Biological molecules — OCR A-Level Biology

Water is a polar molecule: the oxygen atom carries a partial negative charge (δ⁻) and each hydrogen a partial positive charge (δ⁺). The δ⁺ hydrogen of one molecule is attracted to the δ⁻ oxygen of a neighbouring molecule, forming a hydrogen bond. Each water molecule can hydrogen bond with up to four others, giving a network that explains water's properties. High specific heat capacity and high latent heat of vaporisation buffer temperature changes and allow cooling by sweating. Cohesion and surface tension support columns of water in xylem and allow insects to move on water. Being a solvent for ions and polar substances lets water act as a transport medium in blood plasma and as a medium for metabolic reactions. Ice is less dense than liquid water, so it floats and insulates water below.

A monomer is a small, repeating subunit; a polymer is a large molecule made of many monomers joined together. Examples include monosaccharides forming polysaccharides, amino acids forming polypeptides and proteins, and nucleotides forming nucleic acids. Monomers join by condensation reactions, which form a chemical bond and release one molecule of water per bond formed. Polymers are broken down by hydrolysis reactions, which use a molecule of water to break the bond and release the monomers. These reactions are central to building storage and structural molecules (such as starch, glycogen and cellulose) and to digesting food so that soluble products can be absorbed. They also allow polymers to be assembled and dismantled as needed, for example during protein synthesis and digestion.

Biological molecules are built from a small set of chemical elements. The bulk of every carbohydrate, lipid, protein and nucleic acid is carbon, hydrogen and oxygen; proteins and nucleic acids additionally contain nitrogen, and nucleic acids also contain phosphorus. Sulphur appears in some amino acids, so it is present in certain proteins. A useful check is to link each element to a molecule class: C, H and O in all four classes; N in proteins and nucleic acids; P in nucleic acids (and in phospholipids); S in some proteins. In a multiple-choice question you may be asked which element is absent from a named class, or which class contains a named element. Read the option set carefully, eliminate options that add an element to a class that lacks it, and confirm the remaining choice against the class you were given.

Glucose and ribose are both sugars built from carbon, hydrogen and oxygen, but they differ in carbon number and in the ring they form. Glucose is a hexose: six carbons, molecular formula C₆H₁₂O₆. In solution its open chain closes so that carbon 1 (the aldehyde carbon) bonds to the oxygen on carbon 5, giving a six-membered pyranose ring in which five carbons and one oxygen form the ring and carbon 6 sits outside it. The ring closes in two forms, alpha and beta, differing in the position of the –OH on carbon 1. Ribose is a pentose: five carbons, formula C₅H₁₀O₅. Its ring uses four carbons plus one oxygen, a five-membered furanose ring. Both are reducing sugars with free hydroxyl groups, soluble because of hydrogen bonding to water, and glucose is the respiratory substrate.

A condensation reaction joins two monosaccharides: the hydroxyl group of one and the hydrogen of the other combine, water is released, and a glycosidic bond forms. Two monosaccharides give a disaccharide, for example glucose plus fructose forming sucrose; many monosaccharides joined this way give a polysaccharide such as starch or glycogen. The reverse process is hydrolysis: water is added and the glycosidic bond breaks, releasing the monosaccharide units. In the body, enzymes such as amylase and maltase catalyse these hydrolyses; in a test tube, heating with dilute acid achieves the same breakage. Each bond formed or broken releases or consumes one water molecule, so a chain of n residues joined by n−1 glycosidic bonds needs n−1 water molecules to hydrolyse completely.

All three are polymers of glucose but differ in bonding and chain shape. Starch contains amylose, an unbranched helix of α-glucose joined by 1,4-glycosidic bonds, and amylopectin, a branched chain with 1,4 links and 1,6 branches. Glycogen is also α-glucose with 1,4 links and more frequent 1,6 branches, giving a compact store. Cellulose is built from β-glucose; adjacent units are inverted, so each chain is straight and neighbouring chains are held by hydrogen bonds into strong microfibrils. These structural differences explain function: branching gives many ends for rapid hydrolysis, helices pack densely for storage, and straight hydrogen-bonded chains give strength to plant cell walls.

Glucose is a hexose monosaccharide; its soluble, reactive nature makes it the respiratory substrate transported in blood. Two glucose molecules condense to form maltose, and many form starch or glycogen. Starch is a compact, branched or helical polymer of α-glucose stored in plant cells; its insolubility and coiling make it a good storage carbohydrate. Glycogen is a more highly branched polymer of α-glucose stored in animal cells, giving rapid glucose release. Cellulose is a straight, unbranched polymer of β-glucose; alternating inversion lets chains form hydrogen-bonded microfibrils that give plant cell walls tensile strength. Relate each structural feature to the function it enables, and distinguish α- from β-glucose by the position of the hydroxyl group on carbon 1.

A triglyceride forms when one glycerol molecule condenses with three fatty acid molecules, releasing three water molecules and forming three ester bonds. The fatty acids may be saturated or unsaturated, and the triglyceride is a macromolecule used for energy storage because it is compact and insoluble. A phospholipid forms when one glycerol condenses with two fatty acids and one phosphate group, so it has a hydrophilic phosphate head and two hydrophobic fatty acid tails. This amphipathic structure lets phospholipids form bilayers in membranes. Recognise both as macromolecules built by condensation, and distinguish them by the third glycerol position: a fatty acid in a triglyceride, a phosphate group in a phospholipid.

Triglycerides are built when one glycerol molecule bonds with three fatty acid molecules. Each bond forms by a condensation reaction: the hydroxyl group of glycerol reacts with the carboxyl group of a fatty acid, a water molecule is released, and an ester bond (—COO—) links the two. Repeating this three times gives a triglyceride plus three water molecules. Breakdown is the reverse: hydrolysis adds water across each ester bond, splitting the triglyceride back into glycerol and three fatty acids. This happens during digestion, catalysed by lipase, and in cells when fatty acids are respired. Learn the direction of each reaction, the number of water molecules involved and the location of the ester bond, then apply this to unfamiliar diagrams.

Each lipid's function follows from its structure. Triglycerides are non-polar and insoluble, store energy densely and provide insulation and buoyancy; their many carbon–hydrogen bonds release energy on oxidation. Phospholipids have a hydrophilic phosphate head and two hydrophobic fatty acid tails, so in water they form bilayers with tails inward, creating a selectively permeable barrier for membranes. Cholesterol is a small, rigid, amphipathic steroid: its hydrophobic region sits among fatty acid tails while its hydroxyl group faces the aqueous surface, restricting phospholipid movement to regulate membrane fluidity and stability. Link each structural feature to a named function and avoid describing properties without stating the function they enable.

An amino acid is built around a central (alpha) carbon atom. Attached to this carbon are four groups: an amine group (—NH₂), a carboxyl group (—COOH), a hydrogen atom (—H) and a variable R group (side chain). The amine and carboxyl groups are common to every amino acid; it is the R group that differs between the twenty or so standard amino acids and gives each its distinct properties, such as charge or polarity. Because the same carbon carries both an acidic carboxyl group and a basic amine group, amino acids can act as zwitterions and buffer solutions. In an MCQ you may be asked to identify a component, spot a wrongly drawn structure, or recognise that the R group is the only part that varies. Learn the four groups and their positions on the central carbon.

A dipeptide forms when the carboxyl group of one amino acid reacts with the amine group of another in a condensation reaction, releasing one molecule of water and creating a peptide bond between the two residues. Repeating this condensation links many amino acids into a polypeptide, with a peptide bond at each join. Breakdown is the reverse: hydrolysis adds water across each peptide bond, splitting the chain back into amino acids. In an MCQ you may be asked what is released during condensation, what is added during hydrolysis, or where the peptide bond forms. Remember that the bond joins the carbon of one carboxyl group to the nitrogen of the next amine group, and that the number of water molecules released equals the number of peptide bonds formed.

Proteins are built from amino acids joined by peptide bonds, and their shape arises in a hierarchy of levels. The primary structure is the sequence and number of amino acids in the polypeptide chain, held by covalent peptide bonds. The secondary structure is the local folding of the backbone into α-helices and β-pleated sheets, stabilised by hydrogen bonds between the C=O of one amino acid and the N–H of another. The tertiary structure is the further three-dimensional folding of the whole chain, held by hydrogen bonds, ionic bonds, hydrophobic interactions and disulfide bridges between R groups. The quaternary structure exists when two or more polypeptide chains associate, as in haemoglobin. A mutation that changes one amino acid alters the primary structure and can change the tertiary shape and function.

Globular proteins fold so that hydrophobic residues cluster in the core and hydrophilic residues face the aqueous surroundings, giving a compact, roughly spherical shape that is soluble. The precise three-dimensional shape comes from the primary sequence and is held by hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions; this shape creates a specific active site or binding site, so function depends on structure. Examples include enzymes, haemoglobin and antibodies. A conjugated protein contains a non-protein prosthetic group. Haemoglobin is the standard example: four polypeptide chains each associated with a haem group containing an iron ion (Fe²⁺) that binds oxygen. The prosthetic group is essential to function, so removing it destroys oxygen transport.

Fibrous proteins are long, strand-like molecules whose amino acid chains run parallel along one axis and are held together by cross-links, so they are insoluble in water and structurally strong. Their repeating sequence and extensive hydrogen bonding and, where present, disulfide bridges give tensile strength and resistance to stretching. Collagen is the classic example: three polypeptide chains wound into a triple helix, cross-linked in fibrils, giving high tensile strength in tendons, skin and blood-vessel walls. Keratin has many cysteine residues forming disulfide bridges, giving hardness and waterproofing in hair, nails and skin. Elastin is extensible and recoils. Learn to link each structural feature to a named function and to contrast fibrous proteins with globular ones, which are compact and soluble.

Teach the key inorganic ions required for OCR A Level Biology H420: hydrogen (H⁺), sodium (Na⁺), potassium (K⁺), calcium (Ca²⁺), magnesium (Mg²⁺), ammonium (NH₄⁺), nitrate (NO₃⁻), hydrogencarbonate (HCO₃⁻), chloride (Cl⁻), phosphate (PO₄³⁻) and hydroxide (OH⁻). For each ion, link its charge and size to a named biological role, e.g. H⁺ controls pH and enzyme activity; Na⁺ co-transports glucose in the ileum; K⁺ maintains resting potential in neurones; Ca²⁺ triggers muscle contraction and exocytosis; Mg²⁺ is central in chlorophyll; NH₄⁺ is a nitrogen source for plants; NO₃⁻ is absorbed for amino acid synthesis; HCO₃⁻ buffers blood and neutralises stomach acid in the duodenum; Cl⁻ balances charge and forms HCl in the stomach; PO₄³⁻ is in ATP, DNA and phospholipids; OH⁻ contributes to alkaline conditions.

Each test detects a specific molecule through a colour change. Biuret: add an equal volume of biuret solution (sodium hydroxide plus dilute copper(II) sulfate) to the sample; a purple colour indicates peptide bonds, so protein is present, while a blue colour is negative. Benedict's: add Benedict's reagent (blue copper(II) sulfate) and heat in a water bath; a brick-red precipitate shows a reducing sugar. For a non-reducing sugar, first boil with dilute hydrochloric acid to hydrolyse it, neutralise with sodium hydrogencarbonate, then repeat Benedict's; a positive result after hydrolysis but not before indicates a non-reducing sugar such as sucrose. Iodine: add iodine in potassium iodide solution; blue-black indicates starch, orange-brown is negative. Emulsion: add ethanol and shake, then pour into water; a cloudy white emulsion indicates lipid.

Quantitative methods measure how much of a substance is present, not merely whether it is present. A common approach is colorimetry: react the sample with a reagent that produces a coloured product, then measure absorbance with a colorimeter. Prepare a series of known concentrations (standard solutions), measure each absorbance, and plot a calibration curve of absorbance against concentration. Measure the absorbance of the unknown and read its concentration from the curve. Other quantitative methods include titration (for example determining reducing sugar concentration) and using a biosensor or a quantitative Benedict's series comparing precipitate with known standards. Reliable results require controlled volumes, consistent conditions and repeats to reduce error.

Chromatography separates molecules by differential partitioning between a mobile phase and a stationary phase. In paper chromatography the stationary phase is water held in cellulose fibres; in thin layer chromatography (TLC) it is a thin layer of silica gel or cellulose on a glass or plastic plate. The solvent (mobile phase) moves up by capillary action, carrying dissolved molecules. Molecules that interact more strongly with the stationary phase travel more slowly, so each compound moves a characteristic distance. The result is expressed as an Rf value: Rf = distance travelled by the spot ÷ distance travelled by the solvent front. Rf is a ratio with no units and is always less than 1. Because Rf depends on the solvent and conditions, comparisons must use the same solvent and temperature.

A practical chromatography investigation starts with a prepared sample: a small, concentrated spot of the biological solution is applied to the origin line, drawn in pencil, above the level of the solvent. The solvent is allowed to travel up the paper or TLC plate by capillary action. When the solvent front nears the top, the chromatogram is removed and the front is marked immediately in pencil. Spots may be colourless, so they are located using a locating agent such as ninhydrin for amino acids, or viewed under ultraviolet light. Each spot's distance from the origin is measured to its centre, and Rf is calculated as spot distance ÷ solvent-front distance. The sample is identified by comparing its Rf values with those of known standards run on the same chromatogram under identical conditions.