Biomolecules

2.1 Core concepts

• Elemental composition. Elemental analysis of any living tissue (plant tissue, animal tissue, microbial paste) yields the same list of elements as a sample of earth's crust, but the relative abundance of carbon and hydrogen (and oxygen) is higher in living organisms than in earth's crust. Table 9.1 shows representative weights: H 9.5% (body) vs 0.14% (crust), C 18.5% vs 0.03%, O 65.0% vs 46.6%, N 3.3% vs "very little", Si 'negligible' vs 27.7% (NCERT §9 intro and §9.1, pp. 104–105).
• How to analyse chemical composition. Take any living tissue (a vegetable or a piece of liver) and grind it in trichloroacetic acid (Cl₃CCOOH) using a mortar and pestle, producing a thick slurry. Strain through cheesecloth or cotton — two fractions result: the filtrate / acid-soluble pool and the retentate / acid-insoluble fraction. Scientists have found thousands of organic compounds in the acid-soluble pool (NCERT §9.1, p. 104).
• Wet weight, dry weight & ash. Weigh small living tissue → wet weight; dry it → dry weight (water evaporates); burn the dry tissue → all carbon compounds are oxidised to CO₂ and water vapour; the remaining inorganic residue is ash containing Ca, Mg, etc. Inorganic compounds like sulphate and phosphate also occur in the acid-soluble fraction. Table 9.2 lists representative inorganic constituents — Na⁺, K⁺, Ca²⁺, Mg²⁺, water and compounds NaCl, CaCO₃, PO₄³⁻, SO₄²⁻ (NCERT §9.1, p. 105).
• Carbon compounds → 'biomolecules'. From a chemistry viewpoint these can be functional groups (aldehydes, ketones, aromatics); from a biology viewpoint they are classified as amino acids, nucleotide bases, fatty acids etc. (NCERT §9.1, p. 105).
• Amino acids. Organic compounds containing an amino group and an acidic group as substituents on the same carbon — the α-carbon; hence called α-amino acids and they are substituted methanes with four substituents (H, –COOH, –NH₂, variable R). The R group could be hydrogen (glycine), methyl (alanine), hydroxymethyl (serine), etc. There are only 20 types of amino acids in proteins. Based on R-group: acidic (glutamic acid), basic (lysine), neutral (valine), aromatic (tyrosine, phenylalanine, tryptophan). The –NH₂ and –COOH groups are ionizable, so amino-acid structure changes with pH: the doubly-ionised form H₃N⁺–CHR–COO⁻ is the zwitterionic form (B) (NCERT §9.1, pp. 105–106).
• Lipids. Generally water-insoluble. Simple fatty acids carry a –COOH group on an R group of 1–19 carbons; palmitic acid has 16 carbons including the carboxyl carbon; arachidonic acid has 20 carbons. Fatty acids may be saturated (no double bond) or unsaturated (one or more C=C double bonds). Glycerol is trihydroxypropane. Triglycerides are glycerol esterified with three fatty acids; they are also called fats and oils based on melting point — oils have lower melting point (e.g. gingelly oil remains oil in winter). Phospholipids contain phosphorus and a phosphorylated organic group; found in cell membranes (lecithin is one example). Some tissues, especially neural tissues, contain lipids with more complex structures (NCERT §9.1, p. 106).
• Nitrogen bases & nucleotides. Living organisms contain heterocyclic rings — nitrogen bases: adenine, guanine, cytosine, uracil, thymine. When attached to a sugar, they are called nucleosides — adenosine, guanosine, thymidine, uridine, cytidine. With a phosphate group also esterified to the sugar, they are called nucleotides — adenylic acid, thymidylic acid, guanylic acid, uridylic acid, cytidylic acid. Nucleic acids like DNA and RNA consist of nucleotides only and function as genetic material (NCERT §9.1, p. 106).
• Primary and secondary metabolites. A list of biomolecules in animal tissues — amino acids, sugars, etc. — covers primary metabolites, which have identifiable functions and play known roles in normal physiological processes. In contrast, plant, fungal and microbial cells contain thousands of compounds we do not yet understand — secondary metabolites (Table 9.3): Pigments — carotenoids, anthocyanins; Alkaloids — morphine, codeine; Terpenoides — monoterpenes, diterpenes; Essential oils — lemon grass oil; Toxins — abrin, ricin; Lectins — concanavalin A; Drugs — vinblastin, curcumin; Polymeric substances — rubber, gums, cellulose. Many are useful to human welfare (rubber, drugs, spices, scents, pigments); some have ecological importance (NCERT §9.2, p. 108).
• Biomacromolecules. All compounds in the acid-soluble pool have molecular weights ranging from 18 to around 800 Da. The acid-insoluble fraction has only four types of organic compounds — proteins, nucleic acids, polysaccharides and lipids. These have MW in the range of ten thousand daltons and above. Hence biomolecules <1000 Da are micromolecules and those in the acid-insoluble fraction are macromolecules / biomacromolecules. Lipids appear in the macromolecular fraction not because they themselves are large but because cell membranes form vesicles that are not water-soluble and sediment along with proteins/polysaccharides/nucleic acids. Therefore lipids are not strictly macromolecules (NCERT §9.3, pp. 108–109).
• Cellular composition (Table 9.4, p. 109). Water 70–90%, Proteins 10–15%, Carbohydrates 3%, Lipids 2%, Nucleic acids 5–7%, Ions 1% — water is the most abundant chemical in living organisms.
• Proteins. Proteins are polypeptides — linear chains of amino acids linked by peptide bonds; a heteropolymer of 20 amino-acid types (homopolymer would have one monomer repeating n times). Dietary proteins are the source of essential amino acids (those our body cannot make). Proteins carry out many functions — transport, defence, hormones, enzymes, structural support, sensory reception. Table 9.5 lists: Collagen — intercellular ground substance; Trypsin — enzyme; Insulin — hormone; Antibody — fights infectious agents; Receptor — sensory reception (smell, taste, hormone); GLUT-4 — enables glucose transport into cells. Collagen is the most abundant protein in the animal world and RuBisCO (Ribulose bisphosphate Carboxylase-Oxygenase) is the most abundant protein in the whole biosphere (NCERT §9.4, pp. 109–110).
• Polysaccharides. Long chains of sugars (literally cotton threads of monosaccharide building blocks). Cellulose is a polymeric polysaccharide consisting of only one type of monosaccharide (glucose) — a homopolymer, the structural component of plant cell walls (paper and cotton fibre are cellulosic). Starch is the plant storage variant; glycogen is the animal storage variant. Inulin is a polymer of fructose. In a glycogen chain the right end is the reducing end and the left end is the non-reducing end; it has branches (Fig. 9.2). Starch forms helical secondary structures and can hold I₂ molecules in the helical portion — starch-I₂ is blue; cellulose does not contain complex helices and hence cannot hold I₂. More complex polysaccharides have amino-sugars and chemically modified sugars (e.g. glucosamine, N-acetyl galactosamine); chitin in arthropod exoskeletons is a complex polysaccharide (NCERT §9.5, pp. 110–111).
• Nucleic acids. Polynucleotides; building block is the nucleotide with three components — (i) a heterocyclic compound (nitrogen base), (ii) a monosaccharide (pentose sugar: ribose in RNA or 2'-deoxyribose in DNA), and (iii) phosphoric acid / phosphate. Adenine and Guanine are substituted purines, while Cytosine, Uracil and Thymine are substituted pyrimidines. DNA contains deoxyribose; RNA contains ribose (NCERT §9.6, p. 111).
• Structure of proteins (four levels). (a) Primary structure — the sequence of amino acids (positional information: which is first, second, etc.). A protein is imagined as a line with the N-terminal amino acid on the left and the C-terminal amino acid on the right. (b) Secondary structure — the protein thread is folded as a helix (right-handed only) or other forms like β-pleated sheet. (c) Tertiary structure — the long protein chain folds upon itself like a hollow woollen ball, giving a 3-D view; hydrogen bonds and disulphide bonds appear; tertiary structure is absolutely necessary for many biological activities. (d) Quaternary structure — assembly of more than one polypeptide/subunit, e.g. adult human haemoglobin consists of 4 subunits — two α-type + two β-type (NCERT §9.7, pp. 111–112, Fig. 9.3).
• Enzymes — overview. Almost all enzymes are proteins; some catalytic nucleic acids are called ribozymes. Like any protein an enzyme has primary, secondary and tertiary structure; when the chain folds, many crevices/pockets are made and one such pocket is the 'active site' — a crevice into which the substrate fits. Inorganic catalysts work at high temperatures and pressures, while enzymes get damaged above ~40°C. However, enzymes isolated from thermophiles (hot vents, sulphur springs) are stable up to 80–90°C — thermal stability is an important quality (NCERT §9.8, pp. 112–113).
• Chemical reactions — rate & Q₁₀ rule. Rate (or velocity if direction is specified) = δP/δt. General rule of thumb: rate doubles or decreases by half for every 10°C change in temperature. Enzyme-catalysed reactions go vastly faster than uncatalysed; e.g. CO₂ + H₂O ⇌ H₂CO₃: without enzyme ~200 molecules form per hour; with carbonic anhydrase ~600,000 molecules per second — about 10 million times acceleration. A metabolic pathway is a multistep reaction; glucose → 2 pyruvic acid (C₆H₁₂O₆ + O₂ → 2C₃H₄O₃ + 2H₂O) proceeds through ten different enzyme-catalysed reactions (NCERT §9.8.1, pp. 113–114).
• How enzymes act — induced fit & activation energy. A substrate (S) binds the enzyme at its active site within a cleft; an ES complex forms, then a transient transition state structure, then an EP complex, finally release of product P and unchanged enzyme E. Catalytic cycle: E + S → ES → EP → E + P — substrate binding induces the enzyme to alter its shape, fitting more tightly around the substrate (induced fit); active site brings substrate bonds close enough to break/make. Enzymes lower the activation energy — the difference in average energy content of 'S' from that of its transition state (Fig. 9.4). If 'P' lies at a lower energy than 'S', the reaction is exothermic; otherwise it is endothermic (NCERT §9.8.2–9.8.3, pp. 114–115).
• Factors affecting enzyme activity. Temperature and pH — enzymes function in a narrow range; each shows highest activity at an optimum temperature and optimum pH; activity declines on either side; low temperature preserves the enzyme in a temporarily inactive state, high temperature destroys activity by denaturing the protein (Fig. 9.5a, b). Substrate concentration — velocity rises with [S] and reaches maximum velocity V_max that cannot be exceeded by further increase in [S] because enzyme molecules are saturated (Fig. 9.5c). Inhibitors — when binding of a chemical shuts off enzyme activity it is called inhibition and the chemical an inhibitor. When the inhibitor closely resembles the substrate in molecular structure it is a competitive inhibitor; malonate inhibits succinic dehydrogenase because it closely resembles substrate succinate. Competitive inhibitors are often used to control bacterial pathogens (NCERT §9.8.4, pp. 116–117).
• Six IUBMB enzyme classes (with 4–13 subclasses each, four-digit code). (1) Oxidoreductases/dehydrogenases — catalyse oxidoreduction between substrates S and S′. (2) Transferases — transfer of a group G (other than hydrogen) between S and S′. (3) Hydrolases — hydrolysis of ester, ether, peptide, glycosidic, C–C, C-halide or P–N bonds. (4) Lyases — non-hydrolytic removal of groups leaving double bonds. (5) Isomerases — interconversion of optical, geometric or positional isomers. (6) Ligases — linking together of two compounds, e.g. C–O, C–S, C–N, P–O bonds (NCERT §9.8.5, p. 117).
• Cofactors. The protein portion of enzymes that need a non-protein constituent is called the apoenzyme; non-protein constituents required for catalysis are cofactors. Three kinds: (i) Prosthetic groups — organic compounds tightly bound to the apoenzyme; e.g. haem in peroxidase and catalase (catalyse breakdown of H₂O₂ to water + O₂; haem is part of the active site). (ii) Coenzymes — organic, association with apoenzyme is transient, occurring during catalysis; coenzymes serve as cofactors in many different enzyme-catalysed reactions. Essential chemical components of many coenzymes are vitamins, e.g. NAD and NADP contain niacin. (iii) Metal ions — form coordination bonds with side chains at the active site and with the substrate; e.g. zinc is a cofactor for carboxypeptidase. Catalytic activity is lost when the cofactor is removed (NCERT §9.8.6, pp. 117–118).

2.2 Definitions to memorise

2.3 Diagrams / processes to remember

• Figure 9.1 (p. 107) — small-MW organic compounds in living tissue. Sugars (six-membered glucose C₆H₁₂O₆, five-membered ribose C₅H₁₀O₅). Amino acids (Glycine — H, Alanine — CH₃, Serine — CH₂OH on α-carbon). Fats and oils — fatty acid CH₃–(CH₂)₁₄–COOH (palmitic acid), glycerol, triglyceride (R₁, R₂, R₃ are fatty-acid chains). Phospholipid (lecithin) with phosphate and choline group. Cholesterol (steroid ring). Nitrogen bases — adenine (purine, fused 5+6 ring with NH₂), uracil (pyrimidine, 6-membered with two C=O). Nucleosides — adenosine (adenine + ribose), uridine (uracil + ribose). Nucleotide — adenylic acid (adenine + ribose + phosphate).
• Amino-acid ionisation scheme (p. 106). Three protonation states: (A) H₃N⁺–CHR–COOH, (B) H₃N⁺–CHR–COO⁻ — the zwitterionic form, (C) H₂N–CHR–COO⁻.
• Figure 9.2 (p. 110) — branched glycogen cartoon. Right end labelled reducing end; left end labelled non-reducing end; branches off the main chain.
• Figure 9.3 (p. 112) — protein structure. (a) Primary — linear amino-acid string; (b) Secondary — α-helix and β-pleated sheet; (c) Tertiary — folded 3-D ball with hydrogen and disulphide bonds shown; (d) Quaternary — multiple subunits assembled.
• Figure 9.4 (p. 115) — activation energy. Potential-energy plot vs progress of reaction with two humps: a higher hump = activation energy without enzyme; a lower hump = activation energy with enzyme; substrate S on left, product P on right (lower energy if exothermic).
• Figure 9.5 (p. 116) — enzyme activity vs (a) pH (bell), (b) Temperature (bell), (c) [S] hyperbolic rising to V_max with K_m marked at V_max/2.
• Table 9.1 (p. 105) — elemental abundance: C 0.03% (crust) vs 18.5% (body); H 0.14 vs 9.5; O 46.6 vs 65.0; Si 27.7 vs negligible.
• Table 9.4 (p. 109) — cellular composition: water 70–90%, proteins 10–15%, nucleic acids 5–7%, carbohydrates 3%, lipids 2%, ions 1%.
• Tables 9.3 (p. 108) & 9.5 (p. 109) — secondary metabolites and protein-function table (collagen, trypsin, insulin, antibody, receptor, GLUT-4).

2.4 Common confusions / NTA trap points

• Nucleoside vs nucleotide — nucleoside has base + sugar only; the phosphate makes it a nucleotide. NTA frequently swaps these.
• Most abundant protein: collagen is most abundant in animal world; RuBisCO is most abundant in the whole biosphere — distractor option usually flips the two.
• Glycogen branching ends: right end = reducing, left end = non-reducing — NCERT states this explicitly; NTA loves to invert it.
• Lipids in the acid-insoluble fraction — they sediment because cell membranes form vesicles, NOT because they are macromolecules. Lipids are not strictly macromolecules.
• Competitive inhibitor example: malonate inhibits succinic dehydrogenase (substrate = succinate). Distractors often use fumarate or oxaloacetate.
• Purines = 2 members (A, G); pyrimidines = 3 (C, U, T) — a common reversal trap.
• Haemoglobin quaternary structure: two α + two β (not 4 identical, not 2α + 2γ which is foetal Hb — and NCERT does not mention HbF).
• Cellulose vs starch with iodine: starch holds I₂ (blue colour) because of helical secondary structure; cellulose does NOT form helices and cannot hold I₂. NTA flips this.
• Right-handed helix only. In proteins, only right-handed helices are observed — left-handed helices are not natural.
• Q₁₀ rule: rate doubles for +10°C or halves for −10°C — applies in either direction.
• Cofactor terminology: prosthetic = tightly bound; coenzyme = transient binding; many students reverse this.
• NAD/NADP contain niacin, NOT thiamine or riboflavin.
• Carbonic anhydrase numbers: 200 molecules/hour uncatalysed → 600,000/second catalysed; ~10 million-fold acceleration.

2.5 Key processes / classifications