Hi there, I got a C- in orgo 2 (B in orgo 1, A's in genchem - this is all at a top 10 university) and I'm going to Harvard (PhD) in the fall. I also thought my C- would ruin me (I got a B- in both molecular bio and physics, also) but it didn't. I took Biochem and did well, but graduate schools didn't see that grade and I didn't mention it during interviews. I've done a lot of research though and have a publication, so I don't think my 3.5 GPA was a big deal. I also did very well on the GRE (90th percentile in both)
So, if the other parts of your application are strong, I see no reason to count yourself out.
