MERLOT Biology Portal Visit Main MERLOT
 

Searching Genbank

This page authored by Jeff Bell, California State University, Chico, based on an original activity by Dr. Rick Hershberger, Bioactivesite.
Author Profile

This activity has undergone a peer review process.

This activity has undergone a peer review process by which submitted activities are compared to a set of criteria. Activities meeting or revised to meet these criteria have been added to the collection. To learn more about the review criteria, see [http://taste.merlot.org/evaluationcriteria.html]. More information about the peer review process can be found at [http://taste.merlot.org/peerreviewprocess.html].


This page first made public: Mar 17, 2010

This material is replicated on a number of sites as part of the SERC Pedagogic Service Project

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.

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

As the questions vary in difficulty I grade this assignment holistically; full credit if all questions are answered correctly minor deductions for a small number of errors, etc. You could decide on point values for each of the questions and then total them for a simpler grading scheme.

References and Resources

MERLOT description of the "Finding Sequence in Genbank" resource that is used in this activity.

Other Resources:


Main MERLOT Home | MERLOT Communities | About MERLOT | Contact MERLOT
Copyright 1997-2006 MERLOT. All rights reserved.