
Bruce P. answered 10/29/17
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20+ year college biology/genetics teacher; I want you to understand.
Alex--it's useful to think of what a toxin needs to do (or be) in order to be harmful. If it's a functional unit (like a small protein) then it's SHAPE as well as its structure may be critical; in the case of a small molecule (such as a 'drug') then its exact chemical structure is going to be critical to its ability to achieve its nefarious ends.
Either way, your cells need to 'break' the structure or the chemical bonds. There are several ways to do this. Many, many chemical reactions on biological molecules are accelerated at low or high pH, and the lysosome is 'pumped' to very low pH for just this reason* (it also has some tough enzymes that are themselves resistant to low pH and that like to smash things). The peroxisome is another nasty place--it houses chemically active forms of oxygen that are just waiting to get in touch with other molecules and seriously mess them up.
*Your stomach operates on VERY similar principles to your cells' lysosomes.