Gel Electrophoresis - Online Tutor, Practice Problems & Exam Prep

Gel electrophoresis is a technique used to separate and visualize DNA fragments based on size. Negatively charged DNA migrates through a gel matrix towards the positively charged anode when an electrical current is applied. Larger fragments move slower and remain closer to the starting point, while smaller fragments travel further down the gel. This separation allows for comparison against a reference DNA sample, facilitating size estimation of unknown fragments. Understanding this process is crucial for applications in genetics, forensic science, and molecular biology.

Gel Electrophoresis

In this video, we're going to begin our lesson on gel electrophoresis. Gel electrophoresis is a technique used to separate and visualize fragments of DNA using a 3-dimensional gel matrix. It's important to note that DNA itself is a negatively charged molecule. This negatively charged DNA will be separated by its size using gel electrophoresis, by employing an electrical current and an ion buffer solution. The top of this gel used in gel electrophoresis is where the cathode is located, representing the negatively charged end of the gel where the DNA samples are first loaded. DNA samples start towards the cathode and migrate away from it towards the anode, which is at the bottom of the gel. The anode represents the positively charged end of the gel, where the DNA samples migrate towards. Gel electrophoresis separates DNA based on its size; the larger fragments of DNA move slower through the gel, remaining closer to their starting point. Conversely, the smaller fragments of DNA will move faster through the gel and will be found towards the bottom of the gel.

If we look at the image below, we get a better understanding of gel electrophoresis. Notice that the gel is organized into lanes, almost like lanes at a bowling alley, and each lane has numbers. At the top of each lane, there are wells which represent the starting place of the DNA. Each lane typically contains a different DNA sample. Initially, there is a reference DNA sample known for its size and characteristics. Individual DNA samples from different subjects might occupy other lanes. Notice also that lanes 5 and 6 in this image are empty; no DNA samples are present in those lanes.

At the top of the gel is the cathode, the negatively charged end where the DNA samples are loaded. The DNA tends to migrate towards the anode at the bottom of the gel since opposite charges attract. This leads to the separation of DNA through this gel matrix. In this image, you can see that the DNA migrates from the top to the bottom of the gel. The specific numbers indicating base pairs (bp) show that gel electrophoresis separates DNA based on size. Longer DNA fragments, which remain towards the top, travel slower through the gel, while shorter DNA fragments migrate faster to the bottom.

On the right-hand side of the image, a graph demonstrates the relationship between DNA fragment size and the distance the fragment travels through the gel. The y-axis showing molecular size has large fragments at the top; the larger the fragment, the less distance it travels through the gel. A photo of an actual gel electrophoresis being performed is displayed, with references on both sides of the gel and different DNA samples in each lane that can be compared to the reference for size estimation.

This concludes our introduction to gel electrophoresis and how it's used to separate and visualize DNA fragments based on size. As we move forward in our course, we'll get some practice applying these concepts. I'll see you all in our next video.

Gel Electrophoresis Example 1

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, 1, 2, 3. 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 rabbit C 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 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 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.

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.

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.

Gel electrophoresis separates fragments of DNA based on which characteristic?

• A. Sequence.
• B. Level of methylation.
• C. Size.
• D. All of the above.

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.

Here’s what students ask on this topic:

What is gel electrophoresis and how does it work?

Gel electrophoresis is a technique used to separate and visualize DNA fragments based on their size. DNA, being negatively charged, migrates through a gel matrix towards the positively charged anode when an electrical current is applied. The gel matrix acts as a sieve, allowing smaller DNA fragments to move faster and travel further down the gel, while larger fragments move slower and remain closer to the starting point. This separation allows for the comparison of unknown DNA fragments against a reference sample, facilitating size estimation. This method is crucial in genetics, forensic science, and molecular biology for analyzing DNA.

Why do smaller DNA fragments move faster in gel electrophoresis?

In gel electrophoresis, smaller DNA fragments move faster because the gel matrix acts as a sieve. The matrix is composed of a network of pores that DNA fragments must navigate through. Smaller fragments can more easily pass through these pores, encountering less resistance compared to larger fragments. As a result, smaller DNA fragments travel further down the gel towards the anode, while larger fragments move slower and remain closer to the starting point. This differential movement based on size allows for the effective separation and analysis of DNA samples.

What is the role of the cathode and anode in gel electrophoresis?

In gel electrophoresis, the cathode and anode play crucial roles in the movement of DNA fragments. The cathode is the negatively charged end of the gel, where DNA samples are initially loaded. Since DNA is negatively charged, it is repelled by the cathode and migrates towards the anode, which is the positively charged end of the gel. This movement is driven by the electrical current applied across the gel. The separation of DNA fragments occurs as they migrate from the cathode to the anode, with smaller fragments moving faster and traveling further than larger ones.

How is a reference DNA sample used in gel electrophoresis?

A reference DNA sample, also known as a DNA ladder or marker, is used in gel electrophoresis to estimate the size of unknown DNA fragments. The reference sample contains DNA fragments of known sizes, which are loaded into one of the lanes of the gel. As the electrophoresis process runs, these reference fragments migrate through the gel, creating a pattern of bands at specific distances. By comparing the migration distances of unknown DNA fragments in other lanes to the reference bands, researchers can approximate the sizes of the unknown fragments. This comparison is essential for accurate DNA analysis.

What are the applications of gel electrophoresis in molecular biology?

Gel electrophoresis has several important applications in molecular biology. It is used for DNA fingerprinting in forensic science to identify individuals based on their unique DNA patterns. In genetics, it helps in analyzing genetic variations and mutations. The technique is also employed in cloning and sequencing projects to verify the size and integrity of DNA fragments. Additionally, gel electrophoresis is used in the diagnosis of genetic disorders, the study of gene expression, and the purification of specific DNA fragments for further research. Its versatility makes it a fundamental tool in molecular biology.