Biological Molecules
Carbon skeletons
Carbon has four unpaired electrons which can participate in four covalent bonds.
The geometric arrangement of these bonds is tetrahedral.
Such a bond arrangement is ideal for the formation of chains - carbon is the ultimate LEGOŽ
block.
All biological molecules are made of carbon chains.
Polymorphism of carbon chains
Carbon chains can take many forms depending on:
(i) which of the four possible carbon bonds are utilized for carbon-to-carbon linkages
(geometry);
(ii) how many electron pairs are shared (bond multiplicity);
(iii) presence of functional groups and
(iv) functional group arrangement (isomerism).
Chain geometry
"Straight" chain
butane
We often abbreviate the above representation by dropping the symbols. It is implicit that the joint of two
segments contains CH2, the joint of 3 segments has a CH group and each chain ends with a CH3.
butane
Branched chain
isobutane
Ring
cyclohexane
Multiple bonds
The presence of multiple bonds introduces further polymorphism. Two carbon atoms can share
two or three electron pairs.
benzene
Functional groups
The carbon chains, in addition to basic units of carbon and hydrogen, contain various specialized groups.
These substituents give chemical (acid, base) or physical
character (polar) to an otherwise nonpolar carbon chain.
Amino: -NH2
Amino groups are proton acceptors making carbon chains weak bases and increasing
their polarity (and thus solubility in water).
Amino groups are very ubiquitous, present in aminoacids, proteins, nucleic acids, sugars and lipids.
Carboxyl: -COOH
Carboxylic groups are weak acids, their significance and presence matches that of
amino groups.
Phosphate: -O-P(OH)3
Phosphate groups are weak acids. They often are joined together via phospho-ester bonds (P-O-P) which
stores a lot of energy. Phosphate derivatives are often energy intermediates e.g. ATP or
phosphorylated enzymes.
Alcohol: >CH-OH
Alcohol groups are weakly polar and are present in sugars, aminoacids, lipids.
Aldehyde: -CH=O; Keto: >C=O
Aldehyde and keto groups are present in sugars, they give molecules more polar
character.
Isomerism
The presence of functional groups introduces a further complexity: isomerism. The
constituent atoms are the same, but they are connected together differently.
Structural isomerism
Functional groups are different although the constituent atoms are the same: e.g.
C2H6O:
ethanol: CH3CH2OH (pleasantly drinkable - only for those over 21)
ether: CH3OCH3 (pleasantly flammable and explosive);
Geometric stereoisomers
Even when functional groups are identical they can be arranged differently.
In maleic acid, the alcohol groups are cis with respect to the double bond, in fumeric
acid the alcohol groups are trans.
Optical stereoisomers
The tetrahedral bond arrangement of the carbon bonds defines carbon as a chiral
center, when bonded to 4 different atoms. The same four substituents can be bonded to carbon
in two different ways, each of them being a mirror image of the other.
Different spatial arrangement of functional groups will result in different structures and
different affinities for binding other molecules.
One stereoisomer might bind to an enzyme with high affinity, the other might not bind at all, it is like
trying to thread a left-handed screw into a right-handed nut.