This was written by Direncan Boyraz (Izmir Institute of Technology)
Prokaryotic genome has only one chromosome in the cytoplasm, but eukaryotic genome has multiple chromosomes inside a nucleus. Because of multiple number of chromosomes, eukaryotes can be haploid or diploid as difference than always diploid prokaryote. Also Prokaryotic genome own a circular structure, but there are exceptions, besides always linear strands are present in the eukaryotic cells and linear DNA provide telomeres, non-coding DNA ends, for eukaryotic cells. The eukaryotic genome is more complex with longer gene, on the other hand, prokaryotic genome has up to 90% coding sequences than often around 3% in eukaryotic genome. Supercoiling of DNA exist in both, but patterns of them are different because of circular and linear genome. One replication site or Ori is found in prokaryotic genome and it serves quicker division rate more bidirectionally. Eukaryotes have long repeating nucleotides than rare prokaryotic genome (1).
Both of them have some common features about genes. Replication directions, DNA and RNA structures, principles of work of polymerases can be seen as examples. Eukaryotic genes have introns and exons. In mature eukaryotic mRNA, only exons exist. Also eukaryotic genes are clustered, so genes that are related to similar functions are on same region of chromosome and they are controlled independently. Operons or polycistronic mRNAs do not exist in eukaryotes and in prokaryotic gene, regulatory parts are on same place with actual gene (2,3).
3)RNA polII-driven transcription initiation:
In contrast, prokaryotes have simpler transcription. σ factors in prokaryotes attach to promoter with mostly RNA pol and start transcription. Different σ factors bind to different promoters for a responsible gene. In Eukaryotes, transcription initiation are quiet different and more complex. This complexity comes from supercoiled structure and regulator elements. RNA pol can’t initiate transcription. Some DNA binding proteins such as transcription factors and enhancers helps to change conformation of chromatin structure. RNA pol can bind to promoter with help of transcription factors and starts transcription (4).
Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002. Chapter 2, Genome Anatomies. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21120/
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002).Molecular Biology of the Cell(Fourth ed.). New York: Garland Science.
Dvir, Arik & Conaway, Joan & C Conaway, Ronald. (2003). Assays for Investigating the Mechanism of Promoter Escape by RNA Polymerase II. Methods in enzymology. 370. 733-40. 10.1016/S0076-6879(03)70059-7.