Final answer:
The difference between RNA polymerase II in Archaea and Eukarya lies in their helicase activity and transcription initiation factors. Eukaryotic mRNA transcription is monocistronic, while bacterial and archaeal mRNA is polycistronic.
Step-by-step explanation:
RNA polymerase II in Archaea differs from that in Eukarya in a few key ways. First, in eukaryotes, RNA polymerase II does not have helicase activity, while in archaea it does. Instead, eukaryotic gene transcription relies on the multi-subunit TFIIH protein, which contains helicase activity.
Additionally, archaeal mRNA transcription initiation resembles that of eukaryotes, but requires fewer initiation factors. Finally, eukaryotic mRNA transcription is monocistronic, meaning it encodes only one polypeptide, whereas bacterial and archaeal mRNA transcription is polycistronic, encoding multiple polypeptides.