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Elongation
The elongation phase of transcription refers to the process through which nucleotides are added to the growing RNA chain. As the RNA polymerase moves down the DNA template strand, the open complex bubble moves also. The bubble is of a fixed number of nucleotides, meaning that at the leading end of the bubble, the DNA helix is being unwound, while at its trailing end, the single strands are being rejoined. Whereas separation of the DNA helix is permanent in replication, it is only temporary in transcription. Figure 6.07 depicts the beginning steps in transcription up to elongation and the relative positions of the bubble and the polymerase holoenzyme.
Figure 6.07: Steps in Transcription
As the figure shows, within the open complex bubble, the DNA and RNA form a hybrid or joint complex. The exact length of this region is unknown, but it is thought to be between 3 and 12 base pairs long and is found at the growing 3' end of the RNA. The figure also illustrates how the 5' tail end of the RNA chain is separate from, as opposed to base paired to, the DNA template strand. This is another difference between DNA replication and DNA transcription; in replication, the newly synthesized DNA strand remains bound in a helix to the strand with which it has base paired. After the initial stretch of approximately 8 base pairs has been synthesized, the sigma unit, which is responsible for recognition and binding to the promoter region, is released. The core enzyme is left to polymerize the growing RNA chain alone. This leads to the continuous extrusion of the 5' end of the RNA from the enzyme complex. At normal room temperature, the rate of transcription in prokaryotes is 40 nucleotides per second.
Termination
RNA synthesis will continue along the DNA template strand until the polymerase encounters a signal that tells it to stop, or terminate, transcription. This signal can take the form of inverted sequences or the assistance of other protein interactions.
Eukaryotic RNA Polymerases
Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes (including humans) comes in three variations, each encoding a different type of gene.
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RNA polymerase I is responsible for transcribing RNA that codes for genes that become structural components of the ribosome, a protein responsible for the translation of RNA into proteins.
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RNA polymerase II transcribes protein-encoding genes, or messenger RNAs, which are the RNAs that get translated into proteins.
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RNA polymerase III transcribes a different structural region of the ribosome, transfer RNAs, which are also involved the translation process, as well as non-protein encoding RNAs.
Promoter Regions
The promoter regions for RNA polymerases I and II are located upstream of the start site, but the promoter for polymerase III is oddly located downstream.
One key difference between prokaryotic and eukaryotic transcription is that eukaryotic polymerases are unable to recognize promoter regions. They have no direct parallel to the sigma subunit of their prokaryotic counterpart. Instead, eukaryotic polymerases depend on other proteins that bind to the promoter regions and then recruit the RNA polymerases to the correct spots. Polymerase II promoters must have either a "TATA box", a region approximately 25 base pairs upstream from the start-site with the sequence TATAAAA, or an "initiator element". The TATA box, loosely resembles the -10 region found in prokaryotic promoters, but the initiator element is not as well defined. It is known to straddle the start-site. This sequence acts as binding sites for specific transcription factors that then recruit the appropriate RNA polymerases.
