Can someone explain the Fallout 4 faction quests ?

I want to know if doing a quest for a faction means that i've joined them already. Like if i do the first BOS mission do i loose the minutemen or something. Also if i do the "molecular level" or "institutionalized" or whatever the quest that makes you side with someone is (what is it?) do all the railroad and institute quests go to waste (i didnt even meet them yet). And also what is "follow the freedom trail" for ? Is it about finding the railroad and do you have to do it for "the molecular level " ?