MCAT Lab Techniques Part 1: Dinosaurs and Gel Electrophoresis

MCAT

There are a lot of lab techniques tested on the MCAT. Many will be techniques you haven’t seen before in real life. They might have meaningless names like “Western blot” or “SDS-PAGE.” And the MCAT expects you to know not just what they are used for, but also how they work. Sucks, right?

But not to fear – it is possible to learn in an easy, painless way! Here, we will explore the basic principles behind gel electrophoresis.

Basic Rules of the Universe

Understanding gel electrophoresis requires knowing two simple facts about the universe. Like all things in this universe, gel electrophoresis abides by the following rules:

Rule #1: Big dinosaurs can’t fit through small holes

If you’re being chased by a T-rex, where do you run? Toward the open, grassy field? Nope, not unless you can outrun the T-rex’s estimated top speed of 17 mph. How about that thick, dense forest full of giant, sturdy trees instead? That's a much better idea – you, being smaller than a T-rex, can easily fit through gaps in the trees and run away at your top speed. Meanwhile, that hungry T-rex is slowed down by all the trees blocking its way. The bigger the T-rex, the bigger the gaps it needs to find in order for it to fit through, and finding gaps takes time – precious, valuable time you can spend putting distance between yourself and the T-rex. 

Rule #2: Opposites attract

Specifically, positive and negative charges attract. Easy, right? 

Gel Electrophoresis: The Gel is the Forest

Imagine that you have two samples of DNA, and you know that they are of different sizes. Unfortunately, you forgot to label the tubes and you can’t tell which is which. How can you figure it out before your PI yells at you? Run a gel!

A gel is basically a block of unflavored Jello. At the microscopic level, it looks like this:

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It’s a meshwork with holes of varying sizes. DNA molecules move through this meshwork from one end of the gel to the other and, in doing so, they are slowed down proportionately to their size. 

In other words, you and the T-rex are two different DNA molecules. The gel is the forest. Since you’re a tiny molecule, you move through the gel forest pretty quickly and can travel a great distance. The T-rex molecule, meanwhile, is having trouble fitting its giant head through all the gaps, so it’s barely moved in the same amount of time.

Screen Shot 2021-05-13 at 10.11.42 AM

So remember Rule #1: big things can’t fit through small holes.

But how does DNA move through the gel? That brings us to Rule #2: opposites attract.

Recall that DNA is negatively charged due to the phosphodiester bonds that join each nucleotide. The phosphate group joining each nucleotide carries a negative charge, thus giving the entire DNA strand a net negative charge.

Screen Shot 2021-05-13 at 10.11.49 AM

When you make a gel, you stick your DNA samples at one end and then put the entire block inside an electric current. This means that one end of your gel will be next to a negative charge (this is the end your DNA goes), and the other end of your gel will be next to a positive charge. As you apply the current through the gel, the negatively charged DNA molecules will begin to move through the gel towards the positively charged other end.

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If you stand at your gel and watch, you’ll see the race between your two DNA samples. Remember, the gel is the forest. The larger DNA sample, like the T-rex, gets slowed down in the dense gel and moves slowly. The smaller DNA sample moves quickly. If you turn off the current after 20 minutes or so, you’ll see that the smaller sample has moved further along the gel. DNA size is measured in kilobases (kb), so here’s what that might look like:

Screen Shot 2021-05-13 at 10.12.05 AM

In this case, the DNA fragment in lane A is bigger because it has moved more slowly (i.e. traveled less distance) through the gel. The ladder is a mixed sample of many DNA fragments of known size which acts as a ruler to let you estimate the size of your samples. So here, the fragment in lane A is about 20 kilobases (kb) long, while the fragment in lane B is only 4 kb.

In summary, gel electrophoresis is a way to separate DNA fragments based on size. 

Take Home Points

What is the purpose of gel electrophoresis?

Gel electrophoresis is used to separate DNA (or RNA) based on size. 

How does it work?

Gel works by taking negatively charged DNA fragments and pushing them through a dense gel toward a positive pole. Remember, opposites attract.

How do you interpret the results? 

Bigger molecules move slower, so they end up closer to where they started. Smaller molecules move further along the gel. Remember, the gel is the forest and big dinosaurs can’t fit through small holes.

 

The road to medical school is long, and the MCAT is one of its most formidable challenges. You will be relieved to know that what you learned in your premedical courses is actually on the test. But studying for the MCAT is more about taking that knowledge stored way back there in the nooks and crannies of your mind, bringing it to the fore, and then learning to twist and stretch it in the ways the MCAT tests. In reality, studying for the MCAT is no more (or less) difficult than spending late hours on a physics problem set or an entire weekend on an organic chemistry lab report. Just like these other tasks, the MCAT requires endurance and follow-through, but it becomes significantly more manageable when you work with a Cambridge Coaching MCAT tutor to apply a structured, systematic, and strategic approach to your studying.

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Learn more about MCAT tutoring

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