Biological Molecules¶

Part of Module 2: Foundations in biology.

This topic provides the chemical language for the rest of the course. It moves well beyond naming molecules: the central theme is how molecular structure creates biological function. The same pattern appears throughout — small subunits join by condensation to form polymers, bonds can be broken by hydrolysis, and the precise shape and chemistry of each molecule determines what it does.

Learning Objectives¶

The Four Types of Biological Molecule¶

All living cells are built primarily from four classes of molecule: carbohydrates, lipids, proteins, and nucleic acids. All are organic, meaning they contain carbon. Their elemental composition differs:

Lipids differ from the others in an important way: they are not polymers assembled from monomers. Triglycerides and phospholipids are not built by polymerisation the way carbohydrates, proteins, and nucleic acids are.

Monomers, Polymers, Condensation, and Hydrolysis¶

Most carbohydrates, proteins, and nucleic acids are polymers — large molecules assembled from many repeating monomers via a process called polymerisation.

• Condensation reaction: the removal of water to form a covalent bond between two molecules. When monomers are joined, a hydroxyl group on one molecule reacts with a hydrogen on another, releasing water (H₂O) and forming the bond.
• Hydrolysis reaction: the addition of water to break a covalent bond. This reverses condensation, regenerating the monomers.

These two reactions are the fundamental building and dismantling operations of biochemistry, and they appear in every major molecule class in this topic.

Inorganic Ions¶

Inorganic ions are atoms carrying an electric charge; inorganic ions do not contain carbon (with rare exceptions). Cations carry a positive charge; anions carry a negative charge.

Named ions recur throughout the course. Their significance goes beyond this topic:

These ions do not need to be memorised in isolation now; they will be reinforced as they appear in other topics.

Water¶

Molecular Structure and Dipolar Nature¶

A water molecule (H₂O) consists of one oxygen atom covalently bonded to two hydrogen atoms. The bonding electrons are pulled towards the more electronegative oxygen, giving the oxygen a partial negative charge (δ−) and leaving each hydrogen with a partial positive charge (δ+). This charge separation makes water a dipolar molecule — one with both a positive and a negative pole.

Hydrogen Bonding¶

The δ+ hydrogen end of one water molecule is attracted to the δ− oxygen end of a neighbouring molecule. This electrostatic attraction is a hydrogen bond. Each water molecule can form up to four hydrogen bonds simultaneously. Although each hydrogen bond is individually weak, the vast number formed between water molecules gives water its distinctive properties.

Properties of Water and Their Biological Significance¶

Water as a solvent. Many substances inside cells are ionic compounds. Because water is polar, its δ− oxygens attract positive ions and its δ+ hydrogens attract negative ions, causing ionic compounds to dissociate and dissolve. Water is the universal solvent — it dissolves more substances than any other liquid. This is essential because most biological reactions take place in solution (e.g. in the cytoplasm) and dissolved substances can be transported around organisms.

Water as a temperature buffer. Water has a high specific heat capacity — a large amount of energy is needed to raise the temperature of 1 gram of water by 1°C. This is because many hydrogen bonds must be disrupted before the temperature rises. The result is that organisms containing large amounts of water are resistant to rapid temperature fluctuations, allowing stable internal conditions for enzymes.

Water as a cooling mechanism. Water has a high latent heat of vaporisation — a great deal of energy is required to convert liquid water to vapour because so many hydrogen bonds must be broken. When water evaporates from a surface (e.g. from the skin in sweating), it carries a large amount of heat energy away, cooling the organism efficiently without excessive water loss.

Water as a habitat. The same hydrogen bonding that gives water its high specific heat capacity and high latent heat of vaporisation makes it resistant to temperature change, providing a stable environment. At low temperatures, water forms ice. Ice is less dense than liquid water because hydrogen bonds hold water molecules further apart in the crystal lattice, so ice floats. This insulating layer at the surface of ponds and lakes prevents the water below from freezing, allowing aquatic organisms to survive winter.

Water as a metabolite. Water participates directly in chemical reactions: it is a substrate in hydrolysis reactions and is released in condensation reactions. It is also a raw material for photosynthesis.

Water as a transport medium. The tendency of water molecules to stick together via hydrogen bonds is cohesion. Water also sticks to other materials via adhesion. Together, cohesion and adhesion enable water to flow continuously through the xylem of plants in a cohesion-tension mechanism. Cohesion also creates surface tension at the air–water interface, which is strong enough to support small organisms such as pond-skaters.

Carbohydrates¶

General Formula and Functions¶

Carbohydrates contain C, H, and O in an approximate ratio where hydrogen and oxygen are present roughly as in water (2:1). Their general formula is C_x(H₂O)_y.

Roles of carbohydrates in organisms: - Energy supply: the primary energy currency substrate for cells (glucose → respiration → ATP) - Energy storage: complex carbohydrates such as starch (plants) and glycogen (animals) - Structural support: cellulose in plant cell walls; chitin in fungal cell walls and arthropod exoskeletons - Cellular recognition: glycoproteins on cell surfaces mediate cell–cell communication and identification - Building blocks: ribose and deoxyribose form the sugar backbone of RNA and DNA respectively

Monosaccharides¶

Monosaccharides are the simplest carbohydrates — single-unit sugars that are soluble, sweet-tasting, and directly usable in respiration. Their general formula is (CH₂O)_n, where n is 3–7.

They are classified by the number of carbon atoms: - Hexose sugars (6C): glucose, fructose, galactose — formula C₆H₁₂O₆ - Pentose sugars (5C): ribose and deoxyribose — crucial components of nucleotides

Alpha-glucose and beta-glucose are both hexose sugars with the formula C₆H₁₂O₆. They are isomers — the same atoms arranged differently. The only structural difference is the orientation of the hydroxyl group (−OH) on carbon 1 of the ring: in α-glucose, it points downward; in β-glucose, it points upward. This single difference determines whether the resulting polymer will be a storage molecule (starch, glycogen) or a structural molecule (cellulose).

Why glucose functions as an energy source: its hydroxyl groups allow it to be soluble and transportable; its bonds store considerable energy that is released during respiration.

Disaccharides¶

Disaccharides are formed when two monosaccharides are joined by a condensation reaction, forming a glycosidic bond and releasing one molecule of water. The bond typically forms between carbon 1 of one sugar and carbon 4 of another (a 1–4 glycosidic bond), though 1–6 bonds also occur in branched polysaccharides.

Disaccharides are broken down by hydrolysis — the addition of water breaks the glycosidic bond, releasing the constituent monosaccharides.

Polysaccharides¶

Polysaccharides are polymers made from many monosaccharides joined via glycosidic bonds. The three principal examples illustrate how the same monomer type, arranged slightly differently, produces molecules with completely different functions.

Starch¶

Starch is the storage polysaccharide of plants, found in granules in cells. It is hydrolysed back to glucose when energy is needed. Starch has two components:

• Amylose: an unbranched chain of α-glucose joined by 1–4 glycosidic bonds. The angle of these bonds causes the chain to coil into a helix, producing a compact structure.
• Amylopectin: a branched chain of α-glucose joined by 1–4 bonds along the main chain and 1–6 bonds at branch points.

Why starch is well adapted for energy storage: - Insoluble — does not alter the water potential of cells, so water does not rush in by osmosis - Large molecule — cannot diffuse out of cells - Coiled (amylose) — compact, so large amounts of glucose fit in a small volume - Branched (amylopectin) — many free ends available for enzyme attack, enabling rapid release of glucose - Hydrolysis yields α-glucose — directly used in respiration

Glycogen¶

Glycogen is the storage polysaccharide of animals, stored mainly in the liver and muscles. It is very similar to amylopectin in structure but is more highly branched, giving even more free ends for enzyme attack and faster glucose release to meet rapid energy demands. Like starch, it is made of α-glucose, is insoluble, and is large enough not to diffuse out of cells.

Cellulose¶

Cellulose is built from β-glucose and is the main structural polymer of plant cell walls. Its construction differs fundamentally from starch:

Because of the geometry of the β-glucose ring, neighbouring β-glucose monomers cannot align and form a bond unless every other monomer is inverted (rotated 180°). This produces a long, straight, unbranched chain — unlike the helical coiling of amylose. These straight chains run parallel and form extensive hydrogen bonds between adjacent chains. The chains bundle into microfibrils, which aggregate into macrofibrils, forming the strong cellulose fibres of the cell wall.

Why cellulose is well adapted for structural support: - Long, straight, unbranched chains — provide rigidity - Many hydrogen bonds between chains — collectively very strong, giving high tensile strength - Microfibrils — provide additional mechanical strength to the cell wall

Biochemical Tests for Carbohydrates¶

Benedict's Test for Reducing Sugars¶

All monosaccharides and some disaccharides (maltose, lactose) are reducing sugars — they donate electrons to the copper(II) ions in Benedict's reagent.

Procedure: 1. Add 2 cm³ of the food sample to a test tube. 2. Add an equal volume of Benedict's reagent. 3. Heat in a gently boiling water bath for 5 minutes. 4. Observe the colour.

For a quantitative comparison, the precipitate can be filtered and weighed, or a colorimeter used to measure absorbance.

Benedict's Test for Non-Reducing Sugars¶

Non-reducing sugars (e.g. sucrose) do not react directly with Benedict's. They must first be hydrolysed into monosaccharides.

Procedure: 1. Carry out the reducing sugars test first; if the result is negative (remains blue), proceed. 2. Add 2 cm³ of the sample to 2 cm³ of dilute hydrochloric acid. 3. Heat in a boiling water bath for 5 minutes to hydrolyse the disaccharide into monosaccharides. 4. Neutralise by adding sodium hydrogencarbonate solution. 5. Retest with Benedict's reagent. 6. A brick-red precipitate now confirms a non-reducing sugar was originally present.

Iodine Test for Starch¶

1. Add 2 cm³ of the food sample to a test tube.
2. Add a few drops of iodine solution and shake.
3. A colour change from orange-brown to blue-black indicates starch is present.

Lipids¶

Introduction: Elements and General Properties¶

Lipids contain C, H, and O but with a much lower proportion of oxygen than carbohydrates. Unlike carbohydrates, proteins, and nucleic acids, lipids are not polymers — they are not assembled from monomers by polymerisation.

Functions of lipids: - Energy supply and storage: triglycerides are energy-rich and used for long-term storage - Membrane structure: phospholipids form the bilayer framework of all cell membranes - Waterproofing: insoluble lipids form water-resistant barriers (e.g. waxy cuticle on leaves) - Insulation: thermal and electrical insulation (e.g. myelin sheaths around nerve fibres) - Protection: fat surrounding delicate organs acts as a shock absorber

Fatty Acids: Saturated and Unsaturated¶

All lipids contain fatty acids — molecules with a carboxyl group (−COOH) attached to a hydrocarbon chain (R group).

Saturated fatty acids: every carbon in the chain is bonded to the maximum number of hydrogen atoms; there are no carbon–carbon double bonds. The straight chain packs closely with other chains, raising the melting point. Saturated fats are typically solid at room temperature.

Unsaturated fatty acids: contain one or more carbon–carbon double bonds, which introduce kinks in the chain that prevent close packing, lowering the melting point. Unsaturated fats are typically liquid at room temperature (oils). - Monounsaturated: one double bond - Polyunsaturated: two or more double bonds

Triglycerides¶

A triglyceride consists of a glycerol molecule joined to three fatty acids by three ester bonds, one per fatty acid. Each ester bond forms by condensation (releasing one H₂O per bond, so three water molecules total per triglyceride formed).

Features that make triglycerides effective energy stores: - Long hydrocarbon tails with many C–H bonds that release energy when broken - Low mass-to-energy ratio — more energy per gram than carbohydrates or proteins - Insoluble and non-polar — do not affect cell water potential; do not interfere with osmosis - High ratio of H to O — yield metabolic water when oxidised (important for desert animals)

Triglycerides are hydrolysed back to glycerol and three fatty acids by the addition of three water molecules, breaking the ester bonds.

Phospholipids¶

A phospholipid is similar to a triglyceride but one of the three fatty acid tails is replaced by a phosphate group. This gives the molecule two distinct regions: - A hydrophilic head (glycerol + phosphate): attracted to water - A hydrophobic tail (two fatty acid chains): repelled by water

This combination of hydrophilic and hydrophobic regions makes phospholipids amphipathic. When placed in water, phospholipids spontaneously arrange into a bilayer: hydrophilic heads face outward into the water on both sides, while hydrophobic tails face inward, away from the water. This bilayer arrangement forms the structural basis of all cell membranes, creating a barrier that prevents water-soluble substances from freely crossing.

Cholesterol¶

Cholesterol is a sterol — a type of lipid with a characteristic ring structure. Like phospholipids, cholesterol is polar: the hydroxyl group (−OH) is hydrophilic while the rest of the molecule is hydrophobic.

In animal cell membranes, cholesterol molecules intercalate between phospholipid fatty acid tails, causing the phospholipids to pack more closely together. This reduces membrane fluidity and increases stability, modulating permeability.

Cholesterol is also a precursor for vitamin D, steroid hormones (e.g. testosterone, oestrogen), and bile salts.

Emulsion Test for Lipids¶

1. Place the food sample in a test tube.
2. Add 2 cm³ of ethanol and shake (ethanol dissolves lipids).
3. Add 2 cm³ of distilled water.
4. If lipids are present, a milky white emulsion forms as the lipid precipitates out of solution.

Proteins¶

Amino Acid Structure¶

Proteins are polymers of amino acids. There are approximately 20 different amino acids found in living organisms. All share the same general structure: - A central carbon atom - An amino group (−NH₂) - A carboxyl group (−COOH) - A hydrogen atom (−H) - An R group (variable side chain that determines each amino acid's unique properties)

The R group distinguishes amino acids. For example, the amino acid cysteine has an R group containing sulphur, which allows it to form disulfide bonds between polypeptide chains.

Peptide Bond Formation¶

Two amino acids join by condensation: the carboxyl group (−COOH) of one reacts with the amino group (−NH₂) of another, releasing water and forming a peptide bond (between C and N). The result is a dipeptide. Further condensation reactions extend this into a polypeptide — a long chain of amino acids linked by peptide bonds. Hydrolysis reverses this, breaking peptide bonds by addition of water to regenerate individual amino acids.

The Four Levels of Protein Structure¶

Proteins have hierarchical levels of organisation, each maintained by specific interactions.

Primary structure: the unique sequence of amino acids in the polypeptide chain, held together by peptide bonds. A change in even a single amino acid can alter the protein's shape and function.

Secondary structure: hydrogen bonds form between the amino group (−NH) of one amino acid and the carboxyl group (−CO) of another further along the chain. This causes regions of the chain to fold into: - An alpha-helix (a right-handed coil) - A beta-pleated sheet (antiparallel or parallel strands linked by hydrogen bonds)

Tertiary structure: the full polypeptide folds further into a complex, specific 3D shape stabilised by multiple bond types: - Hydrogen bonds (individually weak but collectively strong) - Ionic bonds (between oppositely charged R groups) - Disulfide bridges (covalent bonds between two cysteine R groups containing sulphur) - Hydrophobic and hydrophilic interactions (between non-polar and polar R groups)

Quaternary structure: two or more polypeptide chains associate together, held by the same bonds as tertiary structure. Prosthetic groups (non-protein components) may also be incorporated. Not all proteins have a quaternary structure.

Biuret Test for Proteins¶

The Biuret test detects peptide bonds: 1. Add an equal volume of Biuret solution (sodium hydroxide + copper sulfate) to the food sample. 2. If protein is present, the solution changes from blue to purple (lilac). 3. A negative result remains blue.

Globular and Fibrous Proteins¶

Globular Proteins¶

Globular proteins are compact, spherical, and generally soluble in water. Their solubility allows them to function in solution within cells or the bloodstream. They have specific metabolic roles, and their precise shape is essential for function.

Examples:

Haemoglobin is a globular protein in red blood cells. It has a quaternary structure of four polypeptide chains (two α-chains and two β-chains). Each chain contains a haem prosthetic group that includes an iron atom (Fe²⁺), which reversibly binds one O₂ molecule. A single haemoglobin molecule therefore carries four oxygen molecules simultaneously. Its compact globular shape allows it to fit inside the small volume of a red blood cell.

Insulin is a hormone that regulates blood glucose concentration. It consists of two polypeptide chains held together by disulfide bonds. It must be soluble (to travel in blood plasma) and have a precise shape (to bind to receptors on target cell membranes).

Amylase is an enzyme that breaks down starch into maltose. It is a single polypeptide chain folded using both alpha-helices and beta-pleated sheets. Its active site has a precise shape complementary to the starch substrate.

Fibrous Proteins¶

Fibrous proteins form long strands and are generally insoluble in water. They have structural roles and are not readily broken down.

Collagen is the most abundant protein in the human body, providing structural strength in skin, tendons, cartilage, bones, teeth, and blood vessel walls. It consists of three polypeptide chains wound around each other in a rope-like triple helix, providing both strength and flexibility.

Keratin is found in hair, skin, and nails. Keratin chains contain high numbers of cysteine residues, allowing extensive disulfide bond cross-linking. The number of disulfide bonds determines whether the keratin is soft (hair) or hard (nails). Keratin is strong and insoluble.

Elastin is found in elastic connective tissues such as the walls of blood vessels and the lungs. Unlike collagen, elastin can stretch and recoil to its original shape, providing elasticity to tissues.

Common Confusions¶

• Magnification is not the same as structure. Cellulose and starch are both made of glucose, but the isomer used (β vs α) and the bond geometry create completely different molecules with completely different functions. Cellulose is structural; it is not interchangeable with starch.
• Triglycerides and phospholipids are both lipids but are not interchangeable. Triglycerides store energy; phospholipids form membranes.
• A positive Benedict's test detects reducing sugars, not specifically glucose. Any reducing sugar (all monosaccharides, plus maltose and lactose) will give a positive result.
• Protein function depends on 3D shape, which in turn depends on the specific sequence of amino acids (primary structure). Denaturation (disruption of bonds maintaining tertiary structure) destroys function even if the primary sequence is unchanged.
• Hydrophilic and hydrophobic are not synonyms for water-soluble and water-insoluble in all contexts. Phospholipids are amphipathic — they have both hydrophilic and hydrophobic regions — and it is this combination that enables bilayer formation.
• Not all proteins have a quaternary structure. Amylase and insulin are examples with one or two chains; haemoglobin has four.

Key Terms¶

• Monomer: a small molecular subunit that joins with others to form a polymer.
• Polymer: a large molecule built from many repeating monomers linked by covalent bonds.
• Condensation reaction: formation of a covalent bond between two molecules with simultaneous release of water.
• Hydrolysis: breakage of a covalent bond using water.
• Dipolar molecule: a molecule with partial positive and partial negative charges, such as water.
• Hydrogen bond: a weak electrostatic attraction between a δ+ hydrogen and a δ− atom on a neighbouring molecule.
• Cohesion: the tendency of water molecules to stick together via hydrogen bonds.
• Hexose sugar: a monosaccharide with six carbon atoms (e.g. glucose, fructose, galactose).
• Pentose sugar: a monosaccharide with five carbon atoms (e.g. ribose, deoxyribose).
• Alpha-glucose: an isomer of glucose in which the −OH on carbon 1 points downward; monomer of starch and glycogen.
• Beta-glucose: an isomer of glucose in which the −OH on carbon 1 points upward; monomer of cellulose.
• Glycosidic bond: the covalent bond linking monosaccharides in carbohydrates, formed by condensation.
• Amylose: the unbranched, helical component of starch, formed from α-glucose via 1–4 glycosidic bonds.
• Amylopectin: the branched component of starch, with 1–4 and 1–6 glycosidic bonds.
• Microfibril: a bundle of parallel cellulose chains cross-linked by hydrogen bonds, contributing to cell wall strength.
• Saturated fatty acid: a fatty acid with no carbon–carbon double bonds; solid at room temperature.
• Unsaturated fatty acid: a fatty acid with one or more carbon–carbon double bonds; liquid at room temperature.
• Ester bond: the covalent bond between glycerol and a fatty acid in a lipid, formed by condensation.
• Triglyceride: a lipid made from one glycerol joined to three fatty acids by three ester bonds.
• Phospholipid: a lipid with two fatty acid tails and a phosphate-containing head; amphipathic.
• Amphipathic: having both hydrophilic and hydrophobic regions.
• Cholesterol: a sterol lipid that intercalates between phospholipids in animal cell membranes, reducing fluidity.
• Amino acid: the monomer of proteins; has a central carbon, amino group, carboxyl group, hydrogen, and variable R group.
• Peptide bond: the covalent bond between amino acids in a polypeptide, formed by condensation between carboxyl and amino groups.
• Primary structure: the specific sequence of amino acids in a polypeptide.
• Secondary structure: regular, repeating local folding (alpha-helix or beta-pleated sheet) driven by hydrogen bonds between backbone groups.
• Tertiary structure: the overall 3D shape of a polypeptide, stabilised by hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
• Quaternary structure: the association of two or more polypeptide chains, with optional prosthetic groups.
• Prosthetic group: a non-protein component permanently incorporated into a protein (e.g. haem in haemoglobin).
• Globular protein: a compact, soluble protein with a metabolic function.
• Fibrous protein: a long, insoluble, structurally specialised protein.
• Disulfide bridge: a covalent bond between the sulphur atoms of two cysteine residues, contributing to tertiary and quaternary structure.
• Reducing sugar: a sugar capable of donating electrons to Benedict's reagent, causing a colour change from blue to brick-red.

Connected Pages¶

• 2.1.1 Cell structure
• 2.1.3 Nucleotides and nucleic acids
• 2.1.4 Enzymes