Most secondary applications that I filled out this year have boxes where you mark whether or not you met their "course requirements" for applying. If you do not have a second semester of gen chem you could explain how your school does not offer more than 1 semester of gen chem and combines gen chem 1 and 2 into a single semester but you still learned about all gen chem requirements within that semester. Most schools had text boxes that allowed you to explain why you did or did not meet their requirements.
If your school does offer 2 semesters of gen chem and you only opted to take 1 semester, it will be hard to explain that in the available text box on secondary applications.
Gen chem is a pre-req for physical chem at my alma mater. So if you were very worried about meeting the gen chem requirement, I would take p-chem and then argue that you took upper level chemistry. Final advice is to go to the academic health center, which most colleges have, which contains pre-med advisers who can talk with you about how to fulfill requirements or what previous med school applicants from your university have done in the past to fulfill the gen-chem requirements when they applied for med school.