about retaking C- classes

Graduate School
1

I am a sophomore who transferred from a foreign university to one of the public ivies in 2016 Fall semester.
My major is Chemistry BS.
I plan to attend the graduate school for the Ph.D in Chemistry.

I received A in all science courses in the previous university, and my GPA was 3.9/4.0
In the last term, I received A- in Intro Biology I (100-level, 3 credits) and A in Multivariable Calculus (200-level, 3 credits) and Analytical Chemistry (200-level, 2 credits) in the current school.

However, I got C- in Intro Organic Chemistry I (200-level, 3 credits) and Intro Biology I Lab class (100-level, 1 credit).
My GPA for 2016 Fall semester is 3.158/4.0
Because I got an bicycle accident in the beginning of last September and had to spend a lot of time to get treatment and deal with insurance issues, it was a very hard term for me.
The university says that the permission of the school is required if I want to retake the courses where I did not get F.
I think I might be able to get the permission to retake those two courses I got C- in since I have the clear reason (the accident) that I could not do well in that term.

I wonder whether those two C- courses decreases the chance to attend the graduate school.
Is it better to retake them?

2

A lot will depend on how well you do in the next few terms. If you are able to do much better in the later terms, the first term grades are not as important. Since it looks like you have at least 4 more terms, I think you have plenty of time to improve your performance. The Biology is not as critical but you should ask yourself whether your performance in Organic I is because you have a weak foundation or if it was simply because of the external circumstances. You will have to take Organic II and probably some additional Organic Chemistry courses over the course of your degree. If your foundation is weak, you might have trouble with later courses and that is a very good reason to repeat that course. Realize that the first grade will likely remain on your transcript even if not counted in the GPA.