What you'll learn
Biological molecules and water is the opening topic of CAPE Biology Unit 1 and the foundation for everything that follows. Living organisms are built from a surprisingly small set of molecular families — carbohydrates, lipids, proteins and nucleic acids — and each is assembled from monomers by the same reaction and dismantled by its reverse. Water, though not a macromolecule, is treated alongside them because its unusual properties arise from a single structural feature and those properties determine almost everything about how cells work. By the end of this topic you should be able to explain how hydrogen bonding gives water its biologically important properties, describe condensation and hydrolysis, relate the structure of each biological molecule to its function, distinguish the four levels of protein structure, and carry out and interpret the standard food tests.
Key terms and definitions
Monomer — a small molecule that can be joined to others to form a polymer
Polymer — a large molecule made of many repeating monomer units
Condensation reaction — a reaction joining two molecules with the removal of a molecule of water
Hydrolysis — a reaction splitting a molecule by the addition of water
Hydrogen bond — a weak attraction between a slightly positive hydrogen atom and a slightly negative atom on another molecule
Polar molecule — a molecule with an uneven distribution of charge, giving partial positive and negative regions
Glycosidic bond — the bond joining two monosaccharides
Ester bond — the bond joining glycerol to a fatty acid
Peptide bond — the bond joining two amino acids
Saturated fatty acid — a fatty acid with no carbon–carbon double bonds
Unsaturated fatty acid — a fatty acid containing one or more carbon–carbon double bonds
Denaturation — the loss of a protein's three-dimensional shape, and therefore its function
Core concepts
Water and hydrogen bonding
A water molecule is polar. Oxygen is more electronegative than hydrogen, so it draws the shared electrons towards itself, leaving the oxygen slightly negative and each hydrogen slightly positive. The slightly positive hydrogen of one molecule is attracted to the slightly negative oxygen of another, forming a hydrogen bond.
Individually these bonds are weak, but there are enormous numbers of them, and collectively they give water properties that no molecule of its small size should possess.
The biological importance of water
Water has a high specific heat capacity, because a great deal of energy is needed to break the hydrogen bonds before the temperature can rise. Cells and aquatic habitats therefore experience only gradual temperature changes, which protects enzymes from denaturation.
It has a high latent heat of vaporisation, again because hydrogen bonds must be broken for a molecule to escape. Evaporation of a relatively small quantity of water therefore removes a large amount of energy, which is the basis of cooling by sweating and by transpiration.
It is an excellent solvent for polar and ionic substances, because the polar water molecules surround and separate the charged particles. Most metabolic reactions occur in aqueous solution, and water is the transport medium in blood plasma and in xylem and phloem.
It shows cohesion, with molecules attracted to one another, and adhesion to other polar surfaces. Cohesion produces surface tension, allowing insects to move across a pond surface, and it is what holds the continuous column of water in the xylem as transpiration pulls it upwards.
Ice is less dense than liquid water, because the hydrogen bonds hold the molecules in an open lattice. Ice therefore floats, insulating the water beneath and allowing aquatic organisms to survive in cold climates.
Water is also a reactant in its own right, in photosynthesis and in every hydrolysis reaction, and a product of condensation and of respiration.
Condensation and hydrolysis
Almost every biological polymer is built by condensation and broken down by hydrolysis, and recognising this single pattern simplifies the whole topic.
In a condensation reaction, two monomers join and a molecule of water is released. In hydrolysis, a molecule of water is added and the bond is broken.
Digestion is hydrolysis; synthesis of storage and structural molecules is condensation. The number of water molecules released in forming a chain of n monomers is n minus 1.
Carbohydrates
Carbohydrates contain carbon, hydrogen and oxygen, with hydrogen and oxygen usually in the ratio two to one.
Monosaccharides are the monomers. Glucose, with six carbons, is the most important: it is the immediate substrate for respiration and is soluble and readily transported. Fructose and galactose share its formula but differ in structure. Glucose exists as alpha and beta isomers, differing in the orientation of one hydroxyl group, and this small difference has large structural consequences.
Disaccharides form when two monosaccharides join by a glycosidic bond with the loss of water. Maltose is glucose and glucose, sucrose is glucose and fructose, and lactose is glucose and galactose.
Polysaccharides are polymers of monosaccharides, and three matter.
Starch is the plant storage polysaccharide, made of alpha glucose. Amylose is unbranched and coils into a helix, making it compact; amylopectin is branched, offering many ends for rapid hydrolysis. Starch is insoluble, so it does not affect the water potential of the cell, and it is compact, so large quantities can be stored.
Glycogen is the animal storage polysaccharide, also of alpha glucose but more highly branched than amylopectin, allowing even faster mobilisation of glucose — appropriate to the higher metabolic rate of animals.
Cellulose is the plant structural polysaccharide, made of beta glucose. Because alternate beta glucose molecules must rotate 180 degrees to form the glycosidic bond, the chains are straight rather than coiled. Hydrogen bonds form between adjacent chains, producing microfibrils of great tensile strength, which is why plant cell walls resist the pressure generated by osmosis.
The contrast between starch and cellulose — identical monomer formula, different isomer, completely different properties — is a favourite examination comparison.
Lipids
Lipids contain carbon, hydrogen and oxygen but with proportionally far less oxygen than carbohydrates, which is why they yield more energy per gram on oxidation.
A triglyceride forms by condensation between one molecule of glycerol and three fatty acids, producing three ester bonds and releasing three molecules of water.
Fatty acids may be saturated, with no carbon–carbon double bonds, so the chains are straight and pack closely, giving solids at room temperature such as animal fats. Unsaturated fatty acids contain one or more double bonds, which produce kinks preventing close packing, so they are liquid oils at room temperature.
The functions of lipids are examinable as a set: long-term energy storage, yielding roughly twice the energy per gram of carbohydrate; thermal insulation in adipose tissue; protection of organs; buoyancy in aquatic mammals; waterproofing as waxy cuticles; and a source of metabolic water on oxidation, which matters for desert organisms.
Phospholipids differ in that one fatty acid is replaced by a phosphate group. This creates a molecule with a hydrophilic phosphate head and two hydrophobic hydrocarbon tails. In water such molecules arrange themselves spontaneously into a bilayer with the tails inwards, which is the basis of every membrane and is the link to the membrane topic.
Proteins
Proteins are polymers of amino acids. Every amino acid has the same basic structure: a central carbon carrying an amino group, a carboxyl group, a hydrogen atom and a variable R group. There are twenty R groups, and they are the source of all protein diversity.
Amino acids join by condensation, forming a peptide bond between the amino group of one and the carboxyl group of another.
Four levels of structure are recognised and must be distinguished precisely.
Primary structure is the sequence of amino acids in the polypeptide chain, determined by the base sequence of the gene.
Secondary structure is the regular folding produced by hydrogen bonding between the carboxyl and amino groups of the backbone, giving alpha helices and beta pleated sheets.
Tertiary structure is the overall three-dimensional shape of a single polypeptide, maintained by four kinds of interaction between R groups: hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges between cysteine residues, which are covalent and therefore the strongest.
Quaternary structure exists only in proteins of more than one polypeptide chain, and describes how those chains associate. Haemoglobin, with four chains and four haem groups, is the standard example.
Proteins are classified as globular or fibrous. Globular proteins are roughly spherical with hydrophilic groups outwards, making them soluble; enzymes, haemoglobin and antibodies are examples, and their functions are metabolic. Fibrous proteins are long and insoluble with repetitive sequences; collagen and keratin are examples, and their functions are structural.
Denaturation occurs when high temperature or extremes of pH disrupt the bonds maintaining tertiary structure. The shape is lost and the protein cannot function. Because the peptide bonds of the primary structure are unaffected, denaturation is not the same as hydrolysis.
Food tests
The standard qualitative tests are practical work and are examined.
For starch, add iodine in potassium iodide solution; a blue-black colour is positive.
For reducing sugars, add Benedict's solution and heat in a water bath; the blue colour changes through green and yellow to a brick-red precipitate, with the final colour indicating the approximate concentration.
For non-reducing sugars, first carry out the Benedict's test to confirm a negative result, then hydrolyse a fresh sample with dilute hydrochloric acid and heat, neutralise with sodium hydrogencarbonate, and repeat the Benedict's test. A brick-red precipitate now indicates a non-reducing sugar such as sucrose. Omitting the neutralisation step is the commonest practical error, since Benedict's solution does not work in acid conditions.
For proteins, add biuret reagent at room temperature; a purple or lilac colour is positive.
For lipids, use the emulsion test: dissolve the sample in ethanol, then add an equal volume of water; a cloudy white emulsion is positive.
Worked examples
Example 1: Explaining a property of water (4 marks)
Explain why water's high specific heat capacity is biologically important.
Water molecules are held together by large numbers of hydrogen bonds. A considerable amount of energy must be supplied to break these bonds before the kinetic energy of the molecules, and therefore the temperature, can increase appreciably.
As a result, the temperature of water changes only slowly when energy is gained or lost. Since cytoplasm is largely water, the internal temperature of a cell remains relatively stable, which keeps enzymes within their optimum range and prevents denaturation. Aquatic habitats are likewise thermally stable, providing a constant environment for the organisms living in them.
Example 2: Comparing starch and cellulose (5 marks)
Both starch and cellulose are polymers of glucose, yet they have very different properties. Explain why.
Starch is a polymer of alpha glucose. The glycosidic bonds form between molecules in the same orientation, so the chain coils into a compact helix. Amylose is unbranched and amylopectin branched, and the molecule is insoluble and compact, which suits it to storage: large quantities can be held without affecting the water potential of the cell, and branching provides many ends for rapid hydrolysis.
Cellulose is a polymer of beta glucose. Because the hydroxyl groups are differently oriented, alternate molecules must be rotated 180 degrees for the glycosidic bond to form, so the chain is straight rather than coiled. Adjacent straight chains lie parallel and form hydrogen bonds with one another, producing microfibrils with high tensile strength. This suits cellulose to a structural role in the cell wall, where it resists the turgor pressure generated by osmosis.
Example 3: Levels of protein structure (5 marks)
Explain what happens to an enzyme when it is heated well above its optimum temperature, referring to protein structure.
Heating increases the kinetic energy of the molecule, causing it to vibrate more. This disrupts the relatively weak hydrogen bonds and ionic bonds between R groups that maintain the tertiary structure, and also the hydrogen bonds of the secondary structure.
The polypeptide therefore loses its precise three-dimensional shape. Since the active site of an enzyme is formed by the particular arrangement of R groups produced by the tertiary structure, the active site changes shape and is no longer complementary to the substrate. Enzyme–substrate complexes can no longer form and the enzyme cannot catalyse the reaction; it has been denatured.
The primary structure is unaffected, because the peptide bonds are covalent and are not broken by heating, which is why denaturation is not the same as hydrolysis.
Common mistakes and how to avoid them
The most frequent error is describing denaturation as the enzyme being killed or destroyed. An enzyme is a molecule, not an organism, and its primary structure survives; it is the shape that is lost.
Students often state that the active site is destroyed. It changes shape, which is a different claim and the one the mark scheme requires.
Another routine slip is omitting the neutralisation step in the non-reducing sugar test, or failing to run a preliminary Benedict's test to establish that no reducing sugar was present initially.
Many candidates say that starch is used for storage because it is large. The reasons are that it is insoluble, so it does not affect water potential, and compact.
Finally, candidates frequently attribute water's properties to the hydrogen bonds without first explaining that the molecule is polar because oxygen is more electronegative. The polarity is the cause and the hydrogen bonding the consequence.
Exam technique for "Biological molecules and water"
When asked about a property of water, always give the structural explanation before the biological consequence: polarity, then hydrogen bonding, then the property, then why it matters to an organism.
For structure-and-function questions on polysaccharides, name the isomer of glucose first. Alpha or beta determines everything that follows.
State the bond by name in any question about polymer formation — glycosidic, ester or peptide — and say that water is released.
For the food tests, give the reagent, the condition where one applies such as heating, and the positive result. All three are usually needed.
When describing protein structure, use the four levels explicitly and name the bonds responsible for each, since marks are commonly allocated one per level.
Quick revision summary
Water is polar because oxygen is more electronegative than hydrogen, and the resulting hydrogen bonds give it a high specific heat capacity, a high latent heat of vaporisation, solvent properties, cohesion and adhesion, and a lower density as ice. Polymers form by condensation with the loss of water and break by hydrolysis with its addition. Carbohydrates run from monosaccharides such as glucose through disaccharides joined by glycosidic bonds to polysaccharides: starch and glycogen from alpha glucose for compact insoluble storage, and cellulose from beta glucose forming straight hydrogen-bonded microfibrils for structural strength. Triglycerides form from glycerol and three fatty acids by ester bonds, with saturated chains packing closely as fats and unsaturated kinked chains as oils, serving in energy storage, insulation, protection, buoyancy and waterproofing, while phospholipids with a hydrophilic head and hydrophobic tails form membrane bilayers. Proteins are amino acids joined by peptide bonds, with primary sequence, secondary helices and sheets from backbone hydrogen bonds, tertiary shape from R group interactions including disulfide bridges, and quaternary association of multiple chains. The food tests are iodine for starch, Benedict's for reducing sugars, acid hydrolysis and neutralisation before Benedict's for non-reducing sugars, biuret for protein and the ethanol emulsion test for lipids.