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Okay, so this might not be something that is terrible or anything, but I am just a bit uncomfortable asking it "out in the open".
When I first started college (just finished freshman year), I wasn't really sure what I wanted to do, so my academic advisor suggested getting most of the general ed. requirements my school has out of the way.
That said, I won't be starting the pre-reqs (general bio, general chem, etc) until sophomore year. Is that going to be a problem or am I worrying myself over nothing?
You are worrying over nothing. Many people ultimately going to medical school study for non-science degrees in undergrad, then go back and add-on the science pre-req's. No one will care what order you took your courses.