Chemistry of Life

Water's properties arise from its polar covalent bonds and hydrogen bonding.

Key Properties and Biological Significance

• Carbon has 4 valence electrons → can form 4 covalent bonds
• Creates diverse molecular shapes: chains, branches, rings
• Functional groups modify properties:
  • Hydroxyl ($-OH$): polar, hydrophilic (alcohols)
  • Carboxyl ($-COOH$): acidic, releases $H^+$
  • Amino ($-NH_2$): basic, accepts $H^+$
  • Phosphate ($-PO_4$): negative charge, energy transfer (ATP)
  • Sulfhydryl ($-SH$): disulfide bridges in proteins

All macromolecules are polymers built from monomers via dehydration synthesis (releases $H_2O$) and broken by hydrolysis (consumes $H_2O$).

Carbohydrates

Monomers: Monosaccharides (glucose $C_6H_{12}O_6$, fructose, galactose, ribose)

Key Polymers:

• Starch (plants): α-glucose polymer; helical (amylose) and branched (amylopectin); energy storage
• Glycogen (animals): α-glucose; highly branched; rapid energy mobilisation from liver and muscle
• Cellulose (plants): β-glucose; straight chains with H-bonds between them forming rigid microfibrils; structural
• Chitin (arthropods/fungi): modified sugar polymer; structural exoskeleton

AP Connection: Structure determines function — α vs β linkages create dramatically different properties (storage vs structural).

Lipids

Not true polymers — assembled from smaller molecules.

Triglycerides: Glycerol + 3 fatty acids via ester bonds

• $9 \text{ kcal/g}$ (vs 4 for carbs) — efficient long-term energy storage
• Saturated: straight chains, solid at RT (animal fats)
• Unsaturated: kinked by C=C double bonds, liquid at RT (plant oils)

Phospholipids: Glycerol + 2 fatty acids + phosphate group

• Amphipathic: hydrophilic head + hydrophobic tails
• Form bilayer spontaneously in water → cell membranes

Steroids: 4 fused carbon rings

• Cholesterol: membrane fluidity buffer
• Hormones: testosterone, oestrogen, cortisol

Proteins

Monomer: 20 amino acids (central C with amino group, carboxyl group, H, and R-group)

Peptide bonds form between amino and carboxyl groups (dehydration synthesis).

Levels of Structure:

Functions: Enzymes (catalase, DNA polymerase), structural (collagen, keratin), transport (haemoglobin, channel proteins), defence (antibodies), signalling (insulin), motor (actin/myosin)

Denaturation: Loss of 3D shape (and function) due to extreme pH, temperature, or salt concentration — breaks weak bonds holding tertiary/quaternary structure.

Nucleic Acids

Monomer: Nucleotides (5-carbon sugar + phosphate group + nitrogenous base)

Base pairing: A=T (2 H-bonds), C≡G (3 H-bonds). In RNA: A=U.

Directionality: 5' → 3' (phosphodiester bonds link sugars). Strands are antiparallel.

Enzymes are protein catalysts that lower activation energy without being consumed.

• Active site is complementary to substrate (induced-fit model)
• Affected by: temperature, pH, substrate concentration, competitive/non-competitive inhibitors
• Reaction rate increases with temperature until the optimum, then drops sharply due to denaturation

• Exergonic reactions: release free energy ($\Delta G < 0$); spontaneous (e.g., cellular respiration)
• Endergonic reactions: require free energy ($\Delta G > 0$); not spontaneous (e.g., photosynthesis, protein synthesis)
• ATP couples exergonic and endergonic reactions — energy released from ATP hydrolysis drives cellular work

$ATP + H_2O \rightarrow ADP + P_i + \text{energy} \quad (\Delta G = -30.5 \text{ kJ/mol})$

Question: Explain how the structure of a phospholipid is related to its function in cell membranes. (4 points)

Solution:

A phospholipid has a hydrophilic head (polar phosphate group) and two hydrophobic tails (nonpolar fatty acid chains). This amphipathic nature causes phospholipids to spontaneously form a bilayer in aqueous environments — heads face the water on both sides while tails face inward. This creates a selectively permeable barrier: small nonpolar molecules can cross the hydrophobic core, but ions and large polar molecules cannot without transport proteins. The fluidity of the membrane (modulated by unsaturated tails and cholesterol) enables membrane protein movement and cellular processes like signalling and transport.

• Structure-function is a recurring AP theme — always connect molecular structure to biological role.
• Know the functional groups and which macromolecule classes they appear in.
• Be able to identify macromolecules from structural diagrams or chemical descriptions.
• Understand emergent properties — properties that arise from molecular interactions (e.g., hydrogen bonding → water's unique characteristics).

• Water: polar, hydrogen bonding → cohesion, high specific heat, solvent, ice floats.
• Carbohydrates: monosaccharides → polysaccharides; α-linkages = storage, β-linkages = structural.
• Lipids: triglycerides (energy), phospholipids (membranes), steroids (signalling/structure).
• Proteins: 20 amino acids → 4 levels of structure → vast functional diversity; denaturation = loss of shape/function.
• Nucleic acids: nucleotides → DNA (double helix, genetic storage) and RNA (protein synthesis).
• ATP: couples exergonic and endergonic reactions; universal energy currency.