Nucleosome and histones | Nucleosome structure

[Music] Hello friends welcome to the tutorial and in this tutorial we are going to look the way uh DNA is packed inside uh compact structure which is called chromosome now as we know uh in all of uh the eukariotic organisms or high uh high order organisms we are having much more complex chromosome or much more and much much longer uh DNA segments or Gene segments to be encrypted so need to store them inside uh some compact region so they're storing these DNA materials uh really making them compact now these are the structures called nucleosomes which are helping them to make those compact structure of DNA now if we look at the structure two important things you can notice one is protein and second one is called the DNA now this this strand like parts are the DNA and these bead like sections are the proteins now these proteins are called histone proteins and and rest of the things rest of the thread like structure is called the DNA in this case Okay so two Helix are not uh pictured here or not mentioned here but this is uh that two helical structure of DNA okay now if we zoom in one of these structure we find something like this so if if we look at the structure uh let me take this out okay if you look at the structure yeah now this is the structure now here this is the bead like structure what we have seen before so this is the bead like structure and this is the thread like structure which is DNA now this middle bead like structure is called the histone protein as you can see in this picture this protein is not one unit protein this is made up with multiple subunits as you can see here blue red green yellow and these four different Ty subunits are in uh together to make this kind of proteins okay now actually two different types of uh no actually four different types of subunits those are called histone subunits and they having their own names like histone 2 a histone 2B hisone 3 and histone 4 so H2 a h2b H3 and H4 as abbreviated so they arrange themselves to make this bead and this bead is allowing the DNA structures to wrap themselves around this bead and this bead and uh thread is giving them the way to coil around this bead and that eventually uh compresses the area for the DNA storage that's the actual concept behind this structure okay now we'll go to the detail and advanced structure of this I'm not going to talk about nucleosome in very basic level so this is the nucleome structure how we come to know what is the actual nucleosome structure we can utilize different nucleus enzymes we can actually cleave the DNA strands and if we use these enzymes usually we used the microcal nucleus and this microcal nucleus is a nucleus enzyme which is derived from micro coccus or microcal bacteria so we can take this nucleus we add it and this nucleus can cleave at a particular site if we use a fewer concentration of nucleus this microcal nucleus it will CLE some sites like that if you utilize this uh for more extensive digestion we will finally lead up to the formation of something like that so what we end up with we can see two uh different regions inside that one region is the bead which is uh tightly surrounded by the DNA and the second structure is something small part of the DNA segment which is linking tou two beads with each other so we end up with these two parts one is a bead wrapped wrapped by DNA another one is the Linker uh region this is called the Linker DNA so Linker DNA and the DNA wrapped around the bead so we end up with these two parts now we can we can look at this Parts by running an agaro gel so you can see this uh case in this agaro gel we can look at these different structures okay now if we go on and discuss about the proper arrangement of those subunits because the subunits Arrangement are really important in this case so you can look at the four different subunits H2 H2 bh3 and H4 we can see they're having almost a similar type of folding regions now uh both of them are having this folding Regents if you look at this protein amino acid polypeptide chain now you can see one is n terminal and another one is a c terminal H2 and H2 be resembling very close structure as well as the H3 and H4 with each other but H3 is having extra domain of is folding but otherwise all the other uh subunits are having almost similar kind of folding domains okay the most important thing above all this H3 uh region because this H3 region or H3 subunit is having some extra fold now this extra fold is actually helping uh this uh this H3 to fold uh little bit differently and this H3 is Al is is the most important among all uh due to the regulation step we'll learn them later uh about the histone modification if when we talk about the histone modification these all histone proteins can be modified and why we need to modify the structure we'll find it later but uh just uh for now uh you can uh remember or you can memorize this thing that uh this H3 is the most important among all okay now if I look at the arrangement of these subunits that's uh not like that that four subunit come in and attached with each other to make a tetramic structure like that uh the actual answer is that they come to together to make diers now h2a and h2b come together to make a dimer of H2 h2b and H3 and H4 in turn will come and make a tetramer with each other so this is the actual arrangement from a monomeric form so form a monomer of H3 for a monomer of H4 they will arrange two of the H3 two of the H4 will arrange to make a H3 H4 tetramer this tetramer means they are forming by the four protein subunits two of H3 two of H4 now in case of H2 H2 be Di one h2a one h2b monomer will come and attach with each other to make a DI of H2 h2b now such two dier of H2 h2b can come and make tetramer of H2 h2b now this thing uh just keep in mind this thing so these are the different folding pattern between H3 H4 and H2 h2b H3 and H4 means four monomer so first monomer subunit H3 two monomers H4 two monomers come together to make a to tetr at the first place but in case of H2 H2 be they first make a dimer by attaching one of each monomers then those dimers will come to make a the Teter that is the formation unit these are these are the actual arrangement of this diamond uh this so ultimately we end up with eight subunits so we call it OCTA we call it the histone OCTA okay now if we move on now you can see the arrangement now you can see this H3 and H4 these are the monomers they'll come together to make arrangement like that and H2 H2 come to make a dimer now two such dimer will come and finally make the tetramer okay of H2 a h2b but at the first place the H3 H4 Teter is made directly from the monomers that is the difference between this H2 h2b concept and H3 H4 concept now another important thing which must be noticed in this case is that this two different terminal now as you can see they are made up with both C and N terminal but the N terminal region is slightly more extended than the C terminal region thus this H this inter terminal domain is placed outside of this o of this tetramer of H3 H4 as well as of this dier of H2 h2b you can see importantly so in in in terminals are putting outside uh but in case of in case of H2 H2 one of the C terminal is putting outside but in case of H3 and H4 all of the n terminals are putting outside but the C terminals are embedded inside of this tetramer okay we have a significance for that cell need need this to confirm that the in terminals are putting outside because again when we talk about the hisone modifications which are very very important and key steps of DNA transcription regulation and transcription initiation and all these things uh we need this inter terminal domain to modify these histones and these histone modifications will allow us uh to have DNA as a transcript uh to have DNA to trans as a platform or as a template stand to make a transcript of RNA and then to translate that into proteins okay now the arrangement H3 H4 tetr will come and sit and h2h to be diers again two D two of them diers are come to make a tetr of H2 h2b now again the placement is also specified that means the H3 H H3 and H4 uh tetramer will always be placed at the site where uh the entry and exit side of the DNA comes in so if we think uh this is the entry s of sorry this is the entry side of the DNA and this is the exit side of of the DNA so the entry and exite DNA at that part we have to place the H3 H4 H3 and H4 tetramer and on the opposite side where we are not having any entor exit side of the DNA all the site is closed the H2 h2b Teter is placed okay two of the H2 H2 ders are played so we can call it so let's never think about call like H2 H2 be tetramer so call it H2 a h2b dimer two of the diers come to make a Teter okay so that's it so H3 H4 dimer place and at the site of entry and exit of the DNA and H2 a h2b diers are placed on the closed site of this nucleosome model and you can see right after the arrangement of all those subunits of histone OCTA all the inter terminal in terminal uh sites are putting outside of this construction so no C terminal is putting outward all the n terminals are putting outside okay because again we need to modify this to have access to this DNA and we can do this by modifying this inter terminal domain not the C terminal domain that's why the inter terminal domains are extended and they are putting outside now if we look at the schematic presentation of the arrangement then you can find this is denoted with color now another important thing I must tell you about this part is that the arrangement you can see this blue is H3 and green is H4 so that the arrangement of this two layer two layer of all the subunits are not like that this 2 H3 just play just one top of each other so H3 is here and another H3 is here so it is not like that the two H3 always stay together uh on top of each other to H4 on top of each other not like that this is not arrangement of this this is arranged uh just uh just slightly bending okay so slightly bend it it it arranged like themselves okay now if we if you utilize Proteus enzymes to Cle this n strands we can also CLE this in terminal of this hisone proteins and as a result uh this this histone this compact DNA structure will unable to be reveal the DNA uh during the transcription process okay as a result of the destruction of inter terminal domains now if you look at the arrangement and the symmetry of this histon OCTA and DNA structure you can find something like that so these are the so entry and exit side that means these are the H3 H4 OCT tetr and these are the H2 diers now if we look at the structures so if if if this is the structure this is a schematic presentation of the same structure what we can find we can find one entry site one exit site and if we look at a at at an axis if we imagine an axis throughout so look think about this is a clock if you look this is a clock this is a 12 12:00 this is 6:00 C and 9 so if we draw a line or axis of symmetry from 6 to 12:00 then we can finally find something like that now if you slightly bent it then we can find a structure this is a side view actually so if we rotate it like that so we finally make something like that this is a side view you can notice one important thing is that this side view suggest us that this is this this wrapping of DNA is not almost 90° angle to this bead it is slightly bended look at see this part this is slightly bended so it's not complete 90° turn this is slightly bending okay so this is another important finding so these are all uh small informations about about nucleis structures and all of these actually really count we some of them some of these reasons we know some of them are we don't know but still these are these are the findings and uh the research is going on to know the control of uh the DNA accessibility during the transcription okay now uh again uh so this is called uh so we can say that we have we are having a partially or not partially we having quite uh quite moderate twofold axis of symmetry in this case because we can draw axis and we have two fold on it okay so uh now this is about the interaction of this histones uh with DNA now very important question above all that why these proteins uh are interacting with DNA so if uh we need to wrap this thread around the bead the bead and thread must have an interaction with themselves because otherwise it can easily be pulled out right so there must be an interaction between this histone octomer proteins and the DNA structure and the answer is yes there is an interaction and the interaction is not uncommon the interaction is very common interaction which is called the hydrogen bonding now there is hydrogen bond between these DNA strands uh and as well as uh the DNA phosphodiester backbones actually with this histon oomar proteins now normally uh the phosphor diar bbone contains oxygen and that oxygen is helping them to make the hydrogen bond with this hison octomer subunits okay now another important part about that this this DNA as we know are made up with two different group one is the major group another one is the minor group most of the hydrogen bonding interactions are between the major group of the DNA and the histone proteins but sometimes or fewer in fewer cases we can see The Binding between uh this histone octom with the minor group of the DNA okay but that is rare in uh really rare okay so if we look at here in this case uh some of the cases now this is in this case in normally in H3 H4 Teter structure there are the higher Affinity they are having the higher Affinity with the major group of the DNA not the minor group as you can see in this case this is the major group this is the major group so these are the major group and you can see H3 H4 tetramer is having Affinity much more with the major group rather than the minor group but in case of H2 a h2b and in case of some of the H3 H4 uh Di construction they they may have interaction with the minor group but the actual hydrogen bonding is also always present with the most of the time not always most of the time presented between the hisone protein and uh the major group but sometimes uh for some verifications few residues are uh pop out from the histon octomer protein and uh that uh can have an interaction with the minor group of the DNA sequence and it's actually helped this DNA to bend now another important thing I must tell you is that histon oomar proteins are uh most of most of the the protein subunits and most of the amino acid sequences are made uh with uh the positively charged amino acids and that give the overall histon octomer protein a positive charge now as we know the DNA backbone is as it is made with the phosphate group so it is slightly negative in charge not slightly it's fairly negative in charge so this DNA has higher Affinity with the positively charged histone so that again tells us why his DNA chooses histone protein to wrap themselves around uh because it is made up with those positively charged amino acid sequences and DNA is negatively charged sequences that's why okay now another uh again another important finding so we I'm telling you lot of different uh small small findings so if you all of them are logical though but still if you have a hard time to figure it out just look at these pictures it will tell you it will help you to understand and what is the actual thing now another important finding you can look in this case that H3 and h2b uh this uh n terminals are popping out uh from the in between portion of the DNA stand so again let me explain this picture actually so this is pretty hard for you to understand now this this Parts this uh dark color parts are uh the histone protein and this uh helical structure as you can see in this case the gray helical structure the gray Helix is the DNA and the way we are looking at it it's the side view it's a side horizontal view of the hisone octomer with the DNA sequences now we can see this two uh two DNA strands are going uh are wrapping this uh protein and in and from between these two DNA strands the H3 and H4 uh in terminals are popping out and H2 and H H4 on the other side are poing out from top and the bottom of uh this histone proteins so that's another important assumption another important finding uh I don't know why this is actually happening but we generally see that HCA HC uh terminal is much more vulnerable to the modification than other things because HC is having uh really fairly long inter terminal so it can be modified in several different ways it can be modified by a tilation it can be modified by phosphorilation and also via the methylation and all these cases okay now that's about the basic structure of nucleosome and how nucleosomes are arranged together what is nucleosome uh it's a content between the protein and the DNA protein is called the histone is made up with uh eight different subunits uh H3 four actually four different subunits two of them each we call in that OCTA and H2 H2 bh3 NH H4 are the respective names and they are also having those inter terminals propping out C terminals embedding inside and also there there is a specific arrangement of H3 H4 tetramer as well as H2 h2b dimer to make this structure and there is also uh the different levels of organization to make a DNA structure compact okay and there is also a very important interaction between the histone octomer protein and the DNA structure uh to hold the DNA structure to with this hisona okay so that's all about uh that's a basic overview about nucleosome model and I hope it will help you thank you

Channel: Shomu's Biology

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Keywords: biology education, life sciences, genetics, molecular biology, cell biology, suman bhattacharjee, shomu's biology, DNA, nucleosome model, nucleosome, dna condensetion, histone octamer, core protein, scaffold protein, linker dna, nuclear organization, nucleus, chromosome, chromatin, chromatid, 30 nm fiber, chromonema, Nucleosome and histones | Nucleosome structure, Nucleosome and histones, Nucleosome structure, chromosome structure, nucleosome packaging, nucleosome assembly

Id: F1opjc3PsC4

Length: 19min 2sec (1142 seconds)

Published: Sat Jan 26 2013