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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. They also use the same chemical method of attack by a terminal -OH group of the growing chain on the triphosphate group of an incoming nucleotide. Both replication and transcription are fueled by the hydrolysis of the pyrophosphate group that is released upon attack. There are, however, a number of important differences between these two distinct processes.
One major difference rests on the fact that while DNA replication copies an entire helix, DNA 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. 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.
There are slight differences in the substrates that are used in DNA replication versus transcription. Recall the structural differences between DNA and RNA. RNA's nucleotides are not deoxyribonucleotide triphosphates as in DNA. Instead, they are simply ribonucleotide triphosphates, meaning they do not lack an -OH group. Additionally, in RNA the thymine base is replaced with the base uracil. Both of these differences can be seen in DNA transcription.
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 lay 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 structure of the RNA polymerase is necessary for understanding all of the processes that underlie initiation, elongation, and termination and also explain some of its added capabilities.
There are two main segments of the RNA polymerase molecule: the core enzyme, and the sigma subunit. These two pieces are together referred to as the "holoenzyme". The core enzyme is itself composed of a beta, beta prime, and two alpha subunits; together the core is responsible for carrying out the polymerization or synthesis of RNA. The sigma subunit of RNA polymerase is the part of the enzyme responsible for recognizing the signal on the DNA strand that tells the polymerase to begin synthesizing RNA. It is through this sigma unit that RNA polymerase is able to initiate transcription.
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