The carbon atoms in sugar molecules are
numbered as in the diagram above. In the sugar phosphate backbone of
DNA, the phosphate groups connect to the #3 carbon of one sugar subsegment
and the #5 carbon of the next, linking successive sugars together.
Thus the two ends of a polynucleotide differ. At one end is a free
phosphate group. This is called the 5' end because if the chain
continued, the phosphate group would next be connected to the 5 carbon atom
of the next sugar. At the other end, is a sugar molecule with no
phosphate attached. This is called the 3' end of the chain.
Here, an oxygen and hydrogen molecule, known as a hydroxyl group, are
attached to the #3 carbon of the sugar instead of a phosphate.
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