1. M.Sc. Chemistry- 4th Semester
MCHE-911 (Organic Chemistry Elective-I:
Bio-Organic and Medicinal Chemistry)
Unit 1 (Part A)
Enzymes
2. Enzymes are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which
enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products.
Like all catalysts, enzymes increase the reaction rate by lowering its activation energy. Some enzymes can make their
conversion of substrate to product occur many millions of times faster.
3. Lactase catalyzes the conversion of lactose to glucose and galactose.
Lactose is a disaccharide sugar found in milk, and is composed of two simpler sugars, glucose, a six-sided
molecule, and galactose, another six-sided molecule. The enzyme, lactase (enzyme names often end in -ase)
breaks lactose into its two monosaccharide components.
Note: Lactose intolerance is a shortage of the enzyme needed to digest sugars in milk (lactose) and dairy.
4. Enzymes significantly lower the activation energy required for a reaction to occur, allowing
reactions to proceed efficiently at biologically relevant temperatures and conditions.
There are six different types of enzymes and are mainly categorised into different groups based
on their functions.
1.Lyases
2.Ligases
3.Isomerases
4.Hydrolases
5.Transferases
6.Oxidoreductases
5. Application Enzymes used Uses
Biofuel industry Cellulases Break down cellulose into sugars that can be fermented to produce
cellulosic ethanol
Ligninases Pretreatment of biomass for biofuel production
Biological detergent Proteases, amylases, lipases Remove protein, starch, and fat or oil stains from laundry and dishware.
Mannanases Remove food stains from the common food additive guar gum.
Brewing industry Amylase, glucanases, proteases Split polysaccharides and proteins in the malt.
Betaglucanases Improve the wort and beer filtration characteristics.
Amyloglucosidase and pullulanases Make low-calorie beer and adjust fermentability
Acetolactate decarboxylase (ALDC) Increase fermentation efficiency by reducing diacetyl formation.
Culinary uses Papain Tenderize meat for cooking.
Dairy industry Rennin Hydrolyze protein in the manufacture of cheese.
Lipases Produce Camembert cheese and blue cheeses such as Roquefort.
Food processing Amylases Produce sugars from starch, such as in making high-fructose corn syrup.
Proteases Lower the protein level of flour, as in biscuit-making.
Trypsin Manufacture hypoallergenic baby foods.
Cellulases, pectinases Clarify fruit juices.
Molecular biology Nucleases, DNA ligase and polymerases Use restriction digestion and the polymerase chain reaction to create
recombinant DNA.
Paper industry Xylanases, hemicellulases and lignin peroxidases Remove lignin from kraft pulp.
Personal care Proteases Remove proteins on contact lenses to prevent infections.
Starch industry Amylases Convert starch into glucose and various syrups
6. • Key characteristics of enzymes include:
1. Specificity: Enzymes are highly specific, recognizing and binding to particular substrates based on their unique shapes and chemical
properties. This specificity ensures that the correct reactions occur in the right cellular contexts.
2. Catalytic Efficiency: Enzymes can increase reaction rates by factors ranging from hundreds to billions, making biochemical processes
occur at biologically relevant time scales.
3. Regulation: Enzyme activity can be regulated through various mechanisms, including allosteric regulation (where molecules bind to a site
on the enzyme away from the active site), post-translational modifications, and gene expression control.
4. Active Site: Enzymes possess a region known as the active site, which is a three-dimensional pocket or cleft where the substrate binds and
the catalytic reaction takes place. The active site is highly specific for the substrate and allows enzymes to carry out their functions with
precision.
5. Denaturation: Enzymes are sensitive to changes in temperature, pH, and other environmental factors. High temperatures or extreme pH
levels can cause denaturation, altering the enzyme's structure and rendering it inactive.
6. Naming Conventions: Enzymes are often named according to the type of reaction they catalyze, with names typically ending in "-ase."
For example, the enzyme that breaks down starch is called amylase, while DNA polymerase is responsible for synthesizing DNA strands.
7. • Enzymes have diverse roles in living organisms, including:
Digestion: Enzymes in the digestive system break down complex food molecules into simpler forms for absorption and
energy production.
Metabolism: Enzymes regulate metabolic pathways, facilitating the conversion of substrates into products involved in
energy production, growth, and maintenance.
DNA Replication and Repair: Enzymes are involved in DNA replication, transcription, and repair, ensuring accurate
genetic information transfer.
Cellular Signaling: Enzymes play a role in intracellular signaling cascades, transmitting and amplifying signals within
cells.
Defense Mechanisms: Enzymes are part of the immune system, catalyzing reactions that destroy pathogens and foreign
molecules.
• In summary, enzymes are essential components of life, enabling organisms to perform a wide range of biochemical
reactions necessary for survival and functioning. Their remarkable catalytic abilities make life processes efficient and
finely tuned
8. Brief History on discovery of Enzymes –
1. In 1700 century, the biological scientist initiated the study of stomach secretion to understand its role in digestion.
2. In 1833, French chemist Anselme Payen discovered the first enzyme, diastase. In 1835, the hydrolysis of starch by
diastase was acknowledged as a catalytic reaction by another Swedish scientist Jöns Jacob Berzelius.
3. In 1850s, Louis Pasteur studied fermentation of beer and found that yeasts has something in it which converts
sugar into alcohol. He named the unknown thing as ‘ferments’.
4. In 1897, Eduard Buchner break open the yeasts cells releasing the yeast extract. He showed that yeast extract can
also ferment sugar to alcohol. Hence, he successfully separated the ‘ferments’ from the yeasts proving that
fermentation can also be carried out even after separating ferments from the cells. Eduard Buchner has received the
Nobel Prize for discovering cell free fermentation.
9. • In 1876 Frederick Kunhe named these molecules as enzymes. Discovery of enzymes and
its role in the sustaining life opened the new branch of Life Science called Biochemistry.
• In 1926 James Sumner, and John Northrop and Moses Kunitz crystallized urease,
pepsin and trypsin respectively. The crystallization of enzymes found that chemically they
are proteins.
• It was Haldance 1929 who postulated catalytic ability of enzymes. He suggested that
enzyme interacts with its substrate with weak and non covalent bonds forming the product.
This is the fundamental principle of enzymology till date.
10. • Nomenclature and Classification of Enzymes
• Except for some of the originally studied enzymes such as pepsin, rennin, and trypsin, most enzyme names end in "ase". The
International Union of Biochemistry (I.U.B.) initiated standards of enzyme nomenclature which recommend that enzyme names indicate
both the substrate acted upon and the type of reaction catalyzed.
• Enzyme Nomenclature:
• Enzyme names usually end in "-ase" and are derived from the substrate they act upon or the type of reaction they catalyze.
The name typically consists of two parts: the prefix and the suffix. The prefix indicates the substrate or type of reaction,
while the suffix "-ase" denotes that it's an enzyme.
• For example:
Lipase: Catalyzes the hydrolysis of lipids (fats).
DNA polymerase: Catalyzes the polymerization of DNA strands.
Catalase: Catalyzes the decomposition of hydrogen peroxide into water and oxygen.
11. Main Class Types Of Reaction Catalyzed
Oxidoreductase Oxidation-reduction of all types.
Transferase Transfer of an intact group of atoms from a donor to any acceptor molecule.
Hydrolases The hydrolytic (H2O participates) cleavage of bond.
Lyases The cleavage of bonds by means other than hydrolysis or oxidation.
Isomerases Inter-conversion of various isomers.
Ligases
The bond formation is due to the condensation of two different substances,
with energy provided by ATP.
Enzyme Classification:
Enzymes are classified into several major classes based on the type of reaction they catalyze. The six main
classes are:
12. 1. Oxidoreductases: Catalyze oxidation-reduction reactions, involving the transfer of electrons between molecules.
• Oxidoreductases are a class of enzymes that catalyze redox (oxidation-reduction) reactions in biological systems. These
enzymes facilitate the transfer of electrons between molecules, leading to changes in their oxidation states. Oxidation
involves the loss of electrons, while reduction involves the gain of electrons. Oxidoreductases play a crucial role in
various metabolic pathways, energy production, and many other physiological processes.
• The general reaction catalyzed by oxidoreductases can be represented as follows:
• Substrate A + Substrate B ⇌ Product C + Product D
• Here, one substrate is oxidized (loses electrons) while the other substrate is reduced (gains electrons), leading to the
formation of products.
13. • Oxidoreductases are classified into several subcategories based on the nature of the reactions they catalyze. Some
common subcategories of oxidoreductases include:
1. Dehydrogenases: Catalyze the removal of hydrogen atoms (protons and electrons) from a substrate, often transferring
them to coenzymes like NAD+ (nicotinamide adenine dinucleotide) or FAD (flavin adenine dinucleotide).
2. Oxidases: Transfer electrons from a substrate to molecular oxygen (O2), leading to the formation of hydrogen peroxide
(H2O2) or other reactive oxygen species.
3. Peroxidases: Use hydrogen peroxide or organic hydroperoxides as electron acceptors to catalyze the oxidation of
various substrates.
4. Reductases: Facilitate the reduction of a substrate using electrons provided by a coenzyme or another electron donor.
5. Oxygenases: Incorporate molecular oxygen into substrates, often leading to the formation of hydroxylated compounds.
14. • Examples of oxidoreductases include alcohol dehydrogenase (involved in alcohol metabolism), cytochrome
P450 enzymes (important for drug metabolism), and NADH dehydrogenase (a component of the electron
transport chain in cellular respiration).
• Overall, oxidoreductases are essential for maintaining the balance of electron transfer in biological systems
and are vital for various cellular processes and functions.
15. 2. Transferases: Catalyze the transfer of functional groups (e.g., methyl, phosphate) from one molecule to
another.
Transferases are a class of enzymes that play a crucial role in catalyzing various chemical reactions within
cells. These enzymes facilitate the transfer of specific functional groups (such as methyl, acetyl, phosphate,
etc.) from one molecule to another. The transfer of these groups often leads to important biochemical
processes, including signal transduction, metabolism, and the synthesis of essential molecules.
• There are several subclasses of transferases, each with their own specific functions:
• Aminotransferases: These enzymes transfer amino groups (NH2) between amino acids and α-keto
acids. They are essential for amino acid metabolism and the synthesis of non-essential amino acids.
• Methyltransferases: These enzymes transfer methyl groups (CH3) from one molecule to another. They
are involved in DNA methylation, histone modification, and the regulation of gene expression.
16. • Glycosyltransferases: These enzymes transfer sugar moieties (glycosyl groups) onto target molecules, playing a
critical role in the synthesis of carbohydrates, glycolipids, and glycoproteins.
• Kinases: While often considered a separate class, kinases are a type of transferase that catalyze the transfer of
phosphate groups (PO4) from ATP to target molecules, usually proteins. This process, known as phosphorylation, is
crucial for cellular signaling and regulation.
• Acyltransferases: These enzymes transfer acyl groups, which are typically derived from fatty acids, from one
molecule to another. They are involved in lipid metabolism and the synthesis of various lipids, including phospholipids
and triglycerides.
• Transaminases: These enzymes catalyze the transfer of an amino group from an amino acid to a keto acid, resulting
in the formation of a new amino acid and a new keto acid. This process is important for amino acid metabolism.
• Sulfotransferases: These enzymes transfer sulfate groups (SO4) to target molecules, often playing a role in the
detoxification and elimination of xenobiotics and drugs.
• Phosphotransferases: Similar to kinases, phosphotransferases transfer phosphate groups from one molecule to
another, but they have a broader range of substrates beyond proteins.
17. 3. Hydrolases: Catalyze the hydrolysis of bonds by adding water molecules.
• Hydrolases are a class of enzymes that catalyze the hydrolysis reaction, which involves the breaking of a
chemical bond using a water molecule. In simpler terms, hydrolases help break down larger molecules into
smaller components by adding a water molecule to the bond, leading to the separation of the molecules. This
process is fundamental in various biological and chemical processes.
• There are several types of hydrolases, each with its specific substrate and function. Some common examples
of hydrolases include:
• Lipases: These enzymes break down lipids (fats) into their component fatty acids and glycerol. Lipases play
a crucial role in digestion, as well as in cellular processes involving lipid metabolism.
• Proteases: Proteases, also known as peptidases or proteinases, break down proteins into their constituent
amino acids. They are essential for digestion, protein turnover, and other cellular processes.
18. • Amylases: Amylases break down complex carbohydrates (starches) into simpler sugars such as glucose. They are
involved in the initial stages of carbohydrate digestion in organisms.
• Nucleases: Nucleases hydrolyze nucleic acids, such as DNA and RNA, into nucleotides. These enzymes are critical
for DNA replication, repair, and other nucleic acid processing activities.
• Cellulases: Cellulases break down cellulose, a complex carbohydrate found in plant cell walls, into smaller sugar
units. These enzymes are important for the digestion of plant material in herbivores and for industrial processes like
biofuel production.
• Phosphatases: Phosphatases remove phosphate groups from molecules, often proteins, in a hydrolysis reaction. This
process is crucial for regulating various cellular signaling pathways.
• Esterases: Esterases break down ester bonds found in various molecules, including lipids and certain chemicals.
They play roles in processes like lipid metabolism and detoxification.
• Glycosidases: Glycosidases cleave glycosidic bonds, which link sugar molecules together. These enzymes are
involved in the breakdown of complex carbohydrates and glycoconjugates.
19. 4. Lyases: Catalyze the removal of groups from substrates, resulting in the formation of double bonds.
• Lyases are enzymes that catalyze a type of chemical reaction called "lysis," which involves the cleavage or
formation of chemical bonds in molecules. Unlike many other enzymes, lyases do not require water to carry out
their reactions, and they do not involve the transfer of electrons or hydrogen atoms.
• Lyases can be classified into different subgroups based on the types of reactions they catalyze:
• Carbon-Carbon Lyases: These lyases break or form carbon-carbon bonds. An example is the enzyme fumarase,
which catalyzes the conversion of fumarate to malate in the citric acid cycle.
• Carbon-Oxygen Lyases: These lyases cleave or form carbon-oxygen bonds. An example is ribulose-1,5-
bisphosphate carboxylase/oxygenase (RuBisCO), which is involved in carbon fixation during photosynthesis.
• Carbon-Nitrogen Lyases: These lyases cleave or form carbon-nitrogen bonds. An example is argininosuccinate
lyase, which catalyzes the breakdown of argininosuccinate into arginine and fumarate in the urea cycle.
20. • Phosphorus-Oxygen Lyases: These lyases cleave or form phosphorus-oxygen bonds. An example is adenosine
monophosphate (AMP) deaminase, which catalyzes the deamination of AMP to inosine monophosphate (IMP).
• Sulfur-Sulfur Lyases: These lyases cleave or form sulfur-sulfur bonds. An example is cystathionine β-synthase,
which catalyzes the condensation of homocysteine and serine to form cystathionine.
• Lyases play important roles in various biochemical pathways and processes, contributing to the diversity and
complexity of cellular metabolism. By catalyzing the formation or breaking of specific bonds, lyases are essential
for the synthesis and breakdown of molecules that are crucial for life.
21. 5. Isomerases: Catalyze the rearrangement of atoms within a molecule, creating isomeric forms.
• Isomerases are a class of enzymes that catalyze the conversion of molecules from one isomer to another. Isomers are
molecules that have the same molecular formula but different structural arrangements or spatial orientations. Isomerases
facilitate these transformations by rearranging the atoms within a molecule, resulting in a different isomer.
• There are various types of isomerases, each with specific functions:
• Racemases: These enzymes convert one enantiomer (chiral isomer) into its mirror-image enantiomer, creating a racemic
mixture. Racemization involves the interchange of groups around a chiral center.
• Epimerases: Epimerases catalyze the conversion of one epimer to another. Epimers are stereoisomers that differ in the
configuration of only one chiral center
• Cis-trans Isomerases: These enzymes convert cis-isomers (where substituents are on the same side of a double bond)
into trans-isomers (where substituents are on opposite sides of a double bond) or vice versa.
• Intramolecular Transferases: These isomerases catalyze intramolecular transfers of functional groups, leading to
isomerization.
22. • Phosphatases: Certain phosphatase enzymes can isomerize phosphates within molecules, leading to structural
changes.
• Methyltransferases: Some methyltransferases can catalyze the transfer of a methyl group from one position to
another, causing an isomeric change.
• Mutases: Mutases are a specific type of isomerase that facilitate the movement of functional groups within a
molecule, often involving the migration of a functional group from one atom to another within the same molecule.
• Isomerases play crucial roles in various biochemical processes. For instance, they are involved in carbohydrate
metabolism, amino acid metabolism, nucleotide metabolism, and lipid metabolism. They help maintain the balance
and proper functioning of these pathways by converting molecules between different isomeric forms as needed.
23. 6. Ligases: Catalyze the joining of two molecules using energy from ATP.
• Ligases, also known as synthetases, are a class of enzymes that play a crucial role in the process of ligating or joining
two molecules together through the formation of a covalent bond. These enzymes are essential in various biological
processes, such as DNA replication, repair, and protein synthesis.
• Ligases are involved in several types of reactions, including:
• DNA Replication and Repair: DNA ligases are enzymes that catalyze the joining of DNA strands during DNA
replication and repair. They seal the gaps in the DNA backbone that arise due to the discontinuous synthesis of the
lagging strand during replication. DNA ligases are also involved in repairing damaged DNA by sealing nicks or breaks
in the DNA strands.
• RNA Synthesis: RNA ligases are involved in the synthesis of RNA molecules. They catalyze the ligation of RNA
segments during processes such as splicing, where introns are removed and exons are joined to form a mature RNA
molecule.
24. • Amino Acid Activation: Aminoacyl-tRNA synthetases are ligases that play a vital role in protein synthesis. They
catalyze the attachment of specific amino acids to their corresponding transfer RNA (tRNA) molecules, ensuring
accurate translation of the genetic code during protein synthesis.
• Energy-Intensive Reactions: Ligases are often involved in reactions that require energy input in the form of
adenosine triphosphate (ATP) or another high-energy molecule. For instance, ligases are involved in the formation
of peptide bonds between amino acids during protein synthesis, which requires energy to overcome the
thermodynamic barrier.
• Metabolic Pathways: Ligases are also found in various metabolic pathways, where they catalyze the formation of
important molecules. For example, fatty acid synthase ligase is involved in the synthesis of fatty acids.
26. • Enzymes are much larger than the substrate they act on, and thus there are some specific regions or sites on
the enzyme for binding with the substrate, called active sites. Even in enzymes that differ widely in their
properties, the active site present in their molecule possesses some common features;
1.The active site of an enzyme is a relatively small portion within an enzyme molecule.
2.The active site is a 3-dimensional entity made up of groups that come from different parts of the linear
amino acid sequence.
3.The arrangement and orientation of atoms in the active site are well defined and highly specific, which is
the cause of the marked specificity of the enzymes. However, in some cases, the active site changes its
configuration in order to bind a substance.
4.The interactions or forces between the active site and the substrate molecule are relatively weak.
5.The active sites in the enzyme molecules are mostly present in grooves or crevices from where large
quantities of water are excluded.
27. •The mechanism of action of enzymes in a chemical reaction can occur by several modes; substrate binding,
catalysis, substrate presentation, and allosteric modulation.
•But the most common mode of action of enzymes is by the binding of the substrate.
•An enzyme molecule has a specific active site to which its substrate binds and produces an enzyme-substrate
complex.
•The reaction proceeds at the binding site to produce the products which remain associated briefly with the
enzyme.
•The product is then liberated, and the enzyme molecule is freed in an active state to initiate another round of
catalysis.
•To describe the mechanism of action of enzymes to different models have been proposed
Mechanism of Action of Enzymes
29. • The lock and key model was proposed by Emil Fischer in 1898 and is also known as the template model.
• According to this model, the binding of the substrate and the enzyme takes place at the active site in a manner
similar to the one where a key fits a lock and results in the formation of an enzyme-substrate complex.
• In fact, the enzyme-substrate binding depends on a reciprocal fit between the molecular structure of the
enzyme and the substrate.
• The enzyme-substrate complex formed is highly unstable and almost immediately decomposes to produce the
end products of the reaction and to regenerate the free enzyme.
• This process results in the release of energy which, in turn, raises the energy level of the substrate molecule,
thus inducing the activated or transition state.
• In this activated state, some bonds of the substrate molecule are made susceptible to cleavage.
• This model, however, has few drawbacks as it cannot explain the stability of the transitional state of the
enzyme and also the concept of the rigidity of the active site.
31. • The induced fit hypothesis is a modified form of the lock and key hypothesis proposed by Koshland in 1958.
• According to this hypothesis, the enzyme molecule does not retain its original shape and structure.
• Instead, the contact of the substrate induces some configurational or geometrical changes in the active site of the
enzyme molecule.
• As a result, the enzyme molecule is made to fit the configuration and active centers of the substrate completely.
• Meanwhile, other amino acid residues remain buried in the interior of the molecule.
• However, the sequence of events resulting in the conformational change might be different.
• Some enzymes might first undergo a conformational change, then bind the substrate.
• In an alternative pathway, the substrate may first be bound, and then a conformational change may occur in the
active site.
• Thirdly, both the processes may co-occur with further isomerization to the final confirmation.
32. Summary – Induced Fit vs Lock and Key
The induced fit theory explains the binding of enzyme and substrate when they are
not perfectly matched with each other by their shapes. The binding of substrate
induces the conformation change of the active site of the enzyme for correct binding.
On the other hand lock and key theory explains the binding of perfectly matching or
fitting substrate and enzyme. Similar to a ‘lock and key’, substrate and enzyme fit
with each other very tightly according to this hypothesis. In the induced fit theory,
the active site of the enzyme is not static while it is static in the lock and key
mechanism. This is the difference between induced fit and lock and key.
