The compatibility of a biomolecule with water is seen especially well in genetics. The DNA and RNA molecules that transfer genetic information have a repeating charge in their backbone, carried by the phosphate linkers. This repeating negative charge makes DNA and RNA extremely soluble in water. It also prevents their passing across hydrophobic membranes. Further, the nucleobases that encode the genetic information are, by comparison, hydrophobic. Therefore, they lie inside the double helix, away from water, in base pairs that are well known features of the Watson-Crick model for duplex nucleic acids.
Water, however, carries both nucleophilic and electrophilic centers. This means that water reacts with many biomolecules in a way that damages them. In the case of proteins, as noted above, water reacts with the amide backbone to degrade proteins, generating amino acids as hydrolysis products (see Figure 2.13). This can be disadvantageous if the protein is desired, as it requires that the protein be re-synthesized. The turnover of proteins is important, however, in any system living in a dynamic environment. Thus, the hydrolytic instability of proteins in water is key to maintaining life.
The disadvantageous reactivity of water is especially obvious when considering RNA and DNA (see Figure 2.14). Cytidine, for example, hydrolytically deaminates to give uridine with a half-life of ca. 70 years in water at 300 K.11 Adenosine and guanosine also hydrolytically deaminate in water at only slightly slower rates. A more recent study at the base level affords the following half-lives for the bases at 298 K: cytosine, 340 years; adenine and guanine, about 10,000 years.12 As a consequence, terran DNA in water is continuously damaged in a way that causes it to lose its genetic information. In modern terran life, this continuous water-generated damage is mitigated through continuous repair.