SPEC 3.1.7 & 3.1.8 - BIOLOGICAL MOLECULES
Water & Inorganic Ions
The properties of water arising from hydrogen bonding, and the specific biological roles of the four spec-required inorganic ions
Why Water?
Water makes up approximately 70–95% of most living cells. Every biologically important property of water arises from the same cause: hydrogen bonding between polar water molecules.
Water is a Polar Molecule
Oxygen is more electronegative than hydrogen, pulling shared electrons towards itself. This creates a partial negative charge (δ−) on oxygen and partial positive charges (δ+) on each hydrogen. The resulting dipole allows water molecules to form hydrogen bonds with each other and with other polar/ionic substances.
Water as a Metabolite
Metabolite
A substance that participates directly in metabolic reactions as either a reactant or a product.
Hydrolysis — water REACTANT
Water is used up to break bonds
Digestion: starch + water → glucose
Proteins: peptide bonds hydrolysed → amino acids
ATP + H₂O → ADP + Pᵢ
Condensation — water PRODUCT
Water is released when bonds form
Glucose + glucose → maltose + H₂O
Amino acids joined by peptide bonds → H₂O
ADP + Pᵢ → ATP + H₂O
Also: Photosynthesis
Water is split (photolysis) in the light-dependent reactions: 2H₂O → 4H⁺ + 4e⁻ + O₂. It directly provides electrons and protons to drive the photosynthetic reactions.
Examiner Alert
When explaining water as a metabolite, always specify: "water is a reactant in hydrolysis reactions and a product of condensation reactions." Never just say "water is involved in reactions."
Water as a Solvent
Why Water Dissolves Substances
Water is a polar solvent. Its partial charges attract ionic substances (e.g. Na⁺Cl⁻) and polar molecules (e.g. glucose, amino acids), surrounding them with hydration shells and keeping them in solution.
Metabolic Reactions
Metabolic reactions require reactants in solution
Enzymes and substrates must be dissolved to interact at the active site
The cytoplasm is an aqueous medium for metabolism
Transport
Blood plasma carries dissolved glucose, amino acids, urea, O₂
Xylem sap carries dissolved mineral ions
Phloem carries sucrose dissolved in water
Examiner Alert
Say: "Water is a polar molecule; ionic and polar substances dissolve in it, allowing metabolic reactions to take place in aqueous solution and substances to be transported." Do not write "things dissolve in water" without explaining why.
High Specific Heat Capacity
Specific Heat Capacity
The amount of energy required to raise the temperature of 1 kg of a substance by 1°C. Water has a relatively high specific heat capacity because a large amount of energy is needed to break hydrogen bonds before kinetic energy (temperature) increases.
Biological Significance
Water acts as a thermal buffer — large energy inputs cause only small temperature changes
Cells resist rapid temperature fluctuations, maintaining stable enzyme activity
Aquatic habitats (lakes, seas) have stable temperatures — essential for ectotherms and aquatic organisms
Blood as a transport medium distributes heat without large temperature swings
The Mechanism
When heat energy is absorbed, much of it breaks hydrogen bonds between water molecules rather than increasing molecular kinetic energy. Temperature only rises once bonds begin breaking, so it rises slowly relative to the energy input.
High Latent Heat of Vaporisation
Latent Heat of Vaporisation
The energy required to convert a liquid to a gas without a change in temperature. Water has a relatively large latent heat of vaporisation because the many hydrogen bonds between molecules must all be broken during vaporisation.
Biological Significance
Sweating in mammals: evaporation of a small volume of water from the skin removes a large amount of heat energy — effective cooling with little water loss
Transpiration in plants: water evaporation from leaf surfaces removes heat, cooling the leaf
This makes evaporative cooling energetically efficient for thermoregulation
Examiner Alert
Always state both: (1) large amount of energy removed per unit of water evaporated, AND (2) therefore effective cooling with little water loss. Omitting "little water loss" is a very common reason for losing the mark.
Cohesion & Surface Tension
Cohesion
The attraction between molecules of the same substance, caused by hydrogen bonding between adjacent water molecules.
Xylem Water Columns
Cohesion between water molecules maintains a continuous, unbroken column of water in xylem vessels. As transpiration pulls water from the top, the entire column is drawn upward — the cohesion-tension mechanism. Without cohesion, the column would break and water transport would fail.
Surface Tension
At the water–air interface, cohesion between surface water molecules creates surface tension. This allows small organisms (e.g. pond skaters) to move across the water surface and supports the base of water columns in narrow tubes.
Adhesion (additional detail)
Adhesion is attraction between water molecules and the polar walls of xylem vessels. This also aids the upward movement of water and helps maintain contact between the water column and vessel walls.
Ice Density & Transparency
Ice is Less Dense Than Liquid Water
In ice, hydrogen bonds form a regular lattice that holds molecules further apart than in liquid water
Therefore ice is less dense than liquid water
Ice floats on the surface of bodies of water
This layer of ice insulates the liquid water below, preventing it from freezing solid
Aquatic organisms survive beneath the ice layer in winter
Transparency
Liquid water transmits visible light
Allows light to penetrate aquatic environments
Enables photosynthesis by aquatic plants and algae at depth
Also enables vision underwater for aquatic animals
Root Cause — Always the Same
Every water property traces back to hydrogen bonding between polar water molecules. In any exam answer, link the property to this structural cause for maximum marks.
Water Properties — Full Table
PropertyBiological ImportanceCause
MetaboliteReactant in hydrolysis & photosynthesis; product of condensationPolar; reactive
SolventMetabolic reactions in solution; transport of ions & moleculesPolar → dissolves ionic/polar substances
High heat capacityBuffers temperature in cells & aquatic habitatsMany H-bonds to break before temp rises
High latent heatCooling by evaporation with little water lossMany H-bonds to break to vaporise
CohesionSupports xylem water columns; surface tensionH-bonds between water molecules
TransparencyPhotosynthesis in aquatic environmentsStructure of liquid water
Ice less denseIce floats; insulates aquatic habitats in winterH-bond lattice spaces molecules further apart
Inorganic Ions — Spec Overview
Inorganic ions occur in solution in the cytoplasm and body fluids of organisms, each with a specific role depending on its properties.
The Four Spec-Required Ions (3.1.8)
IonSymbolSpec-Required RoleHydrogenH⁺Determines pH; affects enzyme activityIronFe²⁺/Fe³⁺Component of haemoglobin; O₂ transportSodiumNa⁺Co-transport of glucose and amino acidsPhosphatePO₄³⁻Component of DNA and of ATP
Spec Scope — 3.1.8
The spec explicitly requires students to recognise only these four ions. Other ions (Ca²⁺, Mg²⁺, NO₃⁻) appear elsewhere in the course in specific contexts — they are not required at 3.1.8.
H⁺ Ions & pH
Role of Hydrogen Ions
The concentration of H⁺ ions determines the pH of a solution: pH = −log₁₀[H⁺]
Higher [H⁺] = lower pH (more acidic)
Changes in pH alter enzyme activity: excess H⁺ or OH⁻ ions disrupt the ionic bonds and hydrogen bonds that maintain an enzyme's tertiary structure
This changes the shape of the active site so the substrate no longer fits → reduced reaction rate or denaturation
Synoptic Link — Lesson 1.05: Enzymes
pH effects on enzyme activity link directly to Lesson 1.05. Always specify which bonds are disrupted (ionic bonds and hydrogen bonds in tertiary structure) and the consequence (active site shape change → substrate cannot bind).
Iron Ions (Fe²⁺)
Role: Component of Haemoglobin
Each haemoglobin molecule contains 4 haem groups, each with one Fe²⁺ ion at its centre
Oxygen binds reversibly to the Fe²⁺ ion: haemoglobin + O₂ ⇌ oxyhaemoglobin
This reversible binding allows haemoglobin to load O₂ at the lungs (high pO₂) and unload O₂ at respiring tissues (low pO₂)
Without iron, haemoglobin cannot carry oxygen → iron deficiency causes anaemia
Fe²⁺ vs Fe³⁺
In functional haemoglobin, iron remains as Fe²⁺. If oxidised to Fe³⁺ (methaemoglobin), it can no longer bind oxygen. The spec notation Fe²⁺/Fe³⁺ acknowledges iron's two oxidation states in biological contexts, but haem iron is Fe²⁺.
Sodium Ions (Na⁺)
Role: Co-Transport of Glucose and Amino Acids
Na⁺ ions are actively pumped out of ileum epithelial cells via the Na⁺/K⁺ ATPase pump, creating a low [Na⁺] inside the cell
Na⁺ diffuses back into the epithelial cell down its concentration gradient — but only via a co-transporter protein that simultaneously carries glucose (or amino acid) into the cell
Glucose/amino acids are thus absorbed from the gut lumen against their own concentration gradient, driven by the Na⁺ gradient
Synoptic Link — Topic 2: Membranes & Transport
Co-transport is covered in depth in Topic 2. At 3.1.8 you just need: Na⁺ role = co-transport of glucose and amino acids across ileum epithelial cells.
Phosphate Ions (PO₄³⁻)
Role: Component of DNA and of ATP
In DNA and RNA: phosphate groups form the sugar-phosphate backbone via phosphodiester bonds, linking nucleotide monomers together
In ATP: three phosphate groups are attached to adenosine; the terminal phosphate is released during hydrolysis, transferring energy to cell reactions
Phosphate is therefore essential for both genetic information storage (DNA/RNA) and energy transfer (ATP)
Spec Wording
The spec says: "phosphate ions as components of DNA and of ATP." You must give both roles to score full marks on a question about phosphate ions. A student who says only "component of DNA" will lose a mark if ATP is also credit-worthy.
Practice Question
Explain why water is described as a metabolite in living organisms. Give two specific examples. [4 marks]
1
Water is a metabolite because it participates directly in metabolic reactions as a reactant or product. (1 mark)
2
Water is a reactant in hydrolysis reactions — e.g. water breaks the glycosidic bond between glucose monomers during digestion of starch. (1 mark)
3
Water is a product of condensation reactions — e.g. water is released when two amino acids are joined by a peptide bond. (1 mark)
✓
Additional creditworthy example: water as a reactant in photosynthesis (photolysis: 2H₂O → 4H⁺ + 4e⁻ + O₂). Any two specific examples acceptable. (1 mark)
Practice Question
State the role of each of the following ions in living organisms: (i) Fe²⁺ (ii) Na⁺ (iii) PO₄³⁻ [3 marks]
(i)
Fe²⁺ — component of the haem group in haemoglobin; binds reversibly to oxygen, enabling oxygen transport in red blood cells. (1 mark)
(ii)
Na⁺ — role in the co-transport of glucose and amino acids across the epithelial cells of the ileum; the Na⁺ gradient drives glucose/amino acid uptake into the cell. (1 mark)
(iii)
PO₄³⁻ — component of DNA and of ATP; forms the sugar-phosphate backbone of nucleic acids and provides the phosphate groups of ATP involved in energy transfer. (1 mark — both DNA and ATP must be mentioned for full credit if 1 mark is available per part)
DEEP Framework: Water
"Explain how the properties of water are important to living organisms."
DEEP CHAIN
DDefine: Water is a polar molecule due to unequal electron distribution between oxygen and hydrogen. This polarity allows hydrogen bonding between water molecules, from which all biologically important properties arise.
EExplain mechanism: As a polar solvent, water dissolves ionic and polar substances — metabolic reactions occur in aqueous solution and substances are transported in blood and xylem. High specific heat capacity (many H-bonds to break before temperature rises) buffers temperature in cells and aquatic habitats. High latent heat of vaporisation enables cooling by evaporation with little water loss (e.g. sweating). Cohesion between water molecules supports continuous water columns in xylem and creates surface tension. Water is a metabolite: reactant in hydrolysis and photosynthesis; product of condensation. Ice floats because H-bonds in the lattice hold molecules further apart — insulating aquatic habitats.
EEvidence/example: A 70 kg human at rest loses ~0.5 L of water per hour through sweating. Despite this modest water loss, the evaporation removes substantial heat — demonstrating the high latent heat of vaporisation at work in thermoregulation.
PPractical/significance: Without water's unique combination of properties — all arising from hydrogen bonding — the aqueous chemistry of life would be impossible. No other common solvent provides all these properties simultaneously.
Summary
Water Properties (3.1.7)
PropertyExam-Ready Point
MetaboliteReactant in hydrolysis & photosynthesis; product of condensation
SolventPolar → ionic/polar substances dissolve → transport & metabolism
High heat capacityBuffers temperature; many H-bonds slow temperature rise
High latent heatCooling by evaporation with little water loss
CohesionContinuous xylem column; surface tension
Ice less denseFloats → insulates aquatic habitats in winter
TransparentLight penetrates water → photosynthesis in aquatic habitats
Inorganic Ions (3.1.8) — Spec-Required Four
IonRole
H⁺Determines pH; alters enzyme active site shape via tertiary structure disruption
Fe²⁺/Fe³⁺Component of haem in haemoglobin; reversible O₂ binding
Na⁺Co-transport of glucose and amino acids across ileum epithelium
PO₄³⁻Component of DNA and of ATP (both required)
Top Exam Tip
For every water property: name the cause (hydrogen bonding/polarity) AND give a named biological example. For phosphate ions: always give both roles — DNA and ATP. For latent heat: always include "little water loss."
Next: Why Water?