Structure of Nucleic Acids

Bases, Sugars, and Phosphates

Now that we've looked at the general structure of DNA, we should take a closer look at the structures that make up nucleotides.

The Bases of DNA

The four nitrogen bases found in DNA are adenine, cytosine, guanine, and thymine. Each of these bases are often abbreviated a single letter: A (adenine), C (cytosine), G (guanine), T (thymine). The bases come in two categories: thymine and cytosine are pyrimidines, while adenine and guanine are purines ().

Figure 2.1: DNA Bases

The pyrimidine structure is produced by a six-membered, two-nitrogen molecule; purine refers to a nine-membered, four-nitrogen molecule. As you can see, each constituent of the ring making up the base is numbered to help with specificity of identification.

Base Pairing in DNA

The nitrogen bases form the double-strand of DNA through weak hydrogen bonds. The nitrogen bases, however, have specific shapes and hydrogen bond properties so that guanine and cytosine only bond with each other, while adenine and thymine also bond exclusively. This pairing off of the nitrogen bases is called complementarity. In order for hydrogen bonding to occur at all, a hydrogen bond donor must have a complementary hydrogen bond acceptor in the base across from it. Common hydrogen bond donors include primary and secondary amine groups or hydroxyl groups. Common acceptor groups are carbonyls and tertiary amines ().

Figure 2.2: Common Hydrogen Bond Donors and Acceptors

There are three hydrogen bonds in a G:C base pair. One hydrogen bond forms between the 6' hydrogen bond accepting carbonyl of the guanine and the 4' hydrogen bond accepting primary amine of the cytosine. The second between the 1' secondary amine on guanine and the 3' tertiary amine on cytosine. And the third between the 2' primary amine on guanine and the 2' carbonyl on cytosine ().

Figure 2.3: Guanine : Cytosine Base Pair

Between an A:T base pair, there are only two hydrogen bonds. One is found between the 6' primary amine of adenine and the 4' carbonyl of thymine. The other between the 1' tertiary amine of adenine and the 2' secondary amine of thymine ().

Figure 2.4: Adenine : Thymine Base Pair

The Deoxyribose Sugar

The deoxyribose sugar in DNA is a pentose, a five-carbon sugar. Four carbons and an oxygen make up the five-membered ring; the other carbon branches off the ring. Similar to the numbering of the purine and pyrimidine rings (seen in ), the carbon constituents of the sugar ring are numbered 1'-4' (pronounced "one-prime carbon"), starting with the carbon to the right of the oxygen going clockwise (). The fifth carbon (5') branches from the 4' carbon.

Figure 2.5: Deoxyribose Sugar

It is from this numbering system of the sugar group that DNA gets its polarity. The linkages between nucleotides occur between the 5' and 3' positions on the sugar group. One end has a free 5' end and the other has a free 3' end.

Attached to the remaining free carbons at the 1', 3' and 5' positions is an oxygen-containing hydroxyl group (-OH). The DNA sugar is called a deoxyribose because it is lacking a hydroxyl group at the 2' position. Instead there is just a hydrogen (see ).

Phosphates

A phosphate group consists of a central phosphorous surrounded by four oxygens.

Figure 2.6: Phosphate Group

The phosphorous is single-bonded to three of the oxygens and double-bonded to the fourth. Due to the nature of the chemical bonds, there is a negative charge on each oxygen that has only one bond coming off of it. This negative charge accounts for the overall negative charge on the phosphate backbone of a DNA molecule.

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