The two molecules that alternate to form the backbone of a polynucleotide chain are:

* Sugar (specifically, a pentose sugar like ribose or deoxyribose)

* Phosphate

These molecules are linked together by phosphodiester bonds. The sugar of one nucleotide is connected to the phosphate of the next nucleotide, forming a long chain. The nitrogenous bases (adenine, guanine, cytosine, and thymine or uracil) are attached to the sugar molecules and project outwards from the chain.