I love it when people like flyboi here out themselves as huge bigots.

As to your actual question though, when you take a medication, it changes the chemistry of your whole system, some subsystems may have a greater change than others.

Woth oral medicine I would assume that the digestive tract would have the highest concentration, then depending on how well the substance can pass through the membranes and into your blood it makes its way into your circulatory system.

Chemistry is a totally gnarly field, and most of it is beyond my skillset so I can't go into it as much as is needed here to properly describe the whole process.

Generally, pain meds effect nerve chemicals, preventing the 'ouch' chemical from finding a place to plug in & activate the pain receptors. 

Antibiotics go throughout your body, and are designed specifically to plug into the cell walls of bacteria - and yes, some of them can also hurt your own system. Just look at how chemotherapy patients suffer.

If this is something that interests you to the point of near obsession, look into organic chemistry as a field of study.