How can the Biology Workbench be used in connection with DNA sequencing?
Kathleen Gabric
(kgabric@hinsdale86.org)
(ready to use)
Coauthors
ASK
Partner Projects
| Biology Student Workbench, GK-12 Teaching Fellowships |
Subject Areas
Grade Levels
| 9, 10, 11, 12, Undergraduate |
Unit Keywords
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Biology Workbench, DNA, sequencing, Human Genome Project, GK12 |
Rationale of the Unit
| This unit is designed to introduce students to the Human Genome Project, DNA sequencing, and the Biology Workbench. |
Background and Resources
BACKGROUND -- The overview article on the Human Genome is at U.S. Department of Energy website and is funded by The Human Genome Program. http://www.ornl.gov/hgmis/project/about.html
For a better understanding of DNA sequencing the students are directed "Cracking the Code" at the Nova website. http://www.pbs.org/wgbh/nova/genome/sequencer.html
WEB SITES -- sites for exploration and interaction.
To attempt reading a print out from an electropherogram and deriving the DNA sequence go to http://cstaff.hinsdale86.org/~kgabric/DNAsequences.htm
These graphs were obtained from researcher at Argonne National Laboratories.
To explore and determine what the sequence actually codes for students must use the student interface to the Biology workbench.
http://peptide.ncsa.uiuc.edu/
RESOURCES AND SUPPLEMENT MATERIALS
Computers are all that are required. Students will have to register at the Biology Workbench, but it is free.
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Activities and Open-ended problems
IN-CLASS ACTIVITIES -- Since this was the first experience using Biology Workbench for our students, we did part 3 of the activity in class. During this lab exercise, students had to determine the DNA sequence from an electropherogram. This information is then put into the Workbench and a search is done for similar sequences in rodents (BLASTN) Students then perform an alignment on the sequence(s) they have chosen to determine if it matches the unknown DNA.
LAB ACTIVITIES -- To see the activities that students are requested to do, go to
http://cstaff.hinsdale86.org/~kgabric/sequencing%20DNA.htm
Students have 3 tasks asked of them:
1) Gain a better understanding of the Human Genome Project
2) Learn how DNA is sequenced by scientists through background reading
3) Read a DNA sequence and determine the protein that it most likely codes for.
ACTIVITIES OUTSIDE OF CLASS / INDEPENDENT WORK
Parts 1 and 2 of the activity may either be done in class or out of class. Essentially, they are just background information searches. My preference was to have it done at home, so that it left more in class time for discussion of what they had learned.
OPEN-ENDED PROBLEMS -- creative extensions
Ask students this. If they sequenced the complimentary strand of the DNA, would it code for the same protein. If not, what protein if any does Biology Workbench predict.
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Dialogues, Discussions, and Presentations
FACE-TO-FACE DIALOGUES
There was a lot of face to face dialogues as students became familiar with the Biology Workbench. Students helped each other a lot rather than wait for me to get around to them
IN-CLASS DISCUSSIONS
In class discussions proved important as students attempted to grasp what the supercomputer (Biology Workbench) actually does. Seeing this as a usable tool for scientists is different than most 14 year olds visualize scientists working.
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Assessment, Related Questions, and Story of the Unit
ASSESSMENT
RELATED QUESTIONS
STORY OF THE UNIT -- How did it go?
We used Biology Workbench last year. This was a much simpler way to introduce students to it. Students got the hang of it much faster and were much less intimidated by it. Most students were able to complete the activity on their own with very little assistance. Because they picked it so easily, I believe they will be more receptive to the Biology Workbench than in the past. Also, since sequencing is generally just all paperwork, this added an activity component to it and made it more inquiry oriented.
RESPONSES FROM OTHERS (teachers)
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Uploaded Files:
sequencingDNA.htm
DNAsequences.htm
dnaSequencingExplained.htm
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