Searching Genbank
Summary
In this activity students search the Genbank database for a specific entry on the hemoglobin genes. After finding the entry students learn about the kinds of information available in a Genbank record and some uses for that information by answering a series of guided questions at the Darwin2000 site. The questions are designed to illustrate key aspects of the record and to have students actively use some of the information to learn or review basic molecular biology and molecular evolution. Students turn in answers to the questions.
This assignment has students only go through part of the full assignment at Darwin2000 and includes additional background information not available there to make the assignment more appropriate for introductory biology students.
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Learning Goals
- How to search the Genbank Database
- Appreciation for the amount of genetic information available online
- How to determine the type of sequence (cDNA, genomic, etc.) and what the different types can be used for
- How to locate key molecular features of DNA and RNA sequences, such as promoters, cis-acting regulatory sequences, start codons, stop codons, splice junctions, mutations, etc., in a Genbank record
- The meaning of the terms describing key molecular features of DNA and RNA sequences, such as promoters, cis-acting regulatory sequences, start codons, stop codons, splice junctions, mutations, etc.
- How to use the links in a Genbank record to jump to related information in other databases, such as the protein databases
- Learn about types of mutations and how they might, or might not, effect gene function
- Application of evolutionary principles to DNA sequences
- How to read a protein entry in the protein databases and extract information about amino acid sequences
Context for Use
This assignment is a limited version of the full assignment available at the Darwin2000 site and is designed for introductory biology students who have had some instruction in the basic molecular biology of a eukaryotic gene. The starting web page, Searching Genbank gives background information on hemoglobin, sickle cell anemia and the basics of gene structure and mutation to help students understand the Genbank record. Additional information could be provided to make the assignment appropriate for other audiences such as non-majors. It could also be used as a review assignment for more advanced students.
Students need access to a networked computer to do this assignment and could either do this in a computer lab or on their own. It should take approximately an hour if students do not need to spend a lot of time going over the background material, two hours if they need to review concepts like introns, start codons, etc.
The assignment could be made easier by eliminating some of the harder questions. For instance, question five has the students look for the TATA box without telling them that is what they are looking for - it simply asks them to look for a regulatory sequence. Many students will need more of a hint than is available at the site to remember what the TATA sequence looks like.
The assignment can also be extended, in particular, the Darwin2000 site has several active learning questions at the end where students are asked to come up with additional searches and analysis that would be appropriate for more advanced students.
Description and Teaching Materials
Background material on hemoglobin genes and the basic molecular biology of genes with suggested questions for introductory students is available at Searching Genbank. The Genbank questions and tutorial are at Darwin2000 Finding Sequences in Genbank site, there are links to this site in the "Searching Genbank" page. Included is a Word document with answers to the assigned questions.
Answer key for the assigned questions (Microsoft Word 51kB Jul25 06)Teaching Notes and Tips
This is a fairly simple assignment so most students with a reasonable grasp of basic molecular biology and evolution can follow the guide and use the background material to answer all of the questions. Some of the questions are more challenging, but students who are willing to use the background material as a resource have little difficulty. Part of the goal of this assignment is to have students learn the material by using the background as a resource to develop their answers to the questions.
While fairly easy, the assignment does take a little time and some students may get bored with it unless they see it as part of a larger objective. I usually follow this assignment with the Wikipedia Genetic disease assignment, which has them use some of the skills they learn in this assignment.
Assessment
References and Resources
MERLOT description of the "Finding Sequence in Genbank" resource that is used in this activity.
Other Resources:
- Searching Genbank - Background material and the list of questions appropriate for introductory students
- Darwin2000 Finding Sequences in Genbank - the Genbank tutorial with questions
- Genbank - The Genbank database