How do eukaryotes differ from prokaryotes?
There is an implicit level of complexity that exists in the Eukaryotes over the Prokaryotes.
Eukaryotes have a cellular organelles and a complex structure while prokaryotes have minimal organelles. The levels of complexity directly impact the ability to affect cell metabolism, which is generally the mode of treatment in medicines. The minimal nature of the prokaryote allows them to be defeated easier via medicine, versus the complex eukaryote requires more intricate and sophisticated treatments. You can read about the details of their corresponding structures below.