Polymerization of Nucleotides (Phosphodiester Bonds)

Nucleotides are joined together similarly to other biological molecules, by a condensation reaction that releases a small, stable molecule. Unlike proteins, carbohydrates, and lipids, however, the molecule that is released is not water but pyrophosphate (two phosphate groups bound together). When pyrophosphate is cleaved by the addition of water, a great deal of free energy is released, ensuring that the reverse process (hydrolysis of the phosphodiester bond to give free nucleotides) is very unlikely to occur.

How does releasing free energy
make the reaction go forward?

Click on the step numbers below to see the polymerization of nucleotides. Click on the mouse at left to clear the images and text.

1.

The 5' group of a nucleotide triphosphate is held close to the free 3' hydroxyl group of a nucleotide chain.

2.

The 3' hydroxyl group forms a bond to the phosphorus atom of the free nucleotide closest to the 5' oxygen atom. Meanwhile, the bond between the first phosphorus atom and the oxygen atom linking it to the next phosphate group breaks.

3.

A new phosphodiester bond now joins the two nucleotides. A pyrophosphate group has been liberated.

4.

The pyrophosphate group is hydrolyzed (split by the addition of water), releasing a great deal of energy and driving the reaction forward to completion.