The Ultimate Guide to Enzymes
A Comprehensive Study Resource for Health Sciences & Biochemistry
Hi knowledge lovers! Here in this post you will find basic to advanced level information about one of the most important biological molecule "enzymes". The topics we are going to explore will cover most widely used terms and phenomenons in many exams, such as, BS Nursing, NMDCAT, entry tests preps, BS Biochemistry, NEETS, and other like these.
Enzymes are found in all cells and perform a vast array of biochemical tasks, such as digesting food, synthesizing hormones, and repairing tissues. In this blog post, we will explore the role of enzymes in living organisms and learn about the different types of enzymes and the reactions they catalyze. We will also delve into the classification, structure and function of enzymes, and how they are regulated and controlled.
A. Introduction to Enzymes
Following are the main points to remember about enzymes:
- Enzymes are complex proteins that are made up of one or more polypeptide chains, which are long chains of amino acids (the building blocks of proteins) linked by peptide bonds that catalyze chemical reactions in living organisms.
- They are essential for the metabolic processes that sustain life, including the breakdown of molecules for energy production, the synthesis of new molecules, and the regulation of these processes.
- Enzymes are highly specific and efficient catalysts, meaning they can speed up chemical reactions without being consumed or changed in the process. (This allows them to facilitate a wide range of chemical reactions within living organisms, including those that would be too slow or difficult to occur otherwise).
- Enzymes are classified based on the type of reaction they catalyze, such as hydrolases, which break down molecules by adding water; transferases, which transfer chemical groups from one molecule to another; and ligases, which join molecules together.
- Enzymes are also classified based on the type of substrate they act on, such as carbohydrates, lipids, or nucleic acids.
- Defects in enzymes or the pathways they participate in can lead to various diseases and disorders.
- Enzymes are sensitive to their environment and can be affected by factors such as temperature, pH, and the presence of inhibitors or activators.
- The sequence of amino acids in the polypeptide chain determines the specific three-dimensional structure of the enzyme, which is crucial for its function.
B. How do enzymes catalyze the biochemical reactions?
Here's a more detailed explanation:
1. The substrate(s) bind to the enzyme's active site:
The active site is a small pocket or groove on the surface of the enzyme that is complementary in shape and charge to the substrate(s). When the substrate(s) bind to the active site, the enzyme promotes the formation of a transition state.
2. The transition state is formed:
The transition state is an unstable intermediate stage in which the bonds in the substrate are partially broken and partially formed. It has a higher energy level than the reactants or products.
3. The enzyme stabilizes the transition state:
By stabilizing the transition state through specific interactions at the active site, the enzyme lowers the energy of activation.
4. The product(s) are formed and the enzyme is unchanged:
Once the reaction is complete, the product(s) are formed and the enzyme is unchanged, ready to catalyze another reaction with the same or a different substrate.
C. Structures of Enzyme
The specific three-dimensional structure of an enzyme is determined by the sequence of amino acids in its polypeptide chain(s) and the presence and arrangement of prosthetic groups. This structure is crucial for the enzyme's function, as it determines the shape and properties of the active site, where the substrate(s) bind and the reaction takes place.
D. Enzymes Classification
Enzymes are classified and named using a standardized nomenclature system called the Enzyme Commission (EC) system. This system is based on the type of reaction that the enzyme catalyzes and the type of substrate it acts on.
Enzymes Commission System - EC System
- The EC system is administered by the International Union of Biochemistry and Molecular Biology (IUBMB).
- IUBMB is widely used in the field of biochemistry and molecular biology to identify and describe enzymes.
- It is based on the work of the Enzyme Commission, a group of scientists who were appointed in 1955 to develop a system for naming enzymes.
- The EC system is also widely used in scientific literature and databases, and is an important tool for organizing and communicating information about enzymes.
- It helps to ensure that enzymes are consistently and accurately named and classified, making it easier to search for and compare information about specific enzymes.
According to EC nomenclature system enzymes are classified into the following six main categories, which are further divided into sub-classes and sub-sub classes, based on the type of reaction they catalyze:
1. Oxidoreductases
Enzymes that catalyze oxidation-reduction reactions are known as Oxido-reductase enzymes. There are many subtypes of oxidoreductase enzymes, and they can be further classified based on the specific substrate that they act on and the type of redox reaction that they catalyze. These include:
A. Dehydrogenases:
Dehydrogenases are a type of oxidoreductase enzyme that catalyze the removal of hydrogen atoms from a molecule. They are involved in a wide range of important biochemical reactions, including the metabolism of carbohydrates, lipids, and amino acids. They are further into following categories:
- Alcohol dehydrogenases: These enzymes catalyze the oxidation of alcohols to aldehydes or ketones.
- Aldehyde dehydrogenases: These enzymes catalyze the oxidation of aldehydes to carboxylic acids.
- Lactate dehydrogenases: These enzymes catalyze the conversion of pyruvate to lactate.
- Glutamate dehydrogenases: These enzymes catalyze the conversion of glutamate to alpha-ketoglutarate.
- Succinate dehydrogenases: These enzymes are involved in the citric acid cycle and catalyze the conversion of succinate to fumarate.
- Malate dehydrogenases: These enzymes catalyze the conversion of malate to oxaloacetate.
On the basis of presence or absence of Oxygen for a reaction, dehydrogenases are classified as:
a. Aerobic dehydrogenases are enzymes that catalyze the removal of hydrogen atoms from a molecule using oxygen as an electron acceptor. These reactions occur in the presence of oxygen and produce water as a byproduct.
b. Anaerobic dehydrogenases are enzymes that catalyze the removal of hydrogen atoms from a molecule without using oxygen as an electron acceptor. These reactions occur in the absence of oxygen and produce other compounds as byproducts, such as alcohols or organic acids.
Both aerobic and anaerobic dehydrogenases play important roles in the metabolism of cells. They are involved in processes such as respiration, fermentation, and the breakdown of nutrients to produce energy.
B. Oxidases:
Oxidase enzymes are a type of oxidoreductase enzyme that increases the oxidation state of a molecule by removing electrons from it. They use only Oxygen as hydrogen acceptor. They are involved in a wide range of important biochemical reactions, including the metabolism of carbohydrates, lipids, and amino acids. There are several different types of oxidase enzymes, including:
- Cytochrome oxidase: This enzyme is involved in the electron transport chain and catalyzes the transfer of electrons from cytochrome c to oxygen.
- Diamine oxidase: This enzyme oxidizes diamines to aldehydes.
- Laccase: This enzyme oxidizes a wide range of substrates, including phenols, anilines, and polyphenols.
- Monoamine oxidase: This enzyme oxidizes monoamines to aldehydes.
- Xanthine oxidase: This enzyme catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid.
- Alcohol oxidase: This enzyme oxidizes primary and secondary alcohols to aldehydes and ketones, respectively.
C. Oxygenases:
Oxygenase enzymes are a type of oxidoreductase enzyme that add oxygen atoms to a molecule. They are also involved in a wide range of important biochemical reactions, including the metabolism of carbohydrates, lipids, and amino acids. There are several different types of oxygenase enzymes, including:
- Cytochrome P450 oxygenases: These enzymes are involved in the metabolism of a wide range of substances, including drugs, hormones, and toxins.
- Dioxygenases: These enzymes catalyze the addition of two oxygen atoms to a substrate.
- Monooxygenases: These enzymes catalyze the addition of one oxygen atom to a substrate.
- Amino acid oxygenases: These enzymes catalyze the addition of an oxygen atom to an amino acid.
- Lipoxygenases: These enzymes catalyze the addition of an oxygen atom to a fatty acid.
- Phenylalanine hydroxylase: This enzyme catalyzes the addition of an oxygen atom to phenylalanine, which is an important step in the metabolism of this amino acid.
D. Hydrogen Peroxidases:
Hydrogen peroxide is a molecule that consists of two hydrogen atoms bonded to two oxygen atoms. It is a powerful oxidizing agent and is used in a variety of industrial and medical applications. Hydrogen peroxidases are a type of enzyme that catalyze the breakdown of hydrogen peroxide into water and oxygen. There are several different types of hydrogen peroxidases, including:
- Catalase: This enzyme is found in the cells of many organisms and catalyzes the breakdown of hydrogen peroxide into water and oxygen.
- Glutathione peroxidase: This enzyme is found in the cells of many organisms and catalyzes the breakdown of hydrogen peroxide with the help of the antioxidant glutathione.
- Myeloperoxidase: This enzyme is found in the cells of the immune system and catalyzes the breakdown of hydrogen peroxide as part of the process of killing invading microorganisms.
- Peroxidases: These enzymes are found in a variety of tissues and catalyze the breakdown of hydrogen peroxide as well as other peroxides.
- Thioredoxin peroxidase: This enzyme is found in the cells of many organisms and catalyzes the breakdown of hydrogen peroxide with the help of the protein thioredoxin.
- Tyrosinase: This enzyme is found in the cells of many organisms and catalyzes the breakdown of hydrogen peroxide as well as the oxidation of tyrosine, an amino acid.
2. Transferases
Transferases are a type of enzyme that catalyze the transfer of a specific group of atoms (Except Hydrogen Molecule) from one molecule to another. There are many different types of transferases, and they can be classified based on the type of group that they transfer and the specific reaction that they catalyze e.g Transaminases, Phosphotransferases, Transmethylases, Transpeptidases, and Transacylases. Their detail is given below:
A. Transaminases:
Transaminases are a type of enzyme that catalyze the transfer of an amino group (NH2) from one molecule to another. The exchange of amino group take place between an amin acid and a keto acid as a result amino acid become keto acid and keto acid become amino acid. They are involved in a wide range of important biochemical reactions, including the metabolism of amino acids and the synthesis of proteins.
There are several different types of transaminases, including:
- Alanine transaminase (ALT) or SGPT (Serum Glutamate Pyruvate Transaminase): This enzyme transfers an amino group from alanine to alpha-ketoglutarate, producing pyruvate and glutamate.
- Aspartate transaminase (AST) or SGOT (Serum Glutamate Oxaloacetate Transaminase): This enzyme transfers an amino group from aspartate to alpha-ketoglutarate, producing oxaloacetate and glutamate.
- Glutamate transaminase (GPT): This enzyme transfers an amino group from glutamate to alpha-ketoglutarate, producing 2-oxoglutarate and aspartate.
- Arginine transaminase: This enzyme transfers an amino group from arginine to alpha-ketoglutarate, producing ornithine and glutamate.
- Lysine transaminase: This enzyme transfers an amino group from lysine to alpha-ketoglutarate, producing saccharopine and glutamate.
- Histidine transaminase: This enzyme transfers an amino group from histidine to alpha-ketoglutarate, producing imidazoleacetate and glutamate.
B. Phosphotransferase:
Phosphotransferases are a type of enzyme that catalyze the transfer of a phosphate group from one molecule to another. There are several different types of phosphotransferases, including:
- Kinases: These enzymes transfer a phosphate group from ATP to another molecule.
- Phosphofructokinases: These enzymes transfer a phosphate group from ATP to fructose-6-phosphate, producing fructose-1,6-bisphosphate and ADP.
- Hexokinases: These enzymes transfer a phosphate group from ATP to glucose, producing glucose-6-phosphate and ADP.
- Phosphoglucomutases: These enzymes transfer a phosphate group from glucose-6-phosphate to glucose, or vice versa.
- Phosphotransferases: These enzymes transfer a phosphate group from a molecule of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) to another molecule.
- Phosphoglucoisomerases: These enzymes catalyze the isomerization of glucose-6-phosphate to fructose-6-phosphate.
C. Transmethylases:
Transmethylases are a type of enzyme that catalyze the transfer of a methyl group from one molecule to another. They are involved in a wide range of important biochemical reactions, including the metabolism of amino acids and the synthesis of compounds such as hormones and neurotransmitters. There are several different types of transmethylases, including:
- S-Adenosylmethionine (SAM)-dependent methyltransferases: These enzymes transfer a methyl group from SAM to another molecule.
- Dimethylallyltranstransferase: This enzyme transfers a methyl group from dimethylallyl diphosphate (DMADP) to another molecule.
- Histone lysine N-methyltransferases: These enzymes transfer a methyl group from SAM to a lysine residue on a histone protein.
- Protein lysine N-methyltransferases: These enzymes transfer a methyl group from SAM to a lysine residue on a protein.
- Protein arginine N-methyltransferases: These enzymes transfer a methyl group from SAM to an arginine residue on a protein.
- DNA cytosine N-methyltransferases: These enzymes transfer a methyl group from SAM to a cytosine base in DNA.
D. Transpeptidases:
Transpeptidases are a type of enzyme that catalyze the transfer of a peptide bond from one molecule to another. They are involved in a wide range of important biochemical reactions, including the synthesis of proteins and the modification of other biomolecules. There are several different types of transpeptidases, including:
- Carboxypeptidases: These enzymes hydrolyze a peptide bond at the carboxyl end of a protein or peptide.
- Aminopeptidases: These enzymes hydrolyze a peptide bond at the amino end of a protein or peptide.
- Peptidyl transferases: These enzymes transfer a peptide bond from one molecule to another, such as during the synthesis of proteins.
- Penicillin-binding proteins: These enzymes are involved in the synthesis of the cell wall in bacteria and hydrolyze a peptide bond during this process.
- Endopeptidases: These enzymes hydrolyze a peptide bond within a protein or peptide.
- Exopeptidases: These enzymes hydrolyze a peptide bond at the ends of a protein or peptide.
E. Transacylases:
Transacylases are a type of enzyme that catalyze the transfer of an acyl group from one molecule to another. They are involved in a wide range of important biochemical reactions, including the metabolism of carbohydrates, lipids, and amino acids. There are several different types of transacylases, including:
- Acyltransferases: These enzymes transfer an acyl group from one molecule to another.
- Acyl-CoA synthetases: These enzymes transfer an acyl group from a carboxylic acid to CoA, forming an acyl-CoA molecule.
- Acetyltransferases: These enzymes transfer an acetyl group from acetyl-CoA to another molecule.
- Acyl-CoA thioesterases: These enzymes hydrolyze an acyl-CoA molecule to form a free carboxylic acid and CoA.
- Acyl-CoA dehydrogenases: These enzymes transfer an acyl group from an acyl-CoA molecule to NAD+ or NADP+, producing an aldehyde or ketone and NADH or NADPH.
- Fatty acid synthases: These enzymes synthesize fatty acids by installing an acyl group from one molecule to another.
3. Hydrolases
Hydrolases are a type of enzyme that catalyze the hydrolysis (break down) of a chemical compound by the addition of water into the substrate. They are further classified as:
A. Protein Hydrolyzing Enzymes (Proteinases or Proteases or Proteolytic Enzymes):
Proteases are a type of hydrolase enzyme that catalyze the hydrolysis of proteins into peptides and amino acids. They are involved in a wide range of important biochemical reactions, including the digestion of food proteins, the activation of enzymes, and the regulation of various biological processes.
It has following two sub-types:
i. Exopeptidases:
Exopeptidases are a type of enzyme that catalyze the hydrolysis of peptide bonds at the ends of a protein or peptide. There are several different types of exopeptidases, including:
- Aminopeptidases: These enzymes hydrolyze peptide bonds at the amino end of a protein or peptide.
- Carboxypeptidases: These enzymes hydrolyze peptide bonds at the carboxyl end of a protein or peptide.
- Dipeptidases: These enzymes hydrolyze dipeptides (short chains of two amino acids) into individual amino acids.
- Prolyl endopeptidases: These enzymes hydrolyze peptide bonds within proteins, specifically at the side of proline residues.
- Leucyl aminopeptidases: These enzymes hydrolyze peptide bonds at the amino end of proteins, specifically at the side of leucine residues.
- Prolyl aminopeptidases: These enzymes hydrolyze peptide bonds at the amino end of proteins, specifically at the side of proline residues.
ii. Endopeptidases:
Endopeptidases are a type of enzyme that catalyze the hydrolysis of peptide bonds within a protein or peptide. There are several different types of endopeptidases, including:
- Proteases: These enzymes hydrolyze proteins into peptides and amino acids.
- Prolyl endopeptidases: These enzymes hydrolyze peptide bonds within proteins, specifically at the side of proline residues.
- Leucyl endopeptidases: These enzymes hydrolyze peptide bonds within proteins, specifically at the side of leucine residues.
- Trypsin: This enzyme hydrolyzes proteins by cleaving them at the side of lysine and arginine residues.
What's Next?
This is just the first half! Continue exploring Lyases, Isomerases, Ligases and the Factors affecting enzyme activity in our next post.
Go to Enzymes: Part 2 → |
| The Ultimate Guide to Enzymes - Part 1: Classification & Catalysis |
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