Introduction to Enzymes: Structure and Characteristics-Short Lecture Notes

What are Enzymes?

There are thousands of chemical reactions in a living system. The chemical reactions in the cell are catalyzed by the biological catalysts called enzymes. Almost all enzymes are highly specialized proteins. (Exception: Ribozymes –Ribozymes are RNA with catalytic activity). The current post we will discuss the Characteristics of Enzymes. We will also discuss the features of a Catalyst and the concept of Activation Energy of a reaction.

What are catalysts?

Ø  The catalyst is substances that accelerate the rate of a chemical reaction.

Ø  The catalyst is not consumed or transformed by the reaction.

Ø  It will not change the equilibrium constant of the reaction.

Ø  Catalysts only change the rate to approach equilibrium constant.

Ø  Catalysts are not required in stoichiometric quantities.

Ø  Examples: Platinum, Palladium etc.

Brief History about Enzymes

Ø  The history of biochemistry is the history of enzyme research.

Ø  Louis Pasteur reported fermentation of sugar into alcohol by yeast is catalyzed by “ferments”.

Ø  Frederick W. Kuhne coined the term ENZYME for the ‘ferments’.

Ø  The first enzyme discovered was Diastase from malt by Anselme Payen in 1833.

Ø  The first crystallized enzyme is Urease by James Sumner.

Characteristics of Enzymes

Ø  The enzymes have extraordinary catalytic power.

Ø  Enzymes accelerate reactions up to 1014 to 1020 times.

Ø  Enzymes have a high degree of specificity for their substrates and reactions.

Ø  They function in an aqueous solution.

Ø  Enzymes work under a mild condition of temperature and pH.

Ø  Enzymes make macromolecules from simple precursors.

Ø  The enzymes act in an organized sequence.

Ø  They catalyze the hundreds of step-wise reaction.

Ø  Enzymes can regulate metabolic pathways and these enzymes are regulatory enzymes.

Ø  In some genetic disorders, there may be a deficiency one or several enzymes (Eg. albinism).

Ø  Enzyme reduces the activation energy of the reaction.

Activation Energy

Ø  The term activation energy was introduced by Svante Arrhenius (1889).

Ø  Definition: “The minimum energy that must be input to a chemical system, containing potential reactants, in order for a chemical reaction to occur”.

Ø  In simple term, the minimum energy required to start a chemical reaction.

Ø  For a chemical reaction to proceed at a reasonable rate, there should exist an appreciable number of molecules with energy equal to or greater than the activation energy.

Ø  The activation energy of a reaction is denoted as Ea.

Ø  The Ea is given in units of kilo-joules per mole.

Enzymes Structure

Ø  All enzymes are proteins except Ribozymes. Ribozymes are specialized RNA molecules with catalytic activity.

Ø  The catalytic activity of an enzyme depends on the integrity of the enzyme’s native conformation.

Ø  The primary, secondary, tertiary & quaternary structures of protein are essential for its catalytic properties.

Learn more: Protein Structure (Primary, Secondary, Tertiary & Quaternary)

Ø  The denatured enzyme will not have catalytic activity.

Ø  Most of the enzymes consist of multi-subunits (more than one polypeptide chains).

Ø  Some enzymes require no chemical groups for activity other than their amino acid residues.

Ø  Others enzymes require additional chemical components (one or more) for their activity.

Ø  Enzymes are much larger than their substrates.

Ø  The smallest enzyme 4-oxalocrotonate tautomerase consists of 62 amino acid residues.

Ø  The largest enzyme Fatty acid synthase consists of ~ 2000 amino acid residues.

Ø  Even though most of the enzymes contain thousands of amino acids only 2–4 amino acids are directly involved in the catalysis.

Ø  Binding Sites in the enzyme:

Substrate binding site: the areas of an enzyme where the substrate binding occurs.

Catalytic site: one or many sites, located near to the binding site. They perform the catalysis.

Active site:  Binding site and catalytic site together called active site.

Cofactor site: Additional sites for the binding of cofactors.

Allosteric site: Additional sites for the binding of allosteric modulators. Allosteric modulators are involved in the regulation of enzymatic activity.

Learn more: Regulatory Enzymes

Apoenzyme and Holoenzyme

Ø  Apoenzyme (apoprotein): The protein part of an enzyme is called apoenzyme.

Ø  Prosthetic group: The non-protein part of an enzyme is called the prosthetic group.

Ø  Holoenzyme: The fully functional apoenzyme and the required prosthetic group together are called holoenzyme.

Ø  Holoenzyme = Apoenzyme + Prosthetic Group

Cofactors and Coenzymes

Ø  The prosthetic groups of an enzyme are of different types and they are broadly categorized into two groups.

(1).  Cofactors

(2).  Coenzymes

Cofactors

Ø  Cofactors: A non-protein chemical compound in an enzyme that is bound to an enzyme is called the cofactor.

Ø  They are tightly bound to the enzyme.

Ø  Cofactors may be organic groups or inorganic groups.

Ø  Inorganic cofactors include metal ions such as Fe₂⁺, Mg₂⁺, Mn₂⁺, Zn₂⁺ and iron-sulfur clusters.

Ø  Organic cofactor includes Flavin and Haem.

Ø  Cofactors are required for the proper functioning of enzymes.

Ø  Some enzymes require several cofactors.

Ø  Example: The pyruvate dehydrogenase of the link reaction of respiration requires five cofactors. They are:

(1).      Metal ion

(2).      Loosely bound thiamine pyrophosphate (TPP)

(3).      Covalently bound lipoamide

(4).      Flavin adenine dinucleotide (FAD)

(5).      Co-substrates (NAD, Coenzyme-A and Mg₂⁺)

Coenzymes

Ø  Co-enzyme: Additional chemical component in the enzyme (prosthetic group) which is complex organic or metallo-organic molecules.

Ø  The main difference from cofactor is that coenzymes are NOT tightly bound to the enzyme.

Ø  Coenzymes act as the carriers of specific functional groups.

Ø  They transport chemical groups from one enzyme to another

Ø  Most of the coenzymes are derived from vitamins.

Ø  Co-enzyme is released from the enzyme’s active site during the reaction.

Ø  Usually, coenzymes are chemically modified after the catalytic reaction.

Ø  Thus, the coenzymes are considered as the second substrate.

Ø  Examples for co-enzymes: NADHH⁺, NADPHH⁺, ATP

Ø  One coenzyme is common to many different enzymes.

Ø  Example: The NADHH⁺ is a coenzyme for about 700 different enzymes in human.

Ø  Coenzymes are continuously generated in the cell.

Ø  Their concentration is maintained at a steady level in the cell.

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