Structure of Nucleic Acids: Nucleotides and Nucleic Acids

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Both DNA and RNA are known as nucleic acids. They have been given this name for the simple reason that they are made up of structures called nucleotides. Those nucleotides, themselves comprising a number of components, bond together to form the double-helix first discovered by the scientists James Watson and Francis Crick in 1956. This discovery won the two scientists the Nobel Prize. For now, when we discuss nucleic acids you should assume we are discussing DNA rather than RNA, unless otherwise specified.

Nucleotides

A nucleotide consists of three things:

A nitrogenous base, which can be either adenine, guanine, cytosine, or thymine (in the case of RNA, thymine is replaced by uracil).
A five-carbon sugar, called deoxyribose because it is lacking an oxygen group on one of its carbons.
One or more phosphate groups.

The nitrogen bases are pyrimidine in structure and form a bond between their 1' nitrogen and the 1' -OH group of the deoxyribose. This type of bond is called a glycosidic bond. The phosphate group forms a bond with the deoxyribose sugar through an ester bond between one of its negatively charged oxygen groups and the 5' -OH of the sugar ().

Nucleic Acids

Nucleotides join together through phosphodiester linkages between the 5' and 3' carbon atoms to form nucleic acids. The 3' -OH of the sugar group forms a bond with one of the negatively charged oxygens of the phosphate group attached to the 5' carbon of another sugar. When many of these nucleotide subunits combine, the result is the large single-stranded polynucleotide or nucleic acid, DNA ()

If you look closely, you can see that the two sides of the nucleic acid strand shown above are different, resulting in polarity. At one end of the large molecule, the carbon group is unbound and at the other end, the -OH is unbound. These different ends are called the 5'- and 3'-ends, respectively.

The Helical Structure of DNA

shows a single strand of DNA. However, as stated earlier, DNA exists as a double-helix, meaning two strands of DNA bind together.

As seen above, one strand is oriented in the 5' to 3' direction while the complementary strand runs in the 3' to 5' direction. Because the two strands are oppositely oriented, they are said to be anti-parallel to each other. The two strands bond through their nitrogen bases (marked A, C, G, or T for adenine, cytosine, and guanine). Note that adenine only bonds with thymine, and cytosine only bonds with guanine. The nitrogen bases are held together by hydrogen bonds: adenine and thymine form two hydrogen bonds; cytosine and guanine form three hydrogen bonds.

An important thing to remember about the structure of the DNA helix is that as a result of anti-parallel pairing, the nitrogen base groups face the inside of the helix while the sugar and phosphate groups face outward. The sugar and phosphate groups in the helix therefore make up the phosphate backbone of DNA. The backbone is highly negatively charged as a result of the phosphate groups.

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