I had an issue with this - because I had received credit for the first 2 quarters of Physics via AP, I had to request a waiver from Pritzker (University of Chicago). This involved me sending them a written letter explaining why I was missing the courses, and how I had pursued a well rounded education in the sciences elsewhere (for me, I facilitate in a science workshop program, so I talked about that). Fortunately, my waiver was granted. Pritzker mentioned this directly on its website - but if I were you, I would e-mail/call somebody from admissions at whatever schools you're looking at and get the info directly from them.