From atoms to molecules

Chapter 2

From atoms to molecules

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.

Ring Compounds

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)  


Aldehydes and ketones

If alcohols are dehydrogenated they yield two types of compound, both of which contain the reactive carbonyl –C=O group. Thus removal of 2H from a primary alcohol will yield an aldehyde:


while removal of 2H from a secondary alcohol yields a ketone:


Dehydrogenation reactions of this type frequently occur in metabolic processes and are readily reversible.

Aldehydes and ketones are tautomeric compounds and, as a result of a shift in the position of the double bond and of a hydrogen atom, may exist in either keto or enol forms.


Acetone is formed in the body by the decarboxylation of acetoacetate when this is present in relatively large amounts in the condition of ketosis (page 262).

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.


Oxidation reactions in the body are commonly performed in this manner, i.e. by the addition of water at a double bond followed by removal of 2H atoms.

Dec 10, 2015 | Posted by in General Dentistry | Comments Off on From atoms to molecules
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