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Biological molecules

A-Level Biology 9700 · Topic 2 revision notes

Everything from the 5 lessons of this topic on a few pages: the key idea of each lesson, the diagram to remember, the points to learn and the traps examiners set. Read it, cover it, test yourself.

  1. Testing for biological molecules
  2. Carbohydrates
  3. Lipids
  4. Proteins
  5. Water

1Testing for biological molecules

Syllabus 2.1

Each test pairs a reagent with a colour change. Benedict's (heat) goes from blue to a brick-red precipitate with reducing sugars, through green, yellow and orange as the sugar concentration rises. A non-reducing sugar such as sucrose gives a negative Benedict's until it is hydrolysed by boiling with dilute acid and then neutralised. Iodine in potassium iodide turns blue-black with starch, the emulsion test gives a milky-white emulsion with lipids, and biuret turns lilac with proteins. Standardise the Benedict's test and compare with colour standards, and it becomes a way to estimate concentration.

Benedict's colour standards (glucose concentration) 0%0.1%0.25%0.5%1.0%unknown bluegreenyelloworangebrick redorange more reducing sugar → more Cu⁺ → more red precipitate about 0.5% same volumes, same temperature, same heating time for every tube
Fig. 1: a set of Benedict's colour standards made from known glucose concentrations, used to estimate the concentration of an unknown

Reagent, method, both colours.

  • Benedict's: heat; blue → green, yellow, orange, brick red.
  • Non-reducing sugar: negative Benedict's, boil with HCl, neutralise, retest.
  • Iodine: orange-brown → blue-black. Biuret: blue → lilac.
  • Emulsion: ethanol, then water; milky white means lipid.

Watch out!

Benedict's must be in excess for the semi-quantitative test. If all the Cu2+ is used up, every concentration above a certain value gives the same brick red, and the test can no longer tell them apart.

If the first Benedict's test is already positive, a colour after hydrolysis proves nothing on its own: you would need a deeper colour (more precipitate) after hydrolysis than before to show a non-reducing sugar was there as well.

2Carbohydrates

Syllabus 2.2

Carbohydrates are built from monosaccharides such as glucose (a hexose) and ribose (a pentose). Glucose exists as α-glucose (OH on carbon 1 below the ring) and β-glucose (OH on carbon 1 above). Two monosaccharides join by condensation, losing water and forming a covalent glycosidic bond; hydrolysis adds water to break it. Chains of α-glucose coil into starch and glycogen, compact insoluble energy stores; chains of β-glucose, with alternate units inverted, lie straight and hydrogen-bond into the microfibrils of cellulose.

α-glucoseβ-glucose OO 12345 12345 CH₂OHOHOHH CH₂OHOHOHH OHOH C1 OH below the ringC1 OH above the ring OH on carbon 3 and most H atoms omitted for clarity
Fig. 1: ring forms of α-glucose and β-glucose. The only difference is the position of the OH group on carbon 1

Monomer, bond, shape, job.

  • α-glucose: C1 OH below the ring. β: above.
  • Condensation removes water; hydrolysis adds it.
  • Starch and glycogen: α-glucose, compact, insoluble stores.
  • Cellulose: β-glucose, straight chains, H-bonded microfibrils.

Watch out!

Each hydrogen bond in cellulose is weak; the strength comes from the very large number of them between many parallel chains. And cellulose is not coiled: only α-glucose chains form helices.

3Lipids

Syllabus 2.2

A triglyceride is one glycerol joined to three fatty acids by three ester bonds, each formed by condensation between an OH of glycerol and the COOH of a fatty acid. Triglycerides are non-polar and hydrophobic. Saturated fatty acids have no C=C double bonds and straight tails; unsaturated ones have at least one C=C, which kinks the tail. Their many C-H bonds make triglycerides an energy-dense, insoluble store. In a phospholipid one fatty acid is replaced by a phosphate group, giving a hydrophilic (polar) head and two hydrophobic (non-polar) tails.

triglyceridephospholipid glycerol 3 ester bonds fatty acid tails C=C: kink P polar head(hydrophilic)non-polar tails(hydrophobic) each ester bond forms by condensation, releasing one water molecule
Fig. 1: a triglyceride with one unsaturated fatty acid, and a phospholipid with its phosphate head

Glycerol, three tails, three waters.

  • Ester bond: COOH of fatty acid + OH of glycerol, minus H2O.
  • Saturated: no C=C, straight. Unsaturated: C=C, kinked.
  • Triglyceride: non-polar, hydrophobic, energy-dense store.
  • Phospholipid: hydrophilic phosphate head, hydrophobic tails.

Watch out!

A triglyceride is not a polymer: glycerol and fatty acids are different molecules, not a chain of repeating monomers. And do not call the phospholipid head "hydrophobic because it contains phosphorus": it is hydrophilic because the phosphate group is charged.

4Proteins

Syllabus 2.3

Every amino acid has a central carbon carrying an amine group (NH2), a carboxyl group (COOH), a hydrogen atom and a variable R group. Amino acids join by condensation to form peptide bonds. The primary structure is the sequence of amino acids; secondary structure is the α-helix or β-pleated sheet held by hydrogen bonds in the backbone; tertiary structure is the overall 3D folding held by hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide bonds between R groups; quaternary structure is two or more polypeptides together. Globular proteins such as haemoglobin are soluble with physiological roles; fibrous proteins such as collagen are insoluble with structural roles.

amino aciddipeptide R H₂NCCOOHH amine groupcarboxyl group R group: 20 kinds H₂NCCNCCOOH R₁R₂ OH peptide bond (C-N) condensation: OH from COOH + H from NH₂ → H₂O released hydrolysis: H₂O added to break the peptide bond
Fig. 1: the general structure of an amino acid, and the peptide bond formed when two amino acids condense

Level, then bond.

  • Primary: sequence, peptide bonds.
  • Secondary: α-helix and β-sheet, backbone hydrogen bonds.
  • Tertiary: R-group bonds: hydrophobic, hydrogen, ionic, disulfide.
  • Globular soluble and physiological; fibrous insoluble and structural.

Watch out!

The hydrogen bonds of secondary structure are between atoms of the polypeptide backbone (C=O and N-H), not between R groups. The hydrogen bonds that help hold tertiary structure are between R groups.

5Water

Syllabus 2.4

Oxygen attracts the shared electrons in each O-H bond more strongly than hydrogen, so a water molecule is polar: the O is slightly negative (δ−) and each H slightly positive (δ+). A hydrogen bond is the attraction between a δ+ hydrogen of one molecule and a lone pair on the δ− oxygen of another. Because water is polar it is an excellent solvent for ions and polar molecules. Because hydrogen bonds must be broken first, water has a high specific heat capacity (its temperature changes slowly) and a high latent heat of vaporisation (evaporation removes a lot of heat).

OOO HHHHHH hydrogen bond δ−δ−δ− δ+δ+δ+ covalent O-H attraction between a δ+ H and a lone pair on a δ− O of another molecule each molecule can form up to four hydrogen bonds
Fig. 1: hydrogen bonds between polar water molecules

Always start from the hydrogen bond.

  • Polar: δ− O, δ+ H, bent molecule.
  • Solvent: ions and polar molecules dissolve; transport and reactions.
  • Specific heat capacity: temperature changes slowly.
  • Latent heat of vaporisation: evaporation cools.

Watch out!

Do not mix up the two thermal properties. Specific heat capacity is about how much energy it takes to raise the temperature, so it explains stable temperatures. Latent heat of vaporisation is about the energy needed to evaporate water, so it explains cooling by sweating and transpiration.

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