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CREDITSCreditsCredits/Funding SourceThe Bio-ITEST program is made possible by an Innovative Technology Experiencesfor Students and Teachers grant award from the National Science Foundation (NSF),DRL-0833779.Its contents are solely the responsibility of the authors and do not necessarily representthe official views of the NSF or NWABR’s consultants/advisory board members.Authors and ContributorsJeanne Ting Chowning, MSBio-ITEST Principal InvestigatorDirector of Education, Northwest Association for Biomedical ResearchDina Kovarik, MS, PhDProgram Manager, BioinformaticsNorthwest Association for Biomedical ResearchSandra Porter, PhDBio-ITEST Co-Principal InvestigatorPresident, Digital World BiologyJodie Spitze, NBCTScience Teacher, Kent-Meridian High SchoolCarol L. Farris, PhDSenior Fellow, Biomedical Health InformaticsUniversity of WashingtonKaren Peterson, MEdBio-ITEST Co-Principal InvestigatorCEO, EdLab GroupTamara Caraballo, MEdScience Teacher, Glacier Peak High SchoolContributions, Editing, and Curriculum Design Services:Kristen Clapper Bergsman, MEdLaughing Crow Curriculum LLCProject Assistance:Joanna PrasertongLaughing Crow Curriculum LLCOverview – Using Bioinformatics: Genetic ResearchJoan Griswold, MITEducation Outreach CoordinatorNorthwest Association for Biomedical Research3 Northwest Association for Biomedical Research—Updated October 2012

Graphic Design:Clayton DeFrate DesignCopyediting:Polly Freeman, MACurriculum Development TeamRichard Androsko, MSScience Teacher, Newport High School, Bellevue, WARachelle Carnes, MITScience Teacher, Century High School, Hillsboro, ORMary Glodowski, NBCT, PAEMSTScience Teacher, Meadowdale High School, Lynnwood, WAShannon Hemrich, MAScience Teacher, Ridgefield High School, Ridgefield, WABryan Robles, MSScience Teacher, Issaquah High School, Issaquah, WAMax Rose, MITScience Teacher, Redmond High School, Redmond, WAField Test TeachersTamara Caraballo, MEdScience Teacher, Glacier Peak High School, Snohomish, WARandy Dix, MSScience Teacher, Olathe North High School, Olathe, KSAmy Foote-Wenz, BSScience Teacher, Monroe High School, Monroe, WAUsing Bioinformatics: Genetic ResearchDevin Parry, PhDScience Teacher, Lakeside School, Seattle, WADianne Thompson, MSScience Teacher, Kent-Meridian High School, Kent, WAAdam Waltzer, MSScience Teacher, Eastside Preparatory School, Kirkland, WA4 Northwest Association for Biomedical Research—Updated October 2012

Curriculum ReviewersNatalie FlechsigJD candidate, 2014, U.C. BerkeleyBrian Fox, PhDSenior Scientist, Computational Biology, Novo Nordisk, Seattle, WARyan HauScience Education Web Intern, Northwest Association for Biomedical ResearchMette Peters, PhDDirector, Translational Technologies and Resources CoreInstitute for Translational Health SciencesBio-ITEST Advisory GroupBeth AndersonCEO, ArkitekNitin Baliga, PhDDirector of Integrative Biology, Professor, Institute for Systems BiologyJames DorseyState Director, Washington MESA, University of WashingtonMary Glodowski, NBCT, PAEMSTScience Teacher, Meadowdale High SchoolJim Karkanias, PhDSenior Director, Microsoft CorpConnie Kelly, MSBTBiology Teacher, Shorewood High SchoolEugene Kolker, PhDChief Data Officer, Seattle Children’s Research InstituteMaureen Munn, PhDDirector, Education Outreach, University of WashingtonAnna PavlikProject Manager, Workforce Development Council of Seattle-King CountyKaren Peterson, MEdCEO, EdLab GroupSandra Porter, PhDPresident, Digital World BiologyTim Rose, PhDProfessor, Department of Pediatrics and Medicine, University of Washington5 Northwest Association for Biomedical Research—Updated October 2012

CREDITSStephen Rosenfeld, MD, MBABoard Chair, Quorum ReviewPrincipal at Freeport Research ConsultingTodd Smith, PhDSenior Leader, PerkinElmerBobbie-Jo Webb-Robertson, PhDSenior Research Scientist, Pacific Northwest National LaboratoryBenjamin Wilfond, MDDirector, Treuman Katz Center for Pediatric Bioethics,Seattle Children’s Research InstituteSusie WuACSS Director, Rainier ScholarsRaymond YanChief Operating Officer, DigiPen Institute of TechnologyBio-ITEST ConsultantsCarolyn Cohen, MEdResearcher, Cohen EvaluationDavis Patterson, PhDIndependent ConsultantElizabeth Sanders, PhDMeasurement, Statistics, Research Design, Educational PsychologyUniversity of WashingtonUsing Bioinformatics: Genetic Research6 Northwest Association for Biomedical Research—Updated October 2012

CONTENTS3Credits7Contents11Overview19Lesson 1 — What is Genetic Research?35Resource – Pairwise Comparisons of Canine DNA Sequences37Handout – Bioinformatics: A Tool for Every Trade41Handout – Careers in the Spotlight45Handout – An Introduction to Genetic Research46Handout – Canine DNA Sequences47Handout – The Process of Genetic Research49Key – Bioinformatics: A Tool for Every Trade Teacher Answer Key51Key – An Introduction to Genetic Research Teacher Answer Key52Key – The Process of Genetic Research Teacher Answer Key55Key – Pairwise Comparisons of Canine DNA Sequences Teacher Answer Key57Lesson 2 — DNA Barcoding and the Barcode of Life Database (BOLD)69Class Set – Using BLAST and BOLD for Genetic Research Instructions77Handout – Using BLAST and BOLD for Genetic Research Worksheet79Class Set – Group 1: Class Mammalia80Class Set – Group 2: Class Aves81Class Set – Group 3: Class Osteichthyes (The Bony Fishes)82Class Set – Group 4: Class Chondrichthyes (The Cartilaginous Fishes)83Class Set – Group 5: Class Reptilia85Key – Using BLAST and BOLD for Genetic Research Teacher Answer Key91Lesson 3 — Using Bioinformatics to Study Evolutionary Relationships105Class Set – Using Bioinformatics to Study Evolutionary Relationships Instructions113Handout – Using Bioinformatics to Study Evolutionary Relationships Worksheet115Key – Using BLAST and BOLD for Genetic Research Teacher Answer KeyOverview – Using Bioinformatics: Genetic ResearchContents7 Northwest Association for Biomedical Research—Updated October 2012

CONTENTS121Lesson 4 — Using Bioinformatics to Analyze Protein Sequences143Class Set – Codons and Amino Acid Chemistry144Handout – Understanding Protein Reading Frames Worksheet145Class Set – Using Bioinformatics Tools to Analyze Protein Sequences Instructions151Handout – Using Bioinformatics Tools to Analyze Protein Sequences Worksheet153Key – Understanding Protein Reading Frames Teacher Answer Key154Key – Understanding Protein Reading Frames—Expanded Explanation Teacher Answer Key155Key – Using Bioinformatics Tools to Analyze Protein Sequences Teacher Answer Key159Lesson 5 — Protein Structure and Function: A Molecular Murder Mystery171Class Set – Molecular Murder Mystery Instructions177Key – Molecular Murder Mystery Teacher Answer Key180Resource – Installing Cn3D181Lesson 6 — Writing Research Reports195Class Set – Writing Research Reports197Handout – Research Template Handout199Class Set – Making Scientific Posters in PowerPoint201Handout – Writing a Scientific Abstract about Cytochrome c Oxidase202Resource – Student Research Report Rubric205Resource – Key Words to Include when Writing About Cytochrome c Oxidase206Resource – Student Magazine Article Rubric207Lesson 7 — Who Should Pay? Funding Research on Rare Genetic Diseases219Handout – Issues in Funding Research on Rare Genetic Diseases223Class Set – Group 1: Testimony before Congress Regarding Funding by the NationalUsing Bioinformatics: Genetic ResearchInstitutes of Health for Research on Rare Genetic Diseases224Class Set – Group 2: Testimony before Congress Regarding Funding by the NationalInstitutes of Health for Research on Rare Genetic Diseases225Class Set – Group 3: Testimony before Congress Regarding Funding by the NationalInstitutes of Health for Research on Rare Genetic Diseases226Class Set – Group 4: Testimony before Congress Regarding Funding by the NationalInstitutes of Health for Research on Rare Genetic Diseases227Key – Issues in Funding Research on Rare Genetic Diseases Teacher Answer Key8 Northwest Association for Biomedical Research—Updated October 2012

CONTENTS231Lesson 8 — Exploring Bioinformatic Careers245Class Set – Career Interview 1: Ellen Sisk, MS, Manager, DNA Sequencing Core Facility247Class Set – Career Interview 2: Krishna Veeramah, PhD, Postdoctoral Scientist, DNAand History Program251Class Set – Career Interview 3: Lalita Ramakrishnan, MD, PhD, Microbiologist253Class Set – Career Interview 4: Michael Crawford, PhD, Biological Anthropologist257Class Set – Career Interview 5: James Ferrenberg, Molecular Diagnostics Researcher259Class Set – Career Interview 6: Kris Freeman, MS, Science and Technical Writer263Class Set – Career Interview 7: Russell Saneto, DO, PhD, Pediatric Neurologist265Handout – Spotlight on My Career267Handout – Colleges and Universities in Washington and Oregon268Class Set – Bioinformatics Resume269Handout – Resume Peer-Editing Form271Class Set – Writing a Cover Letter273Handout – Cover Letter Examples275Key – Cover Letter Examples Teacher Answer Key277Handout – Cover Letter Peer-Editing Form279Handout – Mock Interview Grading Rubric281Lesson 9 — Analyzing DNA Sequences and DNA Barcoding301Class Set – Analyzing DNA Sequences Instructions317Handout – Data Table for Editing DNA Sequences318Resource – Installing FinchTV319Wetlab — DNA Barcoding: From Samples to Sequences349Class Set – Lab 1: DNA Purification for DNA Barcoding355Class Set – Lab 2: Copying the DNA Barcoding Gene Using Polymerase ChainReaction (PCR)359Class Set – Lab 3: Analyzing PCR Results with Agarose Gel Electrophoresis363Class Set – Lab 4: Preparation of PCR Samples for DNA Sequencing367Key – Lab 1: DNA Purification for DNA Barcoding Teacher Answer Key369Key – Lab 2: Copying the DNA Barcoding Gene Using Polymerase Chain Reaction (PCR)Teacher Answer Key370Key – Lab 3: Analyzing PCR Results with Agarose Gel Electrophoresis Teacher Answer Key371Key – Lab 4: Preparation of PCR Samples for DNA Sequencing Teacher Answer Key373Resource – Aliquoting DNA Barcoding Reagents for Labs 1–49 Northwest Association for Biomedical Research—Updated October 2012

CONTENTSA1AppendixA2Ethics BackgroundA3Creating Discussion Ground RulesA4Amino Acid Abbreviations and Chemistry ResourcesA5Codons and Amino Acid ChemistryA6Behind the Scenes with the NCBI Databases and the Entrez Search EngineA7Understanding BLASTA9Finding Structures in the NCBI Structure DatabaseUsing Bioinformatics: Genetic Research10 Northwest Association for Biomedical Research—Updated October 2012

OVERVIEWOverviewUnit OverviewThis curriculum unit explores how bioinformatics is used to perform genetic research. Specifically, the bioinformatics toolsBLAST, ORFinder, ClustalW2/JalView, and Cn3D are used to analyze genetic sequences and molecular structures. Thecytochrome c oxidase subunit 1 (COI) gene is introduced as the “DNA barcoding” gene that allows for identification of animalspecies. Students examine DNA sequences from different animal species, investigate the relationship between protein structureand function, and explore evolutionary relationships among eukaryotic organisms. The unit concludes with an optionalauthentic student research project, sequencing the COI genes from samples they collect themselves or samples obtainedthrough partnerships with the National Oceanographic and Atmospheric Association (NOAA) and the Seattle Aquarium, bothbased in Seattle. Throughout the unit, students are exposed to a number of career options where bioinformatics tools areeither developed or used. The career lesson near the end of the unit culminates with resume and cover letter writing activitiesand a mock job interview.Essential Understandings1. Biological molecules store and process information.2. The structure of molecules is closely related to their function. Changes in structure can often impact function.3. Acquisition of biological information has many societal and ethical implications; students need tools to evaluate anddecide how information should be used.4. Technology influences how science is done; bioinformatics gives us new tools to understand biological information.Unit Objectives1. Students will be able to explain how bioinformatics tools are useful in analyzing biological sequence and structureinformation.2. Students will be able to use sequence analysis tools to identify and explore evolutionary relationships between organisms.3. Students will use molecular modeling to investigate and identify foreign substances bound to the active site of cytochromec oxidase.4. Students will be able to identify and critically evaluate the ethical implications of public funding for genetic research.5. Students will be able to design and conduct a research study to isolate and analyze the genetic information of anunknown species or specimen using DNA barcoding techniques and bioinformatics tools (For optional Wet Lab).6. Students will evaluate the use of bioinformatics in the life sciences and describe how bioinformatics tools could beused in various careers.Overview – Using Bioinformatics: Genetic Research5. Bioinformatics is used in many areas of life sciences and related fields.11 Northwest Association for Biomedical Research—Updated October 2012

OVERVIEWInstructional ComponentsThe Curriculum: The Using Bioinformatics: Genetic Research curriculum consists of seven sequential lessons, an eighth lessonthat focuses on careers that make use of bioinformatics tools, and a ninth lesson offering instruction in DNA sequence analysis.Lesson Six is provided as an assessment of the skills obtained in the first five lessons. An optional Wet Lab is also included.Throughout this curriculum, a variety of resources are provided. These materials include: Student “Handouts” that are designed to be printed or copied and given to each student as a “worksheet.” Answersto lesson activity and/or homework questions may be completed on the handouts, on separate sheets of paper, or in labnotebooks, as directed by the teacher. “Class Sets” that contain lesson activity instructions for students and are designed to be printed or copied andre-used as class sets. Questions that students should answer on their handout, piece of paper, or lab notebook areindicated with an icon. Teacher “Resources” that include teacher demonstrations and additional information. Teacher Answer “Keys” that provide suggested answers and scoring information.Time Commitment: Each lesson requires a minimum of one 50 minute class session. Some lessons require two class sessions,in addition to homework assignments. The entire unit (nine lessons) is expected to take 16–20 class periods of 50 minuteseach. The optional wet lab requires an additional 4–6 class periods of 50 minutes each. For a detailed overview of the unittime commitment with and without the optional wet lab, as well as suggested lesson orders, see the Overview section WetLab Component and the summary tables following the Lesson Overview.Prior Knowledge Needed: This curriculum is not designed to introduce students to the “Central Dogma of MolecularBiology” (that information in DNA is transcribed into mRNA and then translated into protein), but to reinforce that concept.Students should already be familiar with DNA replication, transcription, and translation. Student understanding of theseprocesses will be deepened through the use of this curriculum. In addition, this curriculum relies on concepts in taxonomy. Anintroduction to taxonomy before instruction is beneficial.The Bio-ITEST Introductory curriculum, Using Bioinformatics: Genetic Testing, is not a required prerequisite for this curriculum,but it is strongly recommended. The Introductory curriculum develops foundational skills in the bioinformatics programs BLASTand Cn3D, while introducing concepts like sequence alignments.Using Bioinformatics: Genetic ResearchCareer ComponentMost lessons in the curriculum are accompanied by a PowerPoint slide highlighting a person in a career that usesbioinformatics, followed by a slide providing job information about that career. Student Handout—Careers in the Spotlight isgiven to students during the first lesson. Students are expected to take daily notes on this handout at the beginning and endof the class for the duration of the unit.Lesson Eight focuses entirely on careers that use bioinformatics tools. Students consult interview transcripts fromprofessionals, conduct internet research on a specific career, and review the information they have collected on StudentHandout—Careers in the Spotlight. Students then update their resume (developed in the Bio-ITEST Introductory curriculumUsing Bioinformatics: Genetic Testing) and learn how to create a cover letter. The lesson ends with a mock job interview.Although bioinformatics is a career choice in itself, there are also a wide variety of careers that use bioinformatics tools. Thiscurriculum highlights a broad range of career paths, even if the use of bioinformatics is not central to that career.12 Northwest Association for Biomedical Research—Updated October 2012

OVERVIEWWet Lab ComponentAn optional Wet Lab lesson is included in the Bio-ITEST curriculum. This series of four lab experiments is designed to providestudents with hands-on experience in DNA barcoding, through classroom laboratories or as part of an independent researchproject. The four lab experiments include: DNA purification Polymerase chain reaction (PCR) Agarose gel electrophoresis Preparation of samples for DNA sequencingSamples for barcoding could include meat or fish from local grocery stores, markets, or restaurants; samples collected fromlocal parks or other ecosystems; or samples obtained through partnerships with NWABR, zoos, or aquariums.Lesson Order: The Wet Lab lesson is designed to be modular and can be inserted throughout the curriculum as time permits.Many teachers find it best to provide students with a general overview of DNA barcoding (i.e., Lesson One), followed by theWet Lab, then Lessons Two through Eight, and finally, complete the unit with Lesson Nine. This allows students to completethe DNA sequence analyses in Lesson Nine with their own DNA sequence data. This lesson order should allow sufficient timefor classes to send their DNA samples for sequencing and receive their data while completing the other Bio-ITEST lessons.Alternatively, the Wet Lab could be used to start or end the unit.For classes that will not complete the Wet Lab, a collection of sequence data for Lesson Nine has been obtained throughpartnerships with the Seattle Aquarium and the National Oceanographic and Atmospheric Administration (NOAA), and isavailable under the “Resources” tab on the Bio-ITEST advanced bioinformatics webpage at: atics-genetic-research.The Bio-ITEST program will provide PCR primers for DNA barcoding of animal samples. For contact information, visithttp://www.nwabr.org.Technology RequirementsDetailed information regarding computer equipment, files, software, and media requirements can be found in the Materialssection at the beginning of each lesson.For all nine lessons and the optional Wet Lab, teachers will need to be able to project PowerPoint slides for the class tosee. If this is not possible, teachers can print the PowerPoint slides onto transparencies, which can be displayed with anoverhead projector.Lessons One, Two, Five, Nine, and the optional Wet Lab require the capability to show online streaming videos to the class.Lesson One includes an optional video from the Howard Hughes Medical Institute, “Sanger Method of DNA Sequencing.”Lesson Two includes the video “Barcode of Life: Global Diversity Challenge,” produced by the International Barcode of LifeProject Biodiversity Institute of Ontario (available on YouTube), and/or the NWABR animation “DNA Barcoding” (availableunder the “Resources” tab on the Bio-ITEST advanced curriculum webpage at: tics-genetic-research). Lesson Five requires the capability to show the online streaming video, “Electron-TransportChain,” produced by Garland Sciences (available on YouTube). The Howard Hughes Medical Institute’s “Sanger Method ofDNA Sequencing” is also recommended for Lesson Nine. The optional Wet Lab includes a number of recommended onlinestreaming videos to supplement instruction.Lessons One through Six, Lesson Eight, and Lesson Nine require students to use computers with internet access and a searchengine such as Mozilla Firefox. Students may also need a text editing program such as Microsoft Notepad or TextEdit for13 Northwest Association for Biomedical Research—Updated October 2012

OVERVIEWsaving their “unknown” DNA sequences (optional, see Lessons Two and Nine). Students are encouraged to use a wordprocessing program (Microsoft Word) for writing the Student Research Report (Lesson Six), for creating their resume andcover letter (Lesson Eight), and for answering homework questions. Lesson Seven does not require computer use except foranswering homework questions (optional); no internet is required.Lesson Five requires the Cn3D program to be downloaded and installed on all student computers. The program can bedownloaded from: tml. Instructions are also available in the TeacherResource at the end of Lesson Five.Lesson Nine requires the program FinchTV to be downloaded and installed on all student computers. The program can bedownloaded from: http://www.geospiza.com/Products/finchtv.shtml. Instructions are also available in the Teacher Resource atthe end of Lesson Nine.Before Beginning the UnitSet Classroom Discussion Norms: It is especially important to foster a safe classroom atmosphere when discussing ethicalissues about funding research for rare genetic diseases (Lesson Seven) that may involve conflicting moral choices. Please review orcreate classroom discussion ground rules (norms) before proceeding. Instructions for doing this can be found in the Appendix.Install Cn3D and FinchTV on all Computers: Contact your school administrator or IT support staff to be sure theseprograms have been downloaded and installed on all student computers for Lessons Five (Cn3D) and Nine (FinchTV).Instructions for downloading each of these programs can be found in the Teacher Resources sections of each correspondinglesson (Lesson Five and Lesson Nine).Additional ResourcesDNA Structure: Exploring DNA Structure by Dr. Sandra Porter contains information on the discovery and structure of DNA,along with hands-on activities that students can use to explore the structure of DNA first-hand. Students determine wheremolecules bind to DNA, investigate base-pairing, examine the phosphodiester backbone, and study the interaction betweenDNA strands. Exploring DNA Structure is also available on a CD together with 76 DNA structures, Cn3D, and the textbook. Formore information, see http://www.digital-world-biology.com.Ethics: Additional information about ethical theories and perspectives can be found in An Ethics Primer: Lesson Ideas andEthics Background by Jeanne Ting Chowning and Paula Fraser, produced through the Northwest Association for BiomedicalResearch. The complete Ethics Primer is available free for download from http://www.NWABR.org.Using Bioinformatics: Genetic ResearchMolecular Structures: Have you ever wanted to find molecular structures that you can use as class examples? A Beginner’sGuide to Molecular Structure, by Dr. Sandra Porter, navigates through the NCBI databases to help teachers determine whetherstructures come from normal or mutant proteins, and to identify the parts of the protein that are found in the structure.Activities include superimposing influenza structures to see why one strain could become resistant to Tamiflu, working withgreen fluorescent protein, and more. For more information, see http://www.digital-world-biology.com.14 Northwest Association for Biomedical Research—Updated October 2012

OVERVIEWLesson OverviewLesson One: The Process of Genetic ResearchIn this lesson, students are introduced to the process of genetic research. The lesson begins with a Think-Pair-Share activitydesigned to introduce students to the types of research questions people in different career fields might answer usingbioinformatics tools. After a short background explanation provided by the teacher about how genetic research is done,students make their own hypotheses and predictions about the relatedness of canine species, and align paper DNA sequencesto evaluate their hypotheses. The lesson concludes with a group activity introducing students to pairwise comparisons of DNAsequences, which will be explored more fully in later lessons. In Lesson One, students learn how DNA sequencing core labmanagers might use bioinformatics tools in their career.Lesson Two: DNA Barcoding and the Barcode of Life Database (BOLD)In this lesson, students will receive an “unknown” DNA sequence and use the bioinformatics tool Basic Local AlignmentSearch Tool (BLAST) to identify the species from which the sequence came. Students then visit the Barcode of Life Database(BOLD) to obtain taxonomic information about their species and form taxonomic groups for scientific collaboration. Thelesson ends with each student generating a hypothesis about the relatedness of the species within each group. In Lesson Two,students learn how postdoctoral scientists in DNA and history might use bioinformatics tools in their career.Lesson Three: Using Bioinformatics to Study Evolutionary RelationshipsIn this lesson, students learn how to use bioinformatics tools to analyze DNA sequence data and draw conclusions aboutevolutionary relationships. Students collaborate with their group members by pooling their DNA sequences from LessonTwo: DNA Barcoding and the Barcode of Life Database (BOLD) to perform and analyze multiple sequence alignments usingthe computer programs ClustalW2 and JalView. After comparing relatedness among and between the species within theirgroup, students use their sequence alignment to generate a phylogenetic tree, which is a graphical representation of inferredevolutionary relationships. This tree is used to draw conclusions about their research question and hypothesis. In Lesson Three,students learn how microbiologists might use bioinformatics tools in their career.Lesson Four: Using Bioinformatics to Analyze Protein SequencesIn this lesson, students perform a paper exercise designed to reinforce student understanding of the complementary nature ofDNA and how that complementarity leads to six potential protein reading frames in any given DNA sequence. They also gainfamiliarity with the circular format codon table. Students then use the bioinformatics tool ORFinder to identify the readingframes in their DNA sequence from Lesson Two and Lesson Three, and to select the proper open reading frame to use in amultiple sequence alignment using their protein sequences. In Lesson Four, students learn how biological anthropologistsmight use bioinformatics tools in their career.Lesson Five: Protein Structure and Function—A Molecular Murder MysteryPrior to this lesson, students learned how the cytochrome c oxidase subunit 1 (COI) gene is used to barcode animals. In thislesson, students learn more about the cytochrome c oxidase protein and its three-dimensional structure. In particular, studentslearn how to identify the active site in cytochrome c oxidase. Once they can find this site, they look at aligned structures(one of which contains a poison) and then determine the identity of a foreign substance that acts as a poison by bindingto the active site. This lesson allows students to explore the use of the molecular visualization program Cn3D to learn moreabout cytochrome c oxidase, a ubiquitous and important protein. In Lesson Five, students learn how molecular diagnosticsresearchers might use bioinformatics tools in their career.Lesson Six/Assessment: Writing Research ReportsIn this lesson, students compile and synthesize what they have learned in the preceding lessons by writing a research report.The research report includes Introduction, Methods, Results, Discussion, and References sections. Emphasis is placed onrelating previous lesson activities to the original research question and hypothesis. Extensions and lesson alternatives includeinstructions for creating a scientific poster, writing a scientific abstract, or writing a science-related magazine article. In LessonSix, students learn how science and technical writers might use bioinformatics tools in their career.15 Northwest Association for Biomedical Research—Updated October 2012

OVERVIEWLesson Seven: Who Should Pay? Funding Research on Rare Genetic DiseasesIn this lesson, students learn about Leigh’s disease, a rare form of Subacute Necrotizing Encephalomyelopathy (SNEM) that canbe caused by a deficiency in cytochrome c oxidase (complex IV). Deficiencies in the large, 13-subunit cytochrome c oxidasecomplex can result from defects in one of several proteins, including cytochrome c oxidase subunit 1, the protein encoded bythe DNA barcoding gene, and examined in Lesson 5. Without the COI protein, cells are unable to harness usable energy fromglucose. This is a jigsaw exercise. Students are assigned or choose one of four stakeholder parties. They meet in “like” interestgroups to become more familiar with that stakeholder’s position and concerns. Afterwards, they meet in “mixed” groups witha representative from each of the stakeholder groups. Students identify areas of agreement and disagreement, and proposea compromise to recommend to Congress regarding funding for rare disease research. In Lesson Seven, students learn howpediatric neurologists might use bioinformatics tools in their career.Lesson Eight: Exploring Bioinformatics CareersIn this lesson, students synthesize the information they have learned throughout the unit about people in various careers whouse bioinformatics. Students then have the opportunity to

Class Set – Group 1: Class Mammalia Class Set – Group 2: Class Aves Class Set – Group 3: Class Osteichthyes (The Bony Fishes) Class Set – Group 4: Class Chondrichthyes (The Cartilaginous Fishes) Class Set – Group 5: Class Reptilia Key – Using BLAST

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