From my Organic Chemistry days, I remember that the certain isomers (compounds with the same chemical formula but different structures), especially for cis and trans were italicized.
If you look on the Wikipedia page for cis-trans isomerism, it seems to follow this convention, as every cic and every trans is italicized.
Cis is Latin for same side. A cis bond is one where the the substituent groups are both on the same side of the carbon-carbon double bond. Trans is Latin for across, meaning the groups are on opposite sides of the double bond.
I don't know why it started, but it's been done and repeated for so long that it is now conventional to do this.