Hey there,
I'm not a biochem major but I'm actually going to finish taking intro biochem at the end of this summer...I feel like an iPad just wouldn't do you justice at all for some reason. As you said the notes you will be taking will be in-depth and probably involve a lot of mechanisms/curly arrows/all that jazz, and I feel like, even with stylus in hand (something like Pogo Sketch or whatever people are using with the iPad right now) it'd be too slow and get to be real frustrating.
I don't personally have an iPad myself, but I've used one enough to realize that, at the very least, I'm much better off typing notes for biochem (lecturers provided all structures needed on powerpoints, so I can just annotate from there).
Have you ever thought about a LiveScribe pen though? Again, never tried one, but I'd be closer to buying that thing that an iPad personally. Basically it's a digital pen that uses special kind of paper and you can not only keep a paper copy of your notes but you can also transfer those notes to your computer by connecting your pen to your computer and the software does the rest. What's extra cool about the LiveScribe is that it RECORDS what your professor is saying concurrently with what you're writing. Go on the LiveScribe website and check out a demo; it's pretty neat.
Hope this helps!