I'm not so sure about how turning in transcripts work since I will not be applying until this upcoming cycle as well.
Your overall GPA is just about average, but the science GPA is low. I'm kinda in the same situation except I have a lower overall GPA =/ but from what I've picked up from this forum and I've also called various schools to ask about my chances and they said I still have a decent chance. You'll have to do well on MCATs as well and as long as you get involved in activities then you'll get in somewhere. They look at your application overall, so you may be lacking in one area, but hopefully you make it up somewhere else. Hope this helps!