Question

Given a polynucleotide sequence such as GAATTC. Explain what further information you would need in order to identify which is the 5’ end. (See Figure 16.5)

Short answer

Out of the two ends of the DNA molecule, the end with a phosphate group on the 5’ carbon of the sugar is called the 5’ end of the DNA. Thus, the 5’ end of the DNA molecule cannot be identified with the nucleotide sequence.

Step-by-step solution

Structure of DNA molecule

DNA is a polymer of nucleotide molecule. Each nucleotide comprises three components: a pentose sugar (2-deoxy-D-ribose), a phosphate group, and a heterocyclic base. Purine and pyrimidines are two classes of bases found in DNA.

In each nucleotide, the phosphate group is attached to the 5’ C of the sugar moiety, and the nitrogen base is attached to the 1’ C of sugar. A phosphodiester bond links the nucleotides in the DNA molecule.

The phosphate group of one nucleotide forms a covalent bond with the 3’ C of the pentose sugar of the adjacent nucleotide forming the polynucleotide sequence.

Polarity of DNA molecule

DNA is a double-helical molecule as it comprises two strands. The two strands of the molecule have opposite polarity. This is because the ends of the two strands are different. One strand ends with the phosphate group on the 5’ end of the sugar; this end is called the 5’ end of carbon.

The other strand ends with the OH group on the 3’ carbon of the sugar; this end is called the 3’ end. One strand runs in a 5’ to 3’ direction and the other in a 3’ to 5’ direction. Thus, the end of the DNA molecule has both 5’ and 3’ends. As a result, the two strands of DNA molecules are anti-parallel.

To determine the 5’ end of DNA    

To identify the 5’ end of DNA, one must know the end of the DNA molecule with a phosphate group attached to 5’C of the sugar. This is because the phosphate group at 5’C marks the 5’ end of the DNA molecule, and the OH group at 3’C marks the 3’ end of DNA.

Thus, to know the DNA molecule’s 3’ or 5’ ends, one must know the phosphate or OH group present at the end of each strand.