220

15

The Molecules of Life

Fig. 15.1 A water molecule

hydrogen-bonded to its

congeners. The hydrogen

atom is typically 0.10 nm

from the oxygen to which it

is covalently bonded (solid

lines) and 0.18 nm from the

neighbouring oxygen to

which it is hydrogen-bonded

(dotted lines). The energy of

the hydrogen bond (H-bond)

is about 0.1 eV (i.e., about

4 k Subscript upper B Baseline upper T4kBT at room temperature or

about 2.4 kJ/mol)

a redistribution of electron density from the covalent O–H bond to the zone between

the H and the neighbouring O. This loss of electron density from the covalent O–H

bond results in a weaker, more slowly vibrating bond.

Each water molecule can simultaneously accept and donate two hydrogen bonds

(each hydrogen is a donor, and the oxygen bears two lone electron pairs). In flawless

ice, the water molecules are H-bonded together in a tetrahedral arrangement.

The O–H infrared spectrum (of HOD in liquid DSubscript 22O) gives a very broad distribution

of energies, implying a continuum from ice-like to nonbonding. In pure water at room

temperature, about 10% of the O–H groups and lone pairs (LP) are nonbonded; close

to the boiling point, this percentage rises to about 40.

Bonded and nonbonded ions are in equilibrium:

upper H Subscript 2 Baseline upper O Subscript fully bonded Baseline right harpoon over left harpoon OH Subscript free Baseline plus LP Subscript free Baseline commaH2Ofully bonded ⇌OHfree + LPfree ,

(15.1)

where the subscript “free” denotes nonbonded. LPSubscript normal f normal r normal e normal efree and OHSubscript normal f normal r normal e normal efree are, respectively,

an electron donor (Lewis base) and electron acceptor (Lewis acid) and hence can

interact with other species present in the solution. An ion pair such as KCl interacts

with both LPSubscript normal f normal r normal e normal efree and OHSubscript normal f normal r normal e normal efree in roughly equal measure; hence, KCl does not perturb

the equilibrium (15.1), whereas (to take an extreme case) NaB(CSubscript 66HSubscript 5 Baseline right parenthesis Subscript 4 Baseline5)4 can only

interact with LPSubscript normal f normal r normal e normal efree, hence increasing the concentration of free OH groups. This kind

of interaction has profound implications for macromolecular structure, as will be

seen (Sect. 15.5).

15.3

DNA

Deoxyribonucleic acid is considered to be the ultimate repository of potentially

meaningful information in the cell. DNA is poly(deoxyribonucleic acid), and the

information is conveyed by the particular sequence of bases of the polymer.