Biomolecules

2.1 Core concepts

• Carbohydrates are optically active polyhydroxy aldehydes/ketones or compounds that produce such units on hydrolysis; they are also called saccharides (Greek sakcharon = sugar); empirical formula often Cₓ(H₂O)ᵧ, leading to the older name "hydrates of carbon" (NCERT §10.1, p. 281-282).
• Classification on hydrolysis behaviour gives three groups: monosaccharides (cannot be hydrolysed further, ~20 known in nature, e.g. glucose, fructose, ribose, galactose), oligosaccharides (yield 2–10 monosaccharide units, e.g. disaccharides sucrose/maltose/lactose), and polysaccharides (yield many units, e.g. starch, cellulose, glycogen, gums) (NCERT §10.1.1, p. 282).
• Reducing sugars reduce Fehling's solution (Cu²⁺ → Cu₂O, red-brown) and Tollens' reagent (Ag⁺ → Ag mirror); all monosaccharides (aldose or ketose, because of tautomerism via the Lobry de Bruyn-van Ekenstein rearrangement) are reducing; sucrose is non-reducing while maltose and lactose are reducing (NCERT §10.1.1 & §10.1.3, p. 282, 287).
• Monosaccharides are sub-classified by carbon number (triose 3C, tetrose 4C, pentose 5C, hexose 6C, heptose 7C) and by functional group — aldose (–CHO) or ketose (>C=O); glucose is an aldohexose, fructose is a ketohexose, ribose is an aldopentose (NCERT §10.1.2, Table 10.1, p. 282).
• Glucose is prepared (1) commercially from starch by boiling with dilute H₂SO₄ at 393 K under 2-3 atm pressure; (2) from sucrose by boiling with dilute HCl/H₂SO₄ in alcoholic solution giving equimolar glucose + fructose (invert sugar) (NCERT §10.1.2.1, p. 282-283).
• Open-chain structure (Fischer projection) of glucose was assigned from: (a) molecular formula C₆H₁₂O₆; (b) n-hexane on prolonged heating with HI (proves straight chain of six C); (c) oxime + cyanohydrin formation (carbonyl present); (d) gluconic acid with Br₂ water (aldehydic carbonyl); (e) pentaacetate with acetic anhydride (five –OH on different C); (f) saccharic acid with HNO₃ (oxidation of both terminal carbons, primary –OH at C-6) (NCERT §10.1.2.1, p. 283-284).
• D/L notation refers to the configuration of the lowest asymmetric carbon (C-5 in glucose) relative to D-(+)-glyceraldehyde; in D-(+)-glucose the –OH on the lowest asymmetric C is on the right; D/L is unrelated to optical rotation sign (+/−), e.g., D-(−)-fructose is also a D-sugar though laevorotatory (NCERT §10.1.2.1, p. 284-285).
• Open-chain glucose fails Schiff's test, gives no NaHSO₃ addition, pentaacetate gives no oxime with hydroxylamine, and exists as α (m.p. 419 K, [α]D = +112°) and β (m.p. 423 K, [α]D = +19°) crystalline forms — facts explained only by cyclic hemiacetal formation between C-5 –OH and the C-1 –CHO giving a six-membered pyranose ring (NCERT §Cyclic Structure of Glucose, p. 285).
• α- and β-anomers of glucose differ only in configuration of the –OH at C-1 (the anomeric carbon); α has –OH on the same side as D-configuration reference (below ring in Haworth), β on the opposite side; the two cyclic forms exist in dynamic equilibrium with the open chain — basis of mutarotation (equilibrium [α]D = +52.7° starting from either crystal form); the cyclic structure is best shown by the Haworth projection (NCERT §10.1.2.1 Cyclic Structure, p. 285-286).
• Fructose (C₆H₁₂O₆) is a D-(−)-ketohexose with a keto group at C-2; it cyclises by addition of C-5 –OH to the keto group forming a five-membered furanose ring; cyclic anomers shown by Haworth structures; in free state fructose is in pyranose form, but in disaccharides like sucrose it exists as furanose (NCERT §10.1.2.2, p. 286).
• Disaccharides are joined by a glycosidic linkage (oxide bridge formed with loss of H₂O between two anomeric –OH groups, or between one anomeric –OH and another –OH); if the reducing groups of both monosaccharides are tied up in the linkage the sugar is non-reducing (sucrose), otherwise reducing (maltose, lactose) (NCERT §10.1.3, p. 287).
• Sucrose = α-D-glucose (C-1) — β-D-fructose (C-2) joined by α,β-1,2-glycosidic linkage; non-reducing because both anomeric centres are tied up; dextrorotatory ([α]D = +66.5°) but on hydrolysis gives D-(+)-glucose (+52.5°) and D-(−)-fructose (−92.4°); since fructose laevorotation dominates, the hydrolysate is overall laevorotatory and is called invert sugar (NCERT §10.1.3, p. 287).
• Maltose = two α-D-glucose units linked C-1 → C-4 (α-1,4-glycosidic); lactose (milk sugar) = β-D-galactose linked C-1 → C-4 of β-D-glucose (β-1,4); both are reducing because a free aldehyde group can be regenerated at the C-1 of the second sugar (its anomeric –OH is free) (NCERT §10.1.3, p. 287-288).
• Starch is the plant storage polysaccharide; mixture of amylose (water-soluble, 15-20%, unbranched 200-1000 α-D-(+)-glucose units linked by C1–C4 α-glycosidic bonds, gives blue colour with iodine) and amylopectin (insoluble, 80-85%, branched, C1–C4 main chain + C1–C6 branch every 20-25 units, gives violet colour with iodine) (NCERT §10.1.4, p. 288).
• Cellulose is a straight chain polymer of β-D-glucose units joined by C1–C4 β-glycosidic linkages, predominant cell-wall component of plants; humans lack cellulase and cannot digest it; glycogen ("animal starch") is highly branched like amylopectin but more so, stored in liver, muscles and brain; serves as the rapid energy reserve in animals (NCERT §10.1.4, p. 289).
• Carbohydrates serve as energy/storage molecules (starch in plants, glycogen in animals), structural materials (cellulose in cell walls, wood, cotton, chitin in insect exoskeletons), and provide D-ribose and 2-deoxy-D-ribose used in nucleic acids; also provide raw material for industries (textile, paper, sugar, food) (NCERT §10.1.5, p. 289-290).
• Proteins are polymers of α-amino acids; α-amino acids carry –NH₂ and –COOH on the same (α) carbon, with –H and an R side chain making the α-C asymmetric (except in glycine where R = H); only α-amino acids are obtained on hydrolysis of natural proteins (NCERT §10.2.1, p. 290).
• Of 20 natural amino acids, ten are essential (must come from diet because humans cannot synthesise them) — valine, leucine, isoleucine, arginine, lysine, threonine, methionine, phenylalanine, tryptophan, histidine — marked with asterisk in Table 10.2; the remaining ten (glycine, alanine, serine, cysteine, tyrosine, asparagine, glutamine, proline, aspartic acid, glutamic acid) are non-essential (NCERT §10.2.2, Table 10.2, p. 290-291).
• Amino acids are acidic (more –COOH than –NH₂, e.g., aspartic acid), basic (more –NH₂ than –COOH, e.g., lysine) or neutral (equal numbers); they exist as zwitterions/dipolar ions (–COO⁻ and –NH₃⁺ on the same molecule) in solid state and at physiological pH; amphoteric (react with both acids and bases); high-melting crystalline solids with appreciable water solubility; except glycine all are optically active (asymmetric α-C); most natural amino acids have L-configuration (NCERT §10.2.2, p. 291-292).
• Peptide linkage = amide bond (–CO–NH–) formed between –COOH of one amino acid and –NH₂ of the next, with loss of H₂O; sequence of di-, tri-, tetra-, pentapeptide, polypeptide (>10) and protein (>100 residues, molecular mass >10,000 u, e.g. insulin = 51 amino acids in two chains A and B linked by –S–S– disulphide bridges) (NCERT §10.2.3, p. 292).
• By molecular shape: fibrous proteins (parallel polypeptide chains, held by H-bonds and disulphide linkages, insoluble in water — keratin in hair/nails, myosin in muscles, collagen in connective tissue) and globular proteins (chains coiled into spherical shapes, usually water-soluble — insulin, albumins in egg/blood, haemoglobin) (NCERT §10.2.3, p. 292-293).
• Four levels of protein structure: (i) Primary — the unique sequence of amino acids linked by peptide bonds; any change destroys biological activity (e.g., sickle cell anaemia from one residue change in haemoglobin); (ii) Secondary — local shape of the polypeptide chain, two types — α-helix (right-handed coiled screw, stabilised by intramolecular H-bonds between >C=O of one residue and –NH– of the residue four units ahead) and β-pleated sheet (chains stretched out side-by-side, antiparallel, intermolecular H-bonds, like silk fibroin); (iii) Tertiary — overall 3-D folding of the entire chain, stabilised by H-bonds, disulphide linkages, van der Waals, hydrophobic and electrostatic forces — gives fibrous or globular shapes; (iv) Quaternary — spatial arrangement of two or more polypeptide sub-units (e.g., haemoglobin has four sub-units — two α and two β chains) (NCERT §10.2.3, p. 293-294).
• Denaturation = loss of biological activity on heating or change of pH (acids/bases) or addition of urea/heavy metals/organic solvents; H-bonds are disturbed, globules unfold and helix uncoils; secondary and tertiary structures are destroyed but the primary structure (sequence) remains intact — that is, the polypeptide backbone is unbroken. Examples: coagulation of egg white on boiling, curdling of milk by lactic acid produced by bacteria (NCERT §10.2.4, p. 294-295).
• Enzymes are biocatalysts; almost all are globular proteins (a few exceptions are RNA-based ribozymes); very specific for a particular substrate and reaction; usually named after the substrate with the suffix –ase (e.g. maltase hydrolyses maltose to glucose; sucrase hydrolyses sucrose; urease hydrolyses urea); they lower activation energy dramatically — sucrose hydrolysis: Ea = 6.22 kJ mol⁻¹ (acid) vs 2.15 kJ mol⁻¹ (sucrase) (NCERT §10.3 & §10.3.1, p. 295).
• Vitamins are organic compounds required in small amounts in diet whose deficiency causes specific diseases; most cannot be synthesised in the human body (gut bacteria make some vitamin K, B-complex); designated A, B, C, D, ... — "vitamine" came from Funk (1912) from vital + amine, later 'e' was dropped when it was realised many vitamins are not amines (NCERT §10.4, p. 295-296).
• Fat-soluble vitamins (A, D, E, K) dissolve in fat/oil, stored in liver and adipose tissues, deficiency develops slowly; water-soluble (B-complex and C) must be supplied regularly because they are excreted in urine and cannot be stored (except B12, which is stored in liver — uniquely among water-soluble vitamins) (NCERT §10.4.1, p. 296).
• Vitamin-deficiency table: A → xerophthalmia + night blindness; B1 (thiamine) → beri-beri; B2 (riboflavin) → cheilosis (cracking at corners of mouth); B6 (pyridoxine) → convulsions; B12 (cyanocobalamine) → pernicious anaemia; C (ascorbic acid) → scurvy (bleeding gums); D (calciferol) → rickets (children) / osteomalacia (adults); E (tocopherol) → fragile RBCs + muscular weakness; K (phylloquinone) → increased blood clotting time (NCERT §10.4.1, Table 10.3, p. 296-297).
• Nucleic acids are long-chain polymers of nucleotides (polynucleotides); two types — DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) — present in cell nucleus on chromosomes; responsible for heredity (NCERT §10.5, p. 297).
• Complete hydrolysis yields a pentose sugar, phosphoric acid and N-containing heterocyclic bases; sugar = β-D-2-deoxyribose in DNA, β-D-ribose in RNA. Bases: purines adenine (A) and guanine (G) common to both; pyrimidines cytosine (C) common to both; the fourth base is thymine (T) in DNA and uracil (U) in RNA (NCERT §10.5.1, p. 297-298).
• Nucleoside = base attached via N-glycosidic bond to C-1′ of sugar (e.g., adenosine); nucleotide = nucleoside + phosphate ester at C-5′ (e.g., adenosine monophosphate, AMP); nucleotides are joined by 3′–5′ phosphodiester linkages to give the polynucleotide chain (NCERT §10.5.2, p. 298).
• Primary structure = sequence of nucleotides; secondary structure of DNA = Watson–Crick double helix (1953) — two complementary anti-parallel strands held by H-bonds: A pairs with T via two H-bonds, G pairs with C via three H-bonds. RNA has a single-stranded helix that may fold back on itself; three RNAs — m-RNA (messenger, carries genetic code from DNA to ribosome), r-RNA (ribosomal, structural component of ribosome), t-RNA (transfer, brings amino acids to ribosome) (NCERT §10.5.2, p. 298-299).
• Biological functions: DNA is the chemical basis of heredity, self-duplicates during cell division (replication) and passes identical strands to daughter cells; RNA molecules synthesise proteins under instructions encoded in DNA — DNA → mRNA (transcription) → protein (translation); this is the central dogma of molecular biology (NCERT §10.5.3, p. 300).

2.2 Definitions to memorise

2.3 Diagrams / processes to remember

• Open-chain Fischer projection of D-(+)-glucose (p. 283-284) — aldohexose with –CHO at C-1, four asymmetric carbons C-2 to C-5, –OH at C-2/C-4/C-5 on the right and at C-3 on the left, terminal –CH₂OH at C-6; D-configuration assigned from C-5 (lowest asymmetric C).
• Oxidation products of glucose (p. 284) — gluconic acid (C-1 –CHO → –COOH only, by Br₂ water) confirms aldehyde; saccharic acid (both C-1 and C-6 oxidised to –COOH, by HNO₃) confirms primary –OH at C-6.
• Haworth pyranose structures of α- and β-D-glucose (p. 285-286) — six-membered ring with O between C-1 and C-5; α-form has C-1 –OH below the ring plane (trans to C-6 –CH₂OH), β-form has it above (cis to C-6 –CH₂OH); the C-2, C-3, C-4 –OH groups have fixed orientation.
• Open-chain structure of D-(−)-fructose and Haworth furanose structures of its α/β anomers (p. 286) — ketohexose with C=O at C-2, five-membered ring formed between C-2 and C-5; anomeric –OH at C-2 distinguishes α (below) and β (above).
• Disaccharide linkage diagrams (p. 287-288) — sucrose has α-Glc C-1 ↔ C-2 β-Fru (both anomeric carbons tied up, non-reducing); maltose has α-Glc C-1 ↔ C-4 α-Glc (one anomeric C free, reducing); lactose has β-Gal C-1 ↔ C-4 β-Glc (one anomeric C free, reducing).
• Fig. 10.1 α-Helix (p. 293) — coiled right-handed cylinder showing intramolecular H-bonds (dotted lines) between C=O of residue i and N–H of residue i+4; R-groups project outward; example in keratin.
• Fig. 10.2 β-pleated sheet (p. 293) — two anti-parallel stretched chains joined side-to-side by intermolecular H-bonds (C=O ··· H–N), giving the characteristic pleated appearance; example in silk fibroin.
• Fig. 10.3 Four-level protein structure diagram (p. 294) — schematic of primary (linear sequence), secondary (helix or sheet), tertiary (compact 3-D fold of single chain), quaternary (multiple subunits assembled, like haemoglobin's 4 chains).
• Structures of pyrimidine/purine bases (p. 298) — adenine and guanine (purines, two fused rings); cytosine, thymine, uracil (pyrimidines, single ring); thymine has methyl at C-5, uracil does not.
• Fig. 10.5 Nucleoside vs nucleotide (p. 298-299) — nucleoside = base + sugar; nucleotide = nucleoside + phosphate at C-5′; phosphate is the link that connects successive nucleotides in chains.
• Fig. 10.6 Formation of a dinucleotide by phosphodiester linkage (p. 299) — 3′-OH of one nucleotide + 5′-phosphate of next, with loss of H₂O.
• Fig. 10.7 Watson–Crick double-strand helix structure of DNA (p. 299) — two antiparallel strands wound right-handedly, sugar-phosphate backbone outside, base pairs (A=T, G≡C) inside; helical pitch 3.4 nm with 10 base pairs per turn; diameter 2 nm.

2.4 Common confusions / NTA trap points

• D/L notation does NOT indicate optical rotation: D-(+)-glucose is dextrorotatory but D-(−)-fructose is laevorotatory — the (+/−) signs are independent of D/L (p. 284).
• All monosaccharides — including ketoses like fructose — are reducing sugars (p. 282); students often think only aldoses reduce Tollens'. Fructose isomerises to glucose under basic conditions and then reduces the reagent.
• Sucrose is non-reducing because BOTH anomeric carbons are tied up in the glycosidic bond; maltose and lactose are reducing because only ONE anomeric carbon is engaged (p. 287).
• Starch contains both amylose (unbranched, water-soluble, 15-20%) and amylopectin (branched, insoluble, 80-85%); cellulose is β-linked while starch and glycogen are α-linked — humans digest α-glycosidic starch but not β-glycosidic cellulose (p. 288-289).
• Essential amino acids (10) — Val, Leu, Ile, Arg, Lys, Thr, Met, Phe, Trp, His — are marked with asterisk in Table 10.2; Gly, Ala, Ser, Tyr, Pro etc. are non-essential. Memorise the asterisked list (p. 290-291).
• During denaturation, only secondary and tertiary structures are destroyed — primary structure (amino-acid sequence) remains intact (p. 295). The peptide bonds are NOT broken.
• DNA = deoxyribose + (A, G, C, T) and double helix; RNA = ribose + (A, G, C, U) and single helix. Thymine is in DNA only; uracil is in RNA only (p. 297-299). The two strands of DNA are anti-parallel (one 5′→3′, the other 3′→5′).
• Vitamin B12 is water-soluble but unlike other water-soluble vitamins it CAN be stored in the body (specifically in the liver) (p. 296).
• Glycine is the ONLY non-chiral amino acid (R = H, no asymmetric α-C); all other natural amino acids are optically active (p. 291).
• Most natural amino acids have L-configuration (not D); D-amino acids are found only in bacterial cell walls and some antibiotics (p. 292).
• In Haworth projection of D-glucose, the C-6 –CH₂OH points UP; if you draw it down, you are looking at L-glucose. NTA traps confuse the orientation.
• Cellulose's β-1,4 linkage gives a straight chain that packs into microfibrils via H-bonding — that is why cotton, wood are strong fibres but starch is soft and digestible.