Enzymes: Introduction

Most of the history of biochemistry is the history of enzyme research. Enzyme research history can be traced back to 1700 as people suspected how meat digested in the stomach. Louis Pasteur, during 1850 postulated that fermentation of sugar to alcohol by yeast and he named “ferments” for responsible molecules. In 1897 Eduard Buchner discovered that cell-free yeast extracts accountable for fermentation of sugar to alcohol. Later, Frederik W. Kuhne coined the name “ENZYME.” There are many kinds of research afterward in the field of enzymology.

Enzymes are specialized proteins that act as catalysts in biological reactions. They play a crucial role in speeding up chemical reactions in living organisms without being consumed or permanently altered in the process. Enzymes are essential for maintaining the proper functioning and regulation of various biochemical pathways in cells.

Enzymes work by lowering the activation energy required for a specific chemical reaction to occur. Activation energy is the energy barrier that must be overcome for a reaction to proceed. By reducing this energy barrier, enzymes increase the rate at which reactions occur, making them more efficient.

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Definition:

Enzymes are biomolecules, and they speed up the rate of chemical reactions both in vivo and in vitro.

They act as biocatalyst for various biochemical reactions taking place in our bodies. The rate of biochemical reactions is millions of times faster [10⁶ or more] in enzyme-catalyzed reactions compared to that of a noncatalyzed reaction.  Enzymes are essential for all the processes taking place in our body like digestion, metabolism, DNA replication, transcription, translation, etc… Many diseases like inborn errors of metabolism, nutritional disorders are due to defect or deficiency of enzymes.

Characteristics of enzymes

All enzymes are proteins, except ribozymes. Enzymes neither consumed nor permanently altered in any chemical reactions. They transiently involved in a chemical reaction by combining with substrates ad later, they come out as the same enzymes and products. They exhibit specificities like absolute, group, and stereospecificity. Many enzymes may contain or require additional prosthetic groups such as coenzymes or cofactors.

Enzyme nomenclature

Enzymes usually named with a suffix ends with “ase” after the name of the substrate it acts. But still many enzymes have the older name as pepsin, trypsin, amylase. International union of biochemistry and molecular biology [IUBMB] came up with a unique code number and name for each enzyme, and it is called enzyme commission number or enzyme code number.

Enzyme classification

Enzymes are classified by the reaction they catalyze. There are six classes of enzymes.

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

Enzyme commission/ code number

Enzyme Commission (EC) numbers, also known as EC codes or Enzyme Commission numbers, are a classification system developed by the International Union of Biochemistry and Molecular Biology (IUBMB) to categorize enzymes based on their catalytic activities. An enzyme code number is a four-digit number and begins with EC. The first digit represents the class of enzymes (one of 6 classes). The second digit represents a subclass of the enzyme or type of group involved in the reaction. The third digit represents the sub-subclass or acceptor of the group in the reaction. The fourth digit represents a serial number of an enzyme in that list.

The EC number consists of four levels of classification:

1. Class: The first digit represents the broad class of the enzyme based on the type of reaction it catalyzes. There are six main classes:
   • EC 1: Oxidoreductases – Enzymes involved in oxidation and reduction reactions.
   • EC 2: Transferases – Enzymes that transfer functional groups between molecules.
   • EC 3: Hydrolases – Enzymes that catalyze hydrolytic cleavage of bonds.
   • EC 4: Lyases – Enzymes that add or remove groups to form double bonds or rings.
   • EC 5: Isomerases – Enzymes that catalyze isomerization reactions.
   • EC 6: Ligases – Enzymes that catalyze the joining of molecules using ATP.
2. Subclass: The second digit further defines the enzyme’s subclass within the broad class, providing more specific information about the reaction catalyzed.
3. Sub-subclass: The third digit provides additional information on the enzyme’s sub-subclass, specifying the nature of the reaction or the substrate involved.
4. Specific activity: The fourth digit identifies the specific enzyme within the sub-subclass, representing a unique enzyme activity or reaction.

The EC number system provides a standardized way to classify enzymes based on their catalytic functions, facilitating communication and research in the field of enzymology. It allows researchers to quickly identify and compare enzymes with similar activities, aiding in the understanding of their roles in biochemical pathways and their potential applications.

EC 1.1.1.1 [Alcohol dehydrogenase]

EC 1 means this enzyme belongs to class 1 enzymes that are oxidoreductase. EC 1.1 means group involved the reaction catalyzed by this group of enzymes [EC 1.1 series] is CH-OH. EC 1.1.1 means acceptor molecule is NAD+ or NADP+ EC 1.1.1.1 the last digit represents a serial number that is the first enzyme in EC 1.1.1 series

EC 2.7.1.1 [Hexokinase]

EC 2 means this enzyme belongs to class 2 enzymes that are transferase. EC 2.7 means group involved the reaction catalyzed by this group of enzymes [EC 1.1 series] is the phosphorous-containing group. EC 2.7.1 means acceptor is alcohol group EC 2.7.1.1   First enzyme in EC 2.7.1 series that is hexokinase. EC 2.7.1.2   Second enzyme in EC 2.7.1 series that is glucokinase EC 2.7.1.3   Third enzyme in EC 2.7.1 series that is ketohexokinase

Class 1: Oxidoreductases

Class 1 enzymes belong to the EC (Enzyme Commission) classification system and are known as oxidoreductases. Oxidoreductases are enzymes that catalyze oxidation-reduction reactions, also known as redox reactions. These enzymes facilitate the transfer of electrons from one molecule to another.

Oxidoreductases can be further categorized into several subclasses based on the specific type of reaction they catalyze. Here are some examples of subclasses of oxidoreductases:

1. Dehydrogenases: These enzymes catalyze the removal of hydrogen atoms from a substrate, transferring them to an electron acceptor. For example, alcohol dehydrogenase catalyzes the oxidation of alcohols to aldehydes or ketones.
2. Oxidases: These enzymes catalyze the transfer of electrons from a substrate to molecular oxygen (O2), forming hydrogen peroxide (H2O2) or water (H2O) in the process. Cytochrome oxidase, which is involved in the electron transport chain in mitochondria, is an example of an oxidase.
3. Reductases: These enzymes catalyze the reduction of a substrate by transferring electrons from a reduced cofactor, such as NADH (nicotinamide adenine dinucleotide) or NADPH (nicotinamide adenine dinucleotide phosphate). An example of a reductase is dihydrofolate reductase, which participates in the synthesis of DNA.
4. Peroxidases: These enzymes use hydrogen peroxide (H2O2) as an electron acceptor to oxidize substrates. They are involved in various biological processes, including the breakdown of harmful substances and the defense against oxidative stress. Catalase and glutathione peroxidase are examples of peroxidases.

These are just a few examples of subclasses within the class 1 oxidoreductases. Each subclass of oxidoreductases has its own specific function and mechanism of action, allowing for diverse redox reactions to occur within living organisms.

Class 2: Transferases

Class 2 enzymes, according to the Enzyme Commission (EC) classification system, are known as transferases. Transferases are enzymes that facilitate the transfer of functional groups, such as methyl, acyl, or phosphate groups, from one molecule (the donor) to another molecule (the acceptor). These enzymes play a crucial role in various metabolic pathways and cellular processes.

Transferases can be further categorized into different subclasses based on the type of functional group they transfer. Here are some examples of subclasses of transferases:

1. Methyltransferases: These enzymes transfer methyl groups (CH3) from a donor molecule to an acceptor molecule. Methyltransferases are involved in various biological processes, including DNA methylation, histone modification, and biosynthesis of numerous compounds. DNA methyltransferases, which add methyl groups to DNA molecules, are an example of this subclass.
2. Acyltransferases: Acyltransferases transfer acyl groups (RCO-) from one molecule to another. Acyl groups are usually derived from acyl-CoA molecules. This subclass includes enzymes involved in fatty acid metabolism, such as fatty acyl-CoA synthetase and fatty acyl-CoA dehydrogenase.
3. Glycosyltransferases: Glycosyltransferases transfer sugar moieties (glycosyl groups) from a donor molecule to an acceptor molecule, forming glycosidic bonds. These enzymes are essential for the biosynthesis of carbohydrates and glycoconjugates, including glycolipids, glycoproteins, and proteoglycans. Examples include UDP-glucose glycosyltransferases and N-acetylglucosamine transferases.
4. Kinases: Kinases transfer phosphate groups (PO43-) from ATP (adenosine triphosphate) to specific acceptor molecules. This phosphate transfer is crucial for the regulation of cellular signaling pathways and the activation of enzymes. Protein kinases, which phosphorylate proteins to regulate their function, are a well-known example of this subclass.

These are just a few examples of subclasses within the class 2 transferases. Each subclass of transferases has its own specific substrate specificity and catalytic mechanism, allowing for the transfer of a wide range of functional groups and contributing to the complexity of cellular metabolism and regulation.

Class 3: Hydrolases

Class 3 enzymes, according to the Enzyme Commission (EC) classification system, are known as hydrolases. Hydrolases are enzymes that catalyze hydrolysis reactions, which involve the cleavage of chemical bonds through the addition of water molecules. These enzymes play a vital role in breaking down complex molecules into simpler components and are involved in various metabolic processes.

Hydrolases can be further classified into different subclasses based on the type of bond they hydrolyze. Here are some examples of subclasses of hydrolases:

1. Esterases: Esterases catalyze the hydrolysis of ester bonds. These enzymes are involved in the breakdown of various ester-containing compounds, such as lipids, phospholipids, and triglycerides. Lipases, which hydrolyze the ester bonds in fats and oils, are examples of esterases.
2. Proteases: Proteases, also known as peptidases or proteinases, hydrolyze peptide bonds in proteins and peptides. They play a crucial role in protein degradation, digestion, and post-translational modification processes. Examples of proteases include trypsin, chymotrypsin, and pepsin.
3. Glycosidases: Glycosidases catalyze the hydrolysis of glycosidic bonds in carbohydrates or glycoconjugates. These enzymes are involved in the breakdown of complex carbohydrates, such as starch, glycogen, and cellulose. Examples include amylases, which hydrolyze starch, and β-glucosidases, which hydrolyze glycosidic bonds in cellulose.
4. Phosphatases: Phosphatases hydrolyze phosphate groups from various organic molecules, such as proteins, nucleotides, and sugars. These enzymes play a critical role in cellular signaling, metabolism, and regulation by controlling the levels of phosphorylation. Alkaline phosphatase and protein tyrosine phosphatase are examples of phosphatases.
5. Lipases: Lipases are a specific subclass of hydrolases that catalyze the hydrolysis of lipids, specifically triglycerides, into fatty acids and glycerol. These enzymes are involved in fat digestion and lipid metabolism. Pancreatic lipase is a well-known example of a lipase.

These are just a few examples of subclasses within the class 3 hydrolases. Each subclass of hydrolases has its own specific substrate specificity and catalytic mechanism, enabling the hydrolysis of different types of bonds and contributing to the diverse range of biological processes involving the breakdown of complex molecules.

Class 4: Lyases

Class 4 enzymes, as per the Enzyme Commission (EC) classification system, are known as lyases. Lyases are enzymes that catalyze the cleavage or formation of chemical bonds without the involvement of water molecules (hydrolysis) or the transfer of electrons (oxidation/reduction). These enzymes facilitate various non-hydrolytic and non-oxidative reactions, leading to the formation of new double bonds, the addition or removal of functional groups, or the elimination of groups from substrates.

Lyases can be further classified into different subclasses based on the type of reaction they catalyze. Here are some examples of subclasses of lyases:

1. Carbon-Carbon Lyases: These enzymes catalyze the cleavage or formation of carbon-carbon bonds. They play a role in the rearrangement of carbon skeletons and the synthesis of complex molecules. An example is pyruvate decarboxylase, which catalyzes the conversion of pyruvate to acetaldehyde during fermentation.
2. Carbon-Oxygen Lyases: Carbon-oxygen lyases catalyze the cleavage or formation of carbon-oxygen bonds. They are involved in the synthesis or breakdown of compounds containing oxygen. For instance, fumarate hydratase is a carbon-oxygen lyase that participates in the citric acid cycle, converting fumarate to malate.
3. Carbon-Nitrogen Lyases: These enzymes catalyze the cleavage or formation of carbon-nitrogen bonds. They are involved in the synthesis or degradation of nitrogen-containing compounds. One example is the enzyme argininosuccinate lyase, which is part of the urea cycle and catalyzes the conversion of argininosuccinate to arginine.
4. Carbon-Sulfur Lyases: Carbon-sulfur lyases facilitate the cleavage or formation of carbon-sulfur bonds. They are involved in the metabolism of sulfur-containing compounds. Cystathionine β-synthase is an example of a carbon-sulfur lyase that participates in the transsulfuration pathway, converting homocysteine to cystathionine.
5. Other Lyases: Apart from the aforementioned subclasses, there are various other lyases that catalyze unique reactions. These include, for example, decarboxylases (removal of a carboxyl group) and deaminases (removal of an amino group).

Each subclass of lyases has its own specific substrate specificity and catalytic mechanism, allowing for the diverse range of non-hydrolytic and non-oxidative reactions to occur in living organisms.

Class 5: Isomerases

Class 5 enzymes, according to the Enzyme Commission (EC) classification system, are known as isomerases. Isomerases are enzymes that catalyze the rearrangement of atoms within a molecule, resulting in the conversion of one isomer into another. These enzymes play a crucial role in metabolic pathways by interconverting isomeric forms of molecules, facilitating biochemical reactions and maintaining metabolic balance.

Isomerases can be further classified into different subclasses based on the specific type of isomerization reaction they catalyze. Here are some examples of subclasses of isomerases:

1. Racemases: Racemases catalyze the conversion of one enantiomer (optical isomer) into its mirror image (the other enantiomer). This is known as racemization. An example is alanine racemase, which converts L-alanine to D-alanine.
2. Epimerases: Epimerases catalyze the conversion of one epimer (a stereoisomer that differs in the configuration at a single chiral center) into another. Epimerases are involved in the interconversion of sugars and other compounds. For instance, glucose-6-phosphate epimerase catalyzes the conversion of glucose-6-phosphate to fructose-6-phosphate.
3. Isomerases acting on functional groups: These isomerases catalyze the rearrangement of functional groups within a molecule. Examples include:
   • Isomerases that interconvert cis-trans isomers: These enzymes catalyze the interconversion of cis and trans isomers. One example is the enzyme cis-trans isomerase, which converts cis-2-butene to trans-2-butene.
   • Isomerases that interconvert keto-enol tautomers: These enzymes catalyze the interconversion between the keto and enol forms of compounds. An example is enolase, which converts 2-phosphoglycerate to phosphoenolpyruvate in glycolysis.
   • Isomerases that interconvert geometric isomers: These enzymes catalyze the conversion between geometric isomers (e.g., cis and trans) of double bonds. One example is the enzyme maleate isomerase, which interconverts cis-maleate and trans-maleate.
4. Intramolecular transferases: Intramolecular transferases catalyze the transfer of a functional group from one position within a molecule to another position. An example is phosphoglucomutase, which transfers a phosphate group within glucose-1-phosphate to convert it into glucose-6-phosphate.

These are just a few examples of subclasses within the class 5 isomerases. Each subclass of isomerases has its own specific substrate specificity and catalytic mechanism, allowing for the rearrangement of atoms and isomeric interconversions in diverse biological processes.

Class 6: Ligases

Class 6 enzymes, as per the Enzyme Commission (EC) classification system, are known as ligases. Ligases are enzymes that catalyze the joining of two molecules together, often through the formation of a covalent bond. These enzymes play a crucial role in various biosynthetic pathways, DNA repair processes, and the synthesis of macromolecules.

Ligases can be further classified into different subclasses based on the type of bond formation they catalyze. Here are some examples of subclasses of ligases:

1. ATP-dependent ligases: ATP-dependent ligases catalyze the formation of a bond between two molecules using energy derived from the hydrolysis of ATP. These enzymes often play a role in DNA replication, DNA repair, and the synthesis of proteins and other macromolecules. DNA ligase is a well-known example of an ATP-dependent ligase that seals nicks in DNA strands during DNA replication and repair.
2. ATP-independent ligases: ATP-independent ligases, also known as synthetases, catalyze bond formation without utilizing ATP as an energy source. Instead, they often use other high-energy molecules, such as GTP or CTP, as a source of energy. An example is aminoacyl-tRNA synthetase, which catalyzes the attachment of amino acids to their corresponding transfer RNA (tRNA) molecules during protein synthesis.
3. Carboxylate-amine ligases: These ligases catalyze the formation of peptide bonds between carboxylate and amino groups. They are involved in the synthesis of peptides and proteins. Peptide synthetases, which are responsible for the nonribosomal synthesis of peptides in bacteria and fungi, are examples of carboxylate-amine ligases.
4. DNA ligases: DNA ligases specifically catalyze the formation of phosphodiester bonds between the 3′ hydroxyl end of one DNA molecule and the 5′ phosphate end of another DNA molecule. These enzymes play a crucial role in DNA replication, DNA repair, and recombination processes. They are responsible for joining Okazaki fragments during lagging strand synthesis and sealing nicks in the DNA backbone.
5. RNA ligases: RNA ligases catalyze the formation of phosphodiester bonds between RNA molecules. They are involved in various RNA processing and repair processes, such as the ligation of RNA segments during splicing and the repair of broken RNA molecules.

These are just a few examples of subclasses within the class 6 ligases. Each subclass of ligases has its own specific substrate specificity and catalytic mechanism, allowing for the formation of covalent bonds and the synthesis of complex molecules in biological systems.