Organization and Control of Prokaryotic and Eukaryotic Genomes - Part 1

hi everyone hope you are all doing well we are now going to be starting on the next chapter of your h2 biology syllabus and this would be the chapter on organization and control of prokaryotic and eukaryotic genomes this lecture series will be divided into two parts so in the first part we will be looking at the organization of the eukaryotic and programmatic genomes and in the second part we'll be looking at the control of eukaryotic and prokaryotic genomes this chapter is a natural lead up from a chapter you have done previously that would be dna and genomics where you learned about the different aspects of the structure of dna as well as gene expression on how dna is transcribed to rna and how mrna is translated to form proteins you have also learned about semi-conservative dna replication where parental strands have their genome copied to form copies of dna which can then be passed on to their daughter cells in an identical fashion this topic which you're going to be learning right now is going to be a step up from what you have learned from dna and genomics so my first advice to you would be this if you have not read through the lecture notes namely the lecture note on organization and control of prokaryotic and eukaryotic genome 1 please pause this video and read through the lecture notes at least the first set understand and try to understand what is going on in the lecture notes first write down your queries and your doubts on your lecture notes and then thereafter come and view this video the reason is because the content which is going to be covered as part of this particular lecture series is going to be a bit more dense than what you have covered so far so it is important for you to have at least a baseline understanding of what is going to be covered so that you can clarify your doubts with your tutors as you are going through this series of lectures feel free to email or whatsapp your tutors as you have doubts i am not going to say that this is going to be an easy chapter but is one which is going to take a lot of perseverance for you to understand unlearn and relearn concepts so without further ado let's get into this chapter of organization and control of prokaryotic and eukaryotic genomes so as i said earlier we will divide this lecture into a few parts the first part would be the structure and organization of the genome and the second part which is the second part of the lecture notes will look at how regulation of gene expression is influenced by the structure and organization of genomes you would have seen the lecture series on cancer previously and this would be a nice link to see how this regulation or misregulation of gene expression can actually lead to this disease known as cancer which is essentially a disease brought about by mutations so in this lecture series on this lecture we're going to be covering specifically on the structure and organization of genomes so if you look at the learning outcome you realize that the first learning outcome would be to describe the structure and the organization of prokaryotic and eukaryotic genomes so what we need to do as part of this learning outcome would be to look at how we can compare the structured organization of prokaryotic and eukaryotic genomes and also see how the dna is packaged differently in these two genome types we will also be looking at the structure and functions of non-coding dna in eukaryotes i.e dna found in eukaryotes which do not actually lead to the transcription of mrna or their subsequent translation but are rather found in the dna and serve important functions in the control of gene expression so these non-coding sequences include sequences such as introns centromeres telomeres promoters enhancers and silences so these some of these words you might have heard it before but others you may not have so as we go through this series of lectures we will actually be looking specifically at the structure and function of these different types of non-coding dna so let's break down what structure and organization of genome actually means so genome actually refers to the complete set of genetic materials you would find in a cell this cell could either be a prokaryotic cell or it could be a eukaryotic cell so it refers to the complete set of genetic materials both the main chromosome as well as any extracellular chromosomes you might have in a cell all those genetic material is known as a genome and when you talk about the structure and organization then you were to compare the differences in genomes or prokaryotic and eukaryotic genomes you want to look at the distinct features of what defines a prokaryotic cell and eukaryotic cell in terms of its genome and how they are located with respect to each other as we understand and appreciate how this all control how this structure and and organization of genome is found in these different type of cells you will then be able to understand how these lead to effective control of gene expression in these cells so as we talk about the genome uh in in the prokaryotic cells and eukaryotic cells you'd realize that in prokaryotic cells the genome is found in a region known as the nucleoid region so the nucleotide region is where most of the of the eu prokaryotic genome is actually found uh and you know prokaryotic cells they do not have a nucleus okay so they don't have any membrane-bound organelles to have their genetic materials which is found in the form of dna uh compartmentalized within them this is unlike what you would find in a eukaryotic cell where you have a nucleus which is a membrane bound organelle remember nucleus is a double membrane bound organelle and a nucleus is surrounded by this structure known as a nuclear envelope and within the nucleus you would find most of your eukaryotic genome so it is surrounded by the nuclear envelope so that would be one key difference in terms of the location of genomes in prokaryotic cells as compared to in eukaryotic cells in your lecture notes in page four there's a table which actually lists the differences in the features between the structure of genomes of that of a prokaryote and how it is different from that of a eukaryote so please refer to page four for this particular part so now the one thing you would notice generally would be eukaryotic genomes are larger in terms of size and have a greater number of genes as compared to their prokaryotic counterparts so if you look at eukaryotic genomes you can find um in in different species so these are humans in if you find in cockroaches you have ferns and and amoeba um and in different types of plants and even bacterium uh the um the the genome size is actually relatively large okay and yeah you would be surprised to know that a cockroach basically has a larger genome than than yourself so if you look at cockroaches cockroaches basically i've got this many base pairs which is closer to 1 times 10 to the power of 11 number of base pairs while humans have got a lesser number of base pairs as compared to a cockroaches so the length of the genome of a cockroach is actually longer than of that of a human so this actually illustrates an important point over here the complexity of an organism or the physical size of the organism does not necessarily translate to it having a larger genome okay look at a fern a fern is actually a type of plant that has got a larger genome than than a human an amoeba okay a uni uh which which is actually um which is actually a very small organism that also has got a larger genome size than even humans and cockroaches so like what i said the size of organism does not define its genome size okay so you can have a very large organism like a human having a smaller genome size as compared to a very small organism like a cockroach okay so cockroach one human zero also in this sense so that you now now you've got a valid reason to be scared of flying cockroaches okay so if anyone asks you are you scared of cockroaches say yeah because they've got a larger genome size than me okay makes you sound a little bit more brave than than what it seems to be um if you look as compared to bacteria okay of course these bacteria are looking at prokaryotes generally even the largest of bacterial uh species they tend to have genome sizes which are generally smaller than most of the eukaryotes you would find so as compared to the number of genes about 25 000 in eukaryotes about 4500 in in in bacteria the next feature of comparison between eukaryotic and prokaryotic genome genome structure would be that of the appearance of the genome in prokaryotic cells you would find that the double helix dna is organized into one chromosome which is actually the main chromosome you'd find in bacteria and it is found as a single circular molecule which through supercoiling can be made into a more compact structure for eukaryotes however you'll find that the genome is organized into more than one chromosomes and that is how you have deployed numbers or even higher ploidy levels in certain types of organisms so as compared to prokaryotes where you would find the genome to be single and circular in eukaryotes you find that there are multiple chromosomes which appear as part of the genome and these are linear molecules instead of being circular another point of comparison would be the number of origins of replication per chromosome so if you remember your dna and genomics lectures you would remember that the origin of replication is where semiconservative dna replication commences where the parental strand is used as a template for the synthesis of new daughter strands during dna replication in prokaryotes you would find that there's only one origin of replication per chromosome because the chromosome is actually quite it's not very significantly large so one origin of replication is sufficient for you to have successful replication of the genome where else in eukaryotic cells or eukaryotic genomes you'd find that there are multiple origins of replication per chromosome you might ask what the significance of having multiple origins of replication is and if you think about it having many origins of replication would actually help increase the speed of replication and this is this is more necessary for eukaryotic chromosomes because you have a larger genome size telomeres and centromeres are other features of comparisons these are actually non-coding dna sequences which are found in eukaryotic cells so in prokaryotic cells you do not have telomeres where else in eukaryotic cells at the end of the eukaryotic cells you'll find that there are telomeric sequences these telomeres serve important functions and we'll be looking at the functions of telomeres and how they are formed in the later part of this lecture the presence of centromeres is also another distinctive feature of eukaryotic genomes centromeres is what is is a structure of uh of chromosomes you would have seen in the lecture of mitosis and meiosis and it is the part of the chromosome where you would find your kinetochore proteins attached to and to these kinetochore proteins found at the centromere you will have your kinetochore microtubules attaching to them and these kinetochore microtubules serve important functions in separation of sister chromatids during mitosis as well as in meiosis so centromeres they are found in eukaryotic cells and eukaryotic genomes but not in prokaryotic cells another important difference you would find between eukaryotic and programmatic genomes would be the level of dna packing and coiling as you know and as we have seen there is there is a difference in the size as well as the number of chromosomes you'll find in prokaryotic cells as compared to eukaryotic cells so the level of dna packing and coiling is going to be quite different as well especially since the cell is a very small unit to pack as much genetic information a species or an organism would need in every single cell would require very high level of packing and coiling so if you look at a prokaryotic cell you would find that mostly the genome is made of naked dna naked in a sense that there is very little proteins which actually associate with the dna when it comes to the packing of the dna this in comparison to eukaryotic cells is quite different because in eukaryotic cells there is a higher degree of condensation and packaging and you have larger number of proteins including histones and scaffold proteins which come into play to help compact your genetic material into highly condensed chromosomes found in your nucleus so now let's take a closer look at how each one of these condensation of chromosomes work for the respective types of cells so let's start off with the prokaryotic cells if we would look at a prokaryotic cell if this circle a represents a circular chromosomal dna i.e a dna double helix you have the formation of looped domains which come about and these loop domains would actually be found around histone-like proteins so you call this to be histone-like proteins these black structures here they don't call them histone proteins because there is no histones there are no histones which are found in prokaryotic cells so you call this to be histone-like proteins they are like histones but they are not histones so take note of that and further beyond this looped domain you would find that there is super coiling which actually happens so super coiling is a process where you have further compaction of your genome and with further compaction with genome it just about covers a very small area of one micrometer okay from 430 micrometer an e coli bacterial cell has a unfolded chromosome of 430 micrometer to get to one micrometer is is quite an amazing thing actually okay uh it's about a 400 times reduction in terms of the space the genome would occupy and this is going to be very important for the bacterial cell to have a genome found within it um do note that this particular feature of looping is is not just as small as just six loops found around around the histone-like proteins this can be going up to about 50 to 60 loops in in actual number and of course further folding is compacted by super coiling giving rise to highly compact dna in prokaryotes if you thought that was amazing you must check out what happens in eukaryotic genomes okay so this would be for prokaryotic genomes in eukaryotic genomes just imagine this if you were to unwrap or if i were to be able to unwrap all the dna you have in all of just your cells as one individual you can actually reach the moon about 6000 times that's the length of dna you would find to be present in a single person so that's amazing isn't it 6000 times you can build a bridge from the earth to the moon and back and how do you even compact this amount of this length of of of biomolecules in this case uh dna into a single person in all of their cells and that is where the amazing part about condensation and compaction of genomes come in the first level of compacting comes in when where your dna helix begins to associate with these proteins known as histones so histones are special proteins and these proteins actually allow for dna to coil around themselves you know that dna is negatively charged because of the presence of a negatively charged phosphate backbone where else your histone proteins they are made up of amino acids which have got r groups which are generally positively charged so when you have got a negatively charged molecule coiling around a positively charged molecule it helps to hold the dna around the histones due to electrostatic interactions or the presence of ionic bonds so these histones which have got um amino acids which are which have r groups which are positively charged examples of these amino acids would include uh lysine and arginine so the dna is held by around histones by electrostatic interactions forming quite a tight and compact um structure and this structure which is found when uh when when the dna is actually wound around a histone is known as a nucleosome so when most of the dna is wound around an octoma of eight histone proteins so there's not just one histone proteins there's a complex of eight different histone proteins okay you can see this h2a h2h basically referring histone h2a h2b h3h4 and different quantities of this give rise to an octoma and october referring to eight histone proteins when the dna is coiled around it you find that these actually give rise to this structure known as a nucleosome okay so this particular structure of eight histone proteins that there are four different types and you need uh two molecules of each type to give you eight histone proteins and the dna is called around it you call this structure to be a nucleosome and of course different nucleosomes are joined together by the segment of the dna known as a linker dna the width of a nucleosome is approximately 10 nanometers and this is actually a basic unit of chromosomal packing so different optimus actually or rather different nucleosomes which are adjacent to each other are joined by linker dna you also call this particular structure to be the 10 nanometer fiber because the width of a nucleosome is known to be about 10 nanometers so what happens further to this 10 nanometer fibers would be that they would coil around themselves to give you what is known as a 30 nanometer chromatin fiber or a solenoid but before we look at how the 39 nanometer micro chromatin fiber actually looks like this is how a nucleosome actually looks like under an electron microscope so this is a nucleosome and all these different black structures you see here are adjacent nucleosomes and these adjacent nucleosomes they coil around themselves to give you a more compact and condensed structure known as a 30 nanometer chromatin fiber or a solenoid and when you're forming this 30 nanometer chromatin fiber there is another type of histone protein which comes into play that would be the histone h1 protein so you've got another protein which helps in the compaction of your genome so once you have got your 30 nanometer microfiber it doesn't just stop at that that is further compacting where you actually find that your 30 nanometer chromatin fiber would loop uh to form looped domains and these loop domains uh would give rise to 300 nanometer fibers when they associate with different type of proteins known as scaffo proteins so with this scaffold proteins these are actually non-histone proteins you get the 300 nanometer fiber and if that is not enough there is actually a fourth level of compacting and that would be super coiling where the loops would further coil and produce what you would see as a characteristic type of chromosome during metaphase and this is the double arm structure of the chromosome you'd find during mitosis so supercoiling also occurs during uh it to give rise to metaphase chromosomes in a dividing cells so in summary in a eukaryote you'd find that you've got the dna double helix the dna double helix coils around a complex of eight histone proteins to give rise to a nucleosome also known as the 10 nanometer struck structure and further compacting gives rise to the 30 nanometer chromatin fiber or the solenoid followed following that you have got loop domains which come about and further super coiling happens eventually giving rise to your metaphase chromosomes in dividing cells so here's a chance for you to now visualize this through a video so i'm going to play a video on how dna is packaged in an eukaryotic cell to give you a visual representation of what i have just described in this animation we'll see the remarkable way our dna is tightly packed up to fit into the nucleus of every cell the process starts with assembly of a nucleosome which is formed when eight separate histone protein subunits attached to the dna molecule the combined tight loop of dna and protein is the nucleosome multiple nucleosomes are coiled together and these then stack on top of each other the end result is a fiber of packed nucleosomes known as chromatin this fiber which at this point is condensed to a thickness of 30 nanometers is then looped and further packaged using other proteins which are not shown here this remarkable multiple folding allows six feet of dna to fit into the nucleus of each cell in our body an object so small that ten thousand nuclei could fit on the tip of a needle the end result is that the dna is tightly packed into the familiar structures we can see through a microscope chromosomes it is important to realize that chromosomes are not always present they form only when cells are dividing at other times as we can see here at the end of cell division our dna becomes less highly organized so now that we have covered the structure of the genome for the prokaryotic genome and the eukaryotic genome let's move on to table two which is found on page six of your lecture notes which is actually talking about the differences in the organization of the genomes of these two different types of cells so the first point basically talks about the location of functionally related genes on a chromosome so what are functionally related genes so functionally related genes basically refer to genes which code for proteins which are involved in a similar biochemical or metabolic pathway in your cells so in prokaryotes one one very famous type of uh gene struck genome structure which is found in prokaryotic cells which involves the the grouping of genes which code for proteins which similar metabolic uh functions would be that of the lac operon the lac operon is an operon system which you'll be learning more about under this uh the chapter of uh genetics of bacteria where you will learn about how control and organization of prokaryotic genomes actually occur with greater details or in greater details with respect to the lac operon but for at this present moment uh it is important for you just to understand that functionally related genes can be located very close together in prokaryotic cells so when you have got genes which code for proteins for the same metabolic pathway in this case the lac operon which is involved in the uptake of lactose into cells and the breakdown of lactose in in bacterial cells these genes which are involved in this particular pathway they are grouped together under this one single entity known as a single operon a single operon basically has got a single promoter which controls the expression of these genes so uh it it basically means that when one gene is being coded for it will come together with all of the genes within the same operon being coded for being expressed at the same time okay so we'll look into more details about this under the topic of bacteria but it's key for you to understand that you have an operon system in prokaryotes where else in a eukaryote even though you may have you may have genes that code for functionally related proteins they need not necessarily be found very close to each other on a single chromosome they are usually located on different chromosomes another difference would be the the amount of non-coding regions you'd find you'd find that there are very much more non-coding dna sequences in eukaryotes as compared to prokaryotes up to 98 of your genome is actually non-coding okay so isn't that surprising and complex organisms such as uh such as yourself a human ninety-eight percent of the chromosomes you find your 46 chromosomes in your nucleus is non-coding they don't code for proteins then what do they do we will come to that in a short while okay where else in prokaryotes most of the genome is actually made up of coding sequences i.e there are genes which are expressed to give you uh proteins so about less than 15 percent is non-coding um presence of promoters which are important for the expression of genes okay that's the point where the gene actually starts in prokaryotes you find that in both programs and eukaryotes you find that the promoter is present in prokaryotes as i mentioned earlier you can have a single promoter which actually can control all the genes which are found in a operon system where else in a eukaryote each gene comes under the control of its own individual promoter so what this basically means that let's say i've got a promoter sequence here in a prokaryote if i've got gene x gene y and gene z present this single promoter can actually control the expression of these three different genes so these are actually three different genes where else in the eukaryote you don't find this each gene has got its own promoter present so each promo each gene would have its own promoter you don't have a sequence or a structure where a single promoter would control more than one gene introns are non-coding sequences as well and you'd find that introns are present in both prokaryotes and in eukaryotes but this is very low in numbers so as what is stated in your lecture notes introns you can consider them to be even absent even though the introns there are very very little introns present uh in prokaryotes you can actually consider them to be almost absent even though there might be a few but of course in eukaryotes introns which are non-coding sequences found in your genes they are actually interspersed between exons which are the coding regions of your genes enhancers and silences is something you'll learn about shortly as well these are non-coding sequences which either increase the rate of transcription or decrease the rate of transcription respectively of specific genes in prokaryotes you don't find this enhancer and silencers being present but in eukaryotes you do find them to be present enhancers and silences they're said to be control elements because they actually can affect the rate of transcription of genes extra chromosomal dna in prokaryotes they might be they may be present because they can be present in form of plasmids but in eukaryotic genomes you find that a plasmids are absent with the exception of what you might find in mitochondria and chloroplast which may have their own dna now we are done with the first learning outcome which is to describe the structure and organization of prokaryotic and eukaryotic genome let's move on to talk about non-coding dna in eukaryotes and the structure and function of these different types of non-coding dna you would find so when you look at the non-coding dna sequences in a eukaryotic gene or eukaryotic genome you'll find that there are many different types okay but each one of this has got important functions you'll find that you have promoters and terminators and introns you have enhancers and silencers and you also have got features such as centromeres and telomeres which are still non-coding and what we're going to look at is basically structure and function of these different non-coding sequences so as we move into this particular lecture even deeper you'll find that it's quite similar to what you do when you go into a very atas kind of a restaurant okay but you take out the menu card and you realize that what i look at the dish the name of the dish i actually don't understand what the name of the dish is it's the first time i'm actually seeing such it is like how many of you know what uh suno mono is if you look at a jet uh restaurants menu card i for one wouldn't actually know it but the important thing is before you actually uh order it and want to taste it you'd want to actually find out what it is right even though it's a new term you're coming across it's the same thing which actually is going to happen right now you're going to come across different new terms which you might be encountering for the first time but don't give up don't don't just gloss over it but try to and and and please do understand what these terms actually mean and what uh which structures they are referring to okay and the functions of these so uh this is just a different way of saying that there's quite a bit of jargon coming up please pay attention and do clarify if you have doubts okay and if anyone knows what suno mono is you can always drop me a message to to let me know no idea 6.95 hmm okay so um we looked at coding sequences and now we're going to be looking at non-coding sequences which do not code for proteins or rna products and you'll find that in a genome of a eukaryotic cell so now we are looking at eukaryotic genomes uh we are not focusing on prokaryotic genomes here prokaryotic genomes is something you are focusing when we are doing the chapter on bacteria we are also basically focusing on control of gene expression in prokaryotic genomes when we are doing bacteria we are going to be focusing on eukaryotic genomes here okay eukaryotic genome basically genome found in you non-coding dna sequences you would find that 98 of your genome doesn't code for proteins or rna products this is compared to prokaryotes only a small proportion of the genome consists of non-coding regions but a large proportion of the eukaryotic genome is made up of non-coding sequences and the different types of non-coding sequences you have repetitive sequences you have sequences which regulate gene expression you have got even rna genes you have got utr basically sends for untranslated regions and introns which are also uh non-coding sequences which are found within genes where else if you look at the coding part ie the part which is translated or rather transcribed and eventually translated by ribosomes to give you proteins it's only about two percent okay or even less than that you may come across this particular sequence uh this particular term known as tandem repeating dna sequences when you're looking at non-coding sequences what is a tandem repeating dna sequence so repeating dna sequence is fairly straightforward so if i have a sequence like this if i have got t c a t t c a t t c a t d c a t c c a t t c a t this is a repeating sequence and it is tandem basically because it is adjacent to each other it is tandemly repeating but not all random repeating sequences look like this some tandem repeating sequences can have a bit of variation to it okay so tc80 this is taat tca tcat tcat you still consider these sequence to be a tandem repeat sequence okay so when a 10 down repeat sequence actually comes about you would find that it can happen in in different parts of your your genome okay so most of the non-coding sequences uh you find in in your cells are actually made up of tandem repeat sequences and the interesting thing is that tandem repeat sequences may actually vary between individuals of the same species that means the tandem repeat sequence which is found in uh in you in one particular region of your chromosome may actually be different from what you would find in your friend so let's say let's say just just for example let's say this is chromosome 1 and this is you okay and let's say there's a tandem briquettes repeat sequence of maybe five repeats which is found on this part of your chromosome one okay and let's say you've got a friend uh your best friend maybe your best friend also has a chromosome one let's assume your best friend is human so if you've got a best friend who is human best friend is a bff right so best friend you find that with that same part of the the same chromosome in the same region he or she might have 20 repeats of the tandem repeat sequence okay and this is what actually gives rise to variation amongst us okay and you will learn more about this next year when you look at uh how variable number tandem repeats can actually help in identifying uh different people and it comes very useful when you're looking at things like a forensics where you are uh trying to uh see who a particular criminal was or who a thief was or who a murderer was based on forensic evidence is also used for paternity testing if you want to find out who the father or the mother of a particular child is when it comes to certain cases where you need to find out the parents of a particular child okay so it's important for pertinent opportunity testing as well okay more on that later but let's come back to what uh the what we are looking at as part of this particular lecture uh we are looking at uh the gene okay and also the non-coding sequences which we are talking about so what exactly is a gene so everybody basically says ah there are so many genes in in in in humans and and genes are very important and genes are what basically makes you a gene actually refers to an entire specific nucleotide sequence which encodes the synthesis of a polypeptide chain or an rna product basically this is what it looks like a gene basically starts from the promoter and it goes all the way till where you would find the terminator sequences this is a transcription unit okay so this is a transcription unit this is where transcription starts any transcription from your using your rna polymerase will go on all the way till you reach your terminator okay so the coding sequences are known as your exons these are eventually when found in your mr and a are translated and your non-coding sequences are actually known as your introns okay you also find that there are other types of sequences which are found in conjunction with the gene these are known as control elements so you find that their proximal control elements and their distal control elements so these control elements actually regulatory sequences and what these regulatory sequences do as control elements is that they function to either switch on or to switch off the promoter and your uh sorry this this regulatory sequences which i'm talking about the enhancers and silences which are distal or proximal control elements they actually help to regulate the expression or the rate of transcription of a particular gene that basically means that how much of transcription basically happens for this particular gene or how how fast or how slow the rate of transcription is so these enhancers and silencers they have that particular function to either increase or decrease the rate of transcription so beyond the exons which i told you are the coding regions you find that there are the specific non-coding dna sequences they function to either switch on off transcription so that comes about through the action of your promoter and your terminator so your promoter actually is the important feature of a gene which determines whether transcription begins or not because it's a site where rna polymerase actually assembles to give rise to your transcription initiation complex your terminator basically determines when your rna polymerase complex actually falls off from your dna to terminate transcription and as i told you about enhancers and silences enhances and silences what they do is that they either increase or they decrease the frequency of transcription so you can think of them something like a volume button you know you find the volume button on your radios okay so you find that you've got a volume button you can either increase the volume of your radio or you can decrease the volume of your radio right so enhancers and silences are like this the enhancers basically increase the rate of transcription of genes whereas silencers they will reduce the rate of transcription of genes promoters and terminators you can basically think of them as switch on and off buttons of a radio so if you have got on button on a promoter it basically means that the transcription can basically occur where else the off button basically means that transcription is terminated a few terminology before we move on when we talk about transcription we're talking about the direction of transcription happening from the promoter till the terminator and this is known as downstream so when i say downstream from the promoter it basically means from your left to your right whereas upstream basically means upwards from the promoters from the right to the left so let's look at uh the promoter first which is the one of the non-coding sequences which is specifically found as part of a gene structure okay so this the g the promoter it basically refers to the site which is just upstream of the transcription start site so transcription start site basically uh is where transcription actually starts using a dna polymerase the promoter is located just upstream from the transcription start side of a gene and most eukaryotic promoters in fact many eukaryotic promoters they contain a specific sequence within the promoter which is known as the tata box sequence so how a data box sequence actually looks like it's usually t a t a a a although this might differ very slightly uh between species yeah usually this is how a tata box sequence actually looks like uh in in most eukaryotes and this is a distinctive feature which highlights the promoter the function of the promoter is that it is the site where transcription of a gene is initiated so when you have got a when you've got a promoter it is the site where proteins actually bind proteins known as transcription factors okay more specifically general transcription factors they actually bind to your promoter and they recruit your rna polymerase and you know that your rna polymerase is actually the main enzyme which catalyzes the transcription of your mrna or your trna or rrna from the template strand of your dna and as i mentioned there are proteins known as general transcription factors which are very important for the initiation of this particular process of transcription because what they do is that they help they bind to the promoter side and they help to recruit the rna polymerase to the promoter and together with the rna polymerase the transcription factors and the rna polymerase form what you know as the transcription initiation complex which is important for the transcription of a particular gene promoters also have got differing sequences so it is not to say that all promoters of all genes look the same or have the same sequence promoters can differ in the form of certain sequences they might have within them known as critical elements and these short sequences your critical elements within the promoter would determine the strength of the promoter so you could think of it as such when i've got a promoter you can call this okay let's say i've got promoter and i have got gene one and let's say i've got another promoter okay and i've got gene two if i call gene two to be a stronger promoter what does a stronger promoter mean a stronger promoter means that the expression of gene two is generally higher than what i would find in gene one there could be a number of reasons for this okay and one of the reasons could be the short sequences which are found in the promoter of gene two as compared to the promoter of gen1 so the sequence in the promoter of gene 2 can actually differ to h to give rise to a greater binding efficiency of rna polymerase so a stronger promoter would have short sequences within them which actually help for greater binding efficiency of your rna polymerase and this will determine your frequency of transcription and the greater the binding efficiency between your rna polymerase and the promoter the higher the frequency of transcription so that is why you can you sometimes you would say that certain genes have got a stronger promoter as compared to others okay it's not in terms of physical strength but in terms of the sequences which are found within the promoter which will help the binding of a greater which gives the rna polymerase a greater binding efficiency now let's look at the uh the the other part of genes which uh non-coding and that will be actually be introns so what are introns introns they are only found in eukaryotic genes and they are non-coding sequences which are interspersed between coding sequences known as exons so exons when they are eventually translated after being transferred to the mrna sequences these guys will actually give rise to uh proteins or uh will give rise to proteins okay where else introns they are non-coding sequences there are specific functions of introns in some introns you would find that there could be certain regulatory sequences such as uh even even enhances and silences found within introns but generally they are actually non-coding in nature then you might ask what is the what is the significance of having introns okay let's take a look so introns when they are transcribed they are transcribed together with exons to give you a prime uh your pre your primary mrna transcript in eukaryotes or sometimes you might call this to be your pre mrna and at the end of every intron or at the boundary of every intron you would find that there are sites known as splice sites okay so at the boundary of introns you would find that there are splice sites okay and these boundaries are also the boundaries between introns and axons okay so intron exon boundaries you have got splice sites and what these guys what what this is actually important for would be even though introns have got no involvement in the translation of mrna they are actually since they have got no involvement in the translation of mrna they are actually removed or excised during rna splicing and during the process of rna splicing introns are excised that means they're cut off and exons are basically joined together to give you mature mrna at this point of time you're still thinking when intron suggests spliced out and removed from your pre-mrna why are they still important okay they are important because of this concept known as alternative splicing if you look at the number of proteins we have in our body if far outnumbers the number of genes we have in our body there's no way you can have let's say let's say for example this is just a hypothetical number okay let's say there are 50 000 genes in an organism however in the same organism you can find that there are 500 000 proteins how did 50 000 genes give rise to 500 000 proteins you might wonder because if each gene only codes for one protein you only find a maximum of 50 000 genes but there are 500 000 genes herein comes this concept of alternative splicing which actually tells you or or explains the fact that a single gene can actually give rise to different types of mature mrna transcript okay so the presence and and this is this is allowed for due to the presence of introns so the presence of introns within a gene would allow for that particular gene to encode several different polypeptides okay and different exons in the gene can code for different domains of an encoded protein and each domain can actually possess a specific structure and hence function so let's look at this with an example or a scenario okay so let's say that this is a particular pre-mrna which is transcribed from a dna sequence so you've got exon exon one and this is of course an intron and this is intron one and you have got intron two so if both introns are basically removed during rna splicing you'd find that the three exons come together and let's say exon one actually refer is is coding for this part of a protein which forms the binding site domain two which forms part of the activator binding site and domain three allows for the particular protein which is the receptor protein to bind to the cell surface membrane so when one two three and all come together you have got a nice protein product which is called a receptor site it's got an activator binding protein as well as a transmembrane region okay which allows for the receptor to bind to the cell surface membrane however what you can also do because of alternative splicing is when these remove when these introns are removed since there are splice sites at the junction of every intron and exon this entire sequence can be removed that means that in addition to the two introns exon 2 could also be removed during splicing and this what this gives rise to is a totally new mature mrna which only contains exon 1 and exon 3. as compared to the previous example you saw that the mature mrna actually contained all three domains whereas this mature mrna only contains two domains and what this could give rise to would be two different types of another different type of protein altogether with a receptor site and a transmembrane region and this can give rise to a totally new protein which comes from if you think about it it comes from the same gene so in this case alternative splicing with the same gene give rise to different protein products and it depends on the way in which the exons are joined together okay so depending on the number of exons as well as the sequence of exons which are joined together you can have different proteins coming about and this is the idea of alternative splicing where the excision of introns and the joining of exons give rise to different proteins coming about from a single gene okay but one thing to take note of is remember the sequence of your exons does not actually get jumbled up if you've got exon one exon two exon three exon four exon four it's either one two three four one two four or one two three you don't have you won't have a combination of three two one okay it doesn't go that way the sequence actually follows but what actually differs is uh all introns are removed but some exons can be removed along with the introns to give rise to different mature mrnas so with this particular idea you can now see that one gene can code for more than one polypeptide and this is known as alternative splicing and an advantage of alternative splicing would be that it allows for a larger number of proteins to be produced relative to the number of genes present and alternative splicing can produce different proteins from a single gene and do take note that introns are only found in eukaryotes and thus alternative splicing only occurs in eukaryotes let's move on to another non-coding region of of your of your gene which is actually a terminator your terminator is a specific sequence of non-coding dna that signals the stop of transcription its function is to actually allow for your rna polymerase to release the pre mrna and for rna polymerase to detach from your dna template and this happens through the transcript the transcribed dna the transcribe terminator sequence which is found on your mrna so it happens quite differently in eukaryotes and in prokaryotes in prokaryote what happens is that towards the end of your gene your rna polymerase would reach a terminator sequence which actually gives rise to a a very region a region of your mrna which will be very rich in guanine and cytosine so what happens is that when the rna actually codes for region which is rich in guanine and cytosine it allows the formation of a hairpin loop okay in this particular part and following beyond that you would then have a sequence of use which are found in your uracil nucleotides okay which is found in your rna when you have got a hairpin loop which is formed it this particular loop would put a strain on your rna polymerase is your entire rna polymerase okay and would cause it to actually pause for a while and when this pause actually happens this you this sequence of uracil would actually align very nicely with a sequence of adenine nucleotides found on the dna and you know that adenine and uracil base pairs they're actually not very strong there's only two hydrogen bonds within adenine and uracil and because of this particular strain which is put the dna this would cause the rna polymerase to separate from the dna okay and this would then eventually lead to your pre-mrn uh your mature sorry your mrna molecule being released from transcription okay this happens in prokaryotes where else in eukaryotes there are different mechanisms of transcription of termination which is employed okay uh some of these basically include um some of these basically include um the the fact that there is a polyadenylation signal found in your pre-mrna and certain proteins would actually come and cut the pre-mrna and release it from your rna polymerase okay you'll find this in page 12 of your lecture notes enhancers and silences okay are basically sequences as i said previously they are non-coding dna sequences and they are known as control elements okay and enhancers and silencers they are usually known as distal control elements so what enhancers and silencers do is that they actually are located generally yeah they generally located quite far away from the promoter and i said that another silences are like your volume buttons okay if you remember what i went through over here previously when i was describing enhancers and silencers okay they are like your volume buttons of a radio they either can increase the rate of transcription or decrease the rate of transcription enhancers serve to increase the rate of transcription of a specific gene which it controls and silences stuff to decrease the rate of transcription of that particular gene okay so as they are non-coding sequences and their control elements the they can usually be found far away from the promoter but some of them can actually be found within an intron or near a gene so the word distilled over here which tends to uh give you an impression that they're located far away uh may not be applicable all the time because some enhancers and silences are found close to a genome within the gene itself okay and enhancing silences they don't work just or in isolation they need proteins to help them perform their function okay so these proteins which help enhances and silences perform their function they're known as specific transcription factors for enhancers the type of specific transcription factors which bind to them are called activators and when activators actually bind to enhance the sequence they actually promote the assembly of your transcription initiation complex the transcription initiation complex of course it forms at the promoter just before transcription basically starts and since they promote the assembly of transcription initiation complex this leads to an increased rate of gene transcription silences on the other hand work the opposite they are they what they bind to or what what actually binds to them would be repressor proteins specific transcription factors known as repressor proteins notice that for enhance uh for the factors which actually bind to enhancers and silences i we call them to be specific transcription factors okay because general transcription factors bind to the promoter okay remember general transcription factors they bind to the promoter and they help to recruit your rn rna polymerase where else specific transcription factors include your activators as well as your repressors activators bind to enhancer sequences where else the other type of specific transcription factor which is your repressor they actually bind to silences so this is a specific transcription factor okay tf in short okay so repressors as well as activators they are specific transcription factors where else general transcription factors are proteins which bind to your promoter and help in the recruitment of your rna polymerase so please do take note of that okay so when repressors bind to silencers they inhibit the assembly of a transcription initiation complex and this leads to a decreased rate of gene expression we have now done the the the part where we talk about non-coding sequences uh at least part of it in the next lecture we will continue on with the two other features of eukaryotic chromosomes centromeres as well as telomeres do read your lecture notes in advance and we will cover this second part in the next lecture please take care and stay safe and we'll see all in school shortly thank you

hi everyone hope you are all doing well we are now going to be starting on the next chapter of your h2 biology syllabus and this would be the chapter on organization and control of prokaryotic and eukaryotic genomes this lecture series will be divided into two parts so in the first part we will be looking at the organization of the eukaryotic and programmatic genomes and in the second part we&#39;ll be looking at the control of eukaryotic and prokaryotic genomes this chapter is a natural lead up from a chapter you have done previously that would be dna and genomics where you learned about the different aspects of the structure of dna as well as gene expression on how dna is transcribed to rna and how mrna is translated to form proteins you have also learned about semi-conservative dna replication where parental strands have their genome copied to form copies of dna which can then be passed on to their daughter cells in an identical fashion this topic which you&#39;re going to be learning right now is going to be a step up from what you have learned from dna and genomics so my first advice to you would be this if you have not read through the lecture notes namely the lecture note on organization and control of prokaryotic and eukaryotic genome 1 please pause this video and read through the lecture notes at least the first set understand and try to understand what is going on in the lecture notes first write down your queries and your doubts on your lecture notes and then thereafter come and view this video the reason is because the content which is going to be covered as part of this particular lecture series is going to be a bit more dense than what you have covered so far so it is important for you to have at least a baseline understanding of what is going to be covered so that you can clarify your doubts with your tutors as you are going through this series of lectures feel free to email or whatsapp your tutors as you have doubts i am not going to say that this is going to be an easy chapter but is one which is going to take a lot of perseverance for you to understand unlearn and relearn concepts so without further ado let&#39;s get into this chapter of organization and control of prokaryotic and eukaryotic genomes so as i said earlier we will divide this lecture into a few parts the first part would be the structure and organization of the genome and the second part which is the second part of the lecture notes will look at how regulation of gene expression is influenced by the structure and organization of genomes you would have seen the lecture series on cancer previously and this would be a nice link to see how this regulation or misregulation of gene expression can actually lead to this disease known as cancer which is essentially a disease brought about by mutations so in this lecture series on this lecture we&#39;re going to be covering specifically on the structure and organization of genomes so if you look at the learning outcome you realize that the first learning outcome would be to describe the structure and the organization of prokaryotic and eukaryotic genomes so what we need to do as part of this learning outcome would be to look at how we can compare the structured organization of prokaryotic and eukaryotic genomes and also see how the dna is packaged differently in these two genome types we will also be looking at the structure and functions of non-coding dna in eukaryotes i.e dna found in eukaryotes which do not actually lead to the transcription of mrna or their subsequent translation but are rather found in the dna and serve important functions in the control of gene expression so these non-coding sequences include sequences such as introns centromeres telomeres promoters enhancers and silences so these some of these words you might have heard it before but others you may not have so as we go through this series of lectures we will actually be looking specifically at the structure and function of these different types of non-coding dna so let&#39;s break down what structure and organization of genome actually means so genome actually refers to the complete set of genetic materials you would find in a cell this cell could either be a prokaryotic cell or it could be a eukaryotic cell so it refers to the complete set of genetic materials both the main chromosome as well as any extracellular chromosomes you might have in a cell all those genetic material is known as a genome and when you talk about the structure and organization then you were to compare the differences in genomes or prokaryotic and eukaryotic genomes you want to look at the distinct features of what defines a prokaryotic cell and eukaryotic cell in terms of its genome and how they are located with respect to each other as we understand and appreciate how this all control how this structure and and organization of genome is found in these different type of cells you will then be able to understand how these lead to effective control of gene expression in these cells so as we talk about the genome uh in in the prokaryotic cells and eukaryotic cells you&#39;d realize that in prokaryotic cells the genome is found in a region known as the nucleoid region so the nucleotide region is where most of the of the eu prokaryotic genome is actually found uh and you know prokaryotic cells they do not have a nucleus okay so they don&#39;t have any membrane-bound organelles to have their genetic materials which is found in the form of dna uh compartmentalized within them this is unlike what you would find in a eukaryotic cell where you have a nucleus which is a membrane bound organelle remember nucleus is a double membrane bound organelle and a nucleus is surrounded by this structure known as a nuclear envelope and within the nucleus you would find most of your eukaryotic genome so it is surrounded by the nuclear envelope so that would be one key difference in terms of the location of genomes in prokaryotic cells as compared to in eukaryotic cells in your lecture notes in page four there&#39;s a table which actually lists the differences in the features between the structure of genomes of that of a prokaryote and how it is different from that of a eukaryote so please refer to page four for this particular part so now the one thing you would notice generally would be eukaryotic genomes are larger in terms of size and have a greater number of genes as compared to their prokaryotic counterparts so if you look at eukaryotic genomes you can find um in in different species so these are humans in if you find in cockroaches you have ferns and and amoeba um and in different types of plants and even bacterium uh the um the the genome size is actually relatively large okay and yeah you would be surprised to know that a cockroach basically has a larger genome than than yourself so if you look at cockroaches cockroaches basically i&#39;ve got this many base pairs which is closer to 1 times 10 to the power of 11 number of base pairs while humans have got a lesser number of base pairs as compared to a cockroaches so the length of the genome of a cockroach is actually longer than of that of a human so this actually illustrates an important point over here the complexity of an organism or the physical size of the organism does not necessarily translate to it having a larger genome okay look at a fern a fern is actually a type of plant that has got a larger genome than than a human an amoeba okay a uni uh which which is actually um which is actually a very small organism that also has got a larger genome size than even humans and cockroaches so like what i said the size of organism does not define its genome size okay so you can have a very large organism like a human having a smaller genome size as compared to a very small organism like a cockroach okay so cockroach one human zero also in this sense so that you now now you&#39;ve got a valid reason to be scared of flying cockroaches okay so if anyone asks you are you scared of cockroaches say yeah because they&#39;ve got a larger genome size than me okay makes you sound a little bit more brave than than what it seems to be um if you look as compared to bacteria okay of course these bacteria are looking at prokaryotes generally even the largest of bacterial uh species they tend to have genome sizes which are generally smaller than most of the eukaryotes you would find so as compared to the number of genes about 25 000 in eukaryotes about 4500 in in in bacteria the next feature of comparison between eukaryotic and prokaryotic genome genome structure would be that of the appearance of the genome in prokaryotic cells you would find that the double helix dna is organized into one chromosome which is actually the main chromosome you&#39;d find in bacteria and it is found as a single circular molecule which through supercoiling can be made into a more compact structure for eukaryotes however you&#39;ll find that the genome is organized into more than one chromosomes and that is how you have deployed numbers or even higher ploidy levels in certain types of organisms so as compared to prokaryotes where you would find the genome to be single and circular in eukaryotes you find that there are multiple chromosomes which appear as part of the genome and these are linear molecules instead of being circular another point of comparison would be the number of origins of replication per chromosome so if you remember your dna and genomics lectures you would remember that the origin of replication is where semiconservative dna replication commences where the parental strand is used as a template for the synthesis of new daughter strands during dna replication in prokaryotes you would find that there&#39;s only one origin of replication per chromosome because the chromosome is actually quite it&#39;s not very significantly large so one origin of replication is sufficient for you to have successful replication of the genome where else in eukaryotic cells or eukaryotic genomes you&#39;d find that there are multiple origins of replication per chromosome you might ask what the significance of having multiple origins of replication is and if you think about it having many origins of replication would actually help increase the speed of replication and this is this is more necessary for eukaryotic chromosomes because you have a larger genome size telomeres and centromeres are other features of comparisons these are actually non-coding dna sequences which are found in eukaryotic cells so in prokaryotic cells you do not have telomeres where else in eukaryotic cells at the end of the eukaryotic cells you&#39;ll find that there are telomeric sequences these telomeres serve important functions and we&#39;ll be looking at the functions of telomeres and how they are formed in the later part of this lecture the presence of centromeres is also another distinctive feature of eukaryotic genomes centromeres is what is is a structure of uh of chromosomes you would have seen in the lecture of mitosis and meiosis and it is the part of the chromosome where you would find your kinetochore proteins attached to and to these kinetochore proteins found at the centromere you will have your kinetochore microtubules attaching to them and these kinetochore microtubules serve important functions in separation of sister chromatids during mitosis as well as in meiosis so centromeres they are found in eukaryotic cells and eukaryotic genomes but not in prokaryotic cells another important difference you would find between eukaryotic and programmatic genomes would be the level of dna packing and coiling as you know and as we have seen there is there is a difference in the size as well as the number of chromosomes you&#39;ll find in prokaryotic cells as compared to eukaryotic cells so the level of dna packing and coiling is going to be quite different as well especially since the cell is a very small unit to pack as much genetic information a species or an organism would need in every single cell would require very high level of packing and coiling so if you look at a prokaryotic cell you would find that mostly the genome is made of naked dna naked in a sense that there is very little proteins which actually associate with the dna when it comes to the packing of the dna this in comparison to eukaryotic cells is quite different because in eukaryotic cells there is a higher degree of condensation and packaging and you have larger number of proteins including histones and scaffold proteins which come into play to help compact your genetic material into highly condensed chromosomes found in your nucleus so now let&#39;s take a closer look at how each one of these condensation of chromosomes work for the respective types of cells so let&#39;s start off with the prokaryotic cells if we would look at a prokaryotic cell if this circle a represents a circular chromosomal dna i.e a dna double helix you have the formation of looped domains which come about and these loop domains would actually be found around histone-like proteins so you call this to be histone-like proteins these black structures here they don&#39;t call them histone proteins because there is no histones there are no histones which are found in prokaryotic cells so you call this to be histone-like proteins they are like histones but they are not histones so take note of that and further beyond this looped domain you would find that there is super coiling which actually happens so super coiling is a process where you have further compaction of your genome and with further compaction with genome it just about covers a very small area of one micrometer okay from 430 micrometer an e coli bacterial cell has a unfolded chromosome of 430 micrometer to get to one micrometer is is quite an amazing thing actually okay uh it&#39;s about a 400 times reduction in terms of the space the genome would occupy and this is going to be very important for the bacterial cell to have a genome found within it um do note that this particular feature of looping is is not just as small as just six loops found around around the histone-like proteins this can be going up to about 50 to 60 loops in in actual number and of course further folding is compacted by super coiling giving rise to highly compact dna in prokaryotes if you thought that was amazing you must check out what happens in eukaryotic genomes okay so this would be for prokaryotic genomes in eukaryotic genomes just imagine this if you were to unwrap or if i were to be able to unwrap all the dna you have in all of just your cells as one individual you can actually reach the moon about 6000 times that&#39;s the length of dna you would find to be present in a single person so that&#39;s amazing isn&#39;t it 6000 times you can build a bridge from the earth to the moon and back and how do you even compact this amount of this length of of of biomolecules in this case uh dna into a single person in all of their cells and that is where the amazing part about condensation and compaction of genomes come in the first level of compacting comes in when where your dna helix begins to associate with these proteins known as histones so histones are special proteins and these proteins actually allow for dna to coil around themselves you know that dna is negatively charged because of the presence of a negatively charged phosphate backbone where else your histone proteins they are made up of amino acids which have got r groups which are generally positively charged so when you have got a negatively charged molecule coiling around a positively charged molecule it helps to hold the dna around the histones due to electrostatic interactions or the presence of ionic bonds so these histones which have got um amino acids which are which have r groups which are positively charged examples of these amino acids would include uh lysine and arginine so the dna is held by around histones by electrostatic interactions forming quite a tight and compact um structure and this structure which is found when uh when when the dna is actually wound around a histone is known as a nucleosome so when most of the dna is wound around an octoma of eight histone proteins so there&#39;s not just one histone proteins there&#39;s a complex of eight different histone proteins okay you can see this h2a h2h basically referring histone h2a h2b h3h4 and different quantities of this give rise to an octoma and october referring to eight histone proteins when the dna is coiled around it you find that these actually give rise to this structure known as a nucleosome okay so this particular structure of eight histone proteins that there are four different types and you need uh two molecules of each type to give you eight histone proteins and the dna is called around it you call this structure to be a nucleosome and of course different nucleosomes are joined together by the segment of the dna known as a linker dna the width of a nucleosome is approximately 10 nanometers and this is actually a basic unit of chromosomal packing so different optimus actually or rather different nucleosomes which are adjacent to each other are joined by linker dna you also call this particular structure to be the 10 nanometer fiber because the width of a nucleosome is known to be about 10 nanometers so what happens further to this 10 nanometer fibers would be that they would coil around themselves to give you what is known as a 30 nanometer chromatin fiber or a solenoid but before we look at how the 39 nanometer micro chromatin fiber actually looks like this is how a nucleosome actually looks like under an electron microscope so this is a nucleosome and all these different black structures you see here are adjacent nucleosomes and these adjacent nucleosomes they coil around themselves to give you a more compact and condensed structure known as a 30 nanometer chromatin fiber or a solenoid and when you&#39;re forming this 30 nanometer chromatin fiber there is another type of histone protein which comes into play that would be the histone h1 protein so you&#39;ve got another protein which helps in the compaction of your genome so once you have got your 30 nanometer microfiber it doesn&#39;t just stop at that that is further compacting where you actually find that your 30 nanometer chromatin fiber would loop uh to form looped domains and these loop domains uh would give rise to 300 nanometer fibers when they associate with different type of proteins known as scaffo proteins so with this scaffold proteins these are actually non-histone proteins you get the 300 nanometer fiber and if that is not enough there is actually a fourth level of compacting and that would be super coiling where the loops would further coil and produce what you would see as a characteristic type of chromosome during metaphase and this is the double arm structure of the chromosome you&#39;d find during mitosis so supercoiling also occurs during uh it to give rise to metaphase chromosomes in a dividing cells so in summary in a eukaryote you&#39;d find that you&#39;ve got the dna double helix the dna double helix coils around a complex of eight histone proteins to give rise to a nucleosome also known as the 10 nanometer struck structure and further compacting gives rise to the 30 nanometer chromatin fiber or the solenoid followed following that you have got loop domains which come about and further super coiling happens eventually giving rise to your metaphase chromosomes in dividing cells so here&#39;s a chance for you to now visualize this through a video so i&#39;m going to play a video on how dna is packaged in an eukaryotic cell to give you a visual representation of what i have just described in this animation we&#39;ll see the remarkable way our dna is tightly packed up to fit into the nucleus of every cell the process starts with assembly of a nucleosome which is formed when eight separate histone protein subunits attached to the dna molecule the combined tight loop of dna and protein is the nucleosome multiple nucleosomes are coiled together and these then stack on top of each other the end result is a fiber of packed nucleosomes known as chromatin this fiber which at this point is condensed to a thickness of 30 nanometers is then looped and further packaged using other proteins which are not shown here this remarkable multiple folding allows six feet of dna to fit into the nucleus of each cell in our body an object so small that ten thousand nuclei could fit on the tip of a needle the end result is that the dna is tightly packed into the familiar structures we can see through a microscope chromosomes it is important to realize that chromosomes are not always present they form only when cells are dividing at other times as we can see here at the end of cell division our dna becomes less highly organized so now that we have covered the structure of the genome for the prokaryotic genome and the eukaryotic genome let&#39;s move on to table two which is found on page six of your lecture notes which is actually talking about the differences in the organization of the genomes of these two different types of cells so the first point basically talks about the location of functionally related genes on a chromosome so what are functionally related genes so functionally related genes basically refer to genes which code for proteins which are involved in a similar biochemical or metabolic pathway in your cells so in prokaryotes one one very famous type of uh gene struck genome structure which is found in prokaryotic cells which involves the the grouping of genes which code for proteins which similar metabolic uh functions would be that of the lac operon the lac operon is an operon system which you&#39;ll be learning more about under this uh the chapter of uh genetics of bacteria where you will learn about how control and organization of prokaryotic genomes actually occur with greater details or in greater details with respect to the lac operon but for at this present moment uh it is important for you just to understand that functionally related genes can be located very close together in prokaryotic cells so when you have got genes which code for proteins for the same metabolic pathway in this case the lac operon which is involved in the uptake of lactose into cells and the breakdown of lactose in in bacterial cells these genes which are involved in this particular pathway they are grouped together under this one single entity known as a single operon a single operon basically has got a single promoter which controls the expression of these genes so uh it it basically means that when one gene is being coded for it will come together with all of the genes within the same operon being coded for being expressed at the same time okay so we&#39;ll look into more details about this under the topic of bacteria but it&#39;s key for you to understand that you have an operon system in prokaryotes where else in a eukaryote even though you may have you may have genes that code for functionally related proteins they need not necessarily be found very close to each other on a single chromosome they are usually located on different chromosomes another difference would be the the amount of non-coding regions you&#39;d find you&#39;d find that there are very much more non-coding dna sequences in eukaryotes as compared to prokaryotes up to 98 of your genome is actually non-coding okay so isn&#39;t that surprising and complex organisms such as uh such as yourself a human ninety-eight percent of the chromosomes you find your 46 chromosomes in your nucleus is non-coding they don&#39;t code for proteins then what do they do we will come to that in a short while okay where else in prokaryotes most of the genome is actually made up of coding sequences i.e there are genes which are expressed to give you uh proteins so about less than 15 percent is non-coding um presence of promoters which are important for the expression of genes okay that&#39;s the point where the gene actually starts in prokaryotes you find that in both programs and eukaryotes you find that the promoter is present in prokaryotes as i mentioned earlier you can have a single promoter which actually can control all the genes which are found in a operon system where else in a eukaryote each gene comes under the control of its own individual promoter so what this basically means that let&#39;s say i&#39;ve got a promoter sequence here in a prokaryote if i&#39;ve got gene x gene y and gene z present this single promoter can actually control the expression of these three different genes so these are actually three different genes where else in the eukaryote you don&#39;t find this each gene has got its own promoter present so each promo each gene would have its own promoter you don&#39;t have a sequence or a structure where a single promoter would control more than one gene introns are non-coding sequences as well and you&#39;d find that introns are present in both prokaryotes and in eukaryotes but this is very low in numbers so as what is stated in your lecture notes introns you can consider them to be even absent even though the introns there are very very little introns present uh in prokaryotes you can actually consider them to be almost absent even though there might be a few but of course in eukaryotes introns which are non-coding sequences found in your genes they are actually interspersed between exons which are the coding regions of your genes enhancers and silences is something you&#39;ll learn about shortly as well these are non-coding sequences which either increase the rate of transcription or decrease the rate of transcription respectively of specific genes in prokaryotes you don&#39;t find this enhancer and silencers being present but in eukaryotes you do find them to be present enhancers and silences they&#39;re said to be control elements because they actually can affect the rate of transcription of genes extra chromosomal dna in prokaryotes they might be they may be present because they can be present in form of plasmids but in eukaryotic genomes you find that a plasmids are absent with the exception of what you might find in mitochondria and chloroplast which may have their own dna now we are done with the first learning outcome which is to describe the structure and organization of prokaryotic and eukaryotic genome let&#39;s move on to talk about non-coding dna in eukaryotes and the structure and function of these different types of non-coding dna you would find so when you look at the non-coding dna sequences in a eukaryotic gene or eukaryotic genome you&#39;ll find that there are many different types okay but each one of this has got important functions you&#39;ll find that you have promoters and terminators and introns you have enhancers and silencers and you also have got features such as centromeres and telomeres which are still non-coding and what we&#39;re going to look at is basically structure and function of these different non-coding sequences so as we move into this particular lecture even deeper you&#39;ll find that it&#39;s quite similar to what you do when you go into a very atas kind of a restaurant okay but you take out the menu card and you realize that what i look at the dish the name of the dish i actually don&#39;t understand what the name of the dish is it&#39;s the first time i&#39;m actually seeing such it is like how many of you know what uh suno mono is if you look at a jet uh restaurants menu card i for one wouldn&#39;t actually know it but the important thing is before you actually uh order it and want to taste it you&#39;d want to actually find out what it is right even though it&#39;s a new term you&#39;re coming across it&#39;s the same thing which actually is going to happen right now you&#39;re going to come across different new terms which you might be encountering for the first time but don&#39;t give up don&#39;t don&#39;t just gloss over it but try to and and and please do understand what these terms actually mean and what uh which structures they are referring to okay and the functions of these so uh this is just a different way of saying that there&#39;s quite a bit of jargon coming up please pay attention and do clarify if you have doubts okay and if anyone knows what suno mono is you can always drop me a message to to let me know no idea 6.95 hmm okay so um we looked at coding sequences and now we&#39;re going to be looking at non-coding sequences which do not code for proteins or rna products and you&#39;ll find that in a genome of a eukaryotic cell so now we are looking at eukaryotic genomes uh we are not focusing on prokaryotic genomes here prokaryotic genomes is something you are focusing when we are doing the chapter on bacteria we are also basically focusing on control of gene expression in prokaryotic genomes when we are doing bacteria we are going to be focusing on eukaryotic genomes here okay eukaryotic genome basically genome found in you non-coding dna sequences you would find that 98 of your genome doesn&#39;t code for proteins or rna products this is compared to prokaryotes only a small proportion of the genome consists of non-coding regions but a large proportion of the eukaryotic genome is made up of non-coding sequences and the different types of non-coding sequences you have repetitive sequences you have sequences which regulate gene expression you have got even rna genes you have got utr basically sends for untranslated regions and introns which are also uh non-coding sequences which are found within genes where else if you look at the coding part ie the part which is translated or rather transcribed and eventually translated by ribosomes to give you proteins it&#39;s only about two percent okay or even less than that you may come across this particular sequence uh this particular term known as tandem repeating dna sequences when you&#39;re looking at non-coding sequences what is a tandem repeating dna sequence so repeating dna sequence is fairly straightforward so if i have a sequence like this if i have got t c a t t c a t t c a t d c a t c c a t t c a t this is a repeating sequence and it is tandem basically because it is adjacent to each other it is tandemly repeating but not all random repeating sequences look like this some tandem repeating sequences can have a bit of variation to it okay so tc80 this is taat tca tcat tcat you still consider these sequence to be a tandem repeat sequence okay so when a 10 down repeat sequence actually comes about you would find that it can happen in in different parts of your your genome okay so most of the non-coding sequences uh you find in in your cells are actually made up of tandem repeat sequences and the interesting thing is that tandem repeat sequences may actually vary between individuals of the same species that means the tandem repeat sequence which is found in uh in you in one particular region of your chromosome may actually be different from what you would find in your friend so let&#39;s say let&#39;s say just just for example let&#39;s say this is chromosome 1 and this is you okay and let&#39;s say there&#39;s a tandem briquettes repeat sequence of maybe five repeats which is found on this part of your chromosome one okay and let&#39;s say you&#39;ve got a friend uh your best friend maybe your best friend also has a chromosome one let&#39;s assume your best friend is human so if you&#39;ve got a best friend who is human best friend is a bff right so best friend you find that with that same part of the the same chromosome in the same region he or she might have 20 repeats of the tandem repeat sequence okay and this is what actually gives rise to variation amongst us okay and you will learn more about this next year when you look at uh how variable number tandem repeats can actually help in identifying uh different people and it comes very useful when you&#39;re looking at things like a forensics where you are uh trying to uh see who a particular criminal was or who a thief was or who a murderer was based on forensic evidence is also used for paternity testing if you want to find out who the father or the mother of a particular child is when it comes to certain cases where you need to find out the parents of a particular child okay so it&#39;s important for pertinent opportunity testing as well okay more on that later but let&#39;s come back to what uh the what we are looking at as part of this particular lecture uh we are looking at uh the gene okay and also the non-coding sequences which we are talking about so what exactly is a gene so everybody basically says ah there are so many genes in in in in humans and and genes are very important and genes are what basically makes you a gene actually refers to an entire specific nucleotide sequence which encodes the synthesis of a polypeptide chain or an rna product basically this is what it looks like a gene basically starts from the promoter and it goes all the way till where you would find the terminator sequences this is a transcription unit okay so this is a transcription unit this is where transcription starts any transcription from your using your rna polymerase will go on all the way till you reach your terminator okay so the coding sequences are known as your exons these are eventually when found in your mr and a are translated and your non-coding sequences are actually known as your introns okay you also find that there are other types of sequences which are found in conjunction with the gene these are known as control elements so you find that their proximal control elements and their distal control elements so these control elements actually regulatory sequences and what these regulatory sequences do as control elements is that they function to either switch on or to switch off the promoter and your uh sorry this this regulatory sequences which i&#39;m talking about the enhancers and silences which are distal or proximal control elements they actually help to regulate the expression or the rate of transcription of a particular gene that basically means that how much of transcription basically happens for this particular gene or how how fast or how slow the rate of transcription is so these enhancers and silencers they have that particular function to either increase or decrease the rate of transcription so beyond the exons which i told you are the coding regions you find that there are the specific non-coding dna sequences they function to either switch on off transcription so that comes about through the action of your promoter and your terminator so your promoter actually is the important feature of a gene which determines whether transcription begins or not because it&#39;s a site where rna polymerase actually assembles to give rise to your transcription initiation complex your terminator basically determines when your rna polymerase complex actually falls off from your dna to terminate transcription and as i told you about enhancers and silences enhances and silences what they do is that they either increase or they decrease the frequency of transcription so you can think of them something like a volume button you know you find the volume button on your radios okay so you find that you&#39;ve got a volume button you can either increase the volume of your radio or you can decrease the volume of your radio right so enhancers and silences are like this the enhancers basically increase the rate of transcription of genes whereas silencers they will reduce the rate of transcription of genes promoters and terminators you can basically think of them as switch on and off buttons of a radio so if you have got on button on a promoter it basically means that the transcription can basically occur where else the off button basically means that transcription is terminated a few terminology before we move on when we talk about transcription we&#39;re talking about the direction of transcription happening from the promoter till the terminator and this is known as downstream so when i say downstream from the promoter it basically means from your left to your right whereas upstream basically means upwards from the promoters from the right to the left so let&#39;s look at uh the promoter first which is the one of the non-coding sequences which is specifically found as part of a gene structure okay so this the g the promoter it basically refers to the site which is just upstream of the transcription start site so transcription start site basically uh is where transcription actually starts using a dna polymerase the promoter is located just upstream from the transcription start side of a gene and most eukaryotic promoters in fact many eukaryotic promoters they contain a specific sequence within the promoter which is known as the tata box sequence so how a data box sequence actually looks like it&#39;s usually t a t a a a although this might differ very slightly uh between species yeah usually this is how a tata box sequence actually looks like uh in in most eukaryotes and this is a distinctive feature which highlights the promoter the function of the promoter is that it is the site where transcription of a gene is initiated so when you have got a when you&#39;ve got a promoter it is the site where proteins actually bind proteins known as transcription factors okay more specifically general transcription factors they actually bind to your promoter and they recruit your rna polymerase and you know that your rna polymerase is actually the main enzyme which catalyzes the transcription of your mrna or your trna or rrna from the template strand of your dna and as i mentioned there are proteins known as general transcription factors which are very important for the initiation of this particular process of transcription because what they do is that they help they bind to the promoter side and they help to recruit the rna polymerase to the promoter and together with the rna polymerase the transcription factors and the rna polymerase form what you know as the transcription initiation complex which is important for the transcription of a particular gene promoters also have got differing sequences so it is not to say that all promoters of all genes look the same or have the same sequence promoters can differ in the form of certain sequences they might have within them known as critical elements and these short sequences your critical elements within the promoter would determine the strength of the promoter so you could think of it as such when i&#39;ve got a promoter you can call this okay let&#39;s say i&#39;ve got promoter and i have got gene one and let&#39;s say i&#39;ve got another promoter okay and i&#39;ve got gene two if i call gene two to be a stronger promoter what does a stronger promoter mean a stronger promoter means that the expression of gene two is generally higher than what i would find in gene one there could be a number of reasons for this okay and one of the reasons could be the short sequences which are found in the promoter of gene two as compared to the promoter of gen1 so the sequence in the promoter of gene 2 can actually differ to h to give rise to a greater binding efficiency of rna polymerase so a stronger promoter would have short sequences within them which actually help for greater binding efficiency of your rna polymerase and this will determine your frequency of transcription and the greater the binding efficiency between your rna polymerase and the promoter the higher the frequency of transcription so that is why you can you sometimes you would say that certain genes have got a stronger promoter as compared to others okay it&#39;s not in terms of physical strength but in terms of the sequences which are found within the promoter which will help the binding of a greater which gives the rna polymerase a greater binding efficiency now let&#39;s look at the uh the the other part of genes which uh non-coding and that will be actually be introns so what are introns introns they are only found in eukaryotic genes and they are non-coding sequences which are interspersed between coding sequences known as exons so exons when they are eventually translated after being transferred to the mrna sequences these guys will actually give rise to uh proteins or uh will give rise to proteins okay where else introns they are non-coding sequences there are specific functions of introns in some introns you would find that there could be certain regulatory sequences such as uh even even enhances and silences found within introns but generally they are actually non-coding in nature then you might ask what is the what is the significance of having introns okay let&#39;s take a look so introns when they are transcribed they are transcribed together with exons to give you a prime uh your pre your primary mrna transcript in eukaryotes or sometimes you might call this to be your pre mrna and at the end of every intron or at the boundary of every intron you would find that there are sites known as splice sites okay so at the boundary of introns you would find that there are splice sites okay and these boundaries are also the boundaries between introns and axons okay so intron exon boundaries you have got splice sites and what these guys what what this is actually important for would be even though introns have got no involvement in the translation of mrna they are actually since they have got no involvement in the translation of mrna they are actually removed or excised during rna splicing and during the process of rna splicing introns are excised that means they&#39;re cut off and exons are basically joined together to give you mature mrna at this point of time you&#39;re still thinking when intron suggests spliced out and removed from your pre-mrna why are they still important okay they are important because of this concept known as alternative splicing if you look at the number of proteins we have in our body if far outnumbers the number of genes we have in our body there&#39;s no way you can have let&#39;s say let&#39;s say for example this is just a hypothetical number okay let&#39;s say there are 50 000 genes in an organism however in the same organism you can find that there are 500 000 proteins how did 50 000 genes give rise to 500 000 proteins you might wonder because if each gene only codes for one protein you only find a maximum of 50 000 genes but there are 500 000 genes herein comes this concept of alternative splicing which actually tells you or or explains the fact that a single gene can actually give rise to different types of mature mrna transcript okay so the presence and and this is this is allowed for due to the presence of introns so the presence of introns within a gene would allow for that particular gene to encode several different polypeptides okay and different exons in the gene can code for different domains of an encoded protein and each domain can actually possess a specific structure and hence function so let&#39;s look at this with an example or a scenario okay so let&#39;s say that this is a particular pre-mrna which is transcribed from a dna sequence so you&#39;ve got exon exon one and this is of course an intron and this is intron one and you have got intron two so if both introns are basically removed during rna splicing you&#39;d find that the three exons come together and let&#39;s say exon one actually refer is is coding for this part of a protein which forms the binding site domain two which forms part of the activator binding site and domain three allows for the particular protein which is the receptor protein to bind to the cell surface membrane so when one two three and all come together you have got a nice protein product which is called a receptor site it&#39;s got an activator binding protein as well as a transmembrane region okay which allows for the receptor to bind to the cell surface membrane however what you can also do because of alternative splicing is when these remove when these introns are removed since there are splice sites at the junction of every intron and exon this entire sequence can be removed that means that in addition to the two introns exon 2 could also be removed during splicing and this what this gives rise to is a totally new mature mrna which only contains exon 1 and exon 3. as compared to the previous example you saw that the mature mrna actually contained all three domains whereas this mature mrna only contains two domains and what this could give rise to would be two different types of another different type of protein altogether with a receptor site and a transmembrane region and this can give rise to a totally new protein which comes from if you think about it it comes from the same gene so in this case alternative splicing with the same gene give rise to different protein products and it depends on the way in which the exons are joined together okay so depending on the number of exons as well as the sequence of exons which are joined together you can have different proteins coming about and this is the idea of alternative splicing where the excision of introns and the joining of exons give rise to different proteins coming about from a single gene okay but one thing to take note of is remember the sequence of your exons does not actually get jumbled up if you&#39;ve got exon one exon two exon three exon four exon four it&#39;s either one two three four one two four or one two three you don&#39;t have you won&#39;t have a combination of three two one okay it doesn&#39;t go that way the sequence actually follows but what actually differs is uh all introns are removed but some exons can be removed along with the introns to give rise to different mature mrnas so with this particular idea you can now see that one gene can code for more than one polypeptide and this is known as alternative splicing and an advantage of alternative splicing would be that it allows for a larger number of proteins to be produced relative to the number of genes present and alternative splicing can produce different proteins from a single gene and do take note that introns are only found in eukaryotes and thus alternative splicing only occurs in eukaryotes let&#39;s move on to another non-coding region of of your of your gene which is actually a terminator your terminator is a specific sequence of non-coding dna that signals the stop of transcription its function is to actually allow for your rna polymerase to release the pre mrna and for rna polymerase to detach from your dna template and this happens through the transcript the transcribed dna the transcribe terminator sequence which is found on your mrna so it happens quite differently in eukaryotes and in prokaryotes in prokaryote what happens is that towards the end of your gene your rna polymerase would reach a terminator sequence which actually gives rise to a a very region a region of your mrna which will be very rich in guanine and cytosine so what happens is that when the rna actually codes for region which is rich in guanine and cytosine it allows the formation of a hairpin loop okay in this particular part and following beyond that you would then have a sequence of use which are found in your uracil nucleotides okay which is found in your rna when you have got a hairpin loop which is formed it this particular loop would put a strain on your rna polymerase is your entire rna polymerase okay and would cause it to actually pause for a while and when this pause actually happens this you this sequence of uracil would actually align very nicely with a sequence of adenine nucleotides found on the dna and you know that adenine and uracil base pairs they&#39;re actually not very strong there&#39;s only two hydrogen bonds within adenine and uracil and because of this particular strain which is put the dna this would cause the rna polymerase to separate from the dna okay and this would then eventually lead to your pre-mrn uh your mature sorry your mrna molecule being released from transcription okay this happens in prokaryotes where else in eukaryotes there are different mechanisms of transcription of termination which is employed okay uh some of these basically include um some of these basically include um the the fact that there is a polyadenylation signal found in your pre-mrna and certain proteins would actually come and cut the pre-mrna and release it from your rna polymerase okay you&#39;ll find this in page 12 of your lecture notes enhancers and silences okay are basically sequences as i said previously they are non-coding dna sequences and they are known as control elements okay and enhancers and silencers they are usually known as distal control elements so what enhancers and silencers do is that they actually are located generally yeah they generally located quite far away from the promoter and i said that another silences are like your volume buttons okay if you remember what i went through over here previously when i was describing enhancers and silencers okay they are like your volume buttons of a radio they either can increase the rate of transcription or decrease the rate of transcription enhancers serve to increase the rate of transcription of a specific gene which it controls and silences stuff to decrease the rate of transcription of that particular gene okay so as they are non-coding sequences and their control elements the they can usually be found far away from the promoter but some of them can actually be found within an intron or near a gene so the word distilled over here which tends to uh give you an impression that they&#39;re located far away uh may not be applicable all the time because some enhancers and silences are found close to a genome within the gene itself okay and enhancing silences they don&#39;t work just or in isolation they need proteins to help them perform their function okay so these proteins which help enhances and silences perform their function they&#39;re known as specific transcription factors for enhancers the type of specific transcription factors which bind to them are called activators and when activators actually bind to enhance the sequence they actually promote the assembly of your transcription initiation complex the transcription initiation complex of course it forms at the promoter just before transcription basically starts and since they promote the assembly of transcription initiation complex this leads to an increased rate of gene transcription silences on the other hand work the opposite they are they what they bind to or what what actually binds to them would be repressor proteins specific transcription factors known as repressor proteins notice that for enhance uh for the factors which actually bind to enhancers and silences i we call them to be specific transcription factors okay because general transcription factors bind to the promoter okay remember general transcription factors they bind to the promoter and they help to recruit your rn rna polymerase where else specific transcription factors include your activators as well as your repressors activators bind to enhancer sequences where else the other type of specific transcription factor which is your repressor they actually bind to silences so this is a specific transcription factor okay tf in short okay so repressors as well as activators they are specific transcription factors where else general transcription factors are proteins which bind to your promoter and help in the recruitment of your rna polymerase so please do take note of that okay so when repressors bind to silencers they inhibit the assembly of a transcription initiation complex and this leads to a decreased rate of gene expression we have now done the the the part where we talk about non-coding sequences uh at least part of it in the next lecture we will continue on with the two other features of eukaryotic chromosomes centromeres as well as telomeres do read your lecture notes in advance and we will cover this second part in the next lecture please take care and stay safe and we&#39;ll see all in school shortly thank you

Transcript for:Organization and Control of Prokaryotic and Eukaryotic Genomes - Part 1

Transcript for:
Organization and Control of Prokaryotic and Eukaryotic Genomes - Part 1