I can't speak specifically about failing courses, but I too, was in a similar situation a few years ago. The semester I met my wife I received 3 C's in gen chem, calc and general biology. I since have retaken gen chem only (and got a B.) I was really interested in how much retaking classes (and, for that matter, doing poorly in them in the first place) would affect my applications. I spoke with my advisor, who made a few phone calls and asked some schools directly. From the U of U medical school, they said that though my performance was not optimal, but as long as I did well in my other classes I'd be allright. That seemed to be the consensus from the schools he contacted. I think schools will let a bad semester or two pass, it just means you need to kick butt in your upper division classes. It can be done! I pulled my GPA from a 2.3 after two semesters to above a 3.5 during my junior year. Besides, doesn't it say much more that you received an A or B in an advanced biochem course? I certainly think that shows that you're capable of doing the work, and ultimitely, I think that's what opt schools are really looking for.