The spherical object within a cell that controls its activity is the

Nucleus

Modification of protein is done by the Golgi apparatus of the cell and not the nucleus. The nucleus simply has the blue print of proteins and releases these blue prints to mRNA which transports the prints out to the ribosomes where they are read and used to synthesize or make the protein.Once a protein has been made, it is packed into a vesicle which is a "shipping envelope" for a cell. The vesicle moves to the Golgi apparatus which receives it and enzymes within the apparatus modify the vesicle contents, that is the protein, to its final form. The protein is then repacked into a new vesicle which then migrates from the Golgi apparatus to the cell membrane and releases the protein to the outside of the cell.