Unless you're aiming for DO schools, you should not retake classes.
Why? DO schools accept grade replacements and your GPA will go up by their application metrics. MD schools will not do so.
What you should do is learn from your experience and translate that to good grades in upper-level science classes or whatever upper-level material you have to take. Because nothing says you've learned from the past like taking material harder than Introduction to Chemistry and getting better grades.
Most schools will give you the opportunity to explain lapses in grades/extenuating circumstances in your life - you can use that to describe what happened. But don't retake these classes, because while the C's hurt, an upward GPA trend can help undo much of that damage.
Also, what happened? "Rough time" is very vague and may not be received well (for instance, homesickness is simply not comparable to a close relative dying, extreme case of illness or having to work beyond full-time to make ends meet). You may be better off not bringing it up at all depending on what happened, because then it will come across as you making excuses instead of accepting accountability. Plenty of people have had stellar GPAs while maintaining jobs, families, and so forth. Tread carefully.
FWIW, I got a C+ in a class sophomore year and it worked out. This has also happened to numerous people on SDN - it's not the end of the world.
