You can apply before you have fulfilled all prerequisite classes. As far as explaining goes, you would do that on your secondary applications, most of them have a question along the lines of "what are your upcoming plans before matriculation" or "what other classes will you be taking before starting at our school" this is where you would say you are going to finish up your prerequisite classes (assuming you are going to take a physics course with lab). Otherwise you need to contact the schools you are applying to and ask them if your class fulfills their requirements.