I am almost in your same situation, just a little bit worse.
I have a 3.2 as it stands right now going into Senior year. I've received a C+/C in orgo, C+/B- in Gen Chem, and C+/B- in Biology and a B/C in Physics. All of my other grades are usually in the B to B+ range with some B-'s and A's in there, and these C's killed my GPA. I know I won't have much of a chance at any medical school unless I dominate the MCAT, which without a stronger foundation in sciences seems unlikely.
Depending on your GPA, you may be better off, but the sciences are the most important to demonstrate your capacity to handle med school material.
What I am doing, this is just me in my own personal situation, is I am currently retaking both semesters of Orgo in the summer now between junior and senior year. This will probs bring my GPA up to a 3.29 if I get an A both semesters. Then senior year I will be trying to raise my science GPA by taking as many science courses as I can, as well as retaking first semester Bio, then 1st semester Gen Chem in the 2nd semester. The fifth year will allow me to take even more science courses that could raise my GPA as well as complete a double major. However, I need to ace these courses, easier said than done.
My personal point of view right now is this - ok, my GPA is low, and I have decent EC's and I've done well in my other courses besides science courses. This was partially due to a lack of effort in the beginning years of college because of personal problems. I think that if I am able to raise my GPA to above a 3.4 and show an increasing trend these last two years, I might have a shot at some lower selectivity schools in my state granted I do well on the MCAT. It's down to the wire right now.
So, it depends, I'm not retaking my C in Physics, but I will be retaking Orgo, Chem, and Bio. I think it's essential to show to committees that you can do the work in more difficult courses, and the science GPA will be very important.
I would suggest trying to take things in the summer if you still can, or if you had a class that you got two C's in to look at that one first.
