Structural Biochemistry/Nucleic Acid/Nitrogenous Bases

Overview
A DNA nucleotide is composed of 3 main units: a 5-carbon monosaccharide (deoxyribose), a phosphate group, and a nitrogenous base. While the monosaccharide and phosphate group alternate in sequence and form the backbone of the DNA double helix, the nitrogenous bases may differ in every adjoining nucleotide. The four nitrogenous bases present in DNA are adenine (A), guanine (G), cytosine (C) and thymine (T). In RNA, the only differing nitrogenous base is uracil (U) (which replaces thymine in DNA and differs thymine only by the missing methyl group at carbon 5 of the pyrimidine ring). Of the nitrogenous bases, adenine and guanine are purines, which are aromatic compounds attached to an imidazole group, while cytosine and thymine and uracil compose a set of pyrimidines, which are one ring-aromatic compounds. Nitrogenous bases, being hydrophobic, tend to face inwards of the double helix, pointing away from the surrounding aqueous environment. If the phosphate backbones were faced inside of the double helix, then there will be too many charges clustered together such that the double helix would be an unlikely product. Bonds between linking nitrogenous bases of two DNA strands are Hydrogen bonds with 3 H-bonds connecting cytosine and guanine and 2 H-bonds connecting adenine and thymine, while the bonds between the stacking of DNA are kept in close contact via van der waals interactions. The aromaticity of the nitrogenous bases accounts for the DNA absorbance peak at 260nm.