C1 - MOLECULES OF LIFE

1.1 Water

Composed of 1 O + 2 H atoms.
Atoms linked by covalent bonds; bond angle spreads 104.5^{\circ}.
Oxygen is more electronegative → polar molecule (no net charge but unequal e⁻ distribution).
- O atom carries partial \delta^-, each H carries partial \delta^+.
Each molecule can form up to 4 H-bonds with neighbours.

\delta^+ H of one molecule attracts \delta^- O of another ⇒ hydrogen bond (weaker than covalent, yet strong enough to hold water together).
Consequences of polarity:
- Attracts ions/polar solutes (hydrophilic; e.g. NaCl, sugars).
- Repels non-polar solutes (hydrophobic; e.g. oils).

Universal / Versatile Solvent
- Polar H₂O forms hydration shells around ions (e.g. Na⁺, Cl⁻) → dissociation & dispersion.
- Enables biochemical reactions and transport (blood plasma, cytosol).
High Specific Heat Capacity
- Defined as heat (cal) needed to raise 1\,\mathrm g of H₂O by 1^{\circ}\mathrm C.
- Large energy input → small \Delta T.
- Buffers cellular & ocean temperatures; stabilises climate & internal homeostasis.
High Latent Heat of Vaporisation
- Heat required to convert 1\,\mathrm g liquid → gas.
- Evaporative cooling (sweating, panting, bathing) removes large amounts of heat with minimal H₂O loss.
Cohesion & Adhesion
- Cohesion = H₂O–H₂O H-bonds → surface tension (pond-skaters, mosquito larvae).
- Adhesion = H₂O attracted to other polar surfaces (xylem walls) → assists capillary rise; combined with cohesion drives transpiration stream.
Maximum Density at 4^{\circ}\mathrm C
- Ice (0^{\circ}\mathrm C) < density of liquid → floats, insulating aquatic life during winter.

Empirical formula (CH2O)n (C:H:O = 1:2:1).
Three main classes:
1. Monosaccharides (1 sugar unit)
2. Disaccharides (2 units)
3. Polysaccharides (many units)

General traits: sweet, water-soluble, crystallisable, reducing sugars.
Functional groups: carbonyl (aldehyde / ketone) + multiple hydroxyls.
Classification criteria:
1. Carbon skeleton size
- Trioses (C3H6O_3): glyceraldehyde (aldose), dihydroxyacetone (ketose).
- Pentoses (C5H{10}O_5): ribose, deoxyribose (DNA lacks O at C-2).
- Hexoses (C6H{12}O_6): glucose (aldose), fructose (ketose), galactose.
1. Position of carbonyl
- Aldoses – carbonyl at chain end (e.g. glucose).
- Ketoses – carbonyl internal (e.g. fructose).
Ring forms of glucose: α-glucose (−OH at C-1 below plane) vs β-glucose (−OH above).
Biological roles: immediate energy, precursors for larger carbs, structural components (ribose/deoxyribose in nucleotides, RuBP in photosynthesis).

Formed via condensation (dehydration) → glycosidic linkage; broken by hydrolysis.
Common examples:
- Maltose = α-glucose + α-glucose (α-1→4 bond). Found in germinating barley; brewing.
- Sucrose = α-glucose + β-fructose.
- Lactose = β-galactose + α-glucose.
Formation of maltose: \text{α-Glu} + \text{α-Glu} \xrightarrow[-H_2O]{\text{condensation}} \text{Maltose}; breakdown reverse.

General properties: insoluble, colloidal, tasteless, non-crystallisable.

Starch (plant storage)
- Polymer of α-glucose.
- Linkages: α-1→4 (linear) & α-1→6 (branch points).
- Two fractions:
  • Amylose – unbranched helix, 200–1500 residues, only α-1→4.
  • Amylopectin – branched every 25–30 residues (α-1→6).
Glycogen (animal storage)
- Similar to amylopectin but more extensively branched (≈ every 8–12 residues).
- Compact granules in liver & muscle; insoluble, osmotically inert.
Cellulose (plant structural)
- Linear β-glucose polymer with β-1→4 linkages.
- Parallel chains H-bond → microfibrils → fibers (high tensile strength in cell walls).
- Indigestible to humans (lack cellulase); ruminants utilise symbiotic microbes.

Contain C, H, O; hydrophobic due to long non-polar C–H chains.
Not true polymers; diverse structures.
Functions: energy storage (alt to carbs), membrane components, insulation (blubber), vitamin transport, precursors of flavour/odour compounds.

Triglycerides (fats & oils)
- 1 glycerol + 3 fatty acids linked by ester bonds (formed by condensation → release 3 H₂O).
- Hydrolysis (lipase) regenerates glycerol + 3 FAs.
- Fat vs Oil determined by FA saturation:
  • Saturated FA: no C=C, straight chains → tight packing, solid at \sim 20^{\circ}\mathrm C (e.g. stearic, palmitic).
  • Unsaturated FA: ≥1 C=C (cis) → kinks, loose packing, liquid (e.g. oleic). Classified as mono- or poly-unsaturated.
Phospholipids
- Glycerol + 2 FA tails + phosphate-containing head.
- Amphipathic → self-assemble into bilayers; fundamental to membranes.
Steroids
- Four fused carbon rings + variable side chain.
- Cholesterol, sex hormones, corticosteroids.

Fatty acid: long hydrocarbon tail (hydrophobic) + terminal carboxyl (hydrophilic) ⇒ amphiphilic.
Glycerol: C3H8O_3; triol able to form three ester linkages.

General formula: central α-C bonded to H, NH₂, COOH, R (side chain).
At physiological pH (~7.4) exist as zwitterions ((^+NH_3) and (^-COO)().
Grouped by R-group properties:
1. Non-polar (hydrophobic)
2. Polar uncharged (hydrophilic)
3. Acidic (−COOH in R)
4. Basic (−NH₂ in R)

Primary (1°) – linear AA sequence; peptide bonds.
Secondary (2°) – regular coils/folds stabilised by H-bonds along backbone:
- α-helix (every 4th AA; e.g. keratin).
- β-pleated sheet (parallel strands; e.g. fibroin).
Tertiary (3°) – 3-D folding via side-chain interactions:
- Hydrophobic & van der Waals, H-bonds, ionic bonds, disulfide bridges (cys-cys).
- Example: myoglobin (single chain + heme).
Quaternary (4°) – ≥2 polypeptides assemble; same bonds as 3°.
- Examples: collagen (3 helices), hemoglobin (α₂β₂ + four hemes).

Temperature >40^{\circ}\mathrm C & extreme pH disrupt non-covalent bonds → denaturation (loss of function). Sometimes reversible (renaturation).

Condensation: \text{AA}1 + \text{AA}2 \to \text{Dipeptide} + H_2O (peptide bond C-N forms).
Hydrolysis: reverse reaction, adding H₂O.

Fibrous – long, tough, insoluble; mainly 2°; structural (keratin, collagen).
Globular – compact, soluble, functional (enzymes, antibodies, hormones).
Conjugated – protein + prosthetic group (e.g. hemoglobin’s heme, glycoproteins).

Components joined by condensation:
1. Pentose sugar – ribose (RNA) or deoxyribose (DNA; lacks O at C-2).