Lesson 9: What is Genomics

Introduction:

Genomics is the study of all the DNA within an organism. Mapping genomes helps scientists study 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 scientist 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 the DNA fragments to construct a genetic map.

Curriculum alignment:

Biology Goal 3.04 – Human genome project and applications of biotechnology

Classroom time required:

50 minutes

Materials needed:

Cut up copies of paragraph from a children’s book (I used The Magic School Bus since it had small paragraphs sectioned off labeled “From the Desk of Ms. Frizzle.” They were short and simple making piecing the paragraph back together achievable.) You need enough copies of the paragraph for each group of 3 students. The copies all need to be cut at different places in the reading and each needs to 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 to other groups to fill in the gaps. Keep 1 copy of the paragraph together and in order for your key.

Copies of the “What is genomics” information and analysis sheet, 1 per student and copies of the kbp ruler and paper DNA fragments sheet, 1 per group of 3, scissors for each student, 1 roll of clear tape per group of 3

Technology resources:

None required. Optional: Internet connection, computer(s) with media viewer to see animation. Animations mentioned in supplemental section may be shown to the class as a whole with the aid of a data projector or Averkey connection to the television.

Pre-activities:

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.

Be sure that copies are prepared as instructed in the materials section.

Activities:

1. Give each group of 3 students a children’s story paragraph that has been cut into segments where segments have been removed. 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 5 minutes to complete this task.
2. Instruct groups to compare their paragraph 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 2 minutes for this comparison
3. Finally, instruct students to compare with 1 more group to make their paragraph complete and in order. (By the time 3 groups have shared their findings, they should have a complete and correct paragraph.) Allow 1 minute.
4. Ask for 1 group to read their paragraph and see if others in the class agree with the order. Allow another group to help correct the paragraph if necessary and instruct all students to fix their paragraph to match.
5. Explain to students that when scientist 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 “What is genomics” information and analysis sheet. Have different students read each paragraph, up to the “Activity” section, aloud. Be sure to pause and answer question 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 they way which they constructed their paragraphs. Have students look at the BAC clone digest gel on the last page of their handout. 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 6 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 map to the bottom of the analysis questions and to answer these questions.

Assessment:

Check for correctness of analysis questions; this may be done verbally or for an individual grade from the paper. 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.

They following websites have excellent animations of the process 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.
http://www.yourgenome.org/downloads/animations.shtml
http://www.genome.gov/10000002

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

Websites and Resources:

• http://www.poplar.ca/pdf/ellis.pdf: Information about history of genome mapping.
• http://www.nslc.wustl.edu/elgin/genomics/gsc/GoldenPath.pdf: Similar activity, but very cumbersome. This is the basis for my activity, but mine have been simplified (a lot).

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 restore the tree to previous place of importance.