Yeah I agree nucleotides do seem a bit redundant.
The one thing which proteins, fatty acids and dna have which separates them is that
fatty acids are made from pyruvate
proteins are made from pyruvate + ammonia
dna is made from pyruvate + ammonia + phosphate
which does give the player some different goals in the stage. They need a source of sugar just to live and act (to make atp etc) and then they also have to get some phosphate and ammonia somehow.
I guess that could be replaced by saying you just need to produce DNA which requires all of these constituents. It's a little less realistic though.
Yeah I agree that having cells only drop things you can use is a reasonable solution. Having the players cell have an invisible process which breaks things down might be nice but it might also add very little.