My comments are related to AMCAS school expectations, but can probably be generalized to PA schools as well.I was having a hard time with organic chemistry 1 and 2 and I took a WF and it did not affect my gpa at my school but on amcas and caspa they count it as an F towards my gpa which lowers my gpa by alot.
1) What should I do?
2) Does this look bad?
3) I have a good gpa on my transcript but not so great on caspa or amcas.
4) Do I still have a chance of getting into a program?
1) You need to retake both classes, ideally earning an A on your second pass through the material. You need additional A grades as well to counter the hit your science GPA has taken.
2) Yes, it looks bad. That's why you need to counter that negative impression by getting some great grades in upper-level science, and not just in the retakes. Adcomms need to be reassured that you have sufficient academic capability to do well in their program.
3) Adcomms will only look at the application service's transcript when deciding if you should be invited for an interview. For AMCAS they would also be looking at your MCAT score, which will prove you understood the material.
4) Not right now.