I wasn't on the typical pre-medical track because I was in between majors (Kinesiology and Psychology) through my first 2.5 years. However, I took both Chem 1 and Organic Chem 1 in the summers of my freshmen year and junior year. Chem 1 was at my undergrad and Organic Chem 1 was at a community college. It didn't affect me at all. I also applied and was accepted before completing Organic Chem 2, which I finished my last semester at my undergrad. I just needed to get a C or better. When I applied I was approximately 3.35 overall GPA, 3.0 science GPA.
Hopefully that gives you an idea of where you stand