General Genetics/Structure of the DNA Molecule

DNA is generally found as a double helix, composed of two chains, or strands, of nucleotides held together by hydrogen bonds. A good analogy to this would be a spiral staircase, with the sides of the staircase being the strands, and the steps being the hydrogen bonds.

Nucleotides
Nucleotides consist of three parts: sugar, nitrogenous bases, and a monophosphate group. The sugar in DNA is the five-carbon aldose deoxyribose, which has two nucleophilic hydroxyl groups: one at the 5' carbon and the other at the 3' carbon. In a nucleotide, the hydroxyl group at the 5' carbon is replaced with a monophosphate group (PO43-). Nucleotides are joined by bonds between the phosphate group at the 5' carbon on one nucleotide and the hydroxyl group at the 3' carbon on the other nucleotide. These bonds are known as phosphodiesterase bonds, and the string of sugar monomers joined by phosphodiesterase bonds is typically referred to as the sugar-phosphate backbone.

At the 2' carbon, each sugar molecule is joined to a nitrogenous base. There are four nitrogenous bases found in DNA: guanine (G), cytosine (C), thymine (T), and adenine (A). The purines A and G are composed of two rings, whereas the pyrimidines C and T are composed of one ring.

Base Pairing
The two DNA strands in a double helix are held together by hydrogen bonds between pairs of nitrogenous bases. However, not any two nitrogenous bases can form hydrogen bonds. Two purines are are too big to fit in the space between the two strands, whereas two pyrimidines would be too far apart for hydrogen bonds to form. One purine and one pyrimidine are the right size to fit between the strands and have hydrogen bonds form. Adenine and thymine each have one hydrogen bond donor and one hydrogen bond receptor, so two hydrogen bonds form between them. Guanine has two hydrogen bond donors and one hydrogen bond receptor, whereas cytosine has two hydrogen bond receptors and one hydrogen bond donor, so three hydrogen bonds form between them. The relative numbers of hydrogen bonds means that less energy is required to split DNA strands at A-T sites than at C-G sites.