Biomolecules

How to Analyse Chemical Composition?

Biomolecules in Living Organisms & their Analysis

• Living organisms are made of various elements and compounds.
• The elements present in living organisms include carbon, hydrogen, oxygen, nitrogen etc.
• These elements are also found in non-living things like the earth’s crust.
• Carbon and hydrogen are more abundant in living organisms than in the earth’s crust.
• All carbon-containing compounds present in living tissues are called biomolecules.
• The sum total of biomolecules, inorganic compounds and ions present in a cell is known as the cellular pool.
• To find out what organic compounds are in living organisms, we do a chemical analysis.

Steps for Chemical Analysis of Organic Compounds:

1. Take a living tissue (like a vegetable piece or chicken liver piece).
2. Grind it with trichloroacetic acid (Cl₃CCOOH) using a mortar and pestle to form a thick slurry.
3. Strain the mixture through cheesecloth or cotton to get two fractions/parts:
   1. Filtrate (acid-soluble pool)
   2. Retentate (acid-insoluble fraction)
4. The acid-soluble pool contains thousands of organic compounds mainly which are further isolated and purified.
5. Analytical techniques are used to determine the molecular formula and structure of these compounds.

Analysis of Inorganic Elements:

• Weigh a small amount of living tissue (wet weight).
• Dry it to remove all water (dry weight).
• Burn it to oxidize all carbon compounds to gas.
• The remaining material (ash) contains inorganic elements like calcium and magnesium.

• Elemental analysis provides information about the elemental composition of living tissues such as hydrogen, oxygen, carbon, nitrogen and chlorine.
• Compound analysis reveals the organic and inorganic constituents present in living tissues.
• Examples:
  • Organic Compounds: Amino acids, nucleotide bases, fatty acids.
  • Inorganic Elements: Calcium, magnesium.
  • Inorganic Compounds: Sulphate, phosphate.

Biomolecules: Biomicromolecules & Biomacromolecules

Types of Compounds in Living Cells

• During chemical analysis of tissues (discussed above), biomolecules are separated into two fractions:
• Acid-Soluble Pool (Filtrate):
  • This fraction contains compounds with molecular weights ranging from about 18 to 800 daltons (Da).
  • These are simple molecules that dissolve easily in acid.
  • Examples include:
    • Inorganic ions like sulphate, phosphate, nitrate
    • Monomers such as amino acids, monosaccharides, nucleotides
• Acid-Insoluble Fraction (Retentate):
  • This fraction contains large, high-molecular-weight compounds (more than 800 daltons, except Lipids).
  • These molecules are mostly polymers and do not dissolve in acid.
  • Examples include:
    • Proteins
    • Nucleic acids
    • Polysaccharides
    • Lipids
• Even though lipids are not true polymers, they are large and insoluble, so they remain in the acid-insoluble fraction.

Micromolecules vs. Macromolecules

• Micromolecules:
  • Molecular weight less than 1,000 Da.
  • Found in the acid-soluble pool.
  • Include amino acids, sugars, nucleotides and vitamins
• Macromolecules (Biomacromolecules):
  • Found in the acid-insoluble fraction.
  • Include proteins, nucleic acids, and polysaccharides.
  • They are mostly polymeric substances

Lipids

• Although lipids have relatively low molecular weight (below 800 Da), they are found in the acid-insoluble fraction
  • because they form structures like cell membranes.
• During tissue grinding, membranes break into vesicles which are not water-soluble
  • and therefore separate with the acid-insoluble pool.

Chemical Composition of Living Tissues

• The acid-soluble pool mainly represents the cytoplasmic contents.
• Macromolecules from cytoplasm and cell organelles together form the acid-insoluble fraction.
• Both fractions together account for the complete chemical composition of a living cell.

Average Chemical Composition of Living Cells:

• Water: 70–90%
• Proteins: 10–15%
• Carbohydrates: ~3%
• Lipids: ~2%
• Nucleic acids: 5–7%
• Ions: ~1%

Key Points

• Metabolites are classified as primary and secondary.
• Primary metabolites are essential for life processes.
• Secondary metabolites have ecological and economic importance.
• Biomolecules are classified into micromolecules and macromolecules.
• Proteins, nucleic acids and polysaccharides are true biomacromolecules.
• Lipids behave as macromolecules due to their structural role.
• Water is the most abundant chemical in living organisms.

Biomolecules: Biomicromolecules

• Organic compounds from living tissues are called ‘biomolecules.’
• Living organisms also have inorganic elements and compounds.

1. Amino Acids

• “Organic compounds with an amino group and an acidic (carboxyl) group on the same carbon (α-carbon).”
• Hence, they are called α-amino acids or simply Amino Acids.
• Structurally, amino acids are substituted methanes.
• Each amino acid has four groups attached to the α-carbon:
  • A hydrogen atom
  • An amino group (–NH₂)
  • A carboxyl group (–COOH)
  • A variable side chain called the R group
• There are 20 amino acids that commonly participate in protein synthesis and are called protein amino acids.
• Examples:
  • Glycine: R group is hydrogen.
  • Alanine: R group is a methyl group.
  • Serine: R group is hydroxy methyl.
• Classification of Amino Acids (Based on R group properties):
  • Types:
    • Neutral amino acids: e.g., glycine, alanine, valine
    • Acidic amino acids: e.g., aspartic acid, glutamic acid
    • Basic amino acids: e.g., lysine, arginine, histidine
    • Aromatic amino acids: e.g., phenylalanine, tyrosine, tryptophan
    • Sulphur-containing amino acids: e.g., cysteine, methionine
    • Heterocyclic amino acids: e.g., proline, histidine
• Amino acids can ionize in solutions of different pH levels.
  • Amino acids possess ionisable –NH₂ and –COOH groups.
  • Therefore, in solutions of different pH, amino acids exist in different ionic forms such as cation, zwitter ion and anion.

• Except glycine, all amino acids are optically active and laevorotatory.
• Glycine is the simplest amino acid, while tryptophan is the most complex.
• Amino acids that do not participate in protein synthesis are called non-protein amino acids, such as GABA, ornithine and citrulline.

2. Lipids

• Generally water-insoluble organic compounds.
• They dissolve in non-polar organic solvents such as ether, benzene and chloroform, and can form emulsions in water.
• Lipids are mainly composed of carbon and hydrogen, with oxygen present in smaller amounts.
  • Some lipids also contain phosphorus, nitrogen or sulphur.
• Lipids can be simple fatty acids or glycerol-based.
• Fatty acids:
  • Fatty acids are simple lipids having a carboxyl group (–COOH) attached to an R group.
  • The R group may contain 1 to 19 carbon atoms.
  • Examples:
    • Palmitic acid: 16 carbon atoms (including carboxyl carbon).
    • Arachidonic acid: 20 carbon atoms (including carboxyl carbon).
• Based on the presence of double bonds, fatty acids are of two types:
  • Saturated (no double bonds) or unsaturated (one or more double bonds) Fatty acids.
• Glycerol:
  • Glycerol is another simple lipid. It is a trihydroxy propane molecule.
• Fatty acids combine (esterification) with glycerol to form:
  • Monoglycerides
  • Diglycerides
  • Triglycerides (fats and oils).
• Oils have a lower melting point and remain liquid at room temperature (e.g., gingelly oil),
  • whereas fats have a higher melting point and are solid.
• Phospholipids: contain phosphorus and are found in cell membranes (e.g., Lecithin).
• Complex lipids: found in certain tissues like neural tissues.

3. Nucleotides and Nucleic Acids

• Nucleotides are organic compounds containing carbon, hydrogen, oxygen, nitrogen and phosphorus.
• They form about a small fraction of the total cell content and are the basic units of nucleic acids.
• Nitrogenous Bases:
  • Nitrogen bases are heterocyclic carbon compounds and are of two types:
    1. Purines: Adenine and Guanine.
    2. Pyrimidines: Cytosine, Thymine and Uracil.
• Nucleosides:
  • When a nitrogenous base is attached to a pentose sugar, the compound formed is called a nucleoside.
  • Examples: Adenosine, Guanosine, Thymidine, Uridine, Cytidine.
• Nucleotides:
  • When a phosphate group is added to a nucleoside, it becomes a nucleotide.
  • Examples: Adenylic acid, Thymidylic acid, Guanylic acid, Uridylic acid, Cytidylic acid.
• Nucleotides:
  • Nucleic acids are polymers of nucleotides.
  • DNA and RNA are nucleic acids and function as genetic material in living organisms.

4. Carbohydrates

• Carbohydrates are the most abundant organic molecules in nature.
• They are synthesised during photosynthesis in autotrophic plants and are composed of carbon, hydrogen and oxygen.
• They are generally represented by the empirical formula Cₙ(H₂O)ₙ, where ‘n’ is an integer.

Types of Carbohydrates:

Based on the number of sugar units and complexity, carbohydrates are classified into:

1. Monosaccharides
2. Oligosaccharides
3. Polysaccharides

Chemical Nature:

Carbohydrates may be:

1. Aldoses – containing an aldehyde group
2. Ketoses – containing a ketone group
   

Sugar alcohols (polyols) are also found in nature, where the aldehyde or ketone group is reduced to an alcohol group.

Monosaccharides:

Monosaccharides occur in ring forms:

1. Pyranose – hexose ring with 5 carbon atoms and one oxygen atom
2. Furanose – pentose ring with 4 carbon atoms and one oxygen atom

• Hexoses are usually white, crystalline and sweet in nature.
• Fructose is the sweetest naturally occurring sugar and is known as fruit sugar.
• Glucose is the most important monosaccharide in living systems and is called grape sugar.
• Some monosaccharides contain an amino group (–NH₂). Glucosamine forms chitin, hyaluronic acid and chondroitin sulphate.
• Galactosamine is a component of chondroitin sulphate.

Oligosaccharides:

• Oligosaccharides are involved in cell recognition, cell attachment and act as receptor molecules.
• Trehalose is present in the haemolymph of insects.
• Raffinose and stachyose occur in phloem and may be involved in carbohydrate translocation.

Polysaccharides: A biomacromolecule thus discussed further under Biomacromolecules.

Biomolecules: Biomacromolecules

Proteins

• Polypeptides: Proteins are long linear chains of amino acids linked by peptide bonds.
  • Each protein molecule is a polymer made up of amino acid monomers.
• Amino Acids: There are 20 different types of amino acids such as alanine, cysteine, proline, tryptophan and lysine.
  • Since proteins are formed by different kinds of amino acids arranged in specific sequences, proteins are called heteropolymers.
  • They are not homopolymers, which contain only one type of repeating monomer.
• Essential vs. Non-essential Amino Acids: Amino acids are of two types:
  • Essential amino acids cannot be synthesised by the body and must be obtained from the diet.
  • Non-essential amino acids are synthesised by the body itself.
• Functions of Proteins: Proteins perform a wide range of biological functions:
  • They transport substances across membranes.
  • They act as enzymes to catalyse biochemical reactions.
  • They function as hormones.
  • They help in defence by acting as antibodies.
  • They function as receptors and structural components.
• Examples of Important Proteins:
  • Collagen: Most abundant protein in the animal world and forms the intercellular ground substance.
  • RuBisCO: Ribulose bisphosphate carboxylase-oxygenase (RuBisCO) is the most abundant protein in the entire biosphere.

Polysaccharides

• Polysaccharides are macromolecules made of long chains of monosaccharide units joined by glycosidic bonds.
  • Polysaccharides are also called glycans.
• Structure: These chains may be linear or branched and resemble long threads.
• Classification Based on Composition:
  1. Homopolysaccharides (Homoglycans)
     • These are polysaccharides made of only one type of monosaccharide unit.
     • Examples: Cellulose, starch, glycogen, chitin.
  2. Heteropolysaccharides (Heteroglycans)
     • These are polysaccharides formed from two or more different kinds of monosaccharides or their derivatives.
     • Examples: Hyaluronic acid, chondroitin sulphate, heparin.

Reducing and Non-reducing Ends:

• In a polysaccharide chain:
  • The end (usually right) with a free aldehyde or ketone group is called the reducing end.
  • The opposite end is called the non-reducing end.

Storage Polysaccharides

• Storage polysaccharides act as reserve food materials.
• When required, they are hydrolysed to release sugars which provide energy and raw material for biosynthesis.
• 1. Starch
  • Starch is the storage polysaccharide of plants.
  • It is a homopolysaccharide made of α-D-glucose units and is the end product of photosynthesis.
  • Starch has two components:
    • Amylose – a straight, unbranched chain of glucose units linked by α(1→4) glycosidic bonds and arranged in a helical structure.
    • Amylopectin – a branched polymer with α(1→4) linkages in the main chain and α(1→6) linkages at branching points.

Starch forms helical secondary structures and can trap iodine molecules inside the helix, producing a blue colour.

• 2. Glycogen
  • Glycogen is the storage polysaccharide of animals, fungi and bacteria and is also called animal starch.
  • It is chemically similar to starch but is more highly branched.
  • It contains about 30,000 glucose units linked by α(1→4) bonds with α(1→6) bonds at branching points.
• 3. Inulin
  • Inulin is a storage polysaccharide made of fructose units (a fructan).
  • It is found in roots and tubers of plants such as Dahlia.
  • Inulin is not metabolised in the human body and is easily filtered by the kidneys.

Structural Polysaccharides

• These polysaccharides provide strength and support to cells and organisms.
• 1. Cellulose
  • Cellulose is a tough, fibrous, water-insoluble polysaccharide found in plant cell walls, some protists and cotton fibres.
  • It is a homopolysaccharide of β-D-glucose units linked by β(1→4) glycosidic bonds.
  • Cellulose chains are linear and unbranched and do not form helices.
• 2. Chitin
  • Chitin is the second most abundant organic substance after cellulose.
  • It is found in fungal cell walls and the exoskeleton of arthropods.
  • The monomer unit of chitin is N-acetyl glucosamine, a nitrogen-containing glucose derivative.
  • The monomers are linked by β(1→4) glycosidic bonds.
  • Chitin provides both strength and flexibility.

Mucosubstances

• Some heteropolysaccharides form mucus-like substances called mucosubstances.
• 1. Mucopolysaccharides
  • These are slimy substances containing acidic or amino sugars.
  • They are found in both plants and animals and often combine with proteins to form proteoglycans.
  • Proteoglycans form the ground substance of connective tissue.
  • Examples: Hyaluronic acid, chondroitin sulphate, heparin.
• 2. Mucoproteins (Glycoproteins)
  • These are proteins conjugated with carbohydrate chains.
  • They form mucus found in the stomach, intestine, nasal passages and other body linings.
  • They have protective and antibacterial functions.

Nucleic Acids

• Nucleic acids are macromolecules and are found in the acid-insoluble fraction of living tissues.
  • Along with polysaccharides and proteins, they form the true macromolecular fraction of cells.
  • Nucleic acids are polynucleotides, meaning they are long chains made up of repeating nucleotide units.
• Nucleotide Components: Each nucleotide has 3 chemically distinct components:
  1. A nitrogenous base, which is a heterocyclic compound.
  2. A pentose sugar, which may be ribose or deoxyribose.
  3. A phosphoric acid or phosphate group.
• Nitrogenous Bases
  • The nitrogenous bases present in nucleic acids are adenine, guanine, cytosine, thymine and uracil.
  • Adenine and guanine are purines (double-ring structures).
  • Cytosine, thymine and uracil are pyrimidines (single-ring structures).
• Types of Nucleic Acids
• 1. DNA (Deoxyribonucleic Acid)
  • DNA contains the sugar deoxyribose.
  • It serves as the genetic material in most living organisms.
• 2. RNA (Ribonucleic Acid)
  • RNA contains the sugar ribose.
  • It plays an essential role in protein synthesis and gene expression.

Structure of Proteins

• Proteins are macromolecules and form colloidal complexes in water rather than dissolving freely.
• Chemically, proteins contain carbon, hydrogen, oxygen and nitrogen, and often sulphur.
• Some proteins may also contain elements such as phosphorus or iron.
• Heteropolymers: Proteins are heteropolymers, as they are made up of different kinds of amino acids
• Each protein has a unique three-dimensional structure that determines its biological function.

Levels of Protein Structure

• 1. Primary Structure:
  • The primary structure refers to the linear sequence of amino acids in a polypeptide chain.
  • It represents the exact order and number of amino acids present in a protein.
• The two ends of the polypeptide chain are:
  1. N-terminal end – the first amino acid with a free amino group.
  2. C-terminal end – the last amino acid with a free carboxyl group.

The primary structure is the most basic and also the most unstable level of protein structure.

• 2. Secondary Structure:
  • The secondary structure arises due to folding of the polypeptide chain caused by hydrogen bonding between amino acids of the same or different chains.
  • This folding produces regular patterns.
• Two major types of secondary structures are:
  1. Alpha helix – a right-handed, spirally coiled structure stabilised by intramolecular hydrogen bonds. Examples include keratin, myosin and tropomyosin.
  2. Beta-pleated sheet – a zig-zag structure where two or more polypeptide chains are held together by intermolecular hydrogen bonds. Examples include fibroin (silk protein).

Secondary structure proteins are often fibrous and insoluble in water.

• 3. Tertiary Structure
  • The tertiary structure is formed by further bending and folding of the secondary structure, resulting in a compact three-dimensional shape such as spherical, rod-like or fibrous forms.
  • This structure is stabilised by various interactions including hydrogen bonds, ionic bonds, disulphide bonds, hydrophobic interactions and van der Waals forces.
  • The tertiary structure is essential for the biological activity of most proteins and enzymes.

Most proteins present in the protoplasm exhibit tertiary structure.

• 4. Quaternary Structure
  • The quaternary structure is found only in multimeric proteins that consist of two or more polypeptide chains (subunits).
  • Each polypeptide chain has its own tertiary structure and functions as a subunit of the protein.
• Example
  • Haemoglobin has a quaternary structure and is composed of 4 subunits: two alpha (α) chains and two beta (β) chains.

This is the most stable level of protein organisation.

Key Points

• Nucleic acids are polynucleotides made of nucleotides containing a base, sugar and phosphate.
• DNA contains deoxyribose, while RNA contains ribose.
• Proteins are heteropolymers made of amino acids.
• Protein structure is organised into four levels: primary, secondary, tertiary and quaternary.
• The three-dimensional structure of proteins determines their function.
• Haemoglobin is a classic example of a protein with quaternary structure.

Nature of Bonds Linking Monomers in a Polymer

• Polypeptides/Proteins:
  • Peptide Bond: Links amino acids.
  • Formation: Carboxyl group (-COOH) of one amino acid reacts with amino group (-NH₂) of the next amino acid, releasing a water molecule (dehydration).
  • “Peptide bond is a strong covalent bond formed during condensation and is the strongest bond present in proteins.”
• Polysaccharides:
  • Glycosidic Bond: Links monosaccharides.
  • Formation: Dehydration reaction between two adjacent monosaccharides.
  • “The glycosidic bond is formed between carbon atoms of two monosaccharide units and may produce linear or branched polysaccharides.”
• Nucleic Acids:
  • Phosphodiester Bond: Links nucleotides.
  • Formation: Phosphate group links the 3′ carbon of one sugar to the 5′ carbon of the next sugar.
  • “The bond involves two ester linkages on either side of the phosphate group, hence called a phosphodiester bond.”
• DNA Structure (Watson-Crick Model):
  • Double Helix:
    • DNA consists of two polynucleotide strands.
    • Strands run in opposite directions (antiparallel).
  • Backbone: Sugar–phosphate–sugar chain.
    • Bases project inward and pair specifically.
  • Base Pairing:
    • Adenine (A) pairs with Thymine (T) by 2 hydrogen bonds.
    • Guanine (G) pairs with Cytosine (C) by 3 hydrogen bonds.
  • Helix Details:
    • Each step contains one base pair.
    • 36° turn per step or each step rotates by 36°..
    • One complete turn contains 10 base pairs.
    • Pitch of helix = 34 Å.
    • Rise per base pair = 3.4 Å.
    • Form: B-DNA (most common).

“Each strand resembles a helical staircase, where paired bases form the steps.”

Key Points

• Monomers in polymers (proteins, polysaccharides and nucleic acids) are linked by specific covalent bonds formed through dehydration reactions.
• DNA has a double helical structure with strict complementary base pairing (A–T, G–C).

Primary and Secondary Metabolites

Metabolites

• Biomolecules present in living organisms that participate in metabolic reactions are called metabolites.
• Thousands of organic compounds like amino acids, lipids and sugars are metabolites.
• These compounds are continuously converted into one another through enzyme-controlled reactions called metabolic pathways.

Primary Metabolites

• Primary metabolites are organic compounds directly involved in basic life processes such as growth, development and reproduction.
• Examples: Carbohydrates, Proteins, Fats, Nucleic acids, Amino acids and sugars.
• Have clearly defined roles in metabolism like respiration, photosynthesis and biosynthesis (physiological processes).

Secondary Metabolites

• Secondary metabolites are organic compounds mainly produced by plants, fungi and certain microbes.
• They are not directly involved in primary metabolic processes such as growth or reproduction.
• Their exact role in the producing organism may not always be clear, but many have ecological and adaptive significance.
• Many are widely useful to humans (e.g., rubber, drugs, spices, scents, pigments).
• Examples of Secondary Metabolites and their Groups:
  • Alkaloids – e.g., morphine, codeine (medicinal use)
  • Flavonoids and phenolic compounds – pigments, antioxidants ( Found in fruits and vegetables).
  • Terpenoids (isoprenoids) – rubber, steroids, carotenoids
  • Essential oils – scents and perfumes (e.g., lemon grass oil)
  • Antibiotics and drugs – e.g., vinblastine, curcumin
  • Pigments – carotenoids, anthocyanins
  • Toxins – abrin, ricin
  • Polymeric substances – rubber, gums, resins

• Key Points
  • Primary metabolites are essential for survival and normal physiological functions (metabolism).
  • Secondary metabolites often provide protection, attraction or ecological advantages and have economic value.

Dynamic State of Body Constituents – Concept of Metabolism

• Biomolecules: Living organisms contain thousands of organic compounds called biomolecules or metabolites.
• Turnover: Biomolecules are constantly synthesized and broken down.
  • “Continuous formation and breakdown of biomolecules is called turnover.”
• Metabolism:
  • All chemical reactions occurring in living organisms together form metabolism.
  • Examples:
    • Removal of CO2 from amino acids.
    • Removal of amino group from nucleotide base.
    • Hydrolysis of glycosidic bonds in disaccharides.
• Metabolic Pathways:
  • Series of linked reactions converting one metabolite into another.
    • May be linear, circular or interconnected.
• Flow of Metabolites: Occurs in a definite direction and rate, similar to traffic flow.
• Dynamic State: Smooth, coordinated and uninterrupted metabolic activity.
• Catalysis:
  • All metabolic reactions are catalysed.
  • Catalysts are protein molecules called enzymes.

• “There is no uncatalysed metabolic reaction in living systems.”
• Even simple processes like CO₂ dissolving in water in a living system are catalysed.

Metabolic Basis for Living

Metabolic Pathways

• Anabolic Pathways (Biosynthetic)
  • Build complex molecules from simpler ones.
  • Consume energy.
  • Examples
    • Acetic acid → cholesterol.
    • Amino acids → proteins.
• Catabolic Pathways (Degradation)
  • Break complex molecules into simpler ones.
  • Release energy.
  • Examples
    • Glucose → lactic acid in muscles.
    • Glycolysis occurs in 10 enzymatic steps.

Energy in Living Organisms

• Energy is stored in chemical bonds.
• ATP (Adenosine Triphosphate) is the universal energy currency.
• This stored energy is used for:
  • Biosynthetic work (formation of molecules).
  • Osmotic work (maintaining fluid balance).
  • Mechanical work (movement).

“Energy liberated during catabolism is trapped in ATP molecules.”

Bioenergetics

• The study of how organisms obtain, store and use energy..

The Living State

Biomolecules and Metabolites

• Each biomolecule exists at a characteristic concentration.
• Examples:
  • Blood glucose: ~4.5–5.0 mM.
  • Hormones: nanogram per mL range.

Steady-State vs. Equilibrium

• Living organisms exist in a steady-state, not at equilibrium.

Equilibrium: means no work can be done, but living things must always work.
Steady-state: Continuous work possible.

“Living systems constantly prevent reaching equilibrium by continuous energy input.”

• Key point:
  • Metabolism and living state are inseparable.
  • Without metabolism, life cannot exist.

Enzymes

What Are Enzymes?

• Enzymes are organic catalysts that speed up biochemical reactions without being consumed in the process.
• Almost all enzymes are proteins.
• Some nucleic acids act as enzymes, called ribozymes.
• Enzymes have a complex structure:
  • Primary Structure: Sequence of amino acids.
  • Secondary and Tertiary Structure: Protein chain folds and creates pockets.

“Enzymes often occur in an inactive form called proenzymes or zymogens and are converted into active enzymes by specific factors.”

Active Site

• “The active site has a specific three-dimensional shape complementary to the substrate, leading to formation of an enzyme–substrate complex.”
• Active site is like a pocket in the enzyme where the substrate fits.
• Enzymes use their active sites to speed up reactions.

Enzymes vs. Inorganic Catalysts

• Inorganic catalysts work well at high temperatures and pressures.
• “Most enzymes are thermolabile and function best between 25–35°C; they denature (can be damageed) around 50–55°C.”
• Enzymes from organisms in hot environments (like hot springs) are stable at high temperatures (up to 80°-90°C).

Chemical Reactions

Types of Changes in Chemical Compounds

• Physical Change: Shape changes without breaking bonds (e.g., ice melting).
• Chemical Reaction: Bonds are broken and new ones are formed (e.g., Ba(OH)₂ + H₂SO₄ → BaSO₄ + 2H₂O).

Reaction Rate

• The amount of product formed per unit time or change in product concentration per unit time.
• Affected by temperature: Rate doubles or becomes half with every 10°C change.
• Enzyme-catalyzed reactions are much faster than uncatalyzed ones.

Example of Enzyme Action

• Without enzyme: CO₂ + H₂O → H₂CO₃ (very slow, 200 molecules/hour).
• With enzyme (carbonic anhydrase): Reaction rate speeds up to 600,000 molecules/second.

“The enzyme accelerates the reaction rate by nearly ten million times.”

Metabolic Pathways

• Multi-step reactions where each step is catalyzed by specific enzyme.
• Example: Glucose → 2 Pyruvic acid (10 enzyme-catalysed steps).
• Different conditions produce different products:
  • Anaerobic (no oxygen) in muscles: Lactic acid.
  • Aerobic (with oxygen): Complete oxidation via pyruvate.
  • In yeast (fermentation): Ethanol and CO₂.

How Do Enzymes Speed Up Chemical Reactions?

• Active Site: Region of enzyme where substrate binds.
• Substrate (S): The chemical that is converted into a product (P) by the enzyme.
• Enzyme-Substrate Complex (ES): Temporary complex formed when substrate binds to enzyme.
  • “This complex formation is transient and essential for catalysis.”
  • After reaction, product is released and enzyme becomes free again.

Transition State and Activation Energy

• Transition State: A high-energy intermediate state during conversion of substrate to product.
• Activation Energy: Minimum energy required to reach the transition state.
• Enzymes lower activation energy by stabilising the transition state, making reactions faster.

“Even spontaneous reactions must pass through a high-energy transition state.”

• Key Points
  • Enzymes are mostly proteinaceous biological catalysts.
  • Active site determines enzyme specificity.
  • Enzymes are highly efficient and specific.
  • All metabolic reactions in living systems are enzyme-catalysed.
  • Enzymes lower activation energy but do not change reaction equilibrium.

Nature of Enzyme Action

Catalytic Cycle of Enzyme Action

1. Binding: Substrate binds to the enzyme’s active site.
   • “Each enzyme has a specific substrate-binding site that allows formation of a short-lived enzyme–substrate (ES) complex.”
2. Induced Fit: The enzyme changes shape to fit the substrate more tightly.
   • “This binding induces a conformational change in the enzyme, improving contact between enzyme and substrate.”
3. Reaction: The enzyme breaks the substrate’s bonds and forms the enzyme-product complex (EP).
   • “The active site brings reacting groups close together, weakens existing bonds, and facilitates formation of new bonds.”
4. Release: The enzyme releases the product and is ready to start the cycle again with a new substrate.
   • “The enzyme remains unchanged after product release and can repeatedly participate in catalysis.”

Key Points

• Enzymes are proteins with specific three-dimensional structures.
• They speed up reactions by lowering the activation energy.
• The enzyme’s active site is crucial for binding substrates and catalyzing reactions.
• Enzymes are reusable and are not consumed during reactions.

Factors Affecting Enzyme Activity

Temperature and pH

• Enzymes work best at a specific temperature and pH (optimum).
  • “Most animal enzymes function optimally between 30–40°C, while plant enzymes work best around 20–30°C.”
  • Most intracellular enzymes function near neutral pH, though digestive enzymes may work in acidic or alkaline conditions.
• Activity decreases if the temperature or pH is too high or too low.
  • Low temperatures make enzymes temporarily inactive.
  • High temperatures can denature (destroy) enzymes.

“Extreme heat permanently denatures enzymes, whereas low temperature only reduces molecular movement.”

Substrate Concentration

• Increasing substrate concentration initially increases reaction speed.
  • “With increase in substrate concentration, reaction velocity rises due to more frequent enzyme–substrate collisions.”
• Maximum velocity (Vmax) is reached when all enzyme molecules are occupied.
• No further increase in reaction rate occurs after enzyme saturation (Vmax), even if more substrate is added.

Inhibitors

• Inhibitors: Chemicals that decrease/stop enzyme activity.
  1. Competitive Inhibitors: Resemble the substrate and compete for the active site.
     • Example: Malonate inhibits succinic dehydrogenase by resembling succinate.
     • “Competitive inhibition is reversible and can be overcome by increasing substrate concentration.”
  2. Non-competitive Inhibitors: Bind to a site other than the active site (the allosteric site) and alter enzyme shape.
     • “Allosteric inhibition occurs when inhibitors bind at regulatory sites (a site other than the active site), changing active site configuration.”

Classification and Nomenclature of Enzymes

Enzyme Classes

• Enzymes are grouped based on the reactions they catalyze. There are 6 main classes:

1. Oxidoreductases (Dehydrogenases)
   • Catalyze oxidation-reduction reactions.
   • Example: S reduced + S’ oxidized → S oxidized + S’ reduced.
2. Transferases
   • Transfer a functional group (other than hydrogen) between molecules.
   • Example: S–G + S’ → S + S’–G
3. Hydrolases
   • Catalyze hydrolysis reactions (bond breaking) using water.
   • Example: Breaking ester, ether, peptide, or glycosidic bonds.
4. Lyases
   • Remove groups from molecules without hydrolysis, forming double bonds.
5. Isomerases
   • Catalyze the conversion of isomers (same formula, different structure).
   • Catalyze rearrangement of atoms within a molecule.
6. Ligases
   • Join two molecules using energy from ATP.
   • Example: Catalyze the formation of bonds like C–O, C–S, C–N, or P–O bonds

“Each enzyme is assigned a specific numerical code (four-digit) for precise identification.”

Co-factors

• Some enzymes need non-protein helpers called co-factors.
• The protein part of an enzyme is called the apoenzyme.

“Enzyme activity is lost if the required co-factor is removed.”

Types of Co-factors

1. Prosthetic Groups
   • Tightly bound to the apoenzyme.
   • Example: Haem in catalase and peroxidase helps break hydrogen peroxide.
2. Co-enzymes
   • Temporarily bind to the apoenzyme during catalysis.
   • Can assist in various enzyme reactions.
   • Often derived from vitamins.
   • Example: NAD and NADP contain the vitamin niacin.
3. Metal Ions
   • Form coordination bonds with enzyme and substrate.
   • Example: Zinc is a co-factor for the enzyme carboxypeptidase.

• Key Points
  • Enzyme action involves binding, induced fit, catalysis, and release.
  • Enzyme activity depends on temperature, pH, substrate concentration, and inhibitors.
  • Enzymes are highly specific, efficient, and reusable biological catalysts.
  • Co-factors are essential for the catalytic activity of many enzymes.

Chapter Summary:

• Living organisms have diverse forms but have broadly similar chemical composition and metabolic reactions.
• Living tissues and non-living matter show qualitative similarity in elemental composition, though the relative abundance differs.
• Carbon, hydrogen, and oxygen are more abundant in living systems.
• Water is the most abundant chemical constituent of living organisms.

• Living organisms contain a large number of small biomolecules with molecular weight less than 1000 daltons.
  • Examples: Amino acids, sugars, fatty acids, glycerol, nucleotides, nucleosides, and nitrogen bases.
  • 20 types of amino acids and 5 types of nucleotides exist.
• Fats and oils are glycerides in which fatty acids are esterified to glycerol.
• Phospholipids contain a phosphorylated nitrogenous compound and are important membrane components.
• Three major types of macromolecules are present in living systems:
  1. Proteins
  2. Nucleic acids (RNA and DNA)
  3. Polysaccharides
• Lipids are closely associated with membranes and therefore separate along with the macromolecular fraction during chemical analysis.

• Biomacromolecules are polymers formed from specific building blocks:
  • Proteins: Heteropolymers of amino acids.
  • Nucleic acids: polymers of nucleotides.
  • Polysaccharides: serve as structural components (plant cell wall, arthropod exoskeleton) and energy reserves (starch in plants, glycogen in animals).
• Biomacromolecules show hierarchical structural organization at four levels:
  1. Primary
  2. Secondary
  3. Tertiary
  4. Quaternary
• Functions of biomacromolecules:
  • Nucleic acids: act as genetic material.
  • Polysaccharides: Structural components and energy storage.
  • Proteins: diverse Cellular functions (enzymes, antibodies, receptors, hormones, structural proteins).
• Collagen: Most abundant protein in animals.
• RuBisCO: Most abundant protein in the biosphere.

• Enzymes: are protein molecules that catalyze biochemical reactions.
  • Ribozymes: are exceptionally the Nucleic acids with catalytic power.
• Enzymes show substrate specificity, optimal temperature, and pH.
  • High temperatures denature enzymes.
  • Enzymes lower activation energy and speed up biochemical reactions.
• Nucleic acids: store and transmit hereditary information from parents to offspring.