Both grades will be averaged in together if you apply to M.D. schools. Different for D.O. schools though if you were planning on heading towards that path. Your GPA will increase more if you were to take another higher-level Biology class, by far, than retaking that B.
You will hear the "take higher level classes" phrase a lot but it's for a reason. If you were to average in an A from a higher level Bio class it will be more beneficial towards your GPA and your application as a whole. What would look better? Seeing the student obtaining an A in Microbiology or another advanced course or seeing the student's transcript and looking at how many classes were taken over again.
Retaking a C is understandable under some circumstances, a B is fine.