Ubiquitin (there is no e at the end of the word), is a protein, which the eukaryotic cell uses for a variety of purposes. Most notably for signalling that a worn out/misfolded protein be degraded by the proteosome (in this case the ubiquitin protein is attached to the broken protein through a process called ubiquitination, there are some other enzymes involved in this process too!). Ubiquinone is not a protein, it is an enzyme cofactor (I would classify it as a small organic molecule), and is involved in the electron transport chain. Ubiquinone is surely supposed to be there, it's an essential part of cells metabolism/redox pathways. Ubiquitin as you originally stated in your post, would NOT be in a prokaryotic cell ( there are a few homologues found in a few interesting bacteria/Archaea but not many as of yet have been observed ). I restate these things as you still appear a tid bit confised, based on the reply. 

You just have to be careful with your nomenclature, the two things (ubiquitin and ubiquinone) are not even remotely related. :)

Hope this helps.