Unlocking DNA: A Gel Electrophoresis Adventure

Biology Grades High School 10:59 Video
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Lesson Description

Explore the fascinating world of gel electrophoresis, a powerful technique used to separate and analyze DNA fragments. Learn how this method helps scientists understand DNA structure and function.

Video Resource

Gel electrophoresis | Biomolecules | MCAT | Khan Academy

Khan Academy

Duration: 10:59
Watch on YouTube

Key Concepts

  • DNA Fragments Separation
  • Electrophoresis Principle
  • Agarose Gel Properties
  • DNA Ladder Standardization
  • Ethidium Bromide Fluorescence

Learning Objectives

  • Explain the principles of gel electrophoresis and its applications in separating DNA fragments based on size.
  • Describe the function of each component of the gel electrophoresis setup, including the agarose gel, buffer solution, electrodes, and DNA ladder.
  • Interpret gel electrophoresis results to determine the relative sizes of DNA fragments and compare them to a DNA ladder for estimation.
  • Explain the role of ethidium bromide in visualizing DNA fragments under UV light.

Educator Instructions

  • Introduction (5 mins)
    Begin by engaging students with the question of how scientists can determine the size of incredibly small DNA fragments. Introduce the concept of gel electrophoresis as a technique used to separate DNA, RNA, or protein molecules based on size and charge.
  • Video Viewing (10 mins)
    Play the Khan Academy video 'Gel electrophoresis | Biomolecules | MCAT | Khan Academy'. Instruct students to take notes on the key concepts, setup, and principles explained in the video.
  • Components of Gel Electrophoresis (10 mins)
    Discuss the essential components of a gel electrophoresis system: * Agarose gel: A polysaccharide matrix acting as a sieve for separating molecules. * Buffer solution: Maintains pH and conducts electrical current. * Electrodes (positive and negative): Create an electric field to drive DNA migration. * Power source: Supplies the electrical current. * DNA ladder: A standard solution of DNA fragments with known sizes.
  • Mechanism of Separation (10 mins)
    Explain the following steps: * DNA samples are loaded into wells in the agarose gel. * An electric field is applied, causing negatively charged DNA fragments to move towards the positive electrode. * Smaller DNA fragments migrate faster through the gel matrix than larger fragments. * After a set time, the DNA fragments are visualized using a fluorescent dye (e.g., ethidium bromide) under UV light.
  • Interpreting Results (10 mins)
    Guide students on how to interpret gel electrophoresis results: * The distance a DNA fragment migrates is inversely proportional to its size. * Compare the migration distance of unknown DNA fragments to a DNA ladder with known sizes. * Estimate the size of unknown fragments by matching them to bands in the DNA ladder.
  • Applications of Gel Electrophoresis (5 mins)
    Discuss real-world applications: * DNA fingerprinting for forensic science and paternity testing. * Analyzing gene expression by separating RNA molecules. * Checking the size and purity of DNA fragments after PCR amplification. * Diagnosing genetic diseases by identifying abnormal DNA fragment patterns.

Interactive Exercises

  • Gel Electrophoresis Simulation
    Use an online gel electrophoresis simulation (e.g., from LabXchange, Genetic Science Learning Center) to allow students to virtually run a gel and analyze the results. This will provide hands-on experience without the need for laboratory equipment.
  • Fragment Analysis
    Provide students with a mock gel electrophoresis image and a DNA ladder. Ask them to estimate the size of unknown DNA fragments by comparing their migration distances to the ladder. Have students discuss their findings and reasoning.

Discussion Questions

  • Why is it important to use a buffer solution in gel electrophoresis?
  • How does the concentration of agarose in the gel affect the separation of DNA fragments?
  • What would happen if the electrodes were connected in reverse (positive electrode at the well side)?
  • How does gel electrophoresis contribute to our understanding of genetics and molecular biology?

Skills Developed

  • Data Interpretation
  • Analytical Thinking
  • Problem Solving
  • Critical Thinking
  • Scientific Reasoning

Multiple Choice Questions

Question 1:

What is the purpose of gel electrophoresis?

Correct Answer: To separate DNA fragments based on size

Question 2:

What material is commonly used to make the gel in gel electrophoresis?

Correct Answer: Agarose

Question 3:

What property of DNA allows it to migrate through the gel towards the positive electrode?

Correct Answer: Negative charge

Question 4:

Which DNA fragments migrate faster through the gel?

Correct Answer: Smaller fragments

Question 5:

What is the purpose of the DNA ladder in gel electrophoresis?

Correct Answer: To provide a standard for estimating DNA fragment sizes

Question 6:

What is ethidium bromide used for in gel electrophoresis?

Correct Answer: To stain and visualize the DNA fragments

Question 7:

Under what type of light are DNA fragments visualized when ethidium bromide is used?

Correct Answer: Ultraviolet (UV) light

Question 8:

In what field is gel electrophoresis commonly used?

Correct Answer: Forensic science

Question 9:

What is the purpose of the buffer solution in gel electrophoresis?

Correct Answer: To maintain pH and conduct electrical current

Question 10:

What macromolecule CANNOT be analyzed using Gel Electrophoresis?

Correct Answer: Triglycerides

Fill in the Blank Questions

Question 1:

Gel electrophoresis separates DNA fragments based on their __________.

Correct Answer: size

Question 2:

The gel used in gel electrophoresis is typically made of __________.

Correct Answer: agarose

Question 3:

DNA migrates toward the __________ electrode because it has a negative charge.

Correct Answer: positive

Question 4:

The __________ is used as a standard to estimate the sizes of DNA fragments.

Correct Answer: DNA ladder

Question 5:

__________ bromide is a fluorescent dye used to visualize DNA fragments in gel electrophoresis.

Correct Answer: ethidium

Question 6:

The rate of migration of DNA fragments through the gel is __________ proportional to their size.

Correct Answer: inversely

Question 7:

The wells in the gel are where the __________ samples are loaded.

Correct Answer: DNA

Question 8:

The __________ maintains the pH and conducts the electrical current in gel electrophoresis.

Correct Answer: buffer

Question 9:

Ethidium bromide works by ___________ itself between the base pairs of the DNA double helix

Correct Answer: intercalating

Question 10:

Forensic science uses ____________ to match suspects to crime scenes.

Correct Answer: DNA fingerprinting

Educational Standards

B.LS1.1:Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins, which carry out the essential functions of life through systems of specialized cells. B.LS3.1:Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring. B.LS4.1:Communicate scientific information that common ancestry and biological evolution are supported by multiple lines of empirical evidence.

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