Biomolecules — Notes

Carbohydrates are polyhydroxy aldehydes or ketones (or compounds that give them on hydrolysis) and are classified by the number of sugar units.

Monosaccharides cannot be hydrolysed further: glucose (the main fuel, mass 180), ribose and deoxyribose (sugars of RNA and DNA; deoxyribose has one oxygen fewer, 150 against 134), also fructose and galactose.

Disaccharides are two monosaccharides joined by a glycosidic bond with loss of a water molecule: maltose = glucose + glucose; lactose = glucose + galactose (milk sugar); sucrose = glucose + fructose (cane sugar). Each has a mass of 342. Maltose and lactose are reducing sugars (they reduce Benedict’s solution); sucrose is non-reducing until it is hydrolysed. Hydrolysis of 171 g of sucrose takes up 9 g of water and gives 90 g of glucose and 90 g of fructose.

Polysaccharides are long chains of monosaccharides:

• Starch — reserve food of plants (glucose units).
• Glycogen — reserve food of animals, in liver and muscle; highly branched glucose polymer.
• Cellulose — structural polysaccharide of plant cell walls; glucose units joined differently from starch, so humans cannot digest it.
• Inulin — polymer of fructose; a reserve in tubers and roots such as dahlia and chicory.
• Chitin — polymer of an amino sugar; wall of fungi and exoskeleton of arthropods.

Amino acids are the monomers of proteins. Each has an amino group, a carboxyl group, a hydrogen atom and an R group attached to the same (alpha) carbon. They differ only in R: glycine (R = H, 75), alanine (R = CH₃, 89) and serine (R = CH₂OH, 105).

In water, the carboxyl group gives up a proton to the amino group, so the molecule carries both a positive (NH₃⁺) and a negative (COO⁻) charge and no net charge: a zwitterion. In acid it carries a net positive charge, and in alkali a net negative charge.

Classes by R group: neutral (glycine, alanine, serine, valine); acidic (aspartic acid and glutamic acid, with an extra carboxyl group); basic (lysine, arginine, histidine); sulphur-containing (cysteine, methionine). Essential amino acids cannot be made by the body and must come from food: valine, leucine, isoleucine, lysine, methionine, phenylalanine, threonine and tryptophan (histidine is also essential for infants). Non-essential ones such as glycine, alanine and serine can be made.

A peptide bond joins the carboxyl group of one amino acid to the amino group of the next, releasing water. The tripeptide of glycine, alanine and serine weighs 233 (269 − 2 × 18).

Proteins are polymers of amino acids. Four levels of structure:

• Primary — the sequence of amino acids joined by peptide bonds (covalent). A change of one amino acid can change the function of the protein.
• Secondary — regular folding of the chain into an α-helix or β-pleated sheet, held by hydrogen bonds between backbone groups.
• Tertiary — folding of the whole chain into a three-dimensional shape, held by hydrogen bonds, ionic and hydrophobic interactions and disulphide bridges between cysteines.
• Quaternary — association of two or more folded polypeptide chains (subunits) by weak bonds, as in haemoglobin.

Denaturation (by heat, acid or alkali) breaks the weak bonds and unfolds the protein, but the peptide bonds of the primary structure stay intact. Functions: enzymes, structure (collagen, keratin), transport (haemoglobin), hormones (insulin), defence (antibodies), contraction (actin, myosin), storage (casein).

A chain of n amino acids has n − 1 peptide bonds; a protein of 280 amino acids in 4 chains has 276.

Lipids are insoluble in water and soluble in organic solvents. Simple lipids: fats, oils (esters of glycerol and fatty acids) and waxes. Compound lipids: phospholipids and glycolipids. Derived lipids: fatty acids, glycerol and steroids such as cholesterol.

A triglyceride is glycerol (mass 92) joined to three fatty acids by ester bonds with loss of three water molecules; tripalmitin weighs 806. Saturated fatty acids have no double bonds, so the chains pack closely and the fat is solid at room temperature (usually animal fats); unsaturated fatty acids have one or more double bonds that bend the chain, so the oil is liquid (usually plant oils).

Functions: energy store (about 9 kcal per gram, more than twice that of carbohydrate), insulation, protection of organs, waterproofing (wax), structure of membranes (phospholipids, cholesterol) and hormones (steroids).

Enzymes are biological catalysts, almost all proteins. They lower the activation energy, are specific (active site), are not used up, act in small amounts under mild conditions and can act in both directions. Names usually end in -ase (substrate or reaction type).

Six classes: oxidoreductases (oxidation and reduction; lactate dehydrogenase), transferases (transfer of a group; hexokinase), hydrolases (hydrolysis; lipase, lactase), lyases (removal of a group without water; decarboxylase), isomerases (rearrangement; glucose phosphate isomerase), ligases (joining using ATP; DNA ligase).

Cofactors. The protein part is the apoenzyme; with its cofactor it is the holoenzyme. Prosthetic group: organic, tightly bound (haem in catalase). Coenzyme: organic, loosely bound, often from a vitamin (NAD from niacin). Metal ions: zinc, magnesium.

Effects. Activity rises with temperature to an optimum (about 37 °C for a human enzyme; 8, 16, 30, 49, 70, 88, 100, 17, 0 per cent at 5, 10, 15, 20, 25, 30, 37, 45 and 55 °C in the model) and then falls as the enzyme is denatured; each enzyme has an optimum pH (pepsin about 2, trypsin about 8). With rising substrate the rate increases to a maximum (80 units in the model; 26.7, 40, 53.3, 66.7, 72.7, 76.2 at substrate 5, 10, 20, 50, 100, 200).

Competitive inhibition. An inhibitor resembling the substrate occupies the active site; the maximum rate is unchanged but a higher substrate concentration is needed (16, 26.7, 40, 57.1, 66.7, 72.7 with the inhibitor). Example: malonate inhibits succinic dehydrogenase because it resembles succinate.

Primary metabolites (sugars, amino acids, lipids, nucleotides) take part in the basic life of the cell. Secondary metabolites are compounds that are not directly needed for growth, development or reproduction, but have ecological and economic importance.

Examples: alkaloids (morphine, quinine, nicotine, caffeine) — defence against herbivores and medicines; pigments (carotenoids, anthocyanins) — colour to attract pollinators and animals that spread seeds; gums (gum arabic) and resins — seal wounds; terpenoids such as essential oils, rubber; toxins (abrin, ricin) and drugs (vinblastin, curcumin).