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The enzyme RNA polymerase or RNAP is a nucleotidyltransferase that polymerises ribonucleotides in accordance with the information present in DNA. RNA polymerase enzymes are essential and are found in all nucleated cells of all organisms.
RNAP accomplishes de novo synthesis. It is able to do this because specific interactions with the initiating nucleotide hold RNAP rigidly in place, facilitating chemical attack on the incoming nucleotide. Such specific interactions explain why RNAP prefers to start transcripts with ATP (followed by GTP, UTP, and then CTP). In contrast to DNA polymerase, RNAP includes a helicase activity, therefore no separate enzyme is needed to unwind DNA.
RNAP was discovered independently by Sam Weiss and Jerard Hurwitz in 1960.
RNA polymerase in prokaryotes
RNAP is a relatively large molecule. The 5 subunit core enzyme (~410 kDa) α2ββ'ω(with two identical α subunits) functions to bind DNA nonspecifically and catalyze the synthesis of RNA. In order to bind promoter-specific regions, the core enzyme requires a σ factor which greatly reduces affinity for nonspecific DNA while increasing specificity for promoters forming the 5 subunit holoenzyme α2ββ'σω (~480 kDa). The structure RNAP exhibits a groove with a length of 55 Å and a diameter of 25 Å. This groove fits well the 20 Å double strand of DNA. The 55 Å length can accept 16 nucleotides.
RNA polymerase in eukaryotes
Eukaryotes have several types of RNAP:
- RNA polymerase I synthesizes precursors of rRNA.
- RNA polymerase II synthesizes precursors of mRNA. This is the most studied type, and transcription factors are required for its binding to its promoters.
- RNA polymerase III synthesizes tRNA, rRNA 5S and other small RNA's found in the nucleus and cytosol.
- Other RNA polymerase types in mitochondria and chloroplasts.
RNA polymerase can be isolated in the following ways:
- By a phosphocellulose column (PC).
- By glycerol gradient centrifugation (GG).
- By a DNA column (A).
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