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The Chemical Structure of DNA

By the early 1950s, it was well known that DNA was a polymer made up of monomers called nucleotides. Each nucleotide consists of three chemical groups (see Figure 5.1, see also Chapter 2): 
  • A 5 carbon sugar, deoxyribose;
  • A nitrogen rich base attached to the first carbon of the sugar;
  • A phosphate group attached to the fifth carbon of the sugar.


Four types of nucleotides exist, and each differ only at the nitrogenous base: 
  • Adenine (A),
  • Cytosine (C),
  • Guanine (G) and
  • Thymine (T). 
In 1953, James Watson and Francis Crick proposed a model for the structure of DNA by considering a wide variety of data from other researchers. In particular, two observations became crucial to their model:
  • Erwin Chargaff had discovered that, in every molecule of DNA, the amount of A was always equal to the amount of T, and the amount of C was always equal to the amount of G.
  • Rosiland Franklin had obtained X ray diffraction data that showed DNA exists in a double helix, similar in structure to a winding staircase.
From this information, Watson and Crick were able to correctly determine the structure of the polymer (see Figure 5.2).
The monomers of DNA are linked together via the sugar and the phosphate groups in the nucleotides. This is often called the sugar-phosphate backbone, and the bond that forms between the monomeric nucleotides is called a phosphodiester bond. Remember how the phosphate group is attached to the fifth carbon on the deoxyribose? The phosphate from one nucleotide attaches to the sugar of another nucleotide at the third carbon.

The structure of DNA. S: sugar; P: phosphate; A, C, G and T: nitrogenous bases


This actually gives DNA a direction, like north and south, except we call it 5’ and 3’ (pronounced “5 prime” and “3 prime,”). We’ll talk more about this attachment a little later.
One strand (polymer) of DNA is usually found attached to another strand of DNA, forming a double stranded molecule. The bases on each strand bond to form a pair. This pairing follows a strict rule: A always pairs with T, and C always pairs with G (this is what Chargaff saw). We call this complementary base pairing. When the strands of DNA come together to form a double strand, the structure twists around itself, creating a double helix. By knowing the sequence (arrangements of nucleotides) of one strand, the sequence of the second strand can be determined. It is this sequence that determines the structure and function of the cell and the organism.
The base pairs are held together by hydrogen bonds, weak bonds that form between hydrogens and oxygens or hydrogens and nitrogens. The G-C base pairs form 3 hydrogen bonds while the A-T base pairs form only 2. This makes the G-C pairs inherently stronger and more stable.
Another interesting feature of the double helix is that, in order for the bases to pair correctly, the two strands of DNA must run in opposite directions, or in an antiparallel fashion. This means that the 5’ end of one strand pairs with the 3’ end of the other strand.

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