I queried a program about this specifically and the answer was that it doesn't much matter if you're within the few outstanding prereqs that it allows. As to A&P, however, you should most definitely have taken the full sequence before applying. There's no question that it's important to have those grades as part of your application.
Obviously, if you have a lousy prereq GPA, you should take as many prereqs as possible before applying to improve that GPA. In other words, it wouldn't make much sense to apply with a 2.9 GPA with three prereqs outstanding, because you stand a chance to improve on it quite a bit (assuming one has capacity for additional prereqs).
Good luck.
