You previously learned that the Central Dogma of Molecular Biology is a thread that ties together three types of molecules – DNA, RNA, and protein. In this topic, we will dwell in more detail on the second step – the synthesis of RNA from a DNA template. This process is called transcription.
Overlook
Transcription occurs in all cells and is the process by which RNA is synthesized using DNA as a template. A special enzyme called RNA-polymerase unwinds the double stranded DNA and copies it into a strand of messenger RNA (so-called matrix RNA), from which the ribosome will then synthesize a protein.
Why is RNA needed? Why can't proteins be synthesized directly from DNA? There are several reasons. First, ribosomes are rather large molecules and cannot fit in the small space of the nucleus where the DNA resides, so translation cannot take place in the nucleus. ''Pullin'' DNA out of the nucleus is not the best idea, as it risks mutations or errors being introduced to the genetic material and can cause unnecessary stress on cellular structures. The most logical way is to separate large molecules and the processes by which they are made into different compartments and having an intermediate to pass the information from one compartment to the other. So, DNA replication takes place in the nucleus, protein translation takes place in the cytosol, and they are connected by RNA.
Secondly, DNA often contains non-coding sequences. Synthesizing them will disrupt the structure of the protein, so the ribosomes would need to ''know'' which parts to synthesize, which is not something they have evolved to do. Instead, once RNA is copied from DNA, it is processed, and ''corrections'' are introduced into the mRNA to ensure it codes for a functional protein with no extra junk. These corrections include removing unnecessary sections (this is called splicing), as well as protecting the molecule by adding a ''tail'' of adenine (polyadenylation) and a ''cap'' (capping) to it. Making corrections directly to DNA is impractical, as it is meant to be the permanent version of the genome in the cell; it is much easier to do this with an auxiliary disposable molecule like RNA.
A variant of splicing is alternative splicing, when RNA can be ''cut'' in different ways to code for several products with different properties. This ensures the synthesis of several proteins at once with DIFFERENT amino acid sequences. Alternative splicing makes it possible to increase the capacity of the genome, since it proposes to go beyond ''one gene – one protein.''
RNA-polymerase
The general process of transcription can be simply described as follows: a special enzyme RNA polymerase sits on double-stranded DNA and then travels along the chain making a copy of single-stranded RNA. RNA polymerase is a complex protein made up of several subunits. In different organisms, RNA polymerases differ in the number of subunits and amino acid composition. RNA polymerase ''workin'' with DNA is called DNA-dependent (this is opposed to RNA-dependent polymerase, which is capable of making copies on the basis of RNA but exists only in viruses).
DNA and RNA polymerase are the main participants in transcription, but there are several auxiliary proteins. During the process, DNA unravels. One side of the helix become the main side – it is the side where RNA polymerase sits. The enzyme reads the DNA nucleotides and builds RNA. RNA is synthesized according to the principle of complementarity using the same nucleotides as in DNA with one exception: instead of thymine, uracil is used in RNA. The RNA made by this process is called messenger RNA or mRNA.
The activation of RNA polymerase requires transcription factors that trigger transcription. Like most proteins that ''work'' with DNA, polymerases require the presence of magnesium ions as a coenzyme for their work.
Stages of transcription
There are three main stages in transcription – initiation, elongation, and termination. For the initiation step to begin, RNA polymerase needs to recognize a specific nucleotide sequence called a promoter. A promoter is an asymmetric nucleotide sequence that indicates the start site and which chain to copy. Most likely, RNA polymerase sits on the promoter due to blind recognition – so the enzyme goes along the DNA-chain until it finds the desired site. Once the promoter is recognized, the RNA-polymerase and DNA form a closed complex.
For RNA synthesis, RNA-polymerase needs to unwind the DNA helix, which it does at a distance of 13 nucleotides. At the initiation stage, an open complex is formed between RNA polymerase and DNA, which is called the transcription bubble. After that, the polymerase can begin synthesis, and the first bonds of nucleotides are formed: RNA elongation occurs at the 3' end of the chain. The work of the polymerase is often accompanied by errors and interruption of the process at this stage. When about a dozen nucleotides are synthesized, the process becomes more stable and the next stage begins – elongation.
At this stage, the RNA polymerase continues its march, the DNA strand in front of it continues to unwind, and the DNA strand behind it twists again. To regulate this process, there are a number of auxiliary proteins. The speed of polymerase movement at this stage is high – up to 50 nucleotides per second!
For the termination of transcription – its completion – there are several mechanisms. One of the most common in prokaryotes is ρ-dependent termination, when a special protein Rho attaches to certain sections of the synthesized RNA and, with an energy input of ATP, contributes to the breakdown of the RNA-DNA complex. There is also a ρ-independent termination: during this process, a long string of uracils are added to the growing RNA chain, forming a hairpin that mechanically destroys the complex.
Reverse transcription
Retroviruses are capable of a process called reverse transcription that contradicts the original Central Dogma. Reverse transcription produces double-stranded DNA from single-stranded RNA. To do this, there is an enzyme encoded in the genome of these viruses, called reverse transcriptase or revertase.
Reverse transcription is necessary for retroviruses because their genetic information is contained in RNA, and the host cell is not able to synthesize protein based on the incoming RNA. The virus has to synthesize DNA complementary to its RNA and then complete the second chain on this DNA chain. Only in this way can the process of viral protein synthesis begin.
Conclusion
Transcription is the synthesis of RNA from a DNA template. For this, the enzyme RNA polymerase is used. Transcription proceeds in three stages – initiation, elongation and termination. After synthesis, RNA undergoes changes and correction during processing. There are several types of termination, the most frequent being ρ-dependent and ρ-independent. Retroviruses perform reverse transcription, when a new DNA is built on the RNA template.