Biological Molecules

Study guide covering the core biochemistry topics for A-Level Biology examinations.

:::info Board Coverage AQA Paper 1 | Edexcel A Paper 1 | OCR (A) Paper 1 | CIE Paper 2 :::

1. Water

Structure and Properties

Water ($\mathrm{H_2O}$) is a polar molecule. Oxygen is more electronegative than hydrogen, creating a dipole with $\delta^-$ on oxygen and $\delta^+$ on each hydrogen.

Property	Cause	Biological Significance
Solvent	Polarity dissolves ionic/covalent substances	Medium for metabolic reactions; transport in blood and sap
High specific heat capacity	H-bonds absorb energy before breaking	Temperature stability in organisms and environments
High latent heat of vaporisation	Many H-bonds to break	Effective cooling (sweat, transpiration)
Cohesion	H-bonds between water molecules	Water columns in xylem; surface tension
Adhesion	H-bonds with other surfaces	Capillary action in xylem vessels
Lower density as ice	Open H-bonded lattice	Ice floats, insulating aquatic habitats

Hydrogen Bonding in Water

Each water molecule can form up to 4 hydrogen bonds: two as donor (via its H atoms) and two as acceptor (via lone pairs on O). This extensive H-bonding network accounts for water’s unusual physical properties.

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2. Carbohydrates

Structure

Carbohydrates contain only C, H, and O in the ratio $\mathrm{C}_n(\mathrm{H_2O})_n$.

Monosaccharides

Glucose ($\mathrm{C_6H_{12}O_6}$) has two isomers:

• $\alpha$-glucose: OH on C1 is below the plane
• $\beta$-glucose: OH on C1 is above the plane

This single difference has enormous structural consequences (starch vs cellulose).

Other common monosaccharides: fructose, ribose ($\mathrm{C_5}$ pentose in RNA), deoxyribose ($\mathrm{C_5}$ in DNA).

Disaccharides

Formed by a condensation reaction (removal of $\mathrm{H_2O}$) creating a glycosidic bond.

Disaccharide	Monosaccharides	Glycosidic Bond	Found In
Maltose	$\alpha$-glucose + $\alpha$-glucose	$\alpha$-1,4	Digestion
Sucrose	$\alpha$-glucose + fructose	$\alpha$-1,2	Sugar cane/beet
Lactose	$\beta$-galactose + $\beta$-glucose	$\beta$-1,4	Milk

Polysaccharides

Polysaccharide	Monomer	Bonds	Structure	Function
Starch (amylose)	$\alpha$-glucose	$\alpha$-1,4	Coiled, helical	Energy storage in plants
Starch (amylopectin)	$\alpha$-glucose	$\alpha$-1,4 and $\alpha$-1,6	Branched	Energy storage in plants
Glycogen	$\alpha$-glucose	$\alpha$-1,4 and $\alpha$-1,6	Highly branched	Energy storage in animals
Cellulose	$\beta$-glucose	$\beta$-1,4	Straight, cross-linked chains	Structural (cell walls)

Key difference: $\alpha$-glycosidic bonds produce coils (starch); $\beta$-glycosidic bonds produce straight chains that form H-bonds between adjacent chains (cellulose), giving great tensile strength.

Benedict’s Test

1. Add Benedict’s reagent (blue, contains $\mathrm{Cu^{2+}}$)
2. Heat in water bath at 80 °C
3. Positive result: red/orange precipitate ($\mathrm{Cu_2O}$)

• Reducing sugars (all monosaccharides, maltose, lactose): positive directly
• Non-reducing sugars (sucrose): must first hydrolyse with dilute acid, then neutralise and test

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3. Lipids

Triglycerides

Formed from 1 glycerol + 3 fatty acids via ester bonds (condensation reactions).

• Saturated: no C=C bonds; straight chains; solid at room temp (animal fats)
• Unsaturated: one (mono-) or more (poly-) C=C bonds; kinked chains; liquid at room temp (plant oils)

Phospholipids

Modified triglycerides where one fatty acid is replaced by a phosphate group.

• Hydrophilic phosphate head, hydrophobic fatty acid tails
• Form the bilayer of cell membranes
• Essential for membrane fluidity and selective permeability

Cholesterol

• Steroid molecule with a hydrocarbon ring structure
• Small and hydrophobic — fits between phospholipid tails
• Regulates membrane fluidity: prevents crystallisation at low temp, restricts movement at high temp

Emulsion Test

1. Dissolve sample in ethanol
2. Pour into water
3. Positive result: cloudy white emulsion

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4. Proteins

Amino Acids

• 20 standard amino acids
• Each has an amino group ($\mathrm{-NH_2}$), a carboxyl group ($\mathrm{-COOH}$), an R group (variable side chain), and a hydrogen bonded to a central $\alpha$-carbon
• Zwitterions at physiological pH: $\mathrm{-NH_3^+}$ and $\mathrm{-COO^-}$

Peptide Bonds

Formed by condensation between the amino group of one amino acid and the carboxyl group of another:

$\mathrm{amino\ acid_1 + amino\ acid_2 \to dipeptide + H_2O}$

Levels of Protein Structure

Level	Description	Bonds Involved
Primary	Sequence of amino acids	Peptide bonds
Secondary	Regular folding: $\alpha$-helix or $\beta$-pleated sheet	Hydrogen bonds between backbone C=O and N-H
Tertiary	Overall 3D shape of a single polypeptide	H-bonds, ionic bonds, disulfide bridges, hydrophobic interactions
Quaternary	Assembly of two or more polypeptide subunits	Same as tertiary, between subunits

Disulfide bridges form between cysteine residues and are strong covalent bonds critical to tertiary structure stability.

Biuret Test

1. Add Biuret reagent (alkaline copper sulfate, $\mathrm{CuSO_4}$ in $\mathrm{NaOH}$)
2. Positive result: purple/violet colour (presence of peptide bonds)

Fibrous vs Globular Proteins

Feature	Fibrous	Globular
Shape	Long, rope-like	Spherical, compact
Solubility	Insoluble	Soluble
Function	Structural (collagen, keratin)	Metabolic/enzymatic (enzymes, antibodies, haemoglobin)
Bonds	Many cross-links	Hydrophobic interior, H-bonds exterior

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5. Nucleic Acids

DNA Structure

• Double-stranded helix
• Sugar-phosphate backbone on the outside; base pairs on the inside
• Adenine (A) pairs with Thymine (T) — 2 hydrogen bonds
• Guanine (G) pairs with Cytosine (C) — 3 hydrogen bonds
• Antiparallel strands: one runs 5’→3’, the other 3’→5’

DNA Replication (Semi-Conservative)

1. Helicase unwinds and unzips the double helix
2. DNA polymerase adds complementary nucleotides (5’→3’ direction only)
3. Ligase joins Okazaki fragments on the lagging strand
4. Each new molecule contains one original strand + one new strand

RNA

Type	Structure	Function
mRNA	Single-stranded; codons	Carries genetic code from DNA to ribosome
tRNA	Cloverleaf shape; anticodon	Delivers amino acids to ribosome
rRNA	Part of ribosome structure	Catalytic (peptidyl transferase) activity

ATP

Adenosine triphosphate — the universal energy currency:

$\mathrm{ATP} \rightleftharpoons \mathrm{ADP} + P_i + \text{energy}$

Hydrolysis of one phosphate bond releases $\approx 30.6\ \mathrm{kJ\,mol^{-1}}$. ATP is regenerated through respiration and photosynthesis. It is not a long-term energy store.

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6. Enzymes

Lock and Key vs Induced Fit

• Lock and key: substrate fits into a rigid active site (early model)
• Induced fit: active site changes shape slightly upon substrate binding, improving the fit (current model)

Activation Energy

Enzymes lower the activation energy ($E_a$) of a reaction by providing an alternative pathway but do not change the $\Delta H$ or equilibrium position.

Factors Affecting Enzyme Activity

Factor	Effect	Explanation
Temperature	Rate increases then falls sharply	Kinetic energy ↑, then enzyme denatures above optimum
pH	Rate peaks at optimum pH	Changes in charge affect active site shape
Substrate conc.	Rate increases then plateaus	Active sites saturated → Vmax reached
Enzyme conc.	Rate increases linearly	More active sites available

Inhibitors

Type	Mechanism	Effect on Vmax	Effect on $K_m$
Competitive	Binds to active site; competes with substrate	Decreases (but can be overcome by high [S])	Increases
Non-competitive	Binds to allosteric site; changes enzyme shape	Decreases (cannot be overcome)	No change

$K_m$ and Vmax

• $K_m$ = substrate concentration at which rate = $\frac{1}{2}$Vmax
  • Low $K_m$ = high affinity for substrate
  • High $K_m$ = low affinity for substrate
• Vmax = maximum rate when all active sites are saturated

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7. Inorganic Ions

Ion	Role	Example
Iron ($\mathrm{Fe^{2+}}$)	Component of haemoglobin; binds $\mathrm{O_2}$ in transport	Haemoglobin (4 Fe ions per molecule)
Calcium ($\mathrm{Ca^{2+}}$)	Bones and teeth (as calcium phosphate); blood clotting (factor IV)	Bones, teeth, blood clotting cascade
Hydrogen ions ($\mathrm{H}^+$)	Determines pH; affects enzyme activity	Stomach acid (pH 1.5–2.0); enzyme optima
Phosphate ($\mathrm{PO_4^{3-}}$)	ATP, DNA/RNA backbone, phospholipids	ATP, nucleotides, cell membranes
Sodium ($\mathrm{Na^+}$)	Co-transport; nerve impulse transmission; kidney function	$\mathrm{Na^+}/\mathrm{K^+}$ pump; co-transport of glucose
Nitrate ($\mathrm{NO_3^-}$)	Nitrogen source for amino acid synthesis	Protein production in plants

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8. Common Mistakes

1. Confusing $\alpha$- and $\beta$-glucose. This single stereochemical difference determines whether a polysaccharide is a storage molecule (starch) or structural (cellulose).

2. Writing “peptide bonds are between amino acids” without specifying the groups. The bond is between the $\mathrm{-NH_2}$ of one amino acid and the $\mathrm{-COOH}$ of another, with the loss of $\mathrm{H_2O}$.

3. Claiming enzymes are “used up” in reactions. Enzymes are catalysts — they are regenerated at the end of each reaction cycle.

4. Confusing DNA and RNA. Key differences: RNA is single-stranded, has ribose (not deoxyribose), and uses uracil (not thymine).

5. Stating ATP “stores energy.” ATP transfers energy rapidly; it is a short-term energy carrier, not a long-term store (that role belongs to lipids/glycogen/starch).

6. Misidentifying the effect of competitive inhibitors on Vmax. Competitive inhibitors can be overcome by increasing substrate concentration, so Vmax is unchanged; only $K_m$ increases.

7. Forgetting that phospholipids form bilayers, not monolayers. The hydrophilic heads face outward toward water; the hydrophobic tails face inward, away from water.

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Summary

Biological molecules are the building blocks of life. The key themes:

• Water’s unique properties (polarity, H-bonding) underpin all aqueous biochemistry
• Carbohydrates are energy stores (starch, glycogen) and structural components (cellulose)
• Lipids provide energy storage, membrane structure, and insulation
• Proteins have diverse functions determined by their 3D structure
• Nucleic acids store and transmit genetic information
• Enzymes are biological catalysts whose function depends on structure and conditions
• Inorganic ions play essential roles in biological processes

Understanding the link between molecular structure and biological function is central to A-Level Biology.

Worked Examples

Worked examples demonstrating the application of key concepts are covered in the detailed sub-pages linked above.

Common Pitfalls

• Confusing terminology or concepts that appear similar but have distinct meanings.
• Overlooking key assumptions or boundary conditions that limit applicability.