BiomoleculesNEET Zoology · Class 11 · NCERT Chapter 9

Introduction

Every living cell is a chemical factory. The reactions that keep you alive depend on thousands of different molecules working together. This chapter is about those molecules: what they are, how they are built, and what they do.

Expect 1 to 2 NEET questions every year from Biomolecules. The most reliable scoring areas are: the four levels of protein structure, enzyme properties (active site, lock-and-key, factors that affect activity), the difference between storage and structural polysaccharides, and the structure of a nucleotide.

Chemical Composition of Living Tissue

To find out what a cell is made of, you grind up living tissue (like leaf or muscle) and separate the contents. You find two broad categories of molecules:

• Micromolecules (small molecules): molecular weight below about 1000 Da. Include amino acids, simple sugars, organic acids, fatty acids, nucleotides, vitamins and inorganic ions.
• Macromolecules (large molecules): molecular weight in the thousands to millions of Da. Include proteins, polysaccharides, nucleic acids and (loosely) lipids. Macromolecules make up most of the dry weight of a cell.

Acid-Soluble vs Acid-Insoluble Pool

If you treat the ground tissue extract with strong acid (trichloroacetic acid), the large molecules precipitate out and the small molecules stay in solution:

• Acid-soluble pool: micromolecules, inorganic ions and water. This is what stays in solution.
• Acid-insoluble pool: macromolecules (proteins, polysaccharides, nucleic acids, lipids). This is the precipitate.

In a living cell, the macromolecular pool accounts for the bulk of the dry mass. The micromolecular pool turns over rapidly: these molecules are the raw materials and intermediates of metabolism.

Primary and Secondary Metabolites

Organisms make thousands of different compounds. They fall into two broad groups:

• Primary metabolites: compounds with a clear role in growth, reproduction and normal development. Examples: amino acids (protein building blocks), sugars (energy), nucleotides (DNA/RNA building blocks), vitamins, fatty acids.
• Secondary metabolites: compounds whose function in the producing organism is not always obvious. Found mainly in plants and microbes. Examples: alkaloids (morphine, caffeine, nicotine), rubber, resins, terpenes, essential oils, pigments (anthocyanin), toxins, lectins. Many have great economic and medicinal value.

Amino Acids

Amino acids are the building blocks of proteins. Each amino acid has the same basic structure: a central carbon atom (the alpha carbon) with four groups attached to it.

• An amino group (-NH2) on one side
• A carboxyl group (-COOH) on the other side
• A hydrogen atom (-H)
• A variable side chain (R group) that is different for each amino acid and gives it its unique chemical properties

There are 20 standard amino acids used to build proteins. Of these, 8 to 10 are essential amino acids that you cannot synthesise and must get from food.

Two amino acids join through a peptide bond: the carboxyl group of one reacts with the amino group of the next, releasing water (condensation reaction). The resulting -CO-NH- linkage is the peptide bond. A chain of amino acids linked by peptide bonds is called a polypeptide.

Proteins and Protein Structure

Proteins are the most diverse macromolecules in a cell. They perform almost every function: enzymes (catalysis), antibodies (immunity), haemoglobin (transport), collagen (structure), insulin (signalling), actin and myosin (movement), receptors (communication).

The function of every protein depends entirely on its 3D shape. The shape is determined by the sequence of amino acids. Even one wrong amino acid can destroy function (as in sickle-cell anaemia, where one amino acid change in the beta chain of haemoglobin causes the disease).

Four Levels of Protein Structure

1. Primary structure: the linear sequence of amino acids from the N-terminus to the C-terminus, held together by peptide bonds. This sequence is coded directly by the DNA. Even one change in the sequence (a mutation) can alter the protein shape and function.
2. Secondary structure: local regular folding of the polypeptide chain into repeating patterns, held by hydrogen bonds between nearby backbone atoms. Two main forms: the alpha helix (right-handed coil, hydrogen bonds within one chain) and the beta-pleated sheet (hydrogen bonds between adjacent parallel or antiparallel chains).
3. Tertiary structure: the overall 3D shape of the entire polypeptide chain, formed by interactions between side chains (R groups). Held by hydrogen bonds, disulfide bonds (between cysteine residues), ionic interactions and hydrophobic interactions. This is the level at which the active site of an enzyme is formed.
4. Quaternary structure: exists only in proteins made of two or more polypeptide subunits. The subunits assemble and are held by non-covalent interactions. Examples: haemoglobin (4 subunits: 2 alpha + 2 beta), collagen (3 alpha chains wound into a triple helix), insulin (2 chains: A and B linked by disulfide bonds).

Carbohydrates and Polysaccharides

Carbohydrates are molecules made of carbon, hydrogen and oxygen in roughly the ratio Cx(H2O)y. They are the primary fuel molecules and key structural materials.

• Monosaccharides (simple sugars): the building blocks. Cannot be broken down further by hydrolysis. Examples: glucose (C6H12O6, the main fuel), fructose (fruit sugar), ribose (5-carbon, backbone of RNA), deoxyribose (backbone of DNA), galactose.
• Disaccharides: two monosaccharides joined by a glycosidic bond. Sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose + glucose).
• Polysaccharides: long chains of many monosaccharides joined by glycosidic bonds. Formed by condensation reactions.

Polysaccharides have two main jobs:

• Storage: Starch (in plants, made of amylose + amylopectin, alpha-1,4 and alpha-1,6 glycosidic bonds), glycogen (in animals and fungi, more highly branched than starch, stored in liver and muscle).
• Structural: Cellulose (in plant cell walls, beta-1,4 glycosidic bonds, straight chains, very strong), chitin (in fungal cell walls and insect exoskeletons, beta-1,4 bonds with an amino group on each sugar unit).

Lipids and Fatty Acids

Lipids are not true polymers. They are grouped together because they are insoluble in water (hydrophobic) but dissolve in organic solvents like chloroform or ether. They include fats, oils, waxes, sterols and phospholipids.

• Fatty acids: long hydrocarbon chains with a carboxyl group (-COOH) at one end. Saturated fatty acids have no double bonds; they are solid at room temperature (e.g. palmitic acid in butter). Unsaturated fatty acids have one or more double bonds; they are liquid at room temperature (e.g. oleic acid in olive oil).
• Triglycerides (fats and oils): one glycerol molecule joined to three fatty acid chains via ester bonds. Main energy storage in animals.
• Phospholipids: one glycerol, two fatty acids, and a phosphate group linked to a polar head. Amphipathic: hydrophilic head and hydrophobic tails. Form the lipid bilayer of all cell membranes.
• Sterols: four fused carbon rings. Cholesterol is a key component of animal cell membranes and the precursor to steroid hormones and bile acids.

Nucleic Acids

Nucleic acids (DNA and RNA) store and transfer genetic information. They are polymers of nucleotides.

A single nucleotide has three components:

1. A pentose sugar: deoxyribose (in DNA) or ribose (in RNA). Ribose has an -OH at the 2-carbon; deoxyribose has -H there.
2. A phosphate group attached to the 5-carbon of the sugar.
3. A nitrogenous base attached to the 1-carbon of the sugar. Purines: adenine (A) and guanine (G). Pyrimidines: cytosine (C), thymine (T, DNA only) and uracil (U, RNA only).

Nucleotides are joined by phosphodiester bonds (3' to 5') to form the backbone of the nucleic acid strand. In double-stranded DNA, the two strands are held together by hydrogen bonds between complementary base pairs: A with T (2 hydrogen bonds) and G with C (3 hydrogen bonds).

Enzymes

Enzymes are biological catalysts. They speed up chemical reactions inside cells without being used up. Without enzymes, most biological reactions would be too slow to support life.

• Chemical nature: almost all enzymes are proteins. A few RNA molecules also act as enzymes (called ribozymes), for example the rRNA in ribosomes that forms peptide bonds.
• Specificity: each enzyme usually acts on only one or a few substrates. This is because only a molecule with the right shape fits into the enzyme's active site.
• Active site: a specific pocket or groove on the enzyme surface where the substrate binds and the reaction happens. The active site is formed by the enzyme's tertiary (or quaternary) structure.
• Not consumed: the enzyme is released unchanged after the reaction and can catalyse the same reaction again.
• Lower activation energy: enzymes work by lowering the activation energy of the reaction. They do not change the equilibrium of the reaction.

Mechanism of Enzyme Action

The lock-and-key model (Fischer, 1894) says the active site is rigid and has a shape that exactly fits the substrate, like a key fits a lock. Steps:

1. The substrate collides with and binds the active site, forming an enzyme-substrate complex (ES complex).
2. The enzyme lowers the activation energy. The reaction proceeds and the substrate is converted to product(s).
3. The product(s) are released from the active site. The enzyme is unchanged and ready for the next substrate molecule.

The induced-fit model (Koshland, 1958) is a refinement: the active site is not entirely rigid. When the substrate approaches, the enzyme changes shape slightly to wrap around the substrate more tightly. This is a better model for most enzymes.

Factors Affecting Enzyme Activity

• Temperature: activity increases as temperature rises (more kinetic energy, more collisions). Activity peaks at the optimum temperature (about 35 to 40 degrees C for most human enzymes, about 25 degrees C for plant enzymes). Above the optimum, the enzyme denatures: weak bonds holding the 3D structure break, the active site changes shape, substrate can no longer bind, activity falls to zero. Denaturation is usually irreversible.
• pH: each enzyme has an optimum pH. Most enzymes work best between pH 6 and pH 8. Exceptions: pepsin (stomach protease, optimum pH 2), urease (pH 8). At extreme pH values (very acidic or very basic), the enzyme denatures.
• Substrate concentration: at low substrate concentration, increasing substrate increases the reaction rate (more active sites occupied). As concentration rises, a point is reached where all active sites are occupied (the enzyme is saturated). Beyond this point, adding more substrate does not increase the rate. The maximum rate at saturation is called Vmax.

Cofactors

Many enzymes need a non-protein helper molecule to be active. This helper is called a cofactor. There are three types:

• Coenzyme: a small organic molecule (often a vitamin derivative) that binds loosely and temporarily. It carries groups or electrons between enzyme reactions. Examples: NAD+ (from niacin, vitamin B3), FAD (from riboflavin, vitamin B2), Coenzyme A (CoA, from pantothenic acid, vitamin B5).
• Prosthetic group: a cofactor that is tightly and permanently bound to the enzyme. Examples: haem in cytochromes and peroxidase, FAD in succinate dehydrogenase, biotin in carboxylases.
• Metal ion activator: inorganic ions needed for full activity. Examples: Zn2+ (carbonic anhydrase, carboxypeptidase), Mg2+ (hexokinase, many ATP-using enzymes), Fe2+/Fe3+ (cytochromes), Cu2+ (cytochrome oxidase).

An enzyme without its cofactor is called an apoenzyme (inactive). The apoenzyme plus its cofactor is the holoenzyme (active).

Six Classes of Enzymes

1. Oxidoreductases: catalyse oxidation-reduction reactions. Example: alcohol dehydrogenase (oxidises ethanol to acetaldehyde).
2. Transferases: transfer a functional group from one molecule to another. Example: aminotransferases (transfer amino groups in amino acid synthesis).
3. Hydrolases: break bonds using water (hydrolysis). Example: amylase (starch to maltose), lipase (fats to fatty acids + glycerol), protease (proteins to amino acids).
4. Lyases: add groups to double bonds, or remove groups to form double bonds (without water or oxidation). Example: pyruvate decarboxylase (removes CO2 from pyruvate).
5. Isomerases: interconvert isomers. Example: phosphoglucose isomerase (glucose-6-phosphate to fructose-6-phosphate in glycolysis).
6. Ligases: join two molecules using energy (usually from ATP hydrolysis). Example: DNA ligase (joins DNA fragments), aminoacyl-tRNA synthetase (charges tRNA).

Worked NEET Problems

Summary Cheat Sheet

• Acid-soluble pool: micromolecules (amino acids, sugars, nucleotides, organic acids, ions). Acid-insoluble pool: macromolecules (proteins, polysaccharides, nucleic acids, lipids).
• Primary metabolites: amino acids, sugars, nucleotides (clear role in growth). Secondary metabolites: alkaloids, rubber, terpenes, pigments (no obvious immediate role).
• Amino acid structure: alpha-C + amino group + carboxyl group + H + R group (side chain). 20 standard amino acids.
• Peptide bond: between carboxyl of one amino acid and amino of the next; formed by condensation (water released).
• Primary structure: amino acid sequence; held by peptide bonds.
• Secondary structure: alpha helix or beta-pleated sheet; held by hydrogen bonds.
• Tertiary structure: overall 3D shape; held by H-bonds, disulfide bonds, ionic bonds, hydrophobic interactions. Active site formed here.
• Quaternary structure: two or more subunits; e.g. haemoglobin (4 subunits), collagen (3 chains).
• Most abundant protein: RuBisCO (in biosphere). Most abundant protein in animals: collagen.
• Storage polysaccharides: starch (plants, alpha-glucose, alpha-1,4 and 1,6 bonds); glycogen (animals, more branched).
• Structural polysaccharides: cellulose (plants, beta-glucose, beta-1,4 bonds); chitin (fungi and insects, beta-1,4 bonds + amino group).
• Most abundant organic compound: cellulose (in the living world).
• Glycosidic bond: joins monosaccharides in polysaccharides.
• Nucleotide: sugar + phosphate + nitrogenous base. DNA sugar: deoxyribose. RNA sugar: ribose. DNA bases: A, T, G, C. RNA bases: A, U, G, C.
• Phosphodiester bonds: join nucleotides in nucleic acids (3' to 5').
• Lipids: triglycerides (3 fatty acids + glycerol, energy storage); phospholipids (2 fatty acids + phosphate head, membrane bilayer).
• Enzyme: biological catalyst; mostly protein (some are ribozymes).
• Active site: specific pocket where substrate binds and reaction occurs.
• Lock-and-key model: rigid active site; substrate fits like a key. Induced-fit model: active site flexes to wrap substrate.
• Temperature effect: activity rises to optimum, then falls as enzyme denatures above optimum.
• pH effect: each enzyme has an optimum pH; extreme pH denatures the enzyme.
• Substrate concentration: rate increases until Vmax (all active sites saturated).
• Cofactor types: coenzyme (loose, temporary; e.g. NAD+, FAD); prosthetic group (permanent; e.g. haem); metal ion (e.g. Zn2+, Mg2+).
• Apoenzyme (without cofactor, inactive) + cofactor = holoenzyme (active).
• Six enzyme classes: (1) Oxidoreductases, (2) Transferases, (3) Hydrolases, (4) Lyases, (5) Isomerases, (6) Ligases.

Next: explore the interactive learning widgets to classify biomolecule categories, walk through all four levels of protein structure, and see how temperature and pH change enzyme activity on a real bell curve. Practice with the 15+ NEET PYQs with full solutions, or time yourself with the free 10-question mock test.