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 followfollows this convention, as every ciccis 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. TransTrans is Latin for across, meaning the groups are on opposite sides of the double bond.
I don't know why it started (maybe because it was a foreign word), but it's been done and repeated for so long that it is now conventional to do this. Indeed, it is wrong by IUPAC (International Union of Pure and Applied Chemistry) standards to write it any other way (except in contexts where italics are not available; then underlining is necessary.)