Molecular Biology (IB)

Water ($H_2O$) is essential for life due to its unique properties:

• Polarity: Uneven charge distribution ($\delta^+$ on H, $\delta^-$ on O)
• Hydrogen bonding: Between water molecules; gives water its special properties
• Cohesion: Water molecules stick together (transpiration stream, surface tension)
• High specific heat capacity: Resists temperature changes (stable habitats, thermoregulation)
• High latent heat of evaporation: Effective cooling (sweating, transpiration)
• Solvent: Dissolves polar/ionic substances (transport medium, biochemical reactions)
• Less dense as ice: Ice floats, insulating water below (aquatic life survives winter)

Monosaccharides

• General formula: $(CH_2O)_n$
• Examples: glucose ($C_6H_{12}O_6$), fructose, galactose, ribose ($C_5$)
• Quick energy source; building blocks of larger carbohydrates

Disaccharides (formed by condensation, broken by hydrolysis)

Polysaccharides

Triglycerides

• One glycerol + three fatty acids joined by ester bonds (condensation)
• Functions: energy storage (more energy per gram than carbohydrates), insulation, protection
• Saturated: no C=C double bonds; straight chains; solid at room temperature
• Unsaturated: one or more C=C double bonds; kinked chains; liquid at room temperature

Phospholipids

• Two fatty acids + one phosphate group + glycerol
• Amphipathic: hydrophilic head (phosphate), hydrophobic tails (fatty acids)
• Form the phospholipid bilayer in cell membranes

Amino Acids

• 20 different amino acids, each with: amino group ($-NH_2$), carboxyl group ($-COOH$), R-group (variable)
• Joined by peptide bonds (condensation) to form polypeptides

Levels of Structure

Functions of Proteins

Enzymes (catalysis), structural (collagen, keratin), transport (haemoglobin, membrane channels), hormones (insulin), antibodies (immune defence), muscle contraction (actin, myosin)

DNA vs RNA

DNA Replication (Semi-conservative)

1. Helicase unwinds and separates strands
2. Free nucleotides pair by complementary base pairing (A-T, C-G)
3. DNA polymerase III joins nucleotides (5'→3')
4. Leading strand: continuous. Lagging strand: Okazaki fragments joined by DNA ligase
5. Result: two identical DNA molecules, each with one old and one new strand

Transcription (nucleus)

• RNA polymerase binds to promoter; separates DNA strands
• Synthesises mRNA using the template (antisense) strand (5'→3')
• Base pairing: A→U, T→A, C→G, G→C
• In eukaryotes: introns removed (splicing), exons joined; 5' cap and poly-A tail added

Translation (ribosomes)

• mRNA binds to ribosome; start codon AUG is recognised
• tRNA molecules carry amino acids; anticodon pairs with mRNA codon
• Peptide bonds form between amino acids
• Ribosome moves along mRNA until a stop codon (UAA, UAG, UGA) is reached
• Polypeptide released and folds into functional protein

• Biological catalysts — lower activation energy
• Active site complementary to substrate → enzyme-substrate complex → products
• Induced-fit model: active site changes shape slightly upon substrate binding

Factors Affecting Enzyme Activity

• Temperature: increases rate to optimum, then denaturation
• pH: each enzyme has optimum pH; extremes denature
• Substrate concentration: rate increases then plateaus ($V_{max}$)

Inhibition

• Competitive: inhibitor binds active site; overcome by adding substrate
• Non-competitive: inhibitor binds allosteric site; changes active site shape; not overcome by substrate

• Metabolism = all enzyme-catalysed reactions in a cell
• Anabolism: building complex molecules from simpler ones (e.g., protein synthesis, photosynthesis) — requires energy
• Catabolism: breaking down complex molecules (e.g., respiration, digestion) — releases energy

Question: Explain why cellulose is suitable as a structural molecule. (3 marks)

Solution:

Cellulose is made of β-glucose monomers linked by β-1,4 glycosidic bonds. Every other glucose is flipped 180°, creating straight, unbranched chains. These chains form hydrogen bonds with adjacent chains, creating microfibrils with high tensile strength. The microfibrils are arranged in layers at different angles, giving plant cell walls rigidity and the ability to withstand turgor pressure without bursting.

• Water: polar, forms H-bonds; high specific heat capacity, excellent solvent, cohesive, less dense as ice.
• Carbohydrates: monosaccharides → disaccharides → polysaccharides (starch, glycogen, cellulose).
• Lipids: triglycerides (energy storage), phospholipids (membranes). Saturated vs unsaturated.
• Proteins: amino acids joined by peptide bonds; 4 levels of structure; diverse functions.
• Nucleic acids: DNA (double-stranded, deoxyribose, ATCG) vs RNA (single-stranded, ribose, AUCG).
• Enzymes: lower activation energy; induced-fit model; affected by temperature, pH, substrate concentration.