Gel electrophoresis is one of the most widely used techniques in Clinical Chemistry, Biochemistry, and Molecular Biology laboratories. It is introduced to students either in high schools or undergraduate courses. The first time that a person loads their self-casted gel is quite a memorable lab moment. And visualizing the separation of the macromolecules for the first time serves as a cherry on top!
Biological cells are a potpourri of different organelles. Each of these organelles is made up of an array of macromolecules, like the nucleus of a cell largely contains DNA and proteins, while the cell membrane is made up of primarily lipids, carbohydrates, and proteins. None of these macromolecules exists in seclusion; rather their existence is in combination with each other. For studying one specific macromolecule, some separation technique is mandatory.
Gel electrophoresis is one of the many separation techniques. It is used to segregate the macromolecules based on various criteria like size, mass, charge, etc.
If everything is so vibrant, then what makes this technique so unnerving for our young learners?
Can interactive simulations or the utilization of immersive teaching technologies ease the process of explaining this topic to students who often stumble when encountering it for the first time?
For educators and teachers explaining this topic in their classes, this article can offer great help as it highlights the blocks encountered by students and lists practical solutions to resolve them. By the end, we’ll convince you why a virtual lab simulation will prove useful not only for your students but also for you as an educator to deliver concepts more effectively.
There are 3 reasons why students feel dreadful and confused about this topic. Acknowledging these blocks is the first step toward making the topic more approachable.
Being one of the foremost techniques taught to young learners in their early lab training, gel electrophoresis can sometimes come as a mind-boggling sum of variables; buffers, gel concentrations, loading dye, visualization dye, ladder, voltage, dimensions of buffer tank, runtime, etc. Difficulty in visualizing how all of these assemble together in real life can make the theoretical concept appear very complex. Students are also perplexed while imagining how the different macromolecules separate in real time on a gel.
Gel electrophoresis becomes a daunting topic for students when basics related to different macromolecules, their respective structures, overall charges, etc are confused. Not knowing the core concepts about macromolecules like ‘DNA is a negatively charged entity’ or ‘the charge on a protein molecule is determined by the unique amino acids’ further increases the confusion. This lack of knowledge is reflected when students are asked to independently set up the gel electrophoresis unit.
Gel electrophoresis has its own set of sensitivities. You can’t over-run the gel. You can’t overheat the buffer. You can’t overload the well. You can’t pierce the gel with the micropipette while loading. You can’t attach the 2 electrodes to the wrong terminal of the electrophoretic chamber. Students get overwhelmed with so much information. Not knowing the reasons behind each one of these warnings can make it a lot for them to remember and comprehend.
In order to address the blocks encountered while teaching the gel electrophoresis technique, educators can engage the under-listed 5 solutions in their classes. These can clarify many instrumental aspects of this commonplace lab technique. Not only can they make teaching easier for educators like you but will also make lessons clearer and easier to assimilate for your students.
Techniques are best taught when they are explained as ever-evolving processes. No technique or technology in the world should ever be claimed as “the perfect” and “the final” one. With more advancements in Science, an increase in the norm of interdisciplinary learning, and a quest to improvise, researchers keep developing better-off versions of all scientific practices. And, gel electrophoresis is no different...
Starting from Arne Tiselius’ development of the gel electrophoresis technique in 1931 for the molecular separation of serum proteins, the technique has transformed and evolved into different forms through the 20th to 21st century. Engaging students in these development stories can increase their curiosity. One such intriguing story is of Arne Tiselius.
Arne Tiselius joined Theodor Svedberg’s (inventor of ultracentrifuge and after whom Svedberg Unit is named) lab for his Ph.D. He was assigned the task to investigate ‘electricity’ as an analytical tool for protein studies. When Arne Tiselius observed that the passage of electric current through a damp paper beheld the ‘ability to induce the migration of electrically charged molecules/ions of the solution placed over the paper, he knew he could translate it into a separation technique. And he successfully manifested it in the form of the gel electrophoresis technique.
Stories like this can make your students more observant while performing hands-on lab experiments and understanding how things work. Such interest-driven science ensures that your students develop robust core concepts.
Figure: Arne Tiselius demonstrating electrophoresis.
Learning is always more enticing when practical engagement is substantial. Textual reading and tests make the students dull. This holds true for gel electrophoresis too. You can engage your students in setting up the different components of the electrophoretic unit themselves. Let them connect the electrodes to the electrophoretic buffer tank. Let them decide where the anode and cathode should respectively go. This type of engagement will invigorate interest and students will be driven to answer all their “WHYs”!
On the same note, sometimes leaving students in their own ventures with their own intelligence can help them go a long way. For example, verbally telling the ‘importance of tank buffer and its temperature’ might not be readily assimilable for students in your class. In order to make the notion easy to assimilate, you can once let your tank buffer overrun and overheat (by increasing the runtime and voltage beyond the threshold limit). After this little experiment, ask your students to check the pH of your buffer and the DNA on your gel.
When students notice that overrunning and overheating of the tank buffer diminishes the sole purpose of using the buffer in gel electrophoresis and deprives it of its buffering capacity, they could better understand the principles. This small experiment can effectively deliver the importance of small intricacies in lab handling. The fact that ‘buffer solution in electrophoresis plays a vital role in reducing the pH changes due to applied electric field which further ensures that the charge of DNA and RNA remains unchanged’ is effectively delivered by this experiment.
Figure: An interactive GIF showing an operational electrophoretic unit from the Gel Electrophoresis simulation from Labster’s virtual laboratory is available for High School, University / College and Professional classes.
Before letting your students dive into the magnanimous world of complex techniques, it would be advisable to first clarify their basic idea of the biological cells, structures, macromolecules, charges, etc. You can opt for interactive discussions where core concepts are built. Such a practice will ensure that running gel electrophoresis isn’t just a mechanical job but a well-thought and scientifically-planned experiment.
To exemplify, you can discuss a few of the under-listed things.
Is visualization of DNA or proteins possible by the naked eye?Or is their separation is possible by hand? Your students should be clear that visualization of DNA and proteins isn’t possible with the naked eye, let alone separation. To add more to it, it’s not even possible with the aid of a light microscope. This will make them understand the importance of extraction procedures followed by gel electrophoresis.
What happens if DNA and proteins are of the same size? Your students should be clear about why different types of gel electrophoresis exist. The two most commonly used ones are AGE and PAGE. While AGE is used to separate bigger macromolecules like DNA (50–20,000 bp) but with lower resolving power, PAGE is used for smaller ones like proteins (5-250,000 Dalton) or DNA (5-500 bp) and with higher resolving power.
The direction of movement of macromolecules under electric field? This particular discussion should emphasize the structure of the macromolecules. If your students don’t know that DNA is a negatively charged molecule, they will eternally be confused while setting up the electrophoretic apparatus. The direction of the movement of DNA is towards the positively charged anode in the tank buffer. If the gel is placed in the opposite orientation, the loaded sample will run out of the gel.
Importance of the uniform charge-to-mass ratio of DNA in agarose gel electrophoresis? Discussing how different sized DNA molecules separate based on their molecular mass is important. For this to happen, the instrumental role played by the “uniform charge-to-mass ratio of DNA” is undeniable. You might find it useful to inform your students how the overall charge on DNA is derived majorly by the negatively charged phosphate backbone. Adding to it, the proportionate increase in charge as the DNA size increases eventually makes the charge-to-mass ratio ‘uniform’ across DNA of different sizes. This ensures that DNA is separated solely on the basis of its size or mass and not charged in AGE.
Figure: This snippet from the Gel Electrophoresis simulation by Labster’s virtual laboratory shows how the negatively charged DNA moves towards the positively charged anode on an agarose gel. It is available for High School, University / College and Professional classes.
Many science topics become monotonous to learn as they often appear to be absolutely theoretical and of no practical utility. Hence, communicating the real-life examples where gel electrophoresis is applied can catch the attention of your learning audience. In such a way, the technique becomes more promising and worthy to learn.
Listing how gel electrophoresis finds abundant usage in Genetic Disease Testing (elucidation of anomalies at the nucleotide level), Detection of Adulteration (decoding identity of biological material), and Forensic Criminology Tests (unraveling the criminal’s identity from minutest evidence) can make your students stay connected to the topic. You can simply use our Gel Electrophoresis simulation where your students can actively learn about the utilization of this technique in DNA fingerprinting for finding the criminal’s identity. By comparing the band patterns of the suspects’ DNA and sample DNA collected from the crime scene, the thief can be caught. This small engagement can prove promising in your teaching course.
Since gel electrophoresis apparatus or facilities might not be always available, practical demonstrations might become a block. In order to overcome this constraint, you can conveniently switch to virtual laboratory simulations from Labster. Modern-day educators and teachers can make more insightful points as students are rendered with better visual options with our simulations. The 3D simulations will help your students better visualize the important components of the gel electrophoresis unit. They can learn about all the intricacies we discussed above like the direction of macromolecule movement, separation of macromolecules based on their molecular masses, etc.
Your students don’t have to struggle to imagine different steps of gel electrophoresis themselves as our interactive simulation along with gamification elements come to the rescue. By using this way of active and immersive teaching, our virtual learning platform takes an advent in the field of Science to make the upcoming scientists thorough with the “basics of their respective subjects”.
This snippet from the Gel Electrophoresis simulation by Labster’s virtual laboratory shows how 3D simulations can draw active engagement of your students in a virtual electrophoresis workbench. It is available for High School, University / College and Professional classes.
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