From atoms to molecules

Publisher Summary

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.

Before proceeding to the study of the macromolecules which characterize living organisms it may be helpful to give a brief review of the types of compound found in living systems.

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.

Open chain hydrocarbons

These may or may not be branched and may or may not contain double bonds.

Ring Compounds

Hydrocarbon ring compounds

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, so that all the –C–C– bonds are equivalent, is the parent substance of the aromatic series of compounds.

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.

Oxygen-containing ring compounds

and also

Oxygen-containing ring structures of this type occur in the carbohydrates.

Nitrogen-containing ring compounds

These are found in the proteins and nucleic acids. The rings may be five- or six-membered and may contain one or two nitrogen atoms.

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.

Fused ring systems

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.

Functional groups

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.

Table 2.1

Some important functional groups

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)

Hydroxyl groups

Compounds containing a hydroxyl group are known as alcohols. They are customarily referred to as primary, secondary and tertiary alcohols according to the number of hydrocarbon groups

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).