Hey,
I'm also in biochemistry doing the specialization in molecular biology. For second year, the only difference between the two specialization is the chemical engineering course. From what I have heard from my friends that have taken it, there was math in it, but not really difficult. I remember that the exam was open book, so you could bring your notes in.
From the two friends that I know that took it this year, both got a 12. so I guess its not too hard if you're good in math
After second year, there are a few courses that are different, look at it. So it really depends which set of those courses you are more interested. I remember speaking with the biochem advisor about which specialization to pick, and she just told me its just the courses that are different, and to pick according to which type of courses i like more. Both specializations will still be enough to get in to grad school, etc. Molecular bio one has a few more electives i think. So, i guess look at the course lists, and see which ones you like more. I've just finished 2nd year, so i am not sure how 3rd and 4th is yet.
hope that helps.