Gel Electrophoresis

in this video, we're going to begin our lesson on gel electro for Racists. And so gel electrophoresis is really just a technique that's used to separate and visualize fragments of D N A. Using a three dimensional or a three D gel matrix. Now it's important to note that D. N A. Itself is a negatively charged molecule, and so this negatively charged D. N A. Is going to be separated using gel electrophoresis, and it's going to be separated by its size. And so it's going to be separated by its size by using an electrical current and an ion buffer solution. And so, towards the top of this gel that's used in gel, electrophoresis will be the cathode and the cathode represents the negatively charged end of the gel. And this is where the DNA samples are first loaded. So this is where the DNA samples start towards, uh, the cathode and the D. N. A. Will migrate away from the cathode towards the anodes, which is at the bottom of the gel. And so the an ode, which again is at the bottom of the gel, is going to represent the positively charged end of the gel where the DNA sample is going to migrate towards. And so again, gel electrophoresis separates the DNA based on its size. And so the larger fragments of D N A are going to move slower through the gel. And so that means that they remain closer to their starting point. And the starting point is again towards the top of the gel, so the larger fragments of DNA moves slower, and so they remain towards the top of the gel, whereas the smaller fragments of DNA, on the other hand, will move faster through the gel. And so they will be able to get towards the bottom of the gel faster. And so the smaller fragments of DNA are found towards the bottom of the gel. And again, this is because the smaller fragments of D. N A. Will migrate through the gel faster, uh, through that gel apparatus. And so if we take a look at our image down below, we can get a better understanding of gel electrophoresis. And so what you see over here on the left hand side is the gel that's used in gel electrophoresis and so notice that this gel is organized into lanes. And so notice that the lanes are labeled here with numbers. And so the lanes are almost like lanes at a bowling alley in a way so you can see that we have here, uh, six different lanes. And so what happens is, um, at the top of each of the lanes you have these wells and the wells are going to represent the starting place of the DNA. This is where the D N A. Samples are first loaded into the lanes, and each lane will typically have a different d n. A sample. Uh, and so you can see that in the beginning here, what they have is a reference DNA sample, which is basically just a DNA sample that is known. They know exactly the size and things like that of this reference. And then in the other lanes you have different, uh, maybe DNA samples from different individuals like, for example, individual a individual, be individual C. And so on lanes five and six and this, uh, image are empty. So there's no DNA samples in those lanes. And so notice again that at the top of the gel, as we mentioned up above in our text at the top of the gel, we have the cathode, which is going to be the negatively charged end of the gel. And so again, the cathode, which is the negatively charged end of the gel. This is where the D N a samples are going to be loaded. And towards the bottom of the gel, we have the an ode, which is the positively charged the end of the gel, and so recall that opposite charges attract and the d. N A is negatively charged. And so, by placing the d n a towards the cathode, uh, the D n A will end up migrating towards the an ode. And so you get the separation of the DNA through this gel matrix. And so what you can see is that the D. N A. Is going to be migrating from top of the gel to the bottom of the gel in this image. And so over here, what you'll see is, uh, these specific numbers that say BP, and that's referring to the base pairs. So this is referring to the size of the DNA fragments, since gel electrophoresis separates the DNA based on size, and it's the longer DNA fragments that are gonna move slower through the gel. So the longer DNA fragments remain towards the top of the Joe and the smaller the shorter DNA fragments, they move faster through the gel. And so they remain, uh, they will end up being towards the bottom of the gel. And so each of these little bands that you see throughout this gel represents a DNA fragment. And so these are the DNA fragments here. And so what you can see here is, uh, in the reference lane, we have d n a fragments of known size, so you can see that, uh, this fragment at the top is the largest fragment, because again, the longer fragments remain towards the top, it's 1000 base pairs and the smallest fragments, the shortest fragments will migrate fastest through the gel and remain towards the bottom of the gel. And so what you can do is you can use the reference to help give you a general idea of the size of the fragments and these other lanes, and so you can see that individuals, uh, DNA fragments can be compared to the reference to give you an approximate size of those fragments. Now, over here on the right hand side, what we're showing you as a little graph showing you the relationship between the DNA fragment size and the distance that the fragment will travel through the gel. And so, on this axis, right here we have the molecular size of the DNA in base pairs, and on this axis we have the distance that's migrated in the gel. And so what you'll notice is the larger the size. So on this y axis we have large is at the top and small fragments at the bottom, the larger the d n a. The less distance it travels through the gel. And so the larger DNA fragments travel slower and remain towards the top, whereas the smaller fragments are going to be migrating a further distance in the gel. And so that's really what this graph here is emphasizing and then down below right here. What we have is an image of an actual gel electrophoresis that's being performed, and so you can see that you have these mark these references that are on both sides of the gel here, and then in each lane you have a different DNA sample, and that DNA sample can be compared to the reference to give you an approximate size. And so really, this year concludes our introduction to gel electrophoresis and how it's used to separate and visualize fragments of DNA, and it separates the DNA based on size. And so we'll be able to get some practice applying these concepts as we move forward in our course, so I'll see you all in our next video.

so gel electrophoresis can be used for many different reasons. And here we have an example that is showing you how gel electrophoresis can be used. And so it says, using the gel that's being shown down below. Over here on the right hand side, determine which rabbit species are most closely related and we've got these four potential answer options down below. And so, looking at this gel over here, notice that there are three different lanes 12 and three. And within each lane we have different species of rabbits. We have rabbit, a species here, rabbit bi species here and rabbits C species in the third and final count. And so, in order to determine how closely related the species are, what we need to do is compare the band pattern in each of the lanes. And so when you do this, what you'll find is that the band pattern of rabbit eh is very similar to the band pattern of rabbits C and they share more DNA bands that are in common than any other combination. And so what you can see is that, uh, this is going to be the same across both this band here is also the same. Uh, maybe not this one here, but this one and this one, these here are all the same. And so there is a lot of similarity and really, the only difference is that stand out between rabbit A and rabbits C r the circle the bands that are being circled in these positions. These are the only ones that don't match up with each other vertically on the gel. And so because they have such close similarity in that respect, that means that these are going to be the two rabbit species that are most closely related. And so our answer is going to be, uh, answer Option B here, which says rabbit species number one and number three are the ones that are most closely related. And that's simply because their band patterns are the ones that match each other the best. And so option B here is going to be the correct answer for this practice example problem. And, uh, we'll be able to get some practice applying these concepts as we move forward in our course. So I'll see you all in our next video