LESSON 4 Using Bioinformatics to Analyze Protein Sequences

LESSON 4ResourcesThe Howard Hughes Medical Institute (HHMI) Biointeractive site offers a variety of freely-available videos and animations.The following animations may be of particular interest for this lesson:• DNA Transcription (basic detail, 1:54 minutes):http://www.hhmi.org/biointeractive/dna/DNAi_transcription_vo1.html• DNA Transcription (advanced detail, 1:55 minutes):http://www.hhmi.org/biointeractive/dna/DNAi_transcription_vo2.html• Translation (basic detail, 1:48 minutes):http://www.hhmi.org/biointeractive/dna/DNAi_translation_vo1.html• Translation (advanced detail, 1:48 minutes):http://www.hhmi.org/biointeractive/dna/DNAi_translation_vo2.html• Coding Sequences in DNA (1:04 minutes):http://www.hhmi.org/biointeractive/dna/DNAi_coding_sequences.htmlFor more information about DNA sense and anti-sense strands, seeWikipedia: http://en.wikipedia.org/wiki/Sense_(molecular_biology).Dr. Crawford and his collaborators recently published a study in Nature detailingthe sequencing and analysis of DNA isolated from a 4,000-year-old sample.Sequencing of the Y-chromosome confirmed that the remains were male, likelyone of the first settlers of the New World Arctic (northern Alaska, Canada,and Greenland). Also among their findings: the man from whom the DNA wasisolated had type A+ blood; likely had brown eyes, dark hair, and darker skin; hadan increased risk of baldness; and had a dry earwax type more typical of Asiansand Native Americans than the wet ear wax type of other ethnic groups. Studentsmay recall discussions of genetic testing and ear wax type in Lesson One of theBio-ITEST Introductory unit, Using Bioinformatics: Genetic Testing, when theyexplored the Direct-to-Consumer (DTC) genetic testing company 23 and Me.23 and Me, as well as other DTC companies, also offer tests for increased risk ofbaldness. You can read more from the article (Rasmussen et al., 2010) in the free,full-text article available from Nature at: http://www.nature.com/nature/journal/v463/n7282/full/nature08835.html.CreditCrawford, Michael. Personal Interview. 19 March 2010.Direct-to-Consumer (DTC) genetictesting: Sometimes referred to asat-home genetic testing, direct-toconsumergenetic tests are genetictests marketed directly to the consumerwithout necessarily involving a doctor orinsurance company.Rasmussen et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2010; 463: 757–762.The circular format codon table was adapted from: Ellington, A., & Cherry, J.M. (1997). Characteristics of Amino Acids.In F.M. Ausubel, D. Moore, D.D. Moore, R. Brent and J.G. Seidman (Eds.), Current Protocols in Molecular Biology(pp. A.1C.1–A.1C.12). Hoboken, NJ: John Wiley & Sons, Inc.Lesson 4 – Using Bioinformatics to Analyze Protein Sequences141©Northwest Association for Biomedical Research—Updated October 2012