Biomolecules

Monosaccharides are the simplest carbohydrates that cannot be hydrolysed into simpler carbohydrate units. Key features: • General formula: (CH₂O)n where n = 3 to 7 • Named as trioses (n=3), tetroses (n=4), pentoses (n=5), hexoses (n=6), heptoses (n=7) • Further classified as aldoses (contain –CHO, aldehyde group) or ketoses (contain –C=O, keto group) Examples: • Glucose (C₆H₁₂O₆) — aldohexose • Fructose (C₆H₁₂O₆) — ketohexose (isomer of glucose) • Ribose (C₅H₁₀O₅) — aldopentose (in RNA) • Deoxyribose — aldopentose (in DNA) • Galactose — aldohexose (in lactose) Monosaccharides are the building blocks (monomers) of all complex carbohydrates.

Reducing sugars are carbohydrates that can reduce mild oxidising agents such as Fehling's solution (Cu²⁺) or Tollens' reagent (Ag⁺). Structural basis: A sugar is a reducing sugar if it has a free aldehyde group (–CHO) or a free ketone group (–C=O) that is in equilibrium with an open chain form. In practice: reducing sugars have a free anomeric –OH (hemiacetal or hemiketal), which can open to reveal the carbonyl group. Examples of reducing sugars: • All monosaccharides: glucose, fructose, galactose, ribose (all reduce Fehling's/Tollens') • Disaccharides with free anomeric –OH: maltose, lactose Examples of non-reducing sugars: • Sucrose (table sugar): no free –OH at anomeric carbon; both anomeric C atoms are involved in the glycosidic bond → cannot open to free aldehyde/ketone • Trehalose Test: Reducing sugars give brick-red precipitate with Fehling's solution and silver mirror with Tollens' reagent.

α-glucose and β-glucose are anomers — they differ only in the configuration at C-1 (the anomeric carbon). Difference 1 — Position of –OH at C-1: • α-glucose: –OH at C-1 is on the same side as –OH at C-6 in Fischer projection (axial in Haworth; in cyclic form, –OH at C-1 is downward) • β-glucose: –OH at C-1 is on the opposite side from –OH at C-6 (equatorial; –OH at C-1 is upward in Haworth projection) Difference 2 — Optical rotation: • α-glucose: [α]D = +112.2° (in freshly prepared solution) • β-glucose: [α]D = +18.7° Both reach equilibrium optical rotation of +52.7° (mutarotation) Difference 3 — Melting point: • α-glucose: m.p. = 146°C • β-glucose: m.p. = 150°C

Glycogen is the storage polysaccharide of glucose in animals (and fungi), sometimes called 'animal starch.' Structure: • Made of α-glucose units linked by α(1→4) glycosidic bonds (linear portion) • Highly branched: branches occur via α(1→6) glycosidic bonds every 8–10 glucose units Storage: Found mainly in liver and muscle cells. Differences from Starch: | Feature | Starch | Glycogen | |---|---|---| | Found in | Plants | Animals | | Components | Amylose (linear) + Amylopectin (branched) | Single highly branched polymer | | Branching | Amylopectin: every 25–30 units | Every 8–10 units (more branched) | | Colour with I₂ | Blue-black (amylose) | Reddish-brown | | Molecular weight | Lower | Much higher | Both are polymers of α-glucose and serve as energy storage, but glycogen is more extensively branched than amylopectin (the branched component of starch).

(i) Sucrose: Sucrose + H₂O → (acid or enzyme sucrase/invertase) → Glucose + Fructose Details: • Sucrose = α-D-glucose + β-D-fructose linked by α,β(1→2) glycosidic bond • Sucrose is a non-reducing sugar (no free anomeric –OH) • After hydrolysis, the mixture of glucose and fructose is called 'invert sugar' because the optical rotation changes from dextrorotatory (+) to levorotatory (–) (ii) Lactose: Lactose + H₂O → (acid or enzyme lactase) → Glucose + Galactose Details: • Lactose = β-D-galactose + D-glucose linked by β(1→4) glycosidic bond • Lactose is a reducing sugar (glucose unit has free anomeric –OH) • Found in milk; lactase deficiency causes lactose intolerance

Nucleoside: • A compound consisting of a nitrogenous base + a sugar (pentose) • Sugar is ribose (in RNA) or deoxyribose (in DNA) • No phosphate group • Example: Adenosine = Adenine + Ribose; Thymidine = Thymine + Deoxyribose Nucleotide: • A compound consisting of a nitrogenous base + a sugar + one or more phosphate groups • Nucleotide = Nucleoside + Phosphate • Example: Adenosine monophosphate (AMP) = Adenosine + Phosphate Relationship: Nucleoside + Phosphoric acid → Nucleotide Importance: • Nucleotides are the monomers of DNA and RNA • ATP (adenosine triphosphate) is a nucleotide and the primary energy currency of cells • Nucleosides are used in some antiviral drugs (e.g., AZT, a nucleoside analogue)

Secondary structure of proteins refers to the local folding of the polypeptide chain due to hydrogen bonding between amide groups (–CO–NH–). Two main types: 1. α-Helix: • The polypeptide chain coils into a right-handed helical structure • Hydrogen bonds form between the –C=O of one peptide bond and the –N–H of the peptide bond 4 residues ahead • All R groups (side chains) point outward • Stabilised by intramolecular hydrogen bonds • Example: Found in hair keratin, myoglobin 2. β-Pleated Sheet (β-sheet): • The polypeptide chains are almost fully extended and arranged side by side • Hydrogen bonds form between –C=O and –N–H groups on adjacent strands (intermolecular) • Chains can run parallel or antiparallel • R groups alternate above and below the sheet • Example: Found in silk fibroin Both structures are maintained primarily by hydrogen bonds between backbone atoms.

Vitamins are organic compounds required in small amounts in the diet for normal growth, metabolism, and health. They are not synthesised by the body (or in insufficient amounts). Classification: Fat-soluble vitamins (stored in body fat): • Vitamin A (Retinol): vision, immune function, skin health. Deficiency: night blindness, xerophthalmia • Vitamin D (Calciferol): calcium absorption, bone formation. Deficiency: rickets (children), osteomalacia • Vitamin E (Tocopherol): antioxidant, cell membrane integrity. Deficiency: haemolytic anaemia • Vitamin K (Phylloquinone): blood clotting. Deficiency: excessive bleeding Water-soluble vitamins (not stored, must be regularly consumed): • Vitamin B₁ (Thiamine): carbohydrate metabolism. Deficiency: beriberi • Vitamin B₂ (Riboflavin): energy metabolism, vision. Deficiency: ariboflavinosis • Vitamin B₃ (Niacin): energy metabolism. Deficiency: pellagra • Vitamin B₆ (Pyridoxine): amino acid metabolism. Deficiency: anaemia, dermatitis • Vitamin B₁₂ (Cobalamin): red blood cell formation, nerve function. Deficiency: pernicious anaemia • Vitamin C (Ascorbic acid): antioxidant, collagen synthesis, immune function. Deficiency: scurvy • Folic acid: DNA synthesis, cell division. Deficiency: neural tube defects, megaloblastic anaemia

Enzymes are biological catalysts — proteins (mostly) that speed up biochemical reactions without being consumed in the process. Key properties: • Highly specific (one enzyme, one reaction — 'lock and key' or 'induced fit' model) • Extremely efficient — increase reaction rates by 10⁶–10¹² times • Work under mild conditions (physiological T, pH) • Each enzyme has an optimal pH and temperature Mechanism of Action: 1. The enzyme has an active site — a specific region with a shape complementary to the substrate. 2. The substrate (reactant) binds to the active site, forming an enzyme-substrate (E-S) complex: E + S ⇌ E–S complex 3. At the active site, the substrate is stressed, distorted, or positioned optimally to lower the activation energy. 4. The substrate is converted to product(s) and released: E–S → E + P 5. The enzyme is regenerated and can catalyse another reaction. Models of enzyme action: • Lock and key model: Substrate fits exactly into the rigid active site • Induced fit model (Koshland): Active site changes shape to fit the substrate (more accurate) Factors affecting enzyme activity: temperature, pH, substrate concentration, inhibitors, cofactors.

Denaturation is the process by which a protein loses its three-dimensional (native) structure and biological activity without breaking the peptide bonds (primary structure is intact). Causes of denaturation: • High temperature (heat) • Extreme pH (strong acid or base) • Heavy metal ions (Hg²⁺, Pb²⁺) • Organic solvents (ethanol, acetone) • Urea (in high concentration) • Detergents What happens during denaturation: 1. Hydrogen bonds that stabilise α-helices and β-sheets break 2. Disulfide bridges (if any) may or may not break 3. Hydrophobic interactions are disrupted 4. The polypeptide chain unfolds from its compact, organised structure to a random coil 5. The active site (for enzymes) is disrupted → loss of biological activity 6. Protein may precipitate (become insoluble) Examples: • Coagulation of egg white on heating (albumin denatures) • Curdling of milk on adding acid • Sterilisation by heat kills bacteria by denaturing their enzymes Renaturation: In some cases, if denaturing agent is removed gently, the protein can refold into its native structure (renaturation). This shows the native structure is determined by the primary sequence (Anfinsen's experiment).