Re: How exactly does the nucleus of a cell control everything?

Well, that's a pretty complicated question, and the subject of more than 
100 years of research, but I'll give it a shot.  

The nucleus is usually the most prominent structure within a eukaryotic 
cell.  (Bacteria, or prokaryotes, don't contain a nucleus at all.)  The 
nucleus is separated from the rest of the cell by a double lipid bilayer 
known as the nuclear membrane.  The nucleus has two main functions in the 
cell. First, the nucleus is the carrier of herditary information.  The 
chromosomes, which are composed of DNA, are found within the  nucleus.  
Each time the cell divides, the DNA information is copied and passed on the 
the new cells. Second, the nucleus is the supply center for the cell.  The 
nucleus ensures that the complex molecules the cell needs to function are 
supplied in the amounts and variety needed. 

There are many experiments that confirm the role of the nucleus.  In one 
simple experiment, a nucleus was removed from an amoeba.  The amoeba 
stopped dividing and died within a few days.  But, if a new nucleus was 
implanted, the single celled animal lived and divided normally.  This early 
experiment let researchers know that the nucleus was essential for life of 
the cell, and for cell division.  In fact, such experimental findings 
underlie the fields of cell biology, genetics and molecular biology. 

So, how does the nucleus act as the supply center for the cell? The 
chromosomal DNA in the nucleus contains genes.  Genes are the functional 
units of DNA.  The DNA is a complete set of instructions for making all the 
proteins a cell will ever need.  Different genes are activated in different 
cells, creating the specific proteins that give a particular cell type its 
characteristics.  The nucleus regulates the timing and amount of the 
proteins that are made.  It does this by turning the genes off and on.  
Turning a gene on is called transcription.  Transcription is the process by 
which a DNA gene is copied into an RNA message.  These RNA messages exit the 
nucleus and are translated on the ribosomes into proteins.   

How does the nucleus know which genes to turn on and off?  The cell senses 
its environment.  Specialized cellular proteins called receptors detect 
hormones, small molecules, and even ions in the fluids surrounding the 
cell.  By the process called signal transduction, proteins in the cell pass 
the information about the cell environment along to the nucleus.  Signal 
transduction is like a relay race.  For example, a cell surface receptor 
protein might detect a growth factor.  The receptor will pass along the 
information that it has "seen" a growth factor outside of the cell.  The 
passage of information is like one runner passing a baton to another 
runner.  In this case, the "baton" is a high energy phosphate group.  The 
baton (phosphate group) gets passed along from protein to protein, until it 
gets into the nucleus and is passed to a transcription factor.  The 
transcription factors then work together to activate appropriate genes to 
make the cell grow, or deal with any other situation the cell experiences.

For more information, I suggest you check out a textbook such as Molecular 
Biology of the Cell (Alberts).

Hope that was helpful.
Erin