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Similarities between DNA Replication and DNA Transcription
Before we begin our discussion on prokaryotic transcription, it is helpful to first point out some similarities and differences between the process of DNA replication and DNA transcription. The processes that synthesize DNA and RNA are similar in that they use similar nucleotide building blocks. There are, however, several important differences between these two distinct processes.
Differences between Replication and Transcription
One major difference is that while DNA replication copies an entire helix, transcription only transcribes specific regions of one strand of the helix. During DNA transcription, only short stretches (about 60 base pairs) of the template DNA helix are unwound. This strand can also be called the noncoding strand, the minus strand, or the antisense strand. As the RNA polymerase transcribes more of the DNA strand, this short stretch moves along with the transcription machinery. This process is different from that in DNA replication in which the parent helix remains separated until replication is done.
Another major difference is that DNA replication is a highly regulated process that only occurs at specific times during a cell's life. DNA transcription is also regulated, but it is triggered by different signals from those used to control DNA replication.
One final difference lies in the capabilities of RNA polymerase versus DNA polymerase. Remember that a key problem in DNA replication exists in the initiation of the addition of nucleotides. RNA primers are needed to begin replication because DNA polymerase is unable to do it alone. DNA transcription does not have the same problem because RNA polymerase is capable of initiating RNA synthesis.
The Start Site and the Promoter Region
In prokaryotic cells, free RNA polymerase molecules are constantly colliding with DNA helices. The collision leads to a weak association between the DNA and RNA polymerase, which is soon broken. However, when the RNA polymerase binds to a specific sequence on the DNA, it binds tightly, forming a DNA/RNA polymerase complex. This specific site of binding is called the start site. The start site represents the location on the DNA that marks where the first nucleotide of an RNA chain should go; that spot is designated as the "plus one position". Positions that are designated as downstream in the RNA are positively numbered according to their relative position to the plus one position. All positions designated as upstream of the start site are labeled with negative numbers according to their position relative to the start site. Sequences located just upstream of the start site, called the promoter region, contain the information that signals the RNA polymerase to start transcription.
Recognition of the Promoter Region
RNA polymerase binds to the DNA helix at the start site. The RNA polymerase/promoter complex then undergoes a conformational change that breaks a number of base pairs to create a bubble in which the two DNA strands have separated. This new formation is called the "open complex". RNA synthesis is then initiated using one of the DNA strands as a template for adding complementary RNA base pairs. Transcription is usually initiated with a purine, rather than pyrimidine, base. Once initiated, the RNA polymerase moves down the DNA strand in the elongation process, which is covered in the next section.
