Chemistry of Life

Molecular genetics, biochemistry

RNA polymerase

In prokaryotic cells, all RNA classes are synthesized by a single polymerase. In eukaryotic cells there are 3 distinct classes of RNA polymerase, RNA polymerase (pol) I, II and III. Each polymerase is responsible for the synthesis of a different class of RNA.

Nucleolar RNA polymerase I (Pol I) is dedicated to synthesis of pre-rRNA. Nuclear RNA polymerase II (Pol II) initiates transcription at DNA sequences corresponding to the 5' Cap of mRNAs and transcribes the pre-mRNA of class II genes. Nuclear RNA polymerase III (Pol III) transcribes tRNA genes, 5S-rRNA genes, and genes encoding several other small RNAs.

Promoters are DNA sequences that are recognized and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Several proteins termed general transcription factors are necessary for RNA polymerase II binding to chromatin templates: TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH. In order to begin transcription, RNA polymerase requires the general transcription factors, which have been highly conserved in evolution.

All RNA polymerases are dependent upon a DNA template from which to synthesize RNA by addition of complementary bases to an elongating backbone. Transcription, like replication, proceeds 3' to 5' on the template strand and 5' to 3' on the new (nascent) strand. In RNA, U is substituted for T. The transcribed RNA is complementary to the template strand of the DNA duplex, and is a replica of base-sequences in the non-template, coding strand. The non-template strand is called the coding strand because its sequences are identical to those of the mRNA (with U substituted for T).

Eubacterial RNAp : one type; relatively simple subunit composition; binds directly to promoter (can be footprinted).
Archaeal RNAp : one type; complex subunit structure (subunit pattern, genes, and serological properties similar to eukaryal RNA polymerase II); can be footprinted, but still requires basal transcription factors for promoter recognition.
Eukaryotic RNAp : three types; complex subunit compositions; cannot be footprinted; require basal transcription factors for promoter recognition/binding

Table  Comparisons of Eubacteria, Archaea, and Eukaryotes :

p53 - A 3D animation showing the molecule p53 binding to DNA to initiate the transcription of mRNA : diagram - pre-mRNA processing : diagram - intron excision in mRNA precursors : life cycle of an mRNA ~ click on Quicktime Q : alternative splicing - click on fig 1 for animation :NCBI Molecular Cell Biology - Transcription Initiation Complex : Bacterial Transcription Initiation (NCBI MCB) : SUMMARY transcription initiation (NCBI MCB)

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