4. DNA, Chromosomes, and Genomes
The Epigenetic Code
1
concept
Chromatin Structure
3m
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Hi in this video we're gonna be talking about the abbey genetic code. So first before we can talk about the epigenetic code we need to know what we're talking about and how we need to do that is actually make sure we understand the definition of protein. So what is chrome button do you remember? Right so crow maten is the combination of D. N. A. Plus protein. So we're not just focused on the D. N. A. Itself. For focus on this sort of globular picture of D. N. A. And protein or global globular global picture of DNA and protein. And so the chroma tin which is DNA and protein can exist in two forms. So these are you chrome button or hetero comitan. So the these two states are defined based on how condensed the D. N. A. Is so you chroma tin is less condensed. Yeah, D. N. A. Structure. And so because it's not tightly packed that allows the D. N. A. To be accessible to other proteins. Hetero croton on the other hand is more condensed. And so that means that the genes that are found on hetero comment on are generally not expressed because it's so tightly condensed that things that you know transcription factors and things that would express jeans can't bind there, they can't access the D. N. A. And so um these genes are expressed so therefore hetero comitan usually contains only a few genes. Um And so hetero chrome attend is found mainly in regions of the chromosome that don't contain a lot of genes including centrum ears and telomeres now because hetero comitan has this such strong effect of not allowing gene expression. There is this nearby region called the zone of inactivation and this is based on how close the jeans are, too hetero comitan. So the closer they are to hetero comment in the less likely they're going to be expressed or the less highly they're going to be expressed. So um so what this the fancy term for this is position effects, but it just means that the, you know, the closer the gene is too hetero comitan, the less it's going to be expressed. So if we just take a second to look uh this example here, you can see that you chrome aton is here. Um and this sort of is the active form because it's not not as condensed and different proteins or things can come in and they can bind and you know transcribe the gene or do whatever they need to. Whereas hetero chrome aton, these genes are generally silent because they're so tightly packed that really nothing nothing can come in here and access. There's just no points to where it combined. Um So it remains silent and the genes remain unexpressed. So now let's move on.
2
concept
Histone Modifications
4m
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So we now know about the different states of chroma tin. But we haven't or haven't explained yet how they actually formed those different states. And so this video is going to be really focusing on different protein modifications that form the different condensation states of D. N. A. So because chrome aton is made up of DNA and protein and the majority of that protein actually are histone proteins. Histone proteins are proteins responsible for packaging and condensing the D. N. A. So how this happens is because each histone protein contains an interminable tail and on this tale has very um has sort of a long string of amino acids that can be modified. Um And these modifications affect the condensation of D. N. A. So some modifications make it more condensed and some modifications that get less condensed. Now the two most common modifications are assimilation and methylation and I just added in parentheses here what actually is being added um The chemical structure that's being added. Although you usually don't need to know um these exact chemical formulas just sort of know the names of titillation and methylation. So what assimilation does is it removes a positive charged from the histone and this results in a loosening of chromosome structure. So the chroma teen sort of expands a little and genes can be accessed methylation on the other hand tightens chromosome structure and actually can prevent assimilation. So um if we were to just sort of do a quick practice question here assimilation would be what's causing either loosening or tightening of protein. Right assimilation would be loosening and listening and methylation would be tightening. So um sometimes when this happens we kind of think, okay, well, you know each one of these amino acids, you know, there's can be a simulation on this one of methylation on this one. Um and they all happen independently, but sometimes there can actually be this chain reaction. And what happens there is that, you know, one amino acid gets some type of either a methylation or circulation gets some type of modification. But because of that modification it triggers all the rest of the amino acids kind of down the line to have the same modification. So you get this long linear chain of similar histone modifications which can really affect a very um long stretch of protein. And so these um although these chain reactions can't go on forever or everything would be expressed all the time and that would just be complete destruction. Um so eventually they're stopped by barrier sequences which can kind of separate saying, okay, this is condensed protein and this is non condensed protein. And even though there's a chain reaction going on, you're stopping here because you're not going to move on to this condensed chromosomes section. So um assimilation and methylation. So let's actually just let me move out of the way. We'll take a look. So remember you have the nuclear zone core. So these are the histone proteins and they are actually right now formed into a nuclear zone cleo zone and they all have these little tails. You can see them hanging off here um with amino acids on them and each one of these amino acids can be modified various ways. Now I talked about methylation and assimilation, but you'll see there's all these other types of things that can happen to that I didn't ness really talk about but still exists. And so you can see that all of these different amino acids. So here's a long stretch of oscillations, here's a long stretch of methylation. So all of these um all of these amino acids can be modified in so many different ways and these modifications affect protein structure. So now let's move on.
3
concept
Epigenetic Code
5m
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in this video, we're gonna be talking about reading the epigenetic code. So we've talked about how histone proteins can have all these different modifications on them. But you can imagine because there's so many modifications and so many amino acids that reading the genetic epigenetic code which is the histone modification code can be extremely difficult. You know what combinations of modifications do what And so um each nuclear zone has a different set or pattern of modification. And these um modifications are actually really carefully controlled because once the nuclear zone has been modified that these modifications of assimilation or methylation not only affect chromosome condensation but it can also attract other proteins which can do various things to the D. N. A. And so um as the cell is going, you know this is sort of a dynamic process. It's not just stationary. So as the cell needs you know more gene expression or less gene expression or it needs to divide um all of these modifications have to constantly change to adapt to the cells needs in order to allow you know replication of this D. N. A. Or expression of this gene or um you know inhibition of this other gene. So all of these modifications are not only really complex because there's so many different of them but also very complex because they're always changing. So um there is one um complex called the crow metin remodeling complex and this is a complex that uses a T. P. Um energy or energy from a T. P. To change the position of DNA in the nucleus zone So so far we've actually just talked about you know amino acids and modifications but actually there's a second kind of layer of understanding the epigenetic code because the nuclear zones aren't stationary on a specific sequence of D. N. A. They can move to allow access or to constrict a region of D. N. A. And how they do this is through comment and remodeling complexes which allow for specific DNA sequences to become more or less complex. So um here's an example of histone remodeling. So you can see here you have your nuclear zones. Yeah here and there's this protein that wants to come in and bind. But it can't because there's a nuclear zone in the way. So this chromosome complex the chromosome remodeling complexes come in and move histone down. So it exposes this D. N. A. Which then can move forward and do whatever it needs to do express the gene replicate the gene whatever. So that's how that happens. So with ePI genetics there's actually this really unique thing that you've probably never heard of before which is epigenetic inheritance. And so um we can think of inheritance usually as people inheriting D. N. A. Or inheriting genes from their parents. But there's actually this whole field that really just sort of newly discovered. That's very exciting. That is actually epigenetic inheritance. So this is the fact that you can actually inherit chroma tin structure. So not just the D. N. A. And the genes itself but you can actually inherit the condensation state of the D. N. A. And so histone modifications can be passed on to daughter cells. So this can happen through um just sort of normal cell division. So when skin cells divide they can remain they can keep their histone modifications. But there's also some evidence that this can actually happen in germ cells when passing down to offspring. And so how this happens is like it happened with the histone codes. Amino acids on the tail of the his stones are violently modified. They affect the condensation and that is passed down to either you know another generation of skin cells or liver cells but potentially also to offspring. So this inheritance actually allows for this process called uh cell memory which is a type of non genetic inheritance. And so let me scroll up a little non genetic inheritance. So we think of inheritance as being all genetic just genes being passed. But epigenetic inheritance is actually non genetic. And the fact that just these modifications being passed down to cellular offspring. So now let's move on.
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Problem
ProblemWhich of the following terms is associated with condensed chromatin?
A
Acetylation
B
Euchromatin
C
Heterochromatin
D
Cell memory
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Problem
ProblemWhich of the following histone tail modifications is most likely to cause closed chromatin?
A
Acetylation
B
Methylation
C
Phosphorylation
D
Ubiquitination
6
Problem
ProblemThe position of nucleosomes on a region of DNA can never change.
A
True
B
False
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Problem
ProblemHistone protein modifications can be inherited.
A
True
B
False