Lesson 5: Molecules of Life

This lesson covers Theme A — molecules of life (SL and HL): water, carbohydrates, lipids and proteins. The IB skill here is drawing and recognising structures and connecting molecular properties to biological roles — hydrogen bonding explains water's behaviour; condensation reactions build every polymer in the syllabus.

Water: the medium of life

Water is a polar molecule: oxygen carries a partial negative charge, the hydrogens partial positive charges, so hydrogen bonds form between molecules. From this single fact flow the properties examiners test:

• Cohesion — water molecules stick to each other (surface tension; continuous water columns in xylem).
• Adhesion — water sticks to other polar surfaces (capillary action in xylem walls and soil).
• Solvent properties — ionic and polar substances dissolve; most metabolic reactions occur in aqueous solution, and blood plasma, cytoplasm and xylem sap transport dissolved substances.
• High specific heat capacity — large thermal buffer; stabilises aquatic environments and body temperature.
• High latent heat of vaporisation — evaporation cools (sweating, transpiration).
• Buoyancy, transparency and thermal conductivity are also listed in the new guide — relevant to aquatic habitats (e.g. why black-throated loons or seals use water for support) and to light penetration for photosynthesis.

Water is also a reactant/product in metabolism: hydrolysis reactions consume water; condensation reactions release it.

Carbohydrates

Monosaccharides (glucose, ribose, fructose) are single sugars; condensation joins them with glycosidic bonds, releasing water, to form disaccharides (maltose, lactose, sucrose) and polysaccharides. Glucose is drawn as a ring (α or β at carbon 1). The α/β difference is examinable: starch (amylose and amylopectin) is built from α-glucose — helical, compact, ideal for energy storage in plants; cellulose is built from β-glucose with every second monomer inverted, giving straight chains that hydrogen-bond into microfibrils — strong, ideal for cell walls, and indigestible to most animals. Glycogen is the animal storage polymer, like amylopectin but more branched, allowing rapid release. Worked reasoning: storage polysaccharides are insoluble and do not affect water potential — note the direct link to the osmosis lesson.

Lipids

Triglycerides form by condensation of glycerol with three fatty acids (ester bonds). Fatty acids may be saturated (no C=C bonds; straight chains pack tightly; solid fats) or unsaturated (C=C bonds cause bends; oils). *Cis* unsaturated fatty acids have hydrogens on the same side of the double bond (natural, bent); *trans* forms (from industrial hydrogenation) are straighter and associated with increased coronary heart disease risk — a good evaluation topic. Lipids are energy stores: they yield roughly twice the energy per gram of carbohydrates (≈37 kJ g⁻¹ vs ≈17 kJ g⁻¹) because they are more reduced, and they are stored without associated water. Other roles: phospholipids (membranes), insulation (blubber, myelin), buoyancy, waterproofing (waxy cuticles), and steroid hormones (testosterone, oestrogen share the four-ring structure). Health evaluation: epidemiological evidence links saturated and trans fat intake with CHD, but correlation is not causation — examiners reward answers that mention confounding variables (overall diet, smoking, genetics) and that distinguish evidence types (population studies vs controlled trials).

Proteins and amino acids

Amino acids share a common structure: a central carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and a variable R group — 20 standard amino acids differ only in R. Condensation between the amino group of one and the carboxyl group of another forms a peptide bond and a dipeptide; chains are polypeptides. Protein structure has four levels: primary (sequence), secondary (α-helices and β-pleated sheets held by hydrogen bonds), tertiary (folding by interactions between R groups — hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges), and quaternary (multiple polypeptides, sometimes with prosthetic groups, e.g. haemoglobin's haem groups). Denaturation — by heat or pH extremes — breaks the weaker bonds of tertiary structure (not peptide bonds), destroying shape and function without changing the sequence. Protein functions to exemplify: enzymes (amylase), hormones (insulin), antibodies/immunoglobulins, transport (haemoglobin), structure (collagen, keratin), movement (actin/myosin), and membrane receptors and channels. HL adds: the proteome — the full set of proteins a cell produces, unique to each cell type and individual, unlike the genome.

Worked data: energy content

A bomb calorimeter gives: glucose oxidation ≈ 15.6 kJ g⁻¹; a typical fat ≈ 39 kJ g⁻¹; protein ≈ 17 kJ g⁻¹ (but protein is rarely a primary fuel). Question style: an athlete stores 1 kg of energy reserve — as fat this is ~0.44 kg of pure triglyceride equivalent energy vs ~1.1 kg as glycogen (plus glycogen binds ~2 g water per gram, making the real mass penalty larger). This is the quantitative argument for why migrating birds store fat, not carbohydrate.

Nature of Science

Our knowledge of these molecules came from analytical chemistry applied to biology — a reductionist approach. TOK follows naturally: reductionism explains much, but properties such as the behaviour of water in a living cell or the function of a protein in a pathway are emergent — more than the sum of molecular facts. Strong TOK essays keep both truths in view.

Common mistakes (from examiner reports)

• Writing that condensation "joins molecules using water" (it *releases* water; hydrolysis uses it).
• Saying hydrogen bonds are strong, or that they hold the two strands of a water molecule together (bonds *within* water are covalent).
• Claiming fats contain more energy "because they have more bonds" — the reason is their hydrogen-rich, highly reduced carbon chains.
• Stating denaturation breaks peptide bonds.

IB Exam Experience

Paper 1 style. 1. Which reaction joins two amino acids, and what is released? A. Hydrolysis; water B. Condensation; water C. Condensation; oxygen D. Hydrolysis; carbon dioxide 2. Cellulose is strong because its chains are… A. branched and coiled B. straight and hydrogen-bonded into microfibrils C. saturated D. dissolved in water 3. Which property of water results from hydrogen bonding and helps cool mammals by sweating? A. Transparency B. High specific heat capacity C. High latent heat of vaporisation D. Buoyancy Answer key. 1 — B. 2 — B. 3 — C (evaporating sweat absorbs much heat energy per gram). Paper 2 style. (a) Outline how a triglyceride is formed. [3] (b) Explain why lipids are a better long-term energy store than carbohydrates for a migrating bird. [3] (c) State two functions of proteins in the human body, giving a named example for each. [2] *Marking notes.* (a) Glycerol + three fatty acids [1]; condensation reactions form ester bonds [1]; water released (one per bond, three total) [1]. (b) Lipids store ~twice the energy per gram [1]; stored without water, so less mass to carry in flight [1]; insoluble/inert so they do not affect water potential [1]. (c) Any two: enzyme (amylase), hormone (insulin), transport (haemoglobin), immunity (immunoglobulin), structure (collagen) [1 each]. IA idea. Compare the energy content of foods (e.g. nuts vs crisps) by calorimetry — burn a measured mass under a fixed volume of water, calculate energy per gram, and evaluate heat losses against database values.

Extended data: testing for the molecules — Benedict's, iodine, biuret, emulsion

The course's food tests are data generators for Paper 2 and the IA. Iodine turns blue-black with starch (amylose coils trap iodine); Benedict's reagent (heated, alkaline copper sulfate) is reduced by reducing sugars to form a brick-red precipitate through a colour scale — blue → green → yellow → orange → red — semi-quantitative if standards are used; non-reducing sugars (sucrose) need acid hydrolysis first, then neutralisation, then retesting. Biuret (sodium hydroxide + copper sulfate) turns lilac/violet with peptide bonds. The ethanol emulsion test for lipids: dissolve the sample in ethanol, add water — a milky emulsion of lipid droplets forms. Worked semi-quantitative drill: Benedict's colour standards for glucose at 0, 0.1, 0.5, 1.0 and 2.0% give a calibration you can match an unknown against (a colorimeter reading absorbance at ~540 nm converts "orange-ish" into a defensible estimate between standards). Evaluations examiners reward: heating time and temperature held constant, excess Benedict's so reagent is never limiting, and the admission that Benedict's measures *reducing power* — different sugars reduce at different rates, so comparisons are estimates, not exact concentrations.

Why ice floats, and other quantitative consequences of hydrogen bonding

Water expands on freezing because hydrogen bonds lock molecules into an open lattice: ice has a density of ~0.917 g cm⁻³ versus 1.000 for liquid water at 4 °C. The biological consequences cascade: lakes freeze from the surface down, the ice insulates the water below, aquatic life overwinters, and spring turnover mixes nutrients. Anomalous expansion is also why unprotected cells are destroyed by internal ice crystals — and why many organisms evolved antifreeze glycoproteins or accumulate glycerol/sugars (colligative protection), and why laboratories store cells in glycerol or DMSO. Pair this with specific heat data: warming 1 kg of water by 10 °C takes 41.8 kJ — about five times the energy needed for the same mass of dry soil — which is the quantitative core of "water buffers temperature" answers: always give the number, not just the adjective.

One more application: collagen, scurvy and the chemistry of a deficiency disease

Collagen, the body's commonest protein, is a triple helix of polypeptides rich in glycine and proline; its strength depends on hydroxylation of proline residues, a modification that requires vitamin C as a cofactor. Without it (scurvy), collagen is weak: gums bleed, wounds reopen, capillaries leak — a whole-body disease from one missing step in one protein's maturation. The case knits this lesson together: amino acid sequence (primary structure) → helix (secondary) → triple helix assembly (quaternary) → tissue function → deficiency phenotype. It also pairs with the enzymes story (prolyl hydroxylase is an enzyme whose cofactor is a vitamin) and with NOS: scurvy was cured empirically with citrus fruit a century and a half before the molecule responsible was known — effective knowledge can precede mechanistic knowledge.

Examiner's lens: final drills (molecules)

• Condensation/hydrolysis in one picture: condensation builds and releases water; hydrolysis splits and consumes water. Every polymer in this lesson — starch, cellulose, polypeptides, triglycerides (ester bonds) — obeys it.
• Draw the amino acid once, perfectly: central carbon, –NH₂, –COOH, –H, –R. In peptide-bond questions the bond forms between one amino acid's carboxyl group and the next one's amino group — mark schemes check which groups you join.
• Saturated vs unsaturated, functional version: saturated chains pack straight → more van der Waals contacts → higher melting point (solid fats); cis double bonds kink chains → lower melting point (oils). Structure first, property second, example third.
• Self-test: why does the proteome vary between a muscle cell and a liver cell from the same person, while the genome (essentially) does not? (Differential gene expression — see Lesson 4.)