Question

This question is relevant to molecular biology.

When the transcription machinery is compared between prokaryotes and eukaryotes, one finds several similarities as well as many differences. Focusing on each aspect listed below, explain briefly key similarities and differences as specified. Use bullet points to organize your answers and make them clear and short.

1. Compare promoters in prokaryotes versus eukaryotes - what are key similarities and important differences?
2. Compare the RNA polymerases in prokaryotes versus eukaryotes - what are key similarities and

differences?

3. What are key differences between the DNA template being transcribed in eukaryotes versus prokaryotes?

Answer 1

Even though the process of transcription is present in prokaryotes and eukaryotes, there are some differences between both.

A. The promoter is a portion of DNA which is located prior to the gene to be transcribed. They are generally 100-1000 bp long sequences. These are the regulatory regions, controling the binding of RNA polymrase to the DNA template. In prokaryotes only 3 promoter sequences are seen.These are- -10 element, -35 element and UP element.  Prokaryotes carry operons, that is several genes are under the regulation of a single promotr and operator. The -35 promoter sequence is TTGACA. But eukaryotes possess many promoter regions, which are some more complex than that of prokaryotes. Most of the eukaryotic promoters possess a TATAAA sequence called TATA box. CMV, PGK and U6 are some eukaryotic promoters. The regulatory regions in eukaryotic promoters are several base pairs upstream to that of transcription start site, while in prokaryotic promoter they are more nearer to the transcription start site.

B. RNA polymerase is seen as a single form in prokaryotes, but in three different forms in eukaryotes. The three forms are RNA polymerase I, RNA polymerase II and RNA polymerase III. Thes are meant for the transcription of different types of RNA molecules. Pol I transcribe ribosomal RNA, Pol II is for mRNA synthesis and Pol III is for the synthesis of tRNA and other small RNAs. But in prokaryotes all RNAs are synthesized with the help of a single RNA polymerase enzyme. Prokaryotic RNA polymerase have 4 catalytic subunits and a single regulatory subunit. Even though these differences do exist , both prokaryotes and eukaryotes make the common mchanism in transcription.

C. The key difference between template strands in prokaryotes and eukaryotes is that, the eukaryotes possess split gene. That is they carry regions which are expressing called exons and regions which will not get expressed called introns. Both get transcribed into a long pre- mRNA molecule, but later the introns will get removed by the process called RNA splicing.  But the prokaryotes do not possess these distinct regions, but thir entire gene portion gets expressed. In prokaryotes during transcription the double stranded DNA need to be partially unwounded at the 5' region which is called the transcription bubble. Transcription occur at 5'-3' direction using the unwounded single stranded DNA molecules as template strands. In eukaryotes the template strand cannot be directly accessed by the RNA polymerase enzyme, but need the binding of some transcription factors to the promoter region. Then only RNA polymerase can bind and proceed transcription. Here also the double stranded DNA gets unwounded and will follow transcription of template strand in 5'-3' direction.