It will affect your cumulative gpa, and not your pre-req. gpa. Also, keep in mind some schools look at Math/Sci GPA also. So it depends really on the school. I would re-take any class that you got a D or F regardless if its a pre-req or not. As to re-take a C or not, you should check how much your gpa would improve if you did retake that C (sometimes the trouble isn't worth it).