Ubiquitin: forms and functions. Free ubiquitin molecules are present in both the nucleus and the cytosol; the protein is small enough for passive diffusion through the nuclear pore between the two compartments. Ubiquitin conjugation to target proteins plays a central role in many processes of the cell. The best-known function of ubiquitin is its involvement in protein degradation via poly-ubiquitylation in the nucleus and cytoplasm. Mono-ubiquitylation of proteins has various functions depending on the target protein; it can vary from involvement in endocytosis at the plasma membrane, to DNA repair in the nucleus.