Despite the fact that prokaryotes and eukaryotes use the same the same basic method of transcription there are several differences between the two. The structures of prokaryotic and eukaryotic RNA polymerase are basically the same suggesting that they have similar function, and therefore operate in a similar manor. A major difference is the RNA polymerase. Prokaryotes have a single 4 subunit polymerase, while eukaryotes have three RNA polymerase with 10-12 subunites
(5). Each eukaryotic polymerase is responsible for transcribing a different type of RNA, polymerase I transcribes rRNA, polymerase II transcribes mRNA, and polymerase III transcribes tRNA. Another difference is the connection of transcription and translation. In eukaryotes these two mechanisms are separated, transcription within the membrane bound nucleus and translation outside the nucleus. Where as in prokaryotes the nucleus is not membrane bound so translation and transcription are therefore not separated. Translation actually can and does start before transcription stops. One other minor difference is the use of promoters regions. In prokaryotes there are only a few promoters elements while eukaryotes have a wider variety of them. In eukaryotes the promoter can also be in several different location and much farther away from the start site of transcription.