Ubiquitin molecule. Computer artwork of the secondary structure of a ubiquitun molecule. The width of the tubes represents the local flexibility; the broader the more flexible. Ubiquitin is found in all eukaryotic cells. When a protein is damaged or old it will be tagged by several ubiquitin molecules. The protein is then moved to a proteosome, a hollow barrel shaped protein that degrades other proteins into amino acids and small polypeptides.