Great question.
The amino acids from protein are used by the body for just about everything. Every tissue in the body is made from amino acids which are constantly being "turned-over". In other words, the protein that makes up the tissue sin your body isn't static. They are broken down and replaced constantly. Whether it's new skin, new blood cells, new mucus (snot), new bone, new connective tissue, new hair, new fingernails, new cells that line the entire surface of your digestive tract (including your mouth) all require a constant supply of new amino acids.
Amino acids are also required for neurotransmitters.
Amino acids are also used for fuel.
Amino acids are also used by the immune system. In fact, amino acids are the primery fuel source for some immune cells.
Now, all of this protein turnover is controled by the cells themselves. You can't really force them to use the protein you eat.
For muscle cells, when the cell is in an anabolic state you will store more net protein.
Any protein that isn't used immediately is broken down by the liver or oxidized. In other words, its used for the carbon and discarded.
I hope this helps.