 Welcome back everyone. If you're watching this on Moodle later, or if you're watching it on YouTube five years, welcome, welcome. And lecture number three, part number four. So we were talking about transposable elements. Transposable elements are also called jumping genes, which I like much more. Discovered by Barbara McClintock. Yeah, yeah, yeah, that's why I did the intro. I pressed the record button. Don't worry. They were discovered by Barbara McClintock, who won a Nobel Prize in 1983. And for the students that are watching, I have a very particularly favorite thing about Nobel Prize winners. So generally, there is at least a couple of questions about people who won Nobel Prizes on the exam as a tip. So if it says that someone won a Nobel Prize, remember their name because I might ask you what they discovered or what was discovered by whom. So transposals are pieces of DNA that jump around in the DNA making copies of themselves or cutting and pasting themselves. And by doing so, they can disrupt the genes of the host. Not only that, but they are very important in plants where they generate variation since plants cannot move. Yeah, the plant needs to generate variation somehow because it cannot just move to a different country and look for a mate there. It has to do it with the mates that are around itself. So a little bit about transposable elements. Transposable elements are coming in two different classes. So you have a class one, which is called a retros transposal, which is kind of like a retrovirus. So they are generally made of DNA. They recruit the host system and get translated into RNA. Then they are reverse transcriptase into DNA and then they integrate. So there is this reverse transcriptase, which they use. They generally bring their own reverse transcriptase. Transposals are not pieces of DNA that don't do anything. They can code proteins as well. So if a transposal encodes a reverse transcriptase, then it is called a class one retro transposal. Furthermore, there's also things that are DNA transposals and they make direct copies of themselves. So there is no RNA intermediate involved and they use a protein called transposase so that they can jump around in the genome. Besides being able to divide transposals into class one and class two transposals, oh, I first have a picture of them. I added a nice picture. So here we see a retros transposal, right? So the retros transposal is transcribed and then translated into proteins. Then there is the ribonucleoprotein complex being formed, which then makes the reverse transcriptase and then the reverse transcriptase makes the RNA intermediate into DNA, which then integrates into the genome. So the one-ray-through-transposal is then transformed into RNA, the DNA, and then the DNA can integrate into several parts of the genome, disrupting different genes. If we look at class two DNA transposals, a DNA transposal, for example, the Marrior type, yeah, goodbye, testosterone, see you next time. They have this transposase, which is called TASA in T-A-S-E in the DNA. So what happens is that transposase is binding, right? So this thing is transcribed into RNA. The RNA is then... So the transposase is transcribed, not the whole transposal. Proteins are made, and then two of these proteins, they kind of cut out. So they have these tiers areas, which are sequences, which are recognized by the transposase. And they are bound by the protein. The two proteins then bind together, making one of these little loops. And then the whole thing goes and floats away from the genome. And once it hits another part of the genome, it just rolls into the genome over there. So the reverse process by first binding and then extracting again. But where they integrate is not known. So there's no sequence at which DNA transposals are integrated, although you can recognize them by the tier sequences, because the tier sequences, again, is kind of a palindrome, right? So you have a sequence here, which is then mirrored on this side. So interesting and a really funny system of how these DNA transposals jump around. But besides classifying them as class one and class two, you can also classify them as autonomous or non-autonomous. So autonomous transposal elements, they can move by themselves. So they, for example, the mariner type, right? They have their own transposage. So because they have their own transposage, they don't need anything else. They encode the proteins that they need to move around. But you also have non-autonomous transposable elements. And these require the presence of another transposable element to move around. For example, you can have transposable elements which do not have a reverse transcriptase, but they are class one, right? So they do have an RNA intermediate which needs to be transcribed into DNA. But since they do not code for reverse transcriptase themselves, they have to recruit the reverse transcriptase either from the host cell or from another transposable element. And of course, for class two, this means that some class two transposable elements, they don't have any transposage. They don't encode for transposage themselves. So they borrow the transposage of other transposable elements. So you can have a class one autonomous transposable element or you can have a class one, you can have a class one, you can have a class one autonomous or a class one non-autonomous. And then, so in theory, there are four different groups of transposable elements. So a little bit more about regulatory elements, right? Because like we saw, if you have a gene and every gene has a area in front of the gene and a little area in the back of the gene which regulates the expression of this gene. So a regulatory element is defined as a segment of a DNA molecule which is capable of increasing or decreasing the expression of specific genes within this organism. So there are two classes of regulatory elements. There are activators and repressors, right? So either you upregulate a gene or you repress the regulation of a gene. And when we look at regulatory elements, they are generally defined as cis which means that they are located close to the gene which means that around like minus 200 to like 40 base pairs into the gene. Then they are close by. So close by here means like 200 base pairs from the gene which they regulate. And then we also have things which are trans-regulatory and trans-regulatory means that they are located far away and far away can even mean on a different chromosome. The cis-regulation part is actually split into three distal part, is split into three parts. So the distal part is the part which starts at like minus 200 and then is in front of the gene. You have the proximal part which is 50 to 200 base pairs in front of the gene and then you have the core part generally overlaps with the five prime UTR. So the core part itself starts around 50 base pairs in front of the gene and can end around 40 base pairs into the gene. So here you see that visualized as the promoter itself is smaller than 1000 base pairs. And so we have the core promoter region and the proximal elements which regulate and then we have the distal regulatory elements which can be further away. But hey, in total cis means in the neighborhood. So that means that it's close. So if you're talking about it's a million base pairs away then this means that there's a trans-regulator. So some of the most well-known regulatory elements are for example the Tata box also called the Goldberg-Hochnes box. And this is the sequence. So this is how it looks like. So it's T-A-T-A-A. So that's why it's called the Tata box. And this is one of these core regions. So the Tata box is generally located 30 base pairs in front of the gene and proteins bind here to allow transcription of the gene. And again in bioinformatics you can use this sequence to learn if something is a gene. Because if you see T-A-T-A-A in the genome of for example a human then you can be very certain, well not 100% certain but almost always there is a gene next to it. So 30 base pairs downstream of the Tata box there is the start of a gene. So these regulatory elements help us to predict where in the genome are certain genes located. And around 24% of human genes have a Tata box somewhere in the promoter. So it is a very consistent motif that comes back a lot. And it's one of these things that as a bioinformatician you can use the knowledge that a Tata box is generally 30 base pairs in front of a gene to predict genes so that you know where there is. Of course there's a lot of different regulatory elements. There are things which are called frame shift elements which make or which where the polymerase is making RNA and then it hits one of these frame shift elements and because it hits the element it gets pushed back and pushed back like one or two base pairs. So what happens is because every amino acid is coded by three base pairs so it allows genes to be over so it allows one gene to have overlapping codons. So a codon which starts at zero and then at a certain point the thing gets pushed back like a little bit and then it continues on. There are internal ribosomal entry sites which means that a gene can start transcribing the protein halfway through so it doesn't start at the beginning of the messenger RNA but somewhere halfway in the messenger RNA there's another site for the ribosomal entry and it can transcribe. We have things like iron response elements which bind iron so when iron is present in the cell it activates all of the proteins needed to deal with iron located in the cell. Things like leader peptides, pyrolysis insert sequence, ribo switches and RNA thermometers. We have the selenocysteine insertion element so these are all different regulatory elements which in bioinformatics are used to predict genes and if there is a gene and how does this gene look like and if this gene is regulated by for example temperature or if it's responding to iron and so all of these different regulatory elements they have sequence motifs and these sequence motifs we can recognize using a computer and then we can do a prediction to see if there is a gene located at this position in the genome. All right a few words about other types of DNA so for example we have mitochondrial DNA, mitochondrial DNA is DNA which is located in the mitochondria so as you should know as a biologist if you have a cell then this cell has a nucleus and the nucleus holds the DNA so the information which is inherited from father to offspring and from mother to offspring but the mitochondrial DNA is a little bit different because the mitochondria are structures in the cell that produce energy and the structure you only get from your mother so in the egg cell there are mitochondria in the sperm cell there's also mitochondria but when the sperm cell fuses with the egg the tail where all of the mitochondria from the father are located they break away and they do not enter the egg so the sperm only contributes the DNA from the autosomes and the sex chromosome but it does not contribute to the mitochondrial DNA. It's not entirely true because like in one in 10,000 cases one of the mitochondria or two of the mitochondria from the sperm actually are incorporated into the egg so there is some mitochondrial inheritance like one in 10,000 births a child will be born that has a mix of mitochondria from the mother and mitochondria from the father but remember mitochondrial DNA generally is only inherited via the mother the mitochondrial DNA is of bacterial origin which means that it uses not this intron axon structure but it uses this monocystronic messenger RNA so the whole thing is transcribed more or less in one loop and again has since it is from bacteria the whole machinery to transcribe the mitochondrial DNA attaches to the circle, to the little circle of DNA and it just goes round and round to transcribe all of the genes which are located there the goal of mitochondria is to produce ATP so energy for the cell and in total there are 37 genes encoded on the mitochondria if you look at humans so things like cytochrome B, certain subunits which are used in the production of ATP but also the own, the mitochondria come with their own ribosome so the ribosome which makes the proteins within the mitochondria is different from the ribosome which is in the cell which translates the autosomal genes into proteins and this is, so in this part 16S and 12S ribosomal RNA this is why we know that the mitochondria come from a bacteria so originally mitochondria were free living bacteria they got absorbed by a cell and then they collaborated instead of being or less destroyed within the cell so inherited from the mother, how are you going? I'm going well, doing well like almost done with the lecture we need a couple more slides and a couple more slides and then we're done for today so mitochondrial is one of these other types of DNA which is really, really important in multi-cellular organisms because mitochondria produce the energy and you get them from your mother and only one in 10,000 people have mitochondria which come from the father another type of DNA only found in plants is the chloroplast and because plants they do photosynthesis so they are multi-cellular organisms but they, let me, I'm sorry I don't have any water around so I just have to rough through it do I know Guern? No, I don't know Guern so chloroplast DNA is DNA which is only found in plants and algae and only plants which do photosynthesis and the chloroplast is responsible for coding the whole photosynthesis system so they again come with their own RNA polymerase they have their own tRNA so their own ribosomal structure and these structures within the cell they are responsible for photosynthesis so it is kind of the mitochondria of the plant so that's kind of how I always describe the chloroplast they have a cyanobacterial ancestor which is not that much of interest but if you're interested in like how did plants acquire the ability to do photosynthesis well they got that because they kind of captured a cyanobacteria and then the cyanobacteria was kind of in the course of evolution adapted so that had this part of the plant cell can do photosynthesis it encodes between 60 to 100 genes and it has also, it also has their own ribosome and all of the things needed so photosystem one and photosystem two are encoded on there alright, that was it so we're through I told you today about different history so the history of DNA sequencing the history of kind of what we know about DNA so how DNA was invented how we know that it's a double helix I told you about DNA sequencing and the alignment of DNA sequences so I talked a little bit about the fact that hey you start off by trimming the reeds then you align the reeds not only do you align the reeds but after aligning the reeds you have to realign them because there are certain structures which are commonly found in humans and since we only use a single reference genome we have to be sure that the reference genome is that things which occur more often relative to the reference genome are not making it so that reeds are penalized for that hey, if you have a single nucleotide polymorphism then the reed is still perfectly valid and it still maps 100% there besides that we talked about genes things like gene structure what is different between prokaryotes and eukaryotes we talked a little bit about transposals and other regulatory elements although we did that relatively quick and I don't want you guys to know all of the different regulatory elements I just want you guys to know that if you have a gene then in front of the gene there are things which regulate this expression of the gene they can be classified into the core region and then we have the proximal region and besides that we also have transregulations or regulation which could occur from other chromosomes and besides that we have other types of DNA like mitochondria and chloroplast and so the mitochondria are generally called MTDNA which you get from your mother and chloroplasts are more or less the mitochondria that plants use to do photosynthesis and make sure that they get energy as well All right, so for the six people who stayed till the end thank you, thank you very much are there any questions? The homework for today is a little bit of R and it's not on Moodle yet I will put it on Moodle directly for you guys I will actually do that a little bit later if you guys don't mind Misha, you have a question? Sure, sure, it's gonna be a long question Do cloned plants have jumping genes too? Yes, every living organism has jumping genes They are common in plants they are less common in humans but even humans have jumping genes and the jumping genes in humans only become active just after fertilization so when the sperm cell of your father merges with the egg cell of your mother at that point the whole epigenome is wiped so at that point the cell doesn't have the control over the transposions so they start jumping around but every living organism perhaps besides some bacteria because bacteria have a very small genome and they try to get rid of everything that's not useful but almost all more or less higher order living animals or cells like yeast they all have jumping genes and you can't get rid of the jumping genes but because as a plant it is very important to so cloned plants don't have to be genetically identical they will not be genetically identical because there is always things like random mutations because like, hey, if you are a plant or if you have two cloned plants that are standing next to each other one of them might get a little bit UV light which changes a couple of base pairs in the DNA but cloned plants are definitely not genetically identical because of the transposions that are jumping around and causing variation but of course like 99.999% of the genome will be equal and the chances of a transposon jumping into a major gene and disrupting it are also relatively small but it can happen it can happen that for example the FTO locus which is involved in flowering time is disrupted by a transposon making that two cloned plants can have different flowering times there goes months of macrophied cloning why, why, because like in the end like the idea of cloning and making things genetically identical is that you have, that you can exploit that, right that you can predict when a plant will start to flower but in the end like life will do anything to prevent being completely locked into a certain genomic constitution, right because in the end if you are 100% a clone of something then that is very bad because that means that all of the clones are susceptible to for example a single virus and it can wipe out the whole population so life will always do anything it can and use any method possible to get like variants and variation is very important for life to continue because hey you need variation they are identical that's, that's, it's the same with inbred mice mice which are inbred are 99.99% identical but they are not 100% identical that one of the main ways that you can see that is for example the sex chromosomes, right inbred mice still come in a male and in the female form that means that, that they are not genetically identical because the female mouse has two X chromosomes while the main mouse has one X chromosome and one Y chromosome, gotta go thanks for class bye yeah thanks for being here Xanaxin thanks for staying until the end and answering the questions and just participating thank you for being here so yeah but yeah if you clone them right and the same thing holds for cloning plants or cloning other things they are for research purposes you assume that they are identical the same with inbred mice you assume that they are identical you got inbred herds if you want some oh that would be nice, that would be nice like we're almost cycled with the tank I think so it's almost like in harmony or in homeostasis how do you wanna call it so it's time for some new snails in the aquarium as well good if there's no other questions then I will stop the recording so people on YouTube see you later see you next week probably or in a couple of days I don't know exactly the schedule for YouTube so I have to look at that at least see you next time and I hope you enjoyed the lecture if you enjoyed the lecture give it a like and subscribe and all of these things of course on Twitch as well good see you next time