Nucleotides

DNA and RNA are comprised of monomers called nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Three components comprise each nucleotide: a nitrogenous base, a pentose (five-carbon) sugar, and one or more phosphate groups. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

The nitrogenous bases are organic molecules that contain nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).

Scientists classify adenine and guanine as purines. The purine’s primary structure is two carbon-nitrogen rings. Scientists classify cytosine, thymine, and uracil as pyrimidines which have a single carbon-nitrogen ring as their primary structure. Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, we use the symbols A, T, G, C, and U for the nitrogenous bases. DNA contains A, T, G, and C; whereas, RNA contains A, U, G, and C.

The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose’s second carbon and hydrogen on the deoxyribose’s second carbon. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”).

Polynucleotides

A phosphate residue connects the 5′ carbon of one sugar to the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage. A polynucleotide may have thousands or even millions of phosphodiester linkages.

In a polynucleotide, one end of the chain has a free 5′ phosphate, and the other end has a free 3′-OH. These are called the 5′ and 3′ ends of the chain.

The Double Helix

DNA has a double-helix structure. The sugar and phosphate lie on the outside of the helix, forming the DNA’s backbone. The nitrogenous bases are stacked in the interior, like a pair of staircase steps. Hydrogen bonds bind the pairs to each other. Every base pair in the double helix is separated from the next base pair by 0.34 nm. There are about 10 base pairs per turn of the double helix. The helix’s two strands are antiparallel, meaning that they run in opposite directions.

Base pairing is specific.  A can pair with T, and G can pair with C. This is the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is 5′-AATTGGCC-3′, the complementary strand would have the sequence 3′-TTAACCGG-5′.