Professor X is in charge of the school and can actually control living creatures. The nucleus is in charge of the cell and controls all of the organelles.
LIKE THE CELL MEMBRANE IT SEPARATES THE SCHOOL FROM OTHER PEOPLE
The fence is to keep the x-men and the young students from the pain and suffering "normal" people. Similar to how the cell membrane separates the cells from each other like a barrier.
MULTIPLE SMALL AREAS USED TO STORE ITEMS LIKE THE VACUOLE
The dorms that the mutants stay in hold items in multiple small locations. In an animal cell there are multiple small vacuoles that hold food and water.
GUIDES THE STUDENTS TO DIFFERENT PARTS OF THE SCHOOL LIKE THE E.R.
The hallways guide the students from one part of the school to the other. The endoplasmic reticulum guides the proteins from one part of the cell to another.
Cerebro is a machine that can find and track anyone in the world when a telekinetic mutant is controlling it and helps the whole building work. The mitochondria powers the cell and without it the cell could not possibly function.
Without his wheelchair Professor X would not be able to function well and would be pretty vulnerable. If a nucleus didn't have a membrane it wouldn't function as well.
ARE THE WHY THERE IS A SCHOOL SIMILAR TO CHROMOSOMES
The chromosomes are the building blocks of a cell and with out it you would be very different. The mutant powers are the only reason that there is a school.