The interesting thing is that Pharmacology comes easy only if you came to master organic chemistry and biochemistry. They complete each other, fit together nicely in the "master puzzle" and allow you to see the big picture, thus terms like LD50 and bioavailability come naturally and just fit there. Obviously formal training in general makes you think of organic/carbon chemistry and drug classes as totally different things, but it's like saying one's arm is a total different thing from one's leg (which is true), but forgetting that they're both part of one's body, with interactions and dependencies.
I would stress here that the importance of visualizing at least the main (active) parts of the drug molecule when reading what it is is ultimately less important for a practicing clinician, or even researcher. But I find that when it sparks to me whilst reading the drug name that it suddenly becomes clear what that thing does. I can't really explain it, it's become a reflex. I do get strange looks from colleagues, I have to admit.
As another poster said, it all boils down to the teachers. If they are dedicated and talented and you are lucky enough that they all are and they're not smug so that they won't build on the foundation that's already set by their predecessors, then it's a beautiful flow of knowledge. If said flow is interrupted at any point, the damage isn't irreversible, but the whole picture begins to be harder to grasp. As an example, I had excellent chemistry teachers all the way to medical school, but I had terribad physics teacher on the same route and I had (and still have) to compensate by doing ridiculous amounts of reading and self-explaining.
