Biological molecules: the complete AQA A-Level Biology 3.1 guide

What section 3.1 actually demands

Biological molecules is the foundation of the whole AQA A-Level Biology specification. Almost every later section, from cell membranes to respiration, photosynthesis and gene technology, assumes you can already describe these molecules and the reactions that build and break them. Examiners exploit this: 3.1 content appears on all three papers and is a reliable source of marks in both short-answer recall questions and the Paper 3 synoptic essay.

The section rewards two linked skills. The first is precise structural recall: knowing which monomer makes which polymer, which bond joins them, and which reaction forms or breaks that bond. The second is mechanistic explanation: linking a molecule's structure to its function or to the result of a named biochemical test. Strong students drill the structures until they are automatic, then practise the "structure causes function" sentences AQA mark schemes reward.

Monomers, polymers and the two key reactions

A monomer is a small molecule that is a single repeating unit; a polymer is many monomers joined together. AQA names three monomer-polymer relationships you must know: monosaccharides build polysaccharides, amino acids build polypeptides, and nucleotides build polynucleotides (DNA and RNA).

This single pair of reactions recurs in every macromolecule in the section, so it is worth fixing the pattern early. The same logic forms a glycosidic bond between sugars, an ester bond between glycerol and a fatty acid, a peptide bond between amino acids, and a phosphodiester bond between nucleotides; in every case water is released, and in every case adding water back (hydrolysis) reverses it.

Carbohydrates

Monosaccharides

Monosaccharides are the monomers of carbohydrates. The key examples are glucose, fructose and galactose (all hexoses, $\text{C}_6\text{H}_{12}\text{O}_6$). Glucose exists as two isomers that differ in the position of the hydroxyl group on carbon 1: alpha-glucose (OH below the ring) and beta-glucose (OH above the ring). This small difference has large structural consequences in the polysaccharides they form.

Disaccharides and the glycosidic bond

Two monosaccharides join by a condensation reaction to form a disaccharide and a glycosidic bond, releasing water. You must know three:

• Maltose = glucose + glucose
• Sucrose = glucose + fructose
• Lactose = glucose + galactose

Polysaccharides

Testing for carbohydrates

• Reducing sugars (e.g. glucose, maltose): add Benedict's reagent and heat in a water bath. A positive result changes from blue to a brick-red precipitate (through green, yellow and orange as concentration rises).
• Non-reducing sugars (e.g. sucrose): if Benedict's is negative, boil a fresh sample with dilute hydrochloric acid (to hydrolyse it), neutralise with sodium hydrogencarbonate, then repeat the Benedict's test. A brick-red result now confirms a non-reducing sugar.
• Starch: add iodine in potassium iodide solution. A positive result changes from orange-brown to blue-black.

Lipids

Lipids are not polymers (they are not made of repeating monomers), but they are formed by condensation reactions.

Triglycerides

A triglyceride forms when one molecule of glycerol joins to three fatty acids by condensation, forming three ester bonds and releasing three molecules of water. Fatty acids have the general formula $\text{R}-\text{COOH}$. A saturated fatty acid has no carbon-carbon double bonds; an unsaturated fatty acid has one or more C=C double bonds, which create kinks in the chain.

Phospholipids

A phospholipid is like a triglyceride but with one fatty acid replaced by a phosphate group. This gives it a hydrophilic ("water-loving") phosphate head and two hydrophobic ("water-hating") fatty acid tails. In water, phospholipids form a bilayer with heads facing out and tails facing in, the structural basis of all cell membranes.

Testing for lipids

The emulsion test: dissolve the sample in ethanol, then add water and shake. A positive result forms a cloudy white emulsion.

Proteins

Amino acids and the peptide bond

Amino acids are the monomers of proteins. All twenty amino acids share the same general structure: a central carbon bonded to an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom, and a variable R group (the side chain) that differs between amino acids.

Two amino acids join by condensation to form a dipeptide and a peptide bond, releasing water. Many amino acids form a polypeptide.

The four levels of protein structure

Testing for proteins

The biuret test: add sodium hydroxide solution, then a few drops of dilute copper(II) sulfate solution. A positive result (peptide bonds present) changes from blue to purple/lilac. No heating is needed.

Enzymes

Enzymes are biological catalysts. They are globular proteins that lower the activation energy of a reaction, speeding it up without being used up. AQA wants the induced-fit model: the substrate is complementary to the active site, and as it binds, the active site changes shape slightly to mould around the substrate, forming an enzyme-substrate complex and distorting the substrate's bonds so they break (or form) more easily.

Factors affecting enzyme activity

• Temperature: rate increases with temperature as kinetic energy rises and successful collisions become more frequent, up to the optimum. Beyond it, hydrogen and ionic bonds break, the tertiary structure (and active site) is denatured, and the substrate no longer fits.
• pH: each enzyme has an optimum pH. Away from it, $\text{H}^+$ ions disrupt hydrogen and ionic bonds in the tertiary structure, changing the active site's shape and reducing activity.
• Substrate concentration: rate rises with substrate concentration until all active sites are occupied; the enzyme concentration then becomes the limiting factor and the rate plateaus.
• Enzyme concentration: with excess substrate, more enzyme means more active sites and a faster rate.

Inhibitors

Nucleic acids and ATP

Nucleotide structure

A nucleotide is the monomer of DNA and RNA. Each consists of three components joined by condensation reactions:

1. A pentose sugar (deoxyribose in DNA, ribose in RNA)
2. A phosphate group
3. A nitrogen-containing organic base

The bases are adenine (A), thymine (T), cytosine (C) and guanine (G) in DNA; RNA replaces thymine with uracil (U).

DNA structure

Nucleotides join by condensation between the phosphate of one and the sugar of the next, forming a phosphodiester bond and a sugar-phosphate backbone. DNA is a double helix of two antiparallel polynucleotide strands held together by hydrogen bonds between complementary base pairs: A pairs with T (two hydrogen bonds) and C pairs with G (three hydrogen bonds).

Semi-conservative DNA replication

DNA helicase breaks the hydrogen bonds, unwinding the double helix into two template strands. Free DNA nucleotides align opposite their complementary bases, and DNA polymerase catalyses the condensation reactions that join them into a new strand. Each new molecule contains one original ("parent") strand and one new strand, which is why replication is described as semi-conservative. The Meselson and Stahl experiment, using the heavy isotope $^{15}\text{N}$, provided the evidence for this model.

RNA

RNA is a single, relatively short polynucleotide that contains ribose and uracil. Messenger RNA (mRNA) carries a copy of a gene's code out of the nucleus to the ribosomes, where it is translated into a polypeptide.

ATP

Adenosine triphosphate (ATP) is the universal energy currency of cells. It is a nucleotide derivative consisting of the base adenine, the pentose sugar ribose, and three phosphate groups.

ATP is hydrolysed to ADP + inorganic phosphate ($\text{P}_i$), releasing energy for cellular processes; the reaction is catalysed by ATP hydrolase. ATP is resynthesised from ADP and $\text{P}_i$ by condensation, catalysed by ATP synthase, during respiration and photosynthesis.

Water

Water is a small, polar molecule. Oxygen is slightly negative and the hydrogens are slightly positive, so hydrogen bonds form between water molecules. Almost all of water's biologically important properties trace back to this hydrogen bonding.

Inorganic ions

Ions occur in solution in the cytoplasm and body fluids, in high or very low concentrations, each with a specific role. AQA names four you must be able to discuss:

• Hydrogen ions ($\text{H}^+$): determine pH; their concentration affects enzyme activity and is central to chemiosmosis in respiration and photosynthesis.
• Iron ions ($\text{Fe}^{2+}$): a component of haemoglobin, where they bind oxygen for transport.
• Sodium ions ($\text{Na}^+$): involved in the co-transport of glucose and amino acids across cell membranes (e.g. in the ileum and kidney) and in nerve impulse transmission.
• Phosphate ions ($\text{PO}_4^{3-}$): components of DNA, RNA, ATP and phospholipids; phosphorylation of molecules makes them more reactive.

Pulling section 3.1 together for the exam

The smartest way to revise this section is by the unifying patterns, not as a list of facts:

1. One reaction pair builds and breaks everything. Condensation (releases water) makes glycosidic, ester, peptide and phosphodiester bonds; hydrolysis (uses water) breaks them.
2. Structure determines function. Every molecule's job follows from its shape and bonding: branched glycogen for fast hydrolysis, beta-glucose H-bonding for strong cellulose, hydrophilic/hydrophobic phospholipids for bilayers, complementary base pairing for accurate DNA replication.
3. Each macromolecule has a signature test. Benedict's (reducing sugars), iodine (starch), emulsion (lipids), biuret (proteins). Know the reagent, the procedure and the colour change.
4. Water and ions are not afterthoughts. Link every water property back to hydrogen bonding and a consequence, and pair each named ion with one concrete role.

Drill the structures until you can draw them from memory, then convert each one into the "structure causes function" sentence the mark schemes reward, and you will pick up reliable marks across all three papers.