and the reaction will not catalyze at a predictable rate. Inhibitors can be removed by increasing the substrate concentration or by several other factors thus making a reaction reversible. If inhibitors are not removed then the reaction will not be reversed and completely uninformed the activity of an enzyme, such mechanism is used in antibiotics to treat diseases.

References and Sources

Book: David L. Nelson, Michael M. Cox – Lehninger Principles of Biochemistry (2008, W. H. Freeman) – libgen.lc
http://jpkc.scnu.edu.cn/swhx/L/chapt08/bio1.htm https://www.biologydiscussion.com/enzymes/enzymology/enzymology-a-close-look-with-diagram/11211
https://wikispaces.psu.edu/display/230/Enzyme+Kinetics+and+Catalysis
https://slcc.pressbooks.pub/humanbiology/chapter/14-dna-structure-protein-synthesis-and-gene-regulation-2/
https://en.wikipedia.org/wiki/Enzyme
https://wou.edu/chemistry/courses/online-chemistry-textbooks/ch450-and-ch451-biochemistry-defining-lifeat-the-molecular-level/chapter-7-enzyme-kinetics/

Enzymes: Introduction, Enzyme activity and work Mechanism