Biological Molecules

1. Biological Molecules — Overview

4 most common elements in living organisms: Carbon, Hydrogen, Oxygen, Nitrogen (C H O N). Other elements (Fe, Zn, Mg …) = micronutrients — needed in tiny amounts only.

Biological molecule	Elements	Note
① Carbohydrates	C, H, O	direct energy source (→ glucose → ATP)
② Proteins	C, H, O, N	growth & development, enzymes, hormones
③ Lipids	C, H, O	NOT a polymer — only a macromolecule
④ Nucleic acids	C, H, O, N, P	RNA and DNA (studied in Ch. 6 – protein synthesis & DNA)
⑤ Water	H₂O	70–95 % of cell mass; body ≈ 60–65 % water

Carbs → broken to glucose → oxidised → ATP (energy currency of the cell). DNA = identity card of the cell: stores hereditary info; DNA & RNA are used to make protein enzymes / protein hormones. ~90 % of blood plasma is water.

Three key terms

Macromolecule: a giant (large) molecule made up of simpler molecules. (macro = large, micro = small)

Polymer: a large molecule made up of small repeating units called monomers. (poly = many)

Monomer: a small molecule which is the repeating unit of a polymer.

2. Carbohydrates (C – H – O)

All carbohydrates contain only carbon, hydrogen and oxygen. The “hydrate” part of the name = water: H and O are present in a 2 : 1 ratio (like in H₂O).

Old idea: chemists thought carbs were “hydrates of carbon” (carbon + water molecules) — they are not actually joined with water, but the name and formula stayed. e.g. glucose C₆H₁₂O₆ → simplest ratio CH₂O.

Carbohydrates are divided into 3 main groups (saccharide = sugar / sweet):

• Monosaccharide formula (CH₂O)ₓ: hexose x = 6 → C₆H₁₂O₆; pentose x = 5 → C₅H₁₀O₅ (ribose).
• Deoxyribose = ribose with one oxygen less → C₅H₁₀O₄ (like deoxygenated blood has less O₂).
• Disaccharide: 2 monosaccharides joined by a covalent bond, 1 H₂O lost = condensation reaction (two units join → bigger unit + small molecule lost; anabolic).
• Polysaccharide = polymer ⇒ the monomers must be the same repeating unit (disaccharides can have 2 different monosaccharides, e.g. sucrose).

3. Monosaccharide — Glucose (α & β)

Glucose is made in photosynthesis and oxidised for energy → very important in exams (both forms!). In solution the straight-chain form is not stable, so it folds into a ring: C5 bonds with C1 (ring closes through O), and C6 (CH₂OH) sits outside the ring. Each C makes 4 bonds (tetravalent).

Important: in MCQs you must identify whether a disaccharide’s monomers are α or β glucose from the OH position; in drawing questions 1 mark is for the correct ring — drawing β instead of α loses the mark. Practise drawing both rings by heart!

4. Disaccharides (Condensation Reactions)

Formed by the joining of 2 monosaccharides with loss of 1 H₂O (condensation).

Disaccharide	Made of	Bond
① Maltose	α-glucose + α-glucose	α-1,4 glycosidic
② Sucrose	α-glucose + fructose	glycosidic (C1 of glucose – C2 of fructose)
③ Lactose	α-glucose + galactose or β-glucose + galactose	glycosidic
④ Cellobiose	β-glucose + β-glucose	β-1,4 glycosidic

After water is lost, O and C each have an incomplete valency, so the O bridges the two carbons. Both –OH must lie in the same plane; if not, one ring is flipped (see cellobiose). The bond is always between C1 of one and C4 of the other glucose.

Fructose — ring form

Fructose is a ketose (C=O in the middle, C2), a hexose like glucose and galactose.

Sucrose = α-glucose + fructose

Lactose

Lactose = glucose + galactose; it can be made with α-glucose + galactose or β-glucose + galactose (two forms) — joined by a glycosidic bond after loss of H₂O. (Milk sugar.)

Cellobiose = β-glucose + β-glucose

Here a problem: in β-glucose the C1 –OH points up but the C4 –OH of the other β-glucose points down, so the two –OH are not in the same plane and cannot meet. Fix: one β-glucose rotates / flips by 180° — then the C1–OH and C4–OH face each other, H₂O is lost and a β-1,4 glycosidic bond forms.

5. Reducing Sugars & Benedict’s Test

Reducing sugars (= reducing agents) can carry out reduction of another substance; in the process the sugar itself is oxidised.

• Reducing sugars = all monosaccharides + some disaccharides (maltose, lactose, cellobiose).
• Sucrose is NOT a reducing sugar (non-reducing disaccharide).
• Polysaccharides (starch, glycogen, cellulose) = non-reducing.

Benedict’s test

Benedict’s reagent = copper(II) sulfate (CuSO₄) in alkaline solution; blue colour. Reducing sugars reduce the soluble blue Cu²⁺ to insoluble brick-red copper oxide (contains Cu⁺).

Method: ① ~2 cm³ of test solution ② add an equal volume of Benedict’s solution ③ heat in a water bath ④ look for the colour change → brick-red precipitate = reducing sugar present.

Testing for a non-reducing sugar (sucrose)

Sucrose → no change with Benedict’s (stays blue) → hydrolyse with dilute HCl (boil) → breaks glycosidic bond → 2 monosaccharides (glucose + fructose = reducing sugars) → then do Benedict’s again → brick-red ppt.

6. Polysaccharides

Made by joining many monosaccharide molecules (monomers) by condensation. Examples: starch, glycogen, cellulose — all non-reducing and osmotically inactive.

Each time 2 monosaccharides join, 1 H₂O is lost, so the polysaccharide formula has 2 H and 1 O less per unit (C₆H₁₂O₆ → C₆H₁₀O₅). For n monosaccharides, (n − 1) water molecules are lost. (n = number of monosaccharides joining.)

Why store glucose as a polysaccharide?

Glucose is a reactive molecule — it would interfere with normal cell chemistry — and it is osmotically active: dissolved glucose (solute) raises the solute concentration → water potential falls → water enters by osmosis, disturbing the cell. So glucose is converted by condensation into a storage polysaccharide:

Starch (made of α-glucose) — amylose + amylopectin

	Amylose	Amylopectin
Monomer	α-glucose	α-glucose
Shape	helical, unbranched	branched, non-helical
Bonds	α-1,4 glycosidic only	α-1,4 and α-1,6
Digestion (hydrolysis)	more resistant (few free ends)	less resistant — more free ends because of branching
Mᵣ	relatively lower (fewer monomers)	relatively greater
Solubility	—	more water-soluble
With iodine solution	stains blue-black (red-brown → blue-black)	does not cause the same colour change

Glycogen

• Monomer: α-glucose; storage polysaccharide in animal and fungal cells (granules).
• Structure is similar to amylopectin.

Similarities with amylopectin	Differences with amylopectin
• branched • α-1,4 and α-1,6 glycosidic bonds	• more branching in glycogen • Mᵣ greater than amylopectin • glycogen is less resistant to digestion (easier to hydrolyse) than amylopectin

Cellulose (made of β-glucose)

• Structural role — mechanically strong; found in the plant cell wall; most abundant organic molecule.
• Monomer: β-glucose; β-1,4 glycosidic bonds; general formula (C₆H₁₀O₅)ₙ (n = number of monosaccharides joined).

Cellulose molecule = linear, unbranched chain of β-glucose where every alternate β-glucose is rotated by 180° (so that C1-OH and C4-OH can meet).

Comparing polysaccharides

Feature	Amylose	Amylopectin	Glycogen	Cellulose
Monomers	α-glucose	α-glucose	α-glucose	β-glucose
Bonds	1,4 GB	1,4 & 1,6 GB	1,4 & 1,6 GB	β-1,4 GB
H-bonds present	✓	✓	✓	✓ (key feature)
Structure	helical, unbranched	branched, non-helical	branched, non-helical (more branched)	linear, unbranched
Found in	plants	plants	animals / fungi	plants (cell wall)
Exists as	starch grains	starch grains	glycogen granules	fibres
Rotation of monomers	✗	✗	✗	✓ (alternate 180°)
Stains with iodine	✓	✗	✗	✗
Role	energy store	energy store	energy store	structural
Reducing sugar	✗	✗	✗	✗
Osmotically active	✗	✗	✗	✗

7. Lipids (C – H – O)

Fats (animal lipids) → usually solid at room temp · Oils (plant lipids) → usually liquid at room temp.

• A macromolecule but NOT a polymer — not made of repeating units of the same molecule/atoms.
• Organic compounds insoluble in water, soluble in organic solvents.
• Most lipids are formed by fatty acids combining with an alcohol.

① Triglycerides

= 3 fatty acids + 1 glycerol. Fatty acid = organic acid with a –COOH group and a long C–H chain. Glycerol (C₃H₈O₃) = trihydroxy alcohol (3 –OH groups in 1 molecule).

Fatty acids: saturated vs unsaturated

• Saturated (C–C only) · unsaturated (C=C): one double bond = monounsaturated; more than one = polyunsaturated.
• Note: double bonds make fatty acids / lipids melt more easily (loose packing).
• Skeletal formulae: C and H are not shown unless in a group (e.g. –COOH, –CH₃); each corner/end = a carbon. A 12-carbon fatty acid = 12 corners with –COOH at one end.

② Phospholipids

Amphipathic — has both a polar and a non-polar part: phosphate head = hydrophilic (water-loving), soluble; 2 fatty acid tails = hydrophobic (water-hating), insoluble. Fatty acids are joined to glycerol by ester bonds. They form membranes.

Functions / benefits of lipids (stored in adipose tissue)

• Excellent energy store — stored in unlimited amounts (kidney, under the skin, heart …).
• Many C–H bonds (energy-rich) ⇒ yield more energy than carbohydrates on oxidation of the same mass (more than 2×).
• Thermal insulation (under the skin).
• Metabolic source of water to small organisms in dry areas — aerobic respiration releases H₂O; more H atoms ⇒ more water produced.
• Synthesis of steroidal (lipid-based) hormones — testosterone, oestrogen, progesterone (control & coordination).
• Electrical insulation via the myelin sheath — prevents leakage of ions as they move across neurons.

8. Proteins (made of amino acids)

Structure of an amino acid (building block)

Peptide bond (condensation)

–COOH of one amino acid + –NH₂ of the next → –H₂O → peptide bond (–CO–NH–). 2 amino acids = dipeptide; many = polypeptide.

Levels of protein folding

① Primary structure: the sequence of amino acids in a polypeptide chain (held by peptide bonds). Decided by the DNA / gene — always the same for a given protein.

② Secondary structure: regular folding of the polypeptide chain into an α-helix or β-pleated sheet, due to hydrogen bonding between amino acids in the chain: the O of C=O of one amino acid and the H of N–H of another interact via H-bonding ⇒ chain bends back on itself.

R groups (decide tertiary structure)

R group type	Charge	Interaction formed
Polar	partial charge (δ+ / δ–)	hydrogen bonds
Charged	complete (full) charge, + or –	ionic bonds
Non-polar	no charge	hydrophobic interactions (water-hating groups cluster together away from water)
2 cysteines (–SH)	—	disulfide linkage (S–S) after 2 H are lost

③ Tertiary structure: regular 3D folding of a polypeptide chain due to H-bonds (between polar R groups), hydrophobic interactions (non-polar R groups), ionic bonds (charged R groups) and disulfide linkages (between 2 cysteine R groups). Level of folding > secondary.

④ Quaternary structure: forms when 2 or more polypeptide chains (of a protein) associate via H-bonds, hydrophobic interactions, ionic bonds and/or disulfide linkages.

Protein	Polypeptide chains	Quaternary?
Haemoglobin	4	✓ yes
Insulin	2	✓ yes
Myoglobin	1	✗ cannot have a quaternary structure

Globular vs fibrous proteins

	Globular — soluble	Fibrous — insoluble
R groups pointing outwards	hydrophilic ⇒ water soluble	hydrophobic ⇒ water insoluble
Shape	spherical / circular	long, narrow strands
pH & temperature	sensitive to changes	less sensitive
Examples	enzymes, haemoglobin	keratin, collagen

Evidence: nails and hair (keratin) are never seen dissolving in water ⇒ fibrous proteins are insoluble. Enzymes are globular so are sensitive to pH & temperature.

Haemoglobin (globular)

• 1 Hb molecule = 4 polypeptide chains: 2 identical α-chains (α-globins) + 2 identical β-chains (β-globins) → quaternary structure.
• Each chain has a haem group (a prosthetic group) with iron (Fe²⁺) at its centre; Fe²⁺ reversibly binds one O₂ ⇒ 1 Hb holds 4 O₂.

Definition to learn: haemoglobin is an iron-containing protein.

Collagen (fibrous protein)

• Found in skin, tendons, cartilage, bones, teeth, walls of blood vessels; most common protein in animals; structural protein — up to 25 % of total protein of a mammalian body.
• High tensile strength (+ flexible); not easily affected by pH & temperature changes.
• Every 3rd amino acid is glycine (smallest) ⇒ the 3 chains can lie very close and form a tight coil (tropocollagen).

9. Water

70–95 % of cell mass; the human body is ~60–65 % water; ~90 % of blood plasma. Water is a polar molecule with a non-linear, bent shape. δ⁻ O attracts δ⁺ H of neighbours ⇒ hydrogen bonds between molecules.

① Excellent solvent for polar & ionic molecules

δ⁻ O surrounds Na⁺, δ⁺ H surrounds Cl⁻ ⇒ ions separate and dissolve. Water is therefore the transport medium in plants and animals (blood, xylem, phloem) and the medium of reactions in cytoplasm.

② High specific heat capacity

Definition: the amount of heat energy required to raise the temperature of one unit mass of water by 1 °C / 1 K.   Q = m c ΔT  ;  c = Q / mΔT

To raise the temperature of a liquid, molecules must gain energy and move faster. H-bonds make it harder for molecules to move freely, so they must be broken ⇒ MORE heat energy is needed.

③ High latent heat of vaporisation

The heat energy needed to vaporise 1 g of liquid at constant temperature. The network of H-bonds means a high energy input is needed to change 1 g liquid water → vapour.

④ Cohesion & surface tension

Cohesion = attraction between molecules of the same kind. Surface tension = tendency of liquid surfaces at rest to shrink into the minimum surface area possible.

⑤ Adhesion

Attraction of water molecules for molecules of a different kind ⇒ water sticks to the sides of vessels.

⑥ Maximum density at 4 °C — anomalous behaviour

Normal liquid: heated → expands (volume ↑, density ↓); cooled → contracts (volume ↓, density ↑). Density = mass/volume, mass constant ⇒ d ∝ 1/V. Cooling water from 100 °C down to 4 °C: volume ↓, density ↑ (this part is normal contraction, not due to H-bonding). At 4 °C maximum density is reached; on cooling below 4 °C water expands (volume ↑, density ↓) ⇒ anomalous behaviour of water.

10. Quick Recap — Chapter Cheat-Sheet