hey welcome to the Crux in this video we're going to start our discussion on transcription and in particular we start by looking at the procaryotic transcription so transcription is the process of genetic information conversion or transfer from the coding region of the DNA to a messenger RNA in a given piece of DNA for instance a gene you have the coding region which contains information about the protein it codes or a functional RNA it codes like the ribosomal RNA and the start of this coding region is usually referred to as transcription start site or TSS for short and the first base of the coding region is called the plus one position for reference to everything else around it and at the end of the coding region we have the stop site which marks the end of the coding region now from our reference set at the TSS we call all things towards the end of the coding region Downstream and likewise all the things before the plus one site are considered Upstream one important piece of DNA that is located Upstream of the TSS is the promoter region and promoter is involved in promoting or initiating the process of transcription and once transcription is initiated it continues along the coding region in a process called elongation and then it terminates at the stop signal so you could divide the entire process of transcription into three steps since transcription is initiated via the promoters we should first discuss about the organization of the promoter DNA so consider this doubl stranded DNA and let's mark our reference at TSS which is the first base of the coding region and then Downstream of the plus one site you have the plus two plus three and on the Upstream site you have -1 and -2 sites and you can continue writing this notation for all bases in both directions and you should note that there is no site zero now in our promoter region which is the Upstream of the TSS we have three main promoter elements the distal or the farthest is the upe element Upstream promoter element which is at about 58 to- 37th position then we have the -35 element which is located at around -35 to -30 position then you have the most common promoter element the -10 element located at the -12th to -7th position it is also known that the optimal spacing between the -35 and the -10 element is around 17 bases sometimes the- 35 element or the -10 elements are not available in the promoter of some genes in those cases you can find an extended -10 element at the position -17 to -14 and then there are some genes that carry a discriminator promoter element which is usually three bases in length as you may have already read it the -10 element is also sometimes called the pnau box or the pnau sheller box in the UK carots it's homologue can be thought of as the Tata box also known as The Goldberg hogness box functionally speaking the up element is frequently contacted by the RNA polymerase which is the enzyme responsible for making RNA and its binding to the upe stabilizes it the up is commonly found and the promoter of ribosomal RNA genes then the - 35 element extended -10 and the -10 elements are contacted by the sigma factors which are responsible for the transcription initiation process finally the discriminator element is also Bound by the sigma factors and because Sigma factors are bound to the RNA polymerase the discriminator element helps stabilize the polymerase when looking at the sequence structure of each of these elements they have some underlying consensus sequences for instance up has a long consensus the W's and n's that you see in the sequence are iopac symbols check out the link in the description to learn about their meaning the -35 has ttgaca as its consensus sequence the extended -10 has trtg as its consensus and the -10 element has t a t a a t as its consensus and then the discriminator is usually just a g triplet so you should keep in mind that the consensus sequence are just an average representation of the sequence expectation this means that just because you have a consensus sequence does not mean that it is always like that in all genes and therefore it can change a way to get consensus is to align a particular portion of DNA and compute the per base average in that alignment and that gives you a consensus to show you what I mean consider the -10 element whose consensus as we just said is t a t a a t but that is only true because it is bound by Sigma Factor D also known as Sigma 70 or rpod and because Sigma D Factor binds most of the genes and procaryotes the consensus of ta a tat is biased towards it but when you look at the negative T element sequence of certain Sigma H bound genes and these are usually the heat shock genes you find a completely different consensus so there are different Sigma factors involved in the promoter binding and I have a link in the description if you want to read more about them now depending on the promoter sequence the promoters can either be strong or weak that is the measure of how many transcript they can produce in a given time the strong promoters usually match their respective consensus fairly well and weak ones deviate one last thing about promoters you should know is that their sequence composition can cause DNA to form curvatures or bends this is important because the proteins like Sigma factors that bind them have to unfold these DNA sequence and torsion or bend created by these sequence helps these proteins affect L do their job so that is all for the introduction of bacterial promoters