Genomic Variation - Video Tutorials & Practice Problems
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Genomic Variation
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Hi in this video we're gonna be talking about genomic variation. So there are a lot of different variations that exists between and within an individual's genome. So mine and your genome differs a lot. Which is why we aren't clones of each other and that exists for every human organism and also every other organism on earth. Now. Let me talk about some of the genomic variations that are found in humans. Um And we mentioned most of these before briefly, but I want to go over a little bit more detail about what they are and how we identify them and how frequent they are. Just some more detail. So one of them is called a single nucleotide polymorphism or a snip for short. And these are exactly what they sound like. They're single nucleotide changes. So an A to A C. Or a G to a T. Or something like that. Any kind of switch that's made. Now they're actually fairly frequent in the human genome. About one in every 1000 bases is altered. Which is a ton of snips. If you think of how many bases there are that exist in the human genome and then there are about 18 million total snips in humans as a whole. So if you took all human genomes and just threw it together, there'd be about 18 million snips. Um that's a lot of time. So. Um because there's so many, it makes sense that the majority of snips are actually in silent regions. So they're not changing a protein. Um they're not changing an amino acid. They're not having any effect on proteins. Which makes sense because the vast majority of the human genome isn't protein coding only about 2% of the human genome codes for proteins. And therefore most of the snips are going to be in regions that do not code for proteins. Um But they're still important because that allows us to tell the difference between DNA between the individuals. If we do sequencing it helps us identify some sort of evolutionary time scales. So even though they're not affecting proteins, they're still really important for scientists now. How do people identify snips? There's a lot of different ways. One is called a southern blot and that's just a way to visualize different links of D. N. A. So if you are going to identify a snip with different lengths of D. N. A. How you do it is you use proteins called restriction enzymes. And what restriction enzymes do is they cut D. N. A. At one specific region. So some people will have snips that allow the DNA to be cut and some people will have snips that don't allow the DNA to be cut. And so if you take the DNA from those two types of individuals and expose them to this restriction enzyme it'll chop up their D. N. A. But it'll chop up their DNA differently and therefore they'll have different DNA links if you run a southern block. And so by running a southern block you can take DNA. That's been cut by restriction enzymes and say oh well this person has different snips than this person because there are different DNA links after I exposed it to the cutting enzymes. So that's one example you can use PCR um and also the restriction enzymes with that it works the exact same way. But a big one is also DNA micro race which are just sort of these um plates that can bind to different DNA sequences and there can be so specific that they won't bind to a D. N. A sequence with one simple change in it. And that would identify a snip which has a single change in it. So like I said there are multiple different ways to do this. So here's an example of a single nucleotide polymorphism. Notice that the sequence is the same except for this nuclear titan red. And so this is just one single change. It might be in a protein coding region, it might not. And so these types of snips are found very frequently throughout the human genome. So that's kind of the most common. So let's get to some more less common sequences. So one of them is a deletion insertion polymorphism which can also be shortened as a dip or an in del mostly in del but I did see it as dip in a couple of your textbooks. But um essentially what these are is Exactly what they sound right, luckily these things are named very well. So there's small deletions or insertions of some kind of genetic material. They can range from a single base pair to 517 which is the longest identified. And there are nearly 300,000 in the human genome. So about one in every 10 killer bases. So 10,000 bases differs in a deletion or an in del between two individuals. So This like I said, it can be a insertion of one nucleotide, a removal of one nucleotide removal of 20 nucleotides insertion of 20 all the way up to 517. So it's just little sequences that are inserted or deleted and they're found throughout the genome. Another type of genomic variant is simple sequence repeats. And these are generally 12 or three bases. So not very long but they're repeated 15 to 100 times normally. Um Sometimes they cause disease and when they cause the disease they're repeated much more often than that, but normally 15 to 100 times. So a really common one is actually the see a repeat. And this is the repeat of these two nucleotides C. A over and over and over again. And it's found this just this one. So just the see a repeat. It's found about once every 30,000 base pairs in mammalian genomes. And generally they arise through some type of DNA replication error which started you know trying to replicate 50 C. A. S. But then accidentally did 75. And so they are like I said before they're associated with certain diseases. Huntington's disease is one of them. But those are the they're actually a simple sequence repeat of C. A. G. For huntington's. So here's just an example of a C a repeat, right? It's just C A C A C A over and over and over again and it continues 15 200 times. And they're found sprinkled throughout the genome fairly frequently about once every 30,000 base pairs. So finally let's get to the last one where the last couple we're going to talk about and those are many satellites. Many satellites are repeat. Um this is supposed to say base pairs, about 500 base pairs to 20 killer bases. And so 20,000 base pairs. So these are much bigger than what we've been talking about before. Um and these are repeats of these these long sequences that are scattered throughout the genome. Now we have taken advantage of these through what's called the DNA fingerprint. And crime scene investigators used DNA fingerprints all the time. And what they do is they look at these many satellites and they look at the length of them and how frequently they're found throughout the genome. And when you sort of just identify, you know how frequently these regions are repeated throughout the genome. It produces a pattern that's specific to you. So how many many satellites you have and how frequently they are throughout the genome. And when you look at that you have a unique pattern. And every individual on earth has a unique pattern when they look at the length of those on some type of gel which I'll show you in a second. And so um this is how scientists identify whether the crime scene D. N. A. That they found at the crime scene is um is the same D. N. A. As somebody else in the system or somebody that the suspect that they brought in. And they do it through DNA fingerprinting by looking at the pattern of these many satellites in an individual. So that's a really cool thing. I'll show you an example of that in a second. But first I want to talk about large scale deletions which are exactly what they sound like these large regions that are deleted and they can also differentiate human genomes. And an example of a large scale deletion is actually a copy number variants. And this is just you know numbers of copies of alleles or number of copies of larger legal section because they're large scale deletions about to one mega base in length. And so this is another one that's pretty frequent. So what is the DNA fingerprint look like? Well this is what it looks like. These are different DNA links depending on the micro satellites that are present. So if this D. N. A. Here was picked up at the crime scene. And you have three suspects here that you had also done the DNA fingerprint on which one would be most like which one is the one who D. N. A. Was at the crime scene? Would it would be the one that matches this pattern? So if we look across this one has the same this one is the same for all four. This one and this one has it this one and this one has it and this one and this one has it. So if we look at the pattern number two would be the suspect that we could go with. Because this is the the pattern the micro satellite pattern that's most that most resembles the DNA found at the crime scene. That's kind of how that works A little view into C. S. I. For you. But with that let's now move on.
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Problem
Problem
Which of the following is NOT an example of large genomic variations between two individual genomes?
A
Single nucleotide polymorphisms
B
Simple sequence repeats
C
Dominant and Recessive alleles
D
Minisatellites
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Problem
Problem
Which of the following genomic variations can be detected through DNA fingerprinting?
A
SNPs
B
Simple sequence repeats
C
Large scale deletions
D
Minisatellites
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Problem
Problem
Which of the following genomic variations is most common in human genomes?
A
SNPs
B
Simple sequence repeats
C
Large scale deletions
D
Minisatellites
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