Nucleotide

DNA and RNA polymers are constructed by forming phosphodiester bonds between nucleotides. In this arrangement, a phosphate group acts as a bridge between the 5′ position of one sugar and the 3′ position of the next. This arrangement is called the "sugar-phosphate backbone" of DNA or RNA; the bases hang off to the side.

In the cell, DNA or RNA polymers are synthesized using nucleoside triphosphate monomers as precursors. During polymer synthesis, two of the phosphate groups of the incoming nucleoside triphosphate are cleaved off, and this provides the energy needed to power the reaction. The remaining phosphate takes its place in the sugar-phosphate backbone of the growing nucleic acid chain. A pyrophosphate molecule (two linked phosphates) is released.

Just as an arrow has a tip and a tail, DNA or RNA chains have directionality, due to the structure of the sugar. At one end of a chain, a 5′ carbon will be left free. This is known as the 5′ end of the chain. At the other end, the 3′ carbon will be free; this is the 3′ end of the chain. Segments of DNA that are not free at their ends can also be discussed in terms of their 5′ and 3′ ends. This directionality has important consequences. When DNA RNA nucleotides join by linking the 5′ phosphate of one to the 3′ ribose carbon of the next. This linkage is called a phosphodiester bond. replication occurs, it always moves from the 5′ end to the 3′ end, and the incoming triphosphate joins the 3′ end of the chain. Transcription (RNA synthesis from a DNA gene) also moves in this 5′-to-3′ direction. The 5′ end is considered the "upstream" end of the gene, and is the end on which the gene promoter (the transcription initiator) is located.