From atoms to molecules
This chapter discusses the macromolecules that characterize living organisms. Life is based on carbon compounds and is only possible on account of their variety and complexity. As carbon atoms can form stable covalent bonds with other carbon atoms, chains and ring structures can be built up. The parent substances for all other organic compounds are the hydrocarbons that contain hydrogen as the only other element besides carbon. Their molecules contain a number of carbon atoms linked to give either an open chain structure or a closed form containing one or more rings. Certain derivatives of ring hydrocarbons containing five or six carbon atoms and their unsaturated counterparts are biologically important. Benzene, which contains alternate, resonating double bonds, is the parent substance of the aromatic series of compounds. As distinct from benzene and other ring systems that contain carbon as the only ring constituent are a number of heterocyclic ring compounds in which one or more of the carbons is replaced by an oxygen, nitrogen, or sulfur atom. These may be either saturated or unsaturated.
Life is based on carbon compounds and is only possible on account of their variety and complexity. Since carbon atoms can form stable covalent bonds with other carbon atoms, chains and ring structures can be built up; also because carbon is tetravalent, branched as well as straight chain compounds are possible.
The parent substances for all other organic compounds are the hydrocarbons which contain hydrogen as the only other element besides carbon. Their molecules contain a number of carbon atoms linked to give either an open chain structure or a closed form containing one or more rings.
As distinct from benzene and other ring systems which contain carbon as the only ring constituent are a number of heterocyclic ring compounds in which one or more of the carbons is replaced by an oxygen, nitrogen or sulphur atom. These too may be either saturated or unsaturated.
The imidazole ring occurs in the amino acid histidine (page 36) and the pyrrole ring in haem (page 371). Pyrimidine derivatives are found in the nucleotides and nucleic acids.
In addition to the simple ring systems described above, certain more complex systems consisting of two or more rings fused together are found in Nature. The steroids, which include the membrane constituent cholesterol as well as the adrenocortical and sex hormones, are derived from the sterane ring composed of three six-membered and one five-membered hydrocarbon rings containing 17 carbon atoms altogether.
Heterocyclic fused ring systems are found in a variety of biological compounds. The amino acid tryptophan (page 38) contains the indole nucleus, adenine and guanine (page 110) are purine derivatives and riboflavin (page 163) contains the alloxazine ring.
The hydrocarbons and heterocyclic ring compounds described above are rather inert and unreactive but they become more reactive if one or more of their hydrogens is substituted by other groupings, notably those containing oxygen or nitrogen. Biochemically speaking the most important of these functional groups are shown in Table 2.1.
|N containing||O containing||Carbonyl containing||S containing||P containing|
|–NH2 (amino)||–OH (hydroxyl)||–COOH (carboxylic)||–SH (sulphydryl)||–PO4H2 (singly esterified phosphate)|
|=NH (imino)||=CO (carbonyl)||–CONH2 (amide)||–S–S– (disulphide)||–PO4H– (doubly esterified phosphate)|
|–SO3H (sulphonic acid)|
on the C atom which bears the hydroxyl group. Alcohols react with acids to form esters and two important classes of biological substance are compounds of this type, namely the triglycerides and the phosphoric acid esters.
Hydroxyl groups which are directly attached to an aromatic nucleus have rather different properties from aliphatic hydroxyl groups since they can act as proton donors and are therefore weakly acidic as in the case of tyrosine (page 37).
while removal of 2H from a secondary alcohol yields a ketone:
Instead of the addition of 2H to the carbonyl group of aldehydes and ketones, water may be introduced into the molecule to form hydrates that are unstable but that may be important intermediates in the formation of carboxylic acids by subsequent dehydrogenation.
The carboxylic acid grouping (–COOH), as its name suggests, has acidic properties and dissociates in water to form H+ and –COO− ions. Compounds containing a –COOH group can therefore form salts and, in the physiological pH range, most of the organic acids exist in their salt forms, e.g. citrate, oxaloacetate, acetoacetate.