all right welcome back in this second video we're going to jump into the details of transcription how do we get messenger RNA from our DNA we're going to be focusing on transcription and procaryotes although UK carots are very similar where transcription is occurring if I look at the DNA double helix the DNA double helix has to unwind in that region and that unwind portion is known as the transcription bubble transcription always proceeds from the same DNA strand for a particular Gene and that's known as the template strand in this case this is my template I can see that the RNA the sequence of the messenger RNA is going to be complementary to the template strand the other strand of DNA is is going to be known as the non-template this is the non-template Strand and it's also sometimes called the coding strand because interestingly it's going to have a similar SE sequence to the messenger RNA molecule except where instead of having thines we're going to see uracils so if you look at the sequence of the non-template Strand and the messenger RNA it's almost identical again except T's are replaced with u all right so that's that one a couple of other things to know the first five Prime messenger RNA nucleotide and I can see that's here is known as the plus one s or the initiation site so in this case it's the adenine right there anything before that is known as upstream or are known as Upstream nucleotides so it would be something like over here if there was more DNA over here those would be called Upstream nucleotides anything down past that part it are known as Downstream nucleotides and notice notice that the messenger RNA direction of synthesis is just like DNA replication it goes from 5 to 3 Prime where you're adding on to the three prime end because even messenger RNA and the template stram are anti-parallel you're going to be starting at the three prime end of the template strand in order to generate your five Prime end of messenger RNA and you can see you work towards the five Prime end of DNA that will be your three prime end of the messenger RNA there are three basic steps of transcription initiation elongation and termination so in initiation we're going to see that there is a region called the promoter that will be Upstream of the gene of Interest where RNA polymerase will bind and begin transcription after initiation we have elongation which is what it sounds like where RNA polymerase will read the DNA and add the complimentary RNA a nucleotides finally you'll reach termination and there are two types of termination for transcription something called row dependent and then row independent and we'll get into these later when we think about differences in procaryotes versus ukar remember in procaryotes like bacteria there's no nucleus so there's no nuclear membrane everything is happening in the cytoplasm so transcription occurs to make messenger RNA and as soon as there's enough messenger RNA translation can occur before even you finished your messenger RNA these can occur simultaneously so that ribosome will grab onto the messenger RNA and start Translating that into your polypeptide sequence and in UK carots though let's say if this was in UK carots this would be different because ukar let me draw a cell we do have a nucleus so if this were the nucleus then we have transcription is going to occur here transcription going from DNA to my messenger RNA then the messenger RNA has to moveed to the cytoplasm and that's where it's going to be read and converted to proteins through the process of translation so how does RNA polymerase know where to bind and start transcription it looks for a specific region known as the promoter and in this picture this whole part is called a promoter that's where RNA polymerase will bind so that it knows where to begin transcription and the promoters always Upstream of our Gene of Interest so let's jump back to the first step of transcription which is known as initiation it turns out that Upstream of that initiation site there are specific regions known as consensus sequences consensus sequences and these are in a region known as the promoter so promoters are Upstream of the transcription start site and within the promoter there are two consensus sequences that are similar across all promoters and across most bacterial species so in particular there's a region called the minus 10 so minus 10 nucleotides Upstream of the transcription initiation site this is called Theus 10 region and we can see it says ta ta a t and Upstream of that there's another region called the minus 35 region that has a specific sequence again these two sequences don't worry about memorizing them but these are consensus sequences that we see in different species of bacteria and we also see them in all promoters for these bacteria if I look at the RNA polymerase it's a huge enzyme so it's that yellow or creamish color enzyme and it's made up of four subunits in our class I don't require you to memorize them but they're there are several subunits that make up this RNA polymerase I would you I would like you to know the fifth subunit which is the sigma Factor so that's another subunit of the RNA polymerase and more importantly it's the one that recognizes the consensus sequence found in the promoter so it helps us localize where we're going to start the transcription so when we combine the four subunits of RNA polymerase with that Sigma Factor we get the whole RNA polymerase complete enzyme and that is known as the Holo enzyme after initiation we have elongation and here in the RNA polymerase just keeps moving down the template strand of DNA this process starts with the release of the sigma subunit from the RNA polymerase and that's why you don't see that subunit that we saw in the previous picture the messenger RNA again is synthesized in the 5 to3 Prime direction as it unwinds the DNA double helix so you'll see another bubble open up here and the previous region will close up once we no longer need to generate messenger RNA in that region because it's already complete so if we read a for example we would put down U uh T would be put down a c Etc and this continues in that 5 to3 Prime Direction and in procaryotes this is very fast so this is a rate in procaryotes like bacteria 40 nucleotides per second extremely rapid so we had initiation elongation and our last step is termination and we have two types of termination one is called row dependent row dependent termination and in row dependent termination we're going to see that there is a row protein that tracks behind the RNA polymerase and is going to bump into everything and allow it to fall apart in row independent termination we're going to see that there are specific sequences in the DNA template strand that is going to cause a weird shape to be formed in messenger RNA called a hair pin and then everything will break apart so again it's either going to be due to a rope protein so that one is associated with this one or the formation of a hair pin struction H sorry hair pin structure which is associated with this one and both of these cause the release of the messenger RNA strand so that it can start the process of translation here are some pictures of this process on the right we have the row dependent termination and I can see what's happening here is this is my DNA this is my messenger RNA in Red so I have this is my DNA template strand this is my messenger RNA and red so row protein threads itself across the messenger RNA and pushes everything apart so everything falls off and I have my messenger RNA ready to go and in row deep sorry row independent termination which is sh on the left this is row independent we're going to see that there is a specific sequence of nucleotides in the DNA that causes the formation of a hair pin Loop in my messenger RNA so that's a hair pin Loop immediately following the hair pin Loop in the DNA you have a bunch of A's that's my Terminator sequence and of course the complimentary nucleotide are uracils in the messenger RNA because member a and u only pair with two hydrogen bonds it's weaker than G's and C's which pair with three hydrogen bonds this hair pin Loop in combination with the weaker hydrogen bonds between the messenger RNA and DNA cause the structure to fall apart so that releases the messenger RNA and again it's really because of that really bulky hair pin Loop and the weak interaction between A's and U's remember that procaryotes like bacteria since they do not have a nucleus as soon as they create their messenger RNA through transcription they can immediately translate translate that messenger RNA into proteins and that's what's shown in this picture from our book although I don't think it's the best picture it's hard to see what's going on in our book this is DNA the green line is supposed to be DNA and then it looks like it's not shown but we have RNA polymerases that made the blue squiggly lines which are our messenger rnas and at the same time we have ribosomes the red that are bound to the messenger RNA and starting they're going to be starting the translation process if you have multiple ribosomes on a messenger RNA molecule we call that a poly ribosome so really the take home message of this picture is that in bacteria or other procaryotes like archa we can have transcription and translation I'm just going to abbreviate translation happening at the same time everything's happening in the cytoplasm and this will not be true in UK carots because we have a nucleus so this is a picture I found on the internet I thought it was much better but there actually was an error in the 5 to 3 Prime n so I fixed it and here I'm giving it to you guys um it looks like I'm going to start from here on the left this is my DNA double stranded DNA and I have AR plase transcribing the DNA this looks like the template strand is the top one that's the template strand I always read the template strand from 3 to 5 in order to make messenger RNA go from 5 to 3 and then we're zooming in here and this is again in procaryotes cuz we don't have a nucleus we want want to see how things happen at the same time how transcription and translation can happen at the same time so I'm just taking that template strand this top strand this would be the five Prime end of my DNA and I'm making my messenger RNA so this would be the oldest one I transcribed this one first and I can tell because it's the longest one then this one is the second longest third this is the newest messenger RNA in pink that pink line that is been formed so this RNA polymerase latched on first then this one then this one then this one so I can see that as soon as I start transcription with my first RNA polymerase as soon as there's space the next ones can come on and make more messenger RNA and then my ribosomes which are these structures can bind to the five Prime end messenger RNA and start making my polypeptide my amino acid chains and the ribosome is moving from 5 to 3 Prime on the messenger RNA molecule so I can see that's the direction of translation all right similar to what you did at the end of the first video there's an activity and canvas another page after this video where I'd like you to watch this YouTube video I was going to try to embed it but I learned from the previous lecture uh the previous chapter that doesn't work well in my videos so I'm going to post the link on our canvas page please watch the video and again it's also available through our Open Stacks textbook this is a good one to review the transcription process going through initiation elongation and termination and that takes us to the end of our second video and our third video we're going to look at differences between procaryotic and eukariotic transcription