Prokaryotic and eukaryotic polymerases are very similar in structure and have similar function.  However, the first major difference between the two is in their RNA polymerase machinery.  Prokaryotes consists of a smaller four-subunit RNA polymerase, while eukaryotes have three larger 12 subunit RNA polymerases (Hsu, L., 2002).  Furthermore, prokaryotes have only one polymerase to call their own, while eukaryotes have three separate polymerases (RNA Polymerase I, II, and III) capable of producing different RNA.  RNA Polymerase I makes rRNA in the nucleous, RNA Poly II makes mRNA in the nucleoplasm, and RNA Poly III makes tRNA. 

Unlike prokaryotes, eukaryotes are not able to bind by themselves to the promoters.  Eukaryotes require the general transcription factors and gene-specific transcription factors.  Although general transcription factors can attract RNA polymerases to their respective promoter; they can only accomplish basal level transcription.  Even more appealing is the comparison of the promoter regions that lie upstream of the genes.  In the prokaryotic promoter there are two key regions located at -10 and -35 upstream of the start site.  The -10 site has the consensus sequence TATAAT and the -35 region has a sequence which is usually TTGACA (Vassylyev, et al, 2002). These promoters recognize and respond to the s factor of RNA polymerase which is only present in prokaryotes.  Eukaryotes have a similar TATA sequence located between -30 and -100 bp upstream of the start site.  Along with this eukaryotes could contain enhancer regions or an initiator element (Vassylyev, et al, 2002).

            In termination, prokaryotes are believed to follow either a rho-dependent or rho-independent form of termination, while no such termination mechanism exists in eukaryotes.  In rho-dependent termination an extra rho-factor needs to be present in order to initiate termination.  Also, after transcription eukaryotic mRNA must be further processed (capping, poly-A tail, and removal of introns ) while prokaryotic mRNA does not require any further modification and actually tends to be translated while transcription is still taking place.