I am actually confronting this same issue. In my biochemistry program, only one semester of general biology is required. Of course, I've taken several upper-level biology courses by now. In communication with several medical schools, they've indicated that general biology is the minimum and that certainly upper-level courses fulfill the biology requirement.
Take a few minutes and e-mail the admissions departments of the schools you're interested in to make sure. With respect to the MCAT, the general biology you've missed can be easily reviewed on your own.