Right, I’m back to blogging about molecular biology et cetera, and if one were to go back and re-read the last article that I wrote, the first thing they would notice is how the Human Genome Project was extremely significant, since it would enable us to understand how genotypes give rise to phenotypes.
The transition between genotype and phenotype is not very simple or clear cut at all times, since there can be varying numbers of different proteins and interactions between proteins involved in the development of traits from genes. Interactions with the environment can also play a role in this.
One of the central tenets of modern molecular biology is the idea of the central dogma of molecular biology, which forbids the transfer of sequential information from proteins to other proteins or nucleic acids, but allows sequence information transfer from nucleic acids to proteins. You may trawl through the archives on this blog to find that article.
One of the molecular interactions that does happen in all living organisms barring a few viruses with reverse transcription is the process of Transcription. In transcription, an RNA sequence is produced using DNA as a template, and a short introduction to this process will be the focus of my post.
The process of transcription per se can be split into several key stages; Initiation, Promoter Clearance & Elongation, and termination. A brief description of these stages follows…
 Initiation – this is the first stage of the transcription process, which should be bleeding obvious :P, it must be noted that the process of transcription is contingent upon the Transcriptional apparatus beginning to liaise with the DNA that is to be transcribed.
In Eukaryotes (organisms with a proper, double membrane nucleus) the process is slightly more complex than in bacteria, but both involve the binding of the RNA polymerase enzyme’s subunits to DNA sequences called promoters. Promoters are capable of binding to RNA polymerase by means of specific sequence motifs that they carry, and as such they serve as starting points for transcription.
In Eukaryotes, proteins called transcription factors are also required to bind to core promoter regions along with RNA polymerase for initiation to occur properly. The key difference is that while RNA Polymerase is capable of binding directly to promoters in Prokaryotes, in Eukaryotes this is not possible and has to be mediated by transcription factors, this can enable the evolution of genetic systems with a much more complex range of transcriptional regulatory interactions possible, since transcription factors per se can facilitate binding to a wider range of promoter sequences based on the interactions they have with target sequences, and thus enable organisms to develop gene regulatory networks with more flexibility and variability, this can sometimes be a problem in things like cancer since one potential implication is that there are more ways by which dysregulation may be achieved.
RNA polymerase is an enzyme made up of multiple subunits, initiation can be said to have well and truly occurred after we end up with all the requisite factors and enzymes at the promoter. The next step is promoter clearance.
 Promoter Clearance/Abortive Initiation – The fully assembled, active RNA Polymerase complex then begins to move along the unwound DNA (the unwinding is due to the action of a helicase enzyme that is part of the complex), producing very short fragments of RNA, slowly it frees itself from the promoter, at which point a molecule in the complex, called the σ
factor, will have rearranged. From this point onwards, the process of transcription is able to produce full length transcripts.
 Elongation – this is the step in which long, full length transcripts that later undergo translation to form proteins or RNA processing to work as functional RNA molecules are produced. The process is actually quite simple.
i) RNA Polymerase unwinds DNA through helicase activity.
ii) The 3′ – 5′ strand of DNA is used as a template for RNA synthesis, the RNA polymerase incorporates nucleotides through complementary base pairing, like in DNA, but with a noticeable exception, that being that instead of Thymine we have Uracil in RNA, and this binds to Adenine on the DNA template.
iii) And so a strand of RNA is synthesized, as the enzyme complex moves along the template DNA, it allows the hitherto separated strands of DNA to come back in together and the RNA is dissociated. The whole process of elongation is dependent on energy from ATP.
 Termination – This is the final step, where transcription is halted and the RNA transcript is released.
The process again is different in Prokaryotes and Eukaryotes, in prokaryotes there are two known mechanisms.
i) Rho Dependent Termination – here, a protein factor called Rho binds to the transcription termination site, and destabilizes the interaction between the DNA template and the RNA Polymerase complex, resulting in transcription being ended and the transcript being released as a consequence.
ii) Rho independent termination – here, the formation of a hairpin loop in G-C rich regions of the DNA template basically renders it inaccessible to the RNA strand and RNA polymerase, resulting in termination of transcription.
In Eukaryotes there is enzymatic cleavage of the transcript followed by polyadenylation of mRNA to produce the final transcript which may undergo further posttranscriptional modifications before translation, such as splicing.
A little tangent – Reverse Transcription.
Some viruses with RNA genomes (or retroviruses) engage in reverse transcription, that is, production of a DNA sequence using an RNA template, they do this with the help of an enzyme called Reverse Transcriptase. Basically, the process of reverse transcription is as follows…
i) Synthesis of DNA strand complementary to RNA template.
ii) Enzymatic degradation of RNA template.
iii) Conversion of DNA strand synthesized in step i) to a double stranded version through DNA polymerase activity.
Retrotransposons also use Reverse transcription when they do their thing (i.e, self replicate and integrate themselves into other sites in the genome) , Howard Temin, Renato Dulbecco and David Baltimore won a Nobel for their discovery of Reverse Transcriptase, and one may find the apposite Nobel lectures through the link here
More to read, more to learn
 Read an article from Nature Scitable on DNA transcription, here
 Watch a simplified video summary here
Alright then, I guess that is pretty much it for today.