C1 - MOLECULES OF LIFE

1.1 Water

Structure of Water Molecules

• 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.

Hydrogen Bonding & Inter-Molecular Interactions

• $\delta^+$ 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).

Key Properties & Biological Importance

1. Universal / Versatile Solvent
   • Polar H₂O forms hydration shells around ions (e.g. Na⁺, Cl⁻) → dissociation & dispersion.
   • Enables biochemical reactions and transport (blood plasma, cytosol).
2. 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.
3. 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.
4. 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.
5. Maximum Density at $4^{\circ}\mathrm C$
   • Ice ($0^{\circ}\mathrm C$) < density of liquid → floats, insulating aquatic life during winter.

1.2 Carbohydrates

Overview & Classification

• Empirical formula $(CH<em>2O)</em>n$ (C:H:O = 1:2:1).
• Three main classes:
  1. Monosaccharides (1 sugar unit)
  2. Disaccharides (2 units)
  3. Polysaccharides (many units)

Monosaccharides

• General traits: sweet, water-soluble, crystallisable, reducing sugars.
• Functional groups: carbonyl (aldehyde / ketone) + multiple hydroxyls.
• Classification criteria:
  1. Carbon skeleton size
  • Trioses ($C<em>3H</em>6O_3$): glyceraldehyde (aldose), dihydroxyacetone (ketose).
  • Pentoses ($C<em>5H</em>{10}O_5$): ribose, deoxyribose (DNA lacks O at C-2).
  • Hexoses ($C<em>6H</em>{12}O_6$): 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).

Disaccharides

• 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.

Polysaccharides

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

1. 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).

2. Glycogen (animal storage)

   • Similar to amylopectin but more extensively branched (≈ every 8–12 residues).
   • Compact granules in liver & muscle; insoluble, osmotically inert.

3. 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.

1.3 Lipids

General Features

• 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.

Major Types

1. 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.

2. Phospholipids

   • Glycerol + 2 FA tails + phosphate-containing head.
   • Amphipathic → self-assemble into bilayers; fundamental to membranes.

3. Steroids

   • Four fused carbon rings + variable side chain.
   • Cholesterol, sex hormones, corticosteroids.

Structures in Detail

• Fatty acid: long hydrocarbon tail (hydrophobic) + terminal carboxyl (hydrophilic) ⇒ amphiphilic.
• Glycerol: $C<em>3H</em>8O_3$; triol able to form three ester linkages.

1.4 Proteins

Amino Acids – Basic Unit

• 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)

Levels of Protein Structure & Bonds

1. Primary (1°) – linear AA sequence; peptide bonds.
2. 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).
3. 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).
4. Quaternary (4°) – ≥2 polypeptides assemble; same bonds as 3°.
   • Examples: collagen (3 helices), hemoglobin (α₂β₂ + four hemes).

Environmental Effects

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

Peptide Synthesis & Hydrolysis

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

Protein Classification (Structure & Composition)

• 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).

1.5 Nucleic Acids (DNA & RNA)

Nucleotide – Fundamental Unit

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