This animation shows the first couple steps in the degradation of the herbicide 2,4-D. 2,4-D is one of the most well studied herbicides and scientists understand how some microbes break down this molecule. Microbes use a set of enzymes (proteins that can transform one molecule into another) to degrade 2,4-D. These enzymes chew off bits of the 2,4-D molecule a bit at a time in a particular order called a biochemical pathway.
The first step in the pathway is removal of the molecules sticking off from the ring. Just like when you eat the head off a chocolate Easter bunny, the first 2,4-D degrading enzyme chomps off the "head" of the 2,4-D molecule, leaving a carbon ring "body" called 2,4-dichlorophenol.
The next enzyme in the pathway adds oxygen to the remaining carbon ring to make it easier to break (the extra oxygen destabilizes the ring). This oxygen makes the ring easier for the next enzyme in the pathway to break. This reaction then produces the molecule 3,5-dichlorocatechol.
After 3,5-dichlorocatechol is formed, the next enzyme breaks open the ring, and in so doing, one of the chlorine molecules is lost. Other enzymes then chew the straightened carbon molecule into smaller and smaller bits until it is converted entirely to water (H2O), carbon dioxide (CO2), and hydrochloric acid (HCl).