Gel Electrophoresis

Summary

The Amoeba Sisters explore the fascinating world of genetics and biotechnology in this educational video. They recount a childhood experience with guppies, highlighting the inheritance of traits and the role of DNA. The video delves into gel electrophoresis, a technique used to separate DNA molecules by size, and its applications in DNA fingerprinting and species classification. With a DNA ladder for size reference, viewers learn how to compare DNA samples to determine genetic relationships, emphasizing the importance of this biotechnological tool in both scientific research and forensic investigations.

Takeaways

• 🎥 The video script is from the Amoeba Sisters, who use social media platforms like Twitter and Facebook for updates.
• 👶 The speaker had a childhood interest in genetics but initially misunderstood the concept, thinking offspring were a simple blend of their parents.
• 🐟 The speaker's interest in genetics was deepened by observing guppies, which are live-bearing fish with notable genetic traits.
• 👶🐟 The speaker faced challenges in tracking the genetic inheritance of guppies due to multiple mother fish in the tank.
• 🧬 Genetics involves the study of DNA, the genetic material found in the body cells that carries various traits.
• 🔬 Biotechnology, a fusion of biology and technology, includes techniques like PCR, cloning, and genetic engineering.
• 🚀 Gel electrophoresis is a biotechnology method used to separate DNA molecules based on size due to their negative charge.
• 🧪 The gel used in electrophoresis is typically made of agarose, a carbohydrate derived from seaweed, which allows DNA to move through it.
• 🔍 Restriction enzymes are used in gel electrophoresis to cut DNA into specific pieces, aiding in the comparison of genetic material.
• 🧬🔑 DNA samples from different sources can be compared by observing the patterns of DNA bands after electrophoresis.
• 🔑 DNA ladders with known fragment sizes are used as a reference in electrophoresis to estimate the size of unknown DNA fragments.
• 🕵️‍♂️ Gel electrophoresis is important in determining genetic relatedness and is used in DNA fingerprinting for forensic purposes.

Q & A

What sparked the speaker's interest in genetics as a child?

The speaker's interest in genetics was sparked by observing their guppies and noticing the traits carried by their DNA.

What are the two especially cool traits of guppies mentioned in the script?

Guppies have live birth (no eggs) and produce a lot of babies.

What is biotechnology, and why is it relevant to the speaker's guppy observations?

Biotechnology is the merge of biology and technology, including topics like PCR, cloning, and genetic engineering. It is relevant because it could help determine genetic relationships in guppies.

What is gel electrophoresis and how does it work?

Gel electrophoresis is a biotechnology tool used to separate molecules based on size. It uses an electrical charge running through a gel, causing negatively charged DNA to move towards the positive side, with different sized fragments traveling at different speeds.

Why is the negative charge of DNA important in gel electrophoresis?

The negative charge of DNA allows it to move towards the positive side in the gel electrophoresis machine, facilitating the separation of DNA fragments based on size.

What role do restriction enzymes play in gel electrophoresis?

Restriction enzymes cut DNA into pieces at specific sites, which can then be separated by gel electrophoresis to analyze genetic relationships.

How can gel electrophoresis help in identifying genetic relationships between guppies?

By comparing the DNA bands from baby guppies and potential mother guppies, gel electrophoresis can show similarities and differences, helping to determine genetic relationships.

What is a DNA ladder, and how is it used in gel electrophoresis?

A DNA ladder is a sample with known fragment sizes used as a reference to estimate the sizes of DNA fragments in other samples.

Why is gel electrophoresis significant in scientific research?

Gel electrophoresis is used in determining species relatedness, DNA fingerprinting for crime scene investigations, and isolating genes of interest through techniques like southern blotting.

What is DNA fingerprinting, and how does gel electrophoresis contribute to it?

DNA fingerprinting identifies someone's DNA, which can be used to match crime scene samples with suspects. Gel electrophoresis separates DNA fragments to compare patterns between samples.

Outlines

00:00

🐟 Genetics and Guppies

The narrator shares a personal story of their childhood fascination with genetics, particularly through observing their pet guppies. They explain the misconception of genetic blending and how guppies, with their live birth and high offspring numbers, served as an educational tool. The narrator discusses the concept of DNA and genetic material, the importance of tracking inheritance, and the idea of using biotechnology to understand genetic relationships better. Gel electrophoresis is introduced as a biotechnology that could separate DNA molecules based on size, using an agarose gel and electrical charge to facilitate this process.

05:04

🔎 DNA Analysis with Gel Electrophoresis

This paragraph delves into the practical application of gel electrophoresis for DNA analysis. It explains how DNA's negative charge allows it to move through the agarose gel towards a positively charged end. The use of restriction enzymes to cut DNA into specific pieces is highlighted, enabling comparison between different DNA samples, such as those from a baby guppy and its potential mothers. The concept of DNA bands, created by the varying speeds of DNA fragments moving through the gel, is introduced. These bands can be compared to identify genetic relationships and can be visualized with staining and UV light. The paragraph also mentions the use of a DNA ladder for size reference and the broader applications of gel electrophoresis in species classification and DNA fingerprinting, including its role in forensic science.

Keywords

💡Genetics

Genetics is the study of heredity and the variation of inherited characteristics. It is central to understanding how traits are passed from parents to offspring. In the video, the concept of genetics is introduced through the personal experience of the narrator with guppies, highlighting the misconception of blending traits and the actual process of genetic inheritance.

💡Guppies

Guppies are small freshwater fish often kept in home aquariums. They are noted for their vibrant colors and ease of care. The video uses guppies as a practical example to demonstrate genetic inheritance, as the narrator observes the traits of baby guppies and how they inherit characteristics from their parents.

💡DNA

DNA, or deoxyribonucleic acid, is the molecule that carries the genetic instructions for the development, functioning, growth, and reproduction of all known living organisms. In the video, DNA is described as the genetic material found in the cells of guppies, which determines their traits and is passed down through generations.

💡Biotechnology

Biotechnology is the application of biological organisms, systems, or processes to create products and technologies. It merges biology with technology and includes various fields such as genetic engineering. The video discusses how biotechnology, specifically gel electrophoresis, could be used to analyze genetic relationships among guppies.

💡Gel Electrophoresis

Gel electrophoresis is a technique used to separate molecules based on size, commonly used with DNA. The video explains how this technique works, with DNA moving through a gel matrix towards a positive charge, allowing for the separation of DNA fragments of different lengths, which is crucial for genetic analysis.

💡Nucleotides

Nucleotides are the building blocks of DNA, consisting of a base, a sugar molecule, and a phosphate group. The video mentions nucleotides to illustrate the basic structure of DNA and how the negative charge from the phosphates contributes to the movement of DNA in gel electrophoresis.

💡Agarose

Agarose is a type of polysaccharide derived from seaweed, commonly used in gel electrophoresis as the gel matrix. The video describes agarose as the substance that allows DNA molecules to travel through it during the electrophoresis process, facilitating the separation of DNA fragments.

💡Restriction Enzymes

Restriction enzymes are proteins that cut DNA at specific recognition sites. They are essential in molecular biology and genetic engineering. The video explains that these enzymes are used to cut DNA into specific pieces, which can then be analyzed using gel electrophoresis to compare genetic relationships.

💡DNA Bands

DNA bands refer to the visible patterns created when DNA fragments are separated by size during gel electrophoresis. The video uses the concept of DNA bands to explain how different fragments can be compared to determine genetic similarities and differences among guppies.

💡DNA Ladder

A DNA ladder is a sample with known fragment sizes used as a reference in gel electrophoresis. The video mentions DNA ladders to illustrate how they provide a standard for estimating the size of unknown DNA fragments, helping in the analysis of genetic relationships.

💡DNA Fingerprinting

DNA fingerprinting is a technique used to identify an individual based on their unique DNA sequence. The video touches on how gel electrophoresis can be part of the process of DNA fingerprinting, which is useful in forensic science for matching DNA samples from crime scenes to suspects.

Highlights

The speaker's childhood interest in genetics and misconceptions about how traits are inherited.

Introduction to guppies as a model for understanding genetics due to their live birth and high offspring count.

The speaker's experience with tracking guppy inheritance and the idea of using biotechnology for assistance.

Definition and explanation of biotechnology, including its various applications such as PCR, cloning, and genetic engineering.

Introduction of gel electrophoresis as a biotechnology tool for separating DNA molecules based on size.

Description of DNA structure, focusing on the role of nucleotides and their negative charge in gel electrophoresis.

Explanation of the gel electrophoresis machine and its components, such as the agarose gel made from seaweed.

The process of DNA movement in gel electrophoresis due to its negative charge towards the positive side of the gel.

Use of restriction enzymes in cutting DNA into specific pieces for analysis in gel electrophoresis.

Comparison of DNA samples from baby and mother guppies to identify genetic relationships.

Visualization of DNA bands resulting from gel electrophoresis and their significance in genetic analysis.

The concept of a DNA ladder and its use as a reference for estimating fragment sizes in gel electrophoresis.

Practical applications of gel electrophoresis in determining relatedness among species and its role in DNA fingerprinting.

The potential use of gel electrophoresis in solving crime scene mysteries through DNA sample comparison.

Mention of southern blotting as a method to isolate genes of interest from gel electrophoresis results.

Emphasis on the importance of gel electrophoresis as a fundamental tool in biotechnology.

Encouragement to stay curious and explore the fascinating world of genetics and biotechnology.

Transcripts

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Updates on Twitter @AmoebaSisters and Facebook.

When I was a young kid I was really interested in genetics.

Well I didn't really understand genetics.

I kind of thought that when two organisms had a

baby, the baby was just this blend of the two.

Yeah that's a misconception.

But I really saw genetics in action with my guppies.

Guppies are very easy freshwater fish to keep in an aquarium, but they have

two things that I think are especially cool.

They have live birth which means there are no eggs like many

other fish, and second, they have a lot of babies.

They also eat their babies, but I don't think that's especially cool so as you

can see, it's not part of my cool fact list.

Anyway when my surviving baby Guppies grew up they would have all

kinds of cool traits.

These traits were carried by their DNA, their genetic

material, which is found in their body cells.

But sometimes I would forget which mother was the mother of the baby guppy, because

there were several mother fish in the tank, and I wanted to keep track of

inheritance in my guppy notebook.

So what would have been very cool to have at

that time?

Some biotechnology!

Biotechnology is the merge of biology and tech, and it's constantly changing!

It includes topics such as PCR, cloning, and

genetic engineering.

It's also an awesome field.

We're gonna talk about one of the bio technologies that could have, well

potentially, helped me determine the genetic relationships of my guppies... if

you know as a young kid I had access to it.

Although it's becoming way more common in classrooms now.

And that biotechnology is gel electrophoresis!

Gel electrophoresis can be used to separate molecules

based on how big they are (their size) and it's especially useful with

DNA.

Let's look at DNA real quick.

So here is a guppy cell.

Here's the nucleus in the guppy cell.

Here's the DNA in the nucleus of the guppy cell, and if you were

to zoom into the DNA, here is a nucleotide which is a building block of DNA.

See those phosphates in the nucleotides?

They're a bit negative.

Well they contribute a negative charge anyway to the DNA.

So if we look at this whole DNA here it gives that DNA a negative charge.

That's a big deal, because gel electrophoresis which again separates molecules

based on size relies on the fact that DNA molecules have a negative charge.

Okay, here's a gel electrophoresis machine.

The point of the machine is to be able to have an electrical charge

running through a gel so here's the gel typically made of agarose.

Agarose is a polysaccharide polymer, which if you remember

from our biomolecule video, polysaccharides are carbohydrates.

Yeah, usually agarose comes from seaweed.

The agarose gel itself lets the DNA molecules

travel within it.

One end of the gel has these holes called wells.

The wells are where the DNA is placed into The area of the gel where the wells are is

negatively charged, and the area of the gel here is positively charged.

So guess where the DNA will travel towards?

Well since it's negatively charged, it's going to travel to the positive side.

So typically when you're analyzing DNA in electrophoresis

you use these restriction enzymes to cut the DNA up into

tiny pieces.

Restriction enzymes have the ability to cut up DNA in very specific

areas, often related to the specific DNA bases, making restriction enzymes

very useful in biotechnology.

So if I had baby guppy DNA and adult mother guppy

DNA, and I want to compare them, then I would want to use the same types of

restriction enzymes in both DNA samples.

If I used the same type of restriction enzyme, it should be cutting the DNA at the

same identification points in the DNA samples.

However, unless the mother and baby guppy are clones (and they're

not), those pieces that result after the restriction enzyme is done with them may

be differently sized because the DNA of the baby and mother guppy had some

differences in the sequence of their DNA bases.

So the DNA samples both are cut into multiple pieces by the same type of restriction

enzyme and then those samples are loaded into the gel sample1 and

sample2.

If we turn on the machine and let the DNA run through the gel, the DNA

moves towards the positive side.

But some pieces of that cut up DNA will move faster

or slower than other pieces.

Longer DNA pieces tend to have a higher molecular weight and they take more time

to make it across the gel when you compare it to shorter DNA pieces which

move at a faster rate.

So what you end up with is that these DNA fragments spread

out with the longer pieces closer to the wells and the shorter pieces closer to

this opposite side of the gel.

These are called DNA bands, but to see them, you

usually need to stain the gel itself and view it under a UV light.

Now let's compare the DNA bands in this hypothetical

simplified guppy situation.

The bands aren't going to be identical, because these fish are not clones, but I

can compare how similar the bands are and compare that to other mother guppy

samples to look for relationships.

Let's say that we have three mother guppy samples to view and these are the only possible

mothers from the fish tank.

Which one appears to be the most related to the offspring in this case and has a

high likelihood of being the mother?

Well this one.

But we can't be 100% sure with this, It would be helpful for me to know the

father guppy sample too because this will give you more insight.

But if these are the only fish in the tank, it's

a very high likelihood with this case.

Also, you can use something called a DNA ladder!

You can buy them from various science material distributors, but a DNA

ladder is not what it sounds like.

It's basically a sample that has known fragment sizes so if you run it in the electrophoresis

machine, you already know the fragment lengths.

Let's say this DNA ladder only had three bands, which is not

usually the case.

Since it's a DNA ladder, the base pair lengths are known.

They are 500 base pairs, 1,000 base pairs, and 1,500

base pairs.

Think fora minute...where would they fit in?

It would look like this!

You can use this now as a reference to give estimates of

how large the other fragments are when they're run alongside it, and if you want

to be closer to the value, you can use a stand my love graph something to look up.

So why do we care about gel electrophoresis?

It's not likely I'll be actually using this with my guppies anyway,

right?

Well perhaps.

But gel electrophoresis is often a step used in determining

relatedness with different species, which help scientists better classify

organisms!

It's also used as part of DNA fingerprinting.

DNA fingerprinting is a way that one can identify someone's DNA which can be very helpful

if you're trying to solve a mystery involving a crime scene.

If you have a DNA sample from a crime scene, you

can go through the steps of gel electrophoresis to compare it to the

suspect DNA to see the likelihood of a match.

In fact, you can take the results from gel electrophoresis and isolate genes

of interest by something called southern blotting.

Definitely something to look up if you're curious.

Gel electrophoresis is one of many awesome tools

in biotechnology.

Well...that's it for the amoeba sisters, and we remind you

to stay curious.