LESSON 4 Using Bioinformatics to Analyze Protein Sequences

LESSON 442. Explain that genetic researchers use the tools of bioinformatics to help themanalyze DNA sequences and determine which potential protein sequenceis the correct one for their analysis. In particular, a popular tool used byresearchers is called ORF Finder—Open Reading Frame Finder—and is availablethrough the NCBI.43. Ask students to pull out Student Handout—Using Bioinformatics to StudyEvolutionary Relationships from Lesson Three because they will refer to theiranswers on this handout during the next exercise.44. Pass out Student Handout—Using Bioinformatics Tools to Analyze ProteinSequences Instructions and Student Handout—Using Bioinformatics Tools toAnalyze Protein Sequences Worksheet and ask the students to work throughthe handout at the computer either individually, in pairs, or in groups of up tofour students each.PART III: Putting it All Together45. After students have completed their handout and worked with theircollaborators (group members) to answer the questions, ask students to workwithin their groups to prepare a short summary of what they have learned.This could be a short written summary prepared in class or assigned ashomework. Alternatively, student representatives from each group could sharethe following information orally with the class. Some questions to ask include:• How many reading frames did their sequences have that were longer than100 amino acids?Answers will vary, but usually 2-5 frames will contain proteins this long.• Were students surprised to see how many potential reading frames ORFFinder found in their sequences?Students may be surprised to see that more than one frame contained suchlong protein sequences.• Do students predict conservative or non-conservative amino acid changeswill have a larger impact on protein function?ClosureUsually non-conservative changes have a more detrimental effect onprotein function.46. Summarize today’s lesson:• Students have learned how to translate DNA sequences into protein usingcodon tables and using the bioinformatics tool ORF Finder.• In addition, they have learned that they can perform multiple sequencealignments with DNA or protein sequences. Whether scientists use DNAor protein sequences for the alignment often depends on the researchquestion and hypothesis of the genetic researcher.• DNA sequences are easy to obtain and analyze without knowing anythingabout the protein the DNA may encode, and DNA is the material of[Note: Because of the redundancy ofthe genetic code, in which multiplecodons may encode the same aminoacid, the DNA and correspondingprotein sequence may appear to vary atdifferent rates.]Lesson 4 – Using Bioinformatics to Analyze Protein Sequences135©Northwest Association for Biomedical Research—Updated October 2012