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a man in a Forest Service uniform planting a tree

In this lesson, students will examine the American chestnut genome. It has already been digested and made part of a BAC which has been allowed to reproduce. The DNA must be broken down further and students will determine the order of the new fragments.

Genomics is the study of the DNA within an organism. Mapping genomes helps scientists study the location and function of specific genes. The process simulated in this lesson was used in the Human Genome Project and is currently being used by scientists all over the world to map genomes of various organisms. The lesson specifically looks at the use of BAC clones to make a map of DNA fragments which have been cut by the same restriction enzyme (a restriction map).

Learning outcomes

Students will be able to use a DNA fingerprint to determine size of DNA fragments. They will also be able to arrange DNA fragments to construct a genetic map.

Teacher planning

Time required

50 minutes

Materials needed

  • scissors for each student
  • one roll of clear tape per group of three students
  • copies of paragraph from a children’s book

Technology resources

None required.
Optional: You might want to have a computer with internet connectivity and a media player handy to look at the animations mentioned in supplemental section. These may be shown to the class as a whole with the aid of a data projector or Averkey connection to the television.

Student handouts

Genomics lab sheet
one per student
Open as PDF (85 KB, 4 pages; also available as Microsoft Word document)

KBP ruler and DNA fragments
one per group of three students
Open as PDF (59 KB, 1 page; also available as Microsoft Word document)

Pre-activities

  • Make copies of a paragraph from a children’s book. I used The Magic School Bus since it had small paragraphs. They were short and simple making piecing the paragraph back together achievable. You need enough copies of the paragraph for each group of three students. The copies all need to be cut at different places and each should have different segments removed. I removed 2 segments from each paragraph. Each group of three will be putting the paragraph in order and comparing it with other groups to fill in the gaps. Keep one copy of the paragraph for your key.
  • Students should already have knowledge of biotechnology terms such as PCR, restriction enzyme, gel electrophoresis, clone, and the Human Genome Project. This should not be used as an introduction to gel electrophoresis.

Activities

  1. Give each group of three students the paragraph segments. Tell students that there are pieces missing to their story, but it is their job to put the segments in order to make the most sense. Give students about five minutes to complete this task.
  2. Instruct groups to compare their paragraphs with another group’s paragraph and come to an agreement about the order of the sentences. Different groups will have different missing sections, so they will be able to fill in some of the gaps by comparing. Allow two minutes for this comparison
  3. Finally, instruct students to compare with one more group to fill in any information that is still missing and to finalize the sequence. By the time three groups have shared their findings, they should have a complete and correct paragraphs. Allow one minute.
  4. Ask one group to read its paragraph and see if others in the class agree with the order. Allow another group to correct the paragraph if necessary and instruct all students to fix their paragraphs to match.
  5. Explain to students that when scientists are trying to make a DNA map and put DNA fragments in order, they must use must the same process as the one they just simulated. DNA fragments are cut up randomly and then sorted. Several copies of the fragments are sorted at once. Many copies have overlapping segments, while some segments are missing. The overlapping segments are used to make a map just like the overlapping segments each group possessed was used to make a paragraph.
  6. Give each student a copy of the lab sheet. Have different students read each paragraph, up to the Activity section, aloud. Be sure to pause and answer questions about each section if necessary.
  7. Explain to students that they will be simulating making a DNA map using fragments and it will be similar to the way they constructed their paragraphs. Have students look at the BAC clone digest gel on the last page of their handouts. Instruct students to complete Procedure #1.
  8. Hand each group copies of the KBP ruler and paper DNA fragments sheet. Students should now complete the remaining procedures. Be sure to tell students not to cut apart the segments on each of the DNA fragments. They should have six strips and the ruler when they are done cutting. Help students align their fragments if necessary and make sure they are only using fragments 1 and 5 near the end of the procedure to make their map.
  9. Instruct students to attach their completed DNA maps to the bottom of the analysis questions and to answer these questions. Students will answer the following questions:
    • What does BAC stand for?
    • How do scientists get the DNA from another organism into the bacteria?
    • What is a clone?
    • Why do scientists use bacteria to make clones?
    • What is used to separate DNA fragments from each other (based on size)?
    • What does it mean if two or more lanes on a gel are the same size?
    • How can this information be used to make a map?
    • Why was it not necessary to include all of the fragments?
    • What happens to the DNA after a map is made of the overlapping DNA fragments?

Assessment

Check for correctness of analysis questions. A correct DNA map will have lengths of segments in the following order: 4.5, 8, 16, 3, 9, 18.5. Make sure that students understand that this process is used to determine the order of the DNA in a genome, but the actual order of the letters (A, T, G, C) comes from the sequencing machine.

Supplemental information

It may be helpful to have the KBP rulers cut out and laminated in advance, since they may be reused. It will save a small amount of time.

The yourgenome.org has excellent animations of DNA sequencing and information about the Human Genome Project. I highly recommend showing the animations for DNA libraries and subcloning prior to completing the activity.

Critical vocabulary

restriction enzyme
any of the enzymes that cut nucleic acid at specific sites and produce fragments of various lengths
PCR
a technique to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating millions or more copies of a particular DNA sequence.
gel electrophoresis
a technique used for the separation of DNA using an electric current applied to a gel matrix and is generally only used after amplification of DNA via PCR.
Human Genome Project
an international study of the entire human genetic material
clone
genetically identical cells produced asexually

Comments

The method described in the activity is being used to integrate physical maps, genetic maps, and sequencing to determine the genome for American and Chinese chestnut trees. The idea is to find the genes responsible for resistance to the Chestnut blight from the Chinese trees in order to insert them into American trees. This production of a transgenic American chestnut tree will be explored in the final chestnut biotechnology lesson. In real world applications, it will speed up the introduction of a blight-resistant American chestnut tree to its natural habitat and hopefully restore the tree to its previous place of importance.

  • Common Core State Standards
    • English Language Arts (2010)
      • Science & Technical Subjects

        • Grades 11-12
          • 11-12.LS.3 Follow precisely a complex multistep procedure when carrying out experiments, taking measurements, or performing technical tasks; analyze the specific results based on explanations in the text.
        • Grades 9-10
          • 9-10.LS.3 Follow precisely a complex multistep procedure when carrying out experiments, taking measurements, or performing technical tasks, attending to special cases or exceptions defined in the text.

  • North Carolina Essential Standards
    • Science (2010)
      • Biology

        • Bio.3.3 Understand the application of DNA technology. Bio.3.3.1 Interpret how DNA is used for comparison and identification of organisms. Bio.3.3.2 Summarize how transgenic organisms are engineered to benefit society. Bio.3.3.3 Evaluate some of the ethical...

North Carolina curriculum alignment

Science (2005)

Grade 9–12 — Biology

  • Goal 1: The learner will develop abilities necessary to do and understand scientific inquiry.
    • Objective 1.01: Identify biological questions and problems that can be answered through scientific investigations.
    • Objective 1.02: Design and conduct scientific investigations to answer biological questions.
      • Create testable hypotheses
      • Identify variables.
      • Use a control or comparison group when appropriate.
      • Select and use appropriate measurement tools.
      • Collect and record data.
      • Organize data into charts and graphs.
      • Analyze and interpret data.
      • Communicate findings.
    • Objective 1.03: Formulate and revise scientific explanations and models of biological phenomena using logic and evidence to:
      • Explain observations.
      • Make inferences and predictions.
      • Explain the relationship between evidence and explanation.
  • Goal 3: The learner will develop an understanding of the continuity of life and the changes of organisms over time.
    • Objective 3.04: Assess the impact of advances in genomics on individuals and society.
      • Human genome project.
      • Applications of biotechnology.