Concept 6 Review

The Chemistry of DNA

Atoms in each DNA nucleotide can be identified by specific numbers. The ends of a DNA molecule are called 3' and 5' ends, based on the numbering of carbon atoms in deoxyribose sugars.

Chemists identify specific atoms in a molecule by numbering the backbone atoms: C1, C2, etc. In a complex nucleotide, the atoms of the purine or pyrimidine ring are first numbered 1, 2, 3, etc. Carbon atoms in the deoxyribose sugar are then numbered 1', 2', 3', 4', and 5' (shown in red in the figure below).

Notice that phosphate groups are attached to the 5'- and 3'-carbon atoms of each sugar to form the backbone chain of DNA. One end of the chain carries a free phosphate group attached to the 5'-carbon atom; this is called the 5' end of the molecule. The other end has a free hydroxyl (-OH) group at the 3'-carbon and is called the 3' end of the molecule.

When two DNA strands assemble in a double helix, the two strands always face in opposite directions; the 5' end of one strand is paired with the 3' end of the other strand.