Gel Electrophoresis - Video Tutorials & Practice Problems
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concept
Gel Electrophoresis
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7m
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Video transcript
In this video, we're going to begin our lesson on gel electrophoresis. And so gel electrophoresis is really just a technique that's used to separate and visualize fragments of DNA using a 3-dimensional or a 3 d gel matrix. Now it's important to note that DNA itself is a negatively charged molecule, And so this negatively charged DNA is going to be separated using gel electrophoresis and it's going to be separated by its size and so it's gonna 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, the cathode, and the DNA will migrate away from the cathode towards the anode, which is at the bottom of the gel. And so the anode, 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 DNA 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 move 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. So the smaller fragments of DNA are found towards the bottom of the gel. And, again, this is because the smaller fragments of DNA will migrate through the gel faster, 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, 6 different lanes. And so what happens is, 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 DNA samples are first loaded into the lanes. And each lane will typically have a different DNA sample. 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, maybe DNA samples from different individuals like for example, individual a, individual b, individual c, and so on. Lanes 56 in this 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 gonna be the negatively charged end of the gel. And so again, the cathode which the negatively charged end of the gel, this is where the DNA samples are going to be loaded. And towards the bottom of the gel, we have the anode which is the positively charged end of the gel. And so recall that opposite charges attract and then the DNA is negatively charged. And so by placing the DNA towards the cathode, the DNA will end up migrating towards the anode. And so you get the separation of the DNA through this gel matrix. And so, what you can see is that the DNA 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, is, 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 gel and the smaller or the shorter 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, in the reference lane, we have DNA fragments of known size. So you can see that, this fragment at the top is the largest fragment because, again, the longer fragments remain towards the top. It's 1,000 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 in these other lanes. And so you can see that individuals, 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 is 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 DNA, 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 here 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.
2
example
Gel Electrophoresis Example 1
Video duration:
2m
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Video transcript
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 4 potential answer options down below. And so looking at this gel over here, notice that there are 3 different lanes, 123. And within each lane, we have different species of rabbit. We have rabbit a species here, rabbit b species here, and rabbit c, species in the 3rd and final column. 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 a is very similar to the band pattern of rabbitc and they share more DNA bands that are in common than any other combination. And so what you can see is that, this is going to be the same across both. This band here is also the same. 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 differences that stand out between, rabbit a and rabbit c are, the circle the one 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 2 rabbit species that are most closely related. And so our answer is going to be, answer option b here, which says rabbit species number 1 and number 3 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 this example problem. And, 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.
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Problem
Problem
At a crime scene a blood sample was found and investigated using gel electrophoresis. Based on the gel, the blood at the crime scene belongs to which of the suspects?
A
Jenny
B
Bob
C
Mike
D
Lisa
E
The blood at the crime scene does not belong to any of these suspects.
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Problem
Problem
The parents of a new baby believe that the hospital sent them home with someone else’s baby. The hospital
takes DNA samples from both parents and the baby. The DNA is investigated using gel electrophoresis. Do the parents possess their biological child or did the hospital give them the wrong baby?
A
The parents have the correct baby, their DNA matches.
B
The parents have the wrong baby, their DNA does not match.
C
There is no way to tell using this gel.
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Problem
Problem
Gel electrophoresis separates fragments of DNA based on which characteristic?
A
Sequence.
B
Level of methylation.
C
Size.
D
All of the above.
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Problem
Problem
Why do the fragments of DNA in gel electrophoresis move away from the negative cathode?
A
DNA is negatively charged and attracted to the positive anode.
B
DNA is positively charged and attracted to the positive anode.
C
DNA is negatively charged and attracted to the positively charged agarose gel.
D
DNA is positively charged and attracted to the negatively charged agarose gel.