Medical schools look very carefully at both sets of grades.
While it's true that nearly half of all medical school applicants are biology majors, everything from Philosophy to Art is up for grabs. The MCAT , your science GPA, your GPA minus the science classes, your personal statement, your interview, and your extra curricular activities. The last thing a medical school wants to do is enroll a class of students who are likely to drop or fail out. The first step is to have a very honest discussion with the Pre-Professional Advisor. There may be things you can do to enhance your application and simply re-apply for the next cycle.