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

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.

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.

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

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).

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

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.

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

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)

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

• 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

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

• 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 $\mathrm{-COO^-}$

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

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

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

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

• 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’

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

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.

• 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)

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.

• $K_m$ = 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

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.

Biology studies life in all its forms — from microscopic cells to entire ecosystems.

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

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

• Biology
• Cells
• Genetics and DNA