Condensation and hydrolysis

Life is built from a small set of monomers joined into polymers. Every polymer in this topic is made the same way and broken the same way:

• Monosaccharides (glucose, fructose, galactose) → glycosidic bonds → disaccharides and polysaccharides.
• Amino acids → peptide bonds → polypeptides.
• Nucleotides → phosphodiester bonds → DNA and RNA.
• Glycerol + fatty acids → ester bonds → triglycerides (lipids are not polymers — they are macromolecules).

Counting trick you will be examined on: forming a polymer of n monomers requires n − 1 condensation reactions, so n − 1 water molecules are released. A triglyceride, however, always releases exactly 3.

α-glucose, β-glucose and the polysaccharides

Glucose is a hexose monosaccharide, C₆H₁₂O₆, with two isomers that differ only in the orientation of the –OH group on carbon 1. That single difference dictates everything downstream.

• Starch (α-glucose): amylose is unbranched 1,4-glycosidic and coils into a helix; amylopectin adds 1,6 branches. Compact, insoluble (no osmotic effect), many free ends for rapid hydrolysis. Plant storage.
• Glycogen (α-glucose): like amylopectin but more highly branched → even faster mobilisation. Animal storage in liver and muscle.
• Cellulose (β-glucose): every alternate molecule is inverted 180° so 1,4 bonds can form. Chains are straight, held side-by-side by hydrogen bonds into microfibrils — huge tensile strength in the cell wall.

Tests: Benedict's (blue → brick-red) for reducing sugars; boil with acid, neutralise, re-test for non-reducing sugars (e.g. sucrose); iodine in potassium iodide (orange → blue-black) for starch.

Triglycerides and phospholipids

A triglyceride is one glycerol condensed with three fatty acids, forming three ester bonds and releasing three water molecules. Fatty acids are saturated (no C=C) or unsaturated (one or more C=C, which kink the tail and lower the melting point).

• Energy store: the long hydrocarbon tails are highly reduced, so oxidation releases roughly twice the energy per gram of carbohydrate. Storage is also anhydrous — no water of hydration to carry.
• Phospholipid: one fatty acid is replaced by a phosphate group. The phosphate head is hydrophilic, the tails hydrophobic → in water the molecules self-assemble into a bilayer, the basis of every membrane.
• Test: emulsion test — dissolve in ethanol, then add water; a white/milky emulsion indicates lipid.

Exam precision: "triglycerides are insoluble in water" — because the molecule is essentially non-polar, so it cannot form hydrogen bonds with water. That is also why fat stores do not affect the cell's water potential.

Why cellulose is not a food store

Four levels of protein structure

Every amino acid shares a central carbon bonded to an amine group (–NH₂), a carboxyl group (–COOH), a hydrogen and a variable R group. The 20 R groups are the whole of the difference.

• Primary — the sequence of amino acids joined by peptide bonds. It is encoded by the gene, and it determines everything else.
• Secondary — hydrogen bonds between the C=O of one peptide bond and the N–H of another produce the α-helix or β-pleated sheet.
• Tertiary — the chain folds into a precise 3-D shape held by ionic bonds (between charged R groups), disulfide bridges (covalent, between cysteines), further hydrogen bonds, and hydrophobic interactions that bury non-polar R groups in the core.
• Quaternary — two or more polypeptides, sometimes with a prosthetic group. Haemoglobin = 4 polypeptides (2α, 2β) each with an iron-containing haem group; collagen = 3 chains wound into a triple helix.

Denaturation: heat or extreme pH disrupt hydrogen and ionic bonds (not peptide bonds), so the tertiary structure — and the active site — is lost. Biuret test: blue → purple/lilac for peptide bonds.

Your turn — condensation counting

Induced fit and activation energy

Enzymes are globular proteins that act as biological catalysts. The substrate binds the active site to form an enzyme–substrate complex, which lowers the activation energy of the reaction so it proceeds rapidly at body temperature.

The modern model is induced fit, not a rigid lock and key: the active site is not perfectly complementary at first. Substrate binding distorts the active site, moulding it around the substrate. That distortion also strains bonds in the substrate, which is precisely how activation energy is reduced.

Rate factors: temperature (rate rises with kinetic energy until denaturation), pH (charged R groups altered → ionic/H bonds broken → active site changes shape), enzyme concentration (rate ∝ [E] provided substrate is in excess), substrate concentration (rate rises until all active sites are saturated — then V_max).

Always measure the initial rate. As soon as the reaction runs, substrate is used up, so the gradient falls. Only the tangent at t = 0 compares conditions fairly.

Competitive vs non-competitive inhibition

Two mechanisms, and the examiner will test whether you can tell them apart from a graph.

• Competitive: the inhibitor is similar in shape to the substrate and binds the active site, blocking ES complexes. The effect is reduced by increasing substrate concentration, and V_max is eventually still reached.
• Non-competitive: the inhibitor binds elsewhere (an allosteric site), changing the tertiary structure of the active site so the substrate no longer fits. Increasing substrate does not reverse it, and V_max is permanently lowered.

Real examples: statins competitively inhibit HMG-CoA reductase; cyanide non-competitively inhibits cytochrome c oxidase, shutting down oxidative phosphorylation.

Reading an inhibition graph

Your turn — initial rate

DNA, RNA and semi-conservative replication

A nucleotide = pentose sugar + phosphate + nitrogenous base. In DNA the sugar is deoxyribose and the bases are A, T, C, G; in RNA it is ribose with U in place of T.

• Nucleotides join by phosphodiester bonds (condensation) between the phosphate on carbon 5 of one sugar and the –OH on carbon 3 of the next → a sugar-phosphate backbone.
• The two strands are antiparallel (5′→3′ against 3′→5′) and held by hydrogen bonds: A–T (2 bonds) and C–G (3 bonds). Because pairing is complementary, %A = %T and %C = %G (Chargaff's rules).
• DNA is stable, very long (huge information capacity), and the double helix protects the bases inside — ideal as the genetic material.

Semi-conservative replication: DNA helicase breaks the hydrogen bonds and unwinds the helix; each strand acts as a template; free activated DNA nucleotides pair with exposed bases; DNA polymerase catalyses phosphodiester bond formation, moving only along the 3′→5′ template (so the new strand grows 5′→3′). Each daughter molecule contains one original and one new strand.

Meselson & Stahl (1958): bacteria grown on heavy ¹⁵N then switched to ¹⁴N. After one round of replication all the DNA was of intermediate density — impossible under conservative replication. After two rounds: half intermediate, half light — impossible under dispersive replication. Semi-conservative it is.

Your turn — Chargaff

ATP — the universal energy currency

ATP is a phosphorylated nucleotide: adenine + ribose + three phosphate groups.

• The energy released is immediately usable in a single reaction and in a small, manageable quantity — unlike glucose, which would release far too much at once.
• ATP is not a long-term store: it is unstable and is continually resynthesised from ADP + Pi by ATP synthase during respiration and photosynthesis.
• The released inorganic phosphate can phosphorylate another molecule, making it more reactive — for example phosphorylating glucose at the start of glycolysis.

Why water is not just a background solvent

Water is polar: oxygen is δ⁻, hydrogens δ⁺, so molecules form hydrogen bonds with each other. Every property below follows from that one fact.

• High specific heat capacity — hydrogen bonds absorb a lot of energy before the temperature rises, so aquatic habitats and cell contents are thermally stable.
• High latent heat of vaporisation — evaporating water carries away a lot of heat: the basis of sweating and of transpirational cooling.
• Cohesion (and adhesion) — water columns in xylem do not break under tension, and surface tension supports pond-skaters.
• Excellent solvent — polar solutes and ions dissolve, so they can be transported and can react in solution.
• Metabolite — a reactant in hydrolysis and in photolysis; a product of condensation and of respiration.

Inorganic ions, and what they actually do: Fe²⁺ in the haem group binds oxygen; PO₄³⁻ forms the backbone of DNA and the phosphate groups of ATP; H⁺ concentration determines pH and therefore enzyme activity, and drives chemiosmosis; Na⁺ establishes the gradient used in co-transport of glucose and amino acids.

Water as a coolant

Interpreting Meselson and Stahl

Which class of molecule?

Tap a card, then tap the class of biological molecule it belongs to.

Bond, molecule and function

Tap an item on the left, then its partner on the right.

The big ideas to take away

That is the whole of AQA 3.1 Biological molecules. Press Finish to see your score.