Chapter Review

Biological Molecules

Water and Biological Importance · Carbohydrates, Lipids and Proteins · Nucleic Acids, DNA, RNA and Genes · Glycolipids and Glycoproteins

Water — Structure and Polarity

Water is a bent polar molecule (H₂O, bond angle 104.5°) with oxygen's electronegativity creating partial charges that enable hydrogen bonding.

Key Points

  • •
    Oxygen (EN 3.5) is far more electronegative than hydrogen (EN 2.1), creating a permanent dipole
  • •
    Bent geometry (not linear) prevents dipoles from cancelling — two lone pairs on oxygen
  • •
    Partial negative charge (δ⁻) on oxygen, partial positive charges (δ⁺) on hydrogens
  • •
    Polarity underlies all of water's unique biological properties

Hydrogen Bonding, Cohesion and Adhesion

Water molecules attract each other via hydrogen bonds (up to 4 per molecule), collectively giving water high surface tension, cohesion, and enabling capillary action.

Key Points

  • •
    Each water molecule can form up to 4 hydrogen bonds — 2 through H atoms, 2 through O lone pairs
  • •
    Individual H-bonds are weak (~20 kJ/mol) but billions together create strong collective effects
  • •
    Cohesion: water-water attraction → surface tension, droplet formation
  • •
    Adhesion: water-surface attraction → water climbs xylem vessel walls
  • •
    Capillary action = cohesion + adhesion working together
Formula

Water as Solvent and Heat Buffer

Water dissolves polar/ionic substances (universal solvent) and has high specific heat capacity and heat of vaporization, making it a temperature stabilizer for organisms.

Key Points

  • •
    Dissolves ionic compounds (NaCl → Na⁺ + Cl⁻), polar molecules, and gases; insoluble: nonpolar fats/oils
  • •
    Specific heat capacity = 1.0 cal/g°C — absorbed energy breaks H-bonds, not kinetic energy
  • •
    Heat of vaporization = 574 kcal/kg — evaporation of 2 ml from 1 L cools remainder by ~1°C
  • •
    Transpiration (plants) and perspiration (animals) exploit evaporative cooling
  • •
    All enzymes and cellular reactions require aqueous media
Formula

Ionization of Water

Water self-ionizes reversibly to produce equal concentrations of H⁺ and OH⁻ at 25°C (10⁻⁷ mol/L each), establishing the pH scale fundamental to biochemistry.

Key Points

  • •
    H₂O ⇌ H⁺ + OH⁻ — reversible equilibrium producing ions continuously
  • •
    In pure water at 25°C: H⁺ = OH⁻ = 10⁻⁷ mol/L, pH = 7
  • •
    Ion product: Kw = H⁺ × OH⁻ = 10⁻¹⁴ (at 25°C)
  • •
    pH scale: 0–14; below 7 acidic, 7 neutral, above 7 basic
  • •
    Water also serves as reactant in hydrolysis and photosynthesis; as lubricant, cushion, and shock absorber
Formula

Carbohydrates — Classification and Saccharides

Carbohydrates (Cₓ(H₂O)ᵧ) are polyhydroxy aldehydes or ketones classified into monosaccharides, oligosaccharides, and polysaccharides based on chain length.

Key Points

  • •
    General formula Cₓ(H₂O)ᵧ where x ≥ 3 (triose minimum); H:O ratio same as water
  • •
    Monosaccharides: trioses (3C) to heptoses (7C); aldoses (aldehyde) vs ketoses (keto group)
  • •
    Pentoses form 5-membered rings (furanose, e.g., ribose); hexoses form 6-membered rings (pyranose, e.g., glucose)
  • •
    Disaccharides: maltose (Glc+Glc), sucrose (Glc+Fru), lactose (Glc+Gal) — joined by glycosidic bonds (dehydration)
  • •
    Polysaccharides: starch (blue + iodine), glycogen/red + iodine, animal starch), cellulose (no colour + iodine, indigestible by humans)
Formula

Lipids — Fatty Acids and Phospholipids

Lipids are hydrophobic compounds (insoluble in water, soluble in organic solvents) that store more energy per gram than carbohydrates and form membrane structures.

Key Points

  • •
    Defined by solubility, not structure — includes fats, oils, waxes, phospholipids, terpenoids, steroids
  • •
    Triglycerides: glycerol + 3 fatty acids → 3 ester bonds + 3 H₂O released
  • •
    Fatty acids have even-numbered carbons (2–30); saturated (no double bonds, solid) vs unsaturated (double bonds, liquid)
  • •
    Longer chain → higher melting point; more double bonds → lower melting point
  • •
    Phospholipids: glycerol + 2 fatty acids + phosphate + nitrogenous base → amphipathic (hydrophilic head, hydrophobic tail) → membrane building blocks
  • •
    Waxes (C₂₅–C₃₅ alkanes): waterproof coatings on leaves, fruits, insect exoskeletons
Formula

Proteins — Structure and Levels

Proteins are polymers of 20 amino acids linked by peptide bonds, folding into four structural levels that determine their diverse functions.

Key Points

  • •
    Amino acids: amino group (—NH₂) + carboxyl group (—COOH) + H + variable R group on alpha carbon
  • •
    Peptide bond: condensation between carboxyl of one AA and amino of another; n amino acids → (n−1) peptide bonds
  • •
    Primary: linear amino acid sequence (determined by DNA); single substitution can cause disease (sickle cell)
  • •
    Secondary: α-helix (3.6 AA/turn, H-bonds) and β-pleated sheet (folding back, H-bonds)
  • •
    Tertiary: compact globular shape — stabilised by ionic, hydrogen, and disulphide (—S—S—) bonds; hydrophobic residues inside
  • •
    Quaternary: multiple polypeptide subunits held together (e.g., haemoglobin: 2α + 2β chains)
Formula

Protein Classification and Functions

Proteins are classified as fibrous (structural, secondary structure dominant) or globular (functional, tertiary structure dominant) and perform virtually every cellular process.

Key Points

  • •
    Fibrous: elongated fibrils, insoluble, elastic, structural roles — keratin, myosin, fibrin, silk
  • •
    Globular: spherical, soluble, crystallisable, functional roles — enzymes, antibodies, hormones, haemoglobin
  • •
    Functions: structural, enzymatic (all enzymes are proteins), hormonal, transport (Hb), defense (antibodies), clotting (fibrin), movement (myosin)
  • •
    Proteins comprise >50% of total cellular dry weight — most abundant organic compounds in cells

Nucleotides and DNA Structure

DNA is a double helix of antiparallel polynucleotide strands with complementary base pairing (A=T, G≡C), storing genetic information in the nucleus.

Key Points

  • •
    Nucleotide = pentose sugar + nitrogenous base + phosphate; nucleoside = sugar + base (no phosphate)
  • •
    DNA sugar: deoxyribose (no OH at C-2); bases: A, G, C, T
  • •
    Antiparallel strands: one 5'→3', other 3'→5'; linked by phosphodiester bonds
  • •
    A=T via 2 H-bonds; G≡C via 3 H-bonds (GC-rich regions are more thermally stable)
  • •
    1 helix turn = 34 Å ≈ 10 base pairs; discovered by Watson & Crick (1953), built on Chargaff's rule and Franklin's X-ray data
  • •
    DNA amount is species-specific; germ cells contain half the DNA of somatic cells
Formula

RNA Types and Genes

RNA is single-stranded (uses uracil instead of thymine, ribose sugar) and exists in three types — mRNA, tRNA, and rRNA — each essential for protein synthesis. A gene is a DNA segment coding for a polypeptide.

Key Points

  • •
    mRNA (3–4% of RNA): carries genetic code from DNA to ribosomes; length = amino acids × 3 nucleotides
  • •
    tRNA (10–20%): 75–90 nucleotides; transfers amino acids to ribosome; one specific tRNA per amino acid
  • •
    rRNA (~80%): most abundant; structural + catalytic core of ribosomes
  • •
    Gene: segment of DNA coding for a specific polypeptide (E. coli: 4,639,221 bp → 4,288 genes)
  • •
    DNA vs RNA: deoxyribose/ribose, double/single-stranded, T/U, nucleus/cytoplasm, store/express info
Formula

Glycolipids and Glycoproteins

Conjugated molecules formed by covalently attaching carbohydrate chains to proteins (glycoproteins) or lipids (glycolipids), serving as cell recognition markers and structural components.

Key Points

  • •
    Glycoproteins: oligosaccharide + protein; O-linked (serine/threonine) or N-linked (asparagine) glycosylation
  • •
    Glycolipids: oligosaccharide + sphingolipid; anchored in membrane with sugar chain projecting outward
  • •
    Glycolipids found exclusively on the outer (extracellular) leaflet of the plasma membrane
  • •
    Glycocalyx: sugar-rich coat formed by both glycoproteins and glycolipids on cell surface — enables cell recognition
  • •
    Three roles: (1) membrane components for recognition/adhesion, (2) structural in animal extracellular matrix, (3) structural in bacterial cell wall

Formulas

Specific Heat Capacity of Water

Heat energy for temperature change of water; c = 1.0 cal/g°C

Heat of Vaporization of Water

Heat absorbed during evaporation; Hv = 574 kcal/kg

Ion Product of Water

Relates [H⁺] and [OH⁻] at 25°C

pH Formula

Calculate pH from hydrogen ion concentration

Complementary Base Pairing

A pairs with T (2 H-bonds); G pairs with C (3 H-bonds)

Chargaff's Rule

In DNA: A = T, G = C, and all bases sum to 100%

mRNA Length from Amino Acids

Each amino acid needs 3 nucleotides on mRNA

Peptide Bond Count

n amino acids produce (n−1) peptide bonds and release (n−1) water molecules

Triacylglycerol Formation

Glycerol + 3 fatty acids form triacylglycerol with 3 ester bonds, releasing 3 H₂O