[QUOTE][b]Afterall if every piece of DNA coded for a protein, what would be left to tell those proteins what to do and where to do it?[[/QUOTE]
[/b]
Proteins are told neither what to do nor where to do it. They are large, (for a molecule) dumb surfaces upon which chemical reactions occur. Telling a protein what to do is like telling the catalytic converter in your car what to do. What they "do" is determined by the laws of chemistry, and one protein's function is set apart from the other proteins on the basis of the 1 level (the composition of the protein) and that protein's conformation, that is its shape as determined by various things like hydrogen bonds throughout the molecule and the local temperature inside the cell. A protein "does" something because its substrate (the molecule it manipulates) bumps into its active site and the component atoms and bonds of the substrate are stretched or rearranged in the collision. Aside from that, the thing just drifts. A protein, after being synthesized cannot be "told" what to do, it can simply be deactivated by having its active site blocked by another molecule or packaged by the Golgi apparatus. But most "control" over proteins come from switching genes on and off in the nucleus and so varying the concentration of those proteins.
These "orders" don't originate from the nucleus, they are results of environmental conditions and interactions other proteins.
There is some speculation that introns ("junk DNA") might play a role in protein folding (the manner in which proteins acquire their conformations) but they aren't "command centers" and to say that they control proteins is simply not accurate.