Human Genetics

BIO 310 – Human Genetics Module 8 Worksheet Name: Exploring Genomics In this lecture we examined the cause of different types of mutations and how mutations affect phenotype by altering the structure and function of proteins. The emergence of genomics, bioinformatics, and proteomics as key disciplines in modern genetics has provided geneticists with an unprecedented set of tools fro identifying and analyzing mutations in gene and protein sequences. In this exercise we will use the ExPASy (expert protein analysis system) site, which is hosted by the Swiss Institute for Bioinformatics and provides a wealth of resources for studying proteins. Here we will use an ExPASy program called SIM to compare two polypeptide sequences so as to pinpoint a mutation. Once the mutation ahs been identified, you will learn more about the gene encoding these polypeptides and about a human disease condition associated with this gene. Download the “Instructions for Module 8 Worksheet” to obtain the two gene sequences to be compared, and follow the directions on that handout to perform your searches. Use the results to answer the following questions: 1. How many amino acids (called residues on the SIM result) are in each polypeptide sequence that was analyzed? 2. Look carefully at the alignment results. Can you find any differences in amino acid sequence when comparing these two polypeptides? What did you find? Use the BLAST link from the ExPASy site to identify the polypeptide you have been studying. Explore the BLAS reports for the top three protein sequences that aligned with your query sequence by clicking on the link for each. Once you know the sequence, go to PubMed (http://www.ncbi.nlm.nih.gov/pubmed) and search for a review article by the authors Vajo, Z., Francomano, C.A., and Wilkin, D.J. Use all of this information to answer the following: 3. What gene codes for the polypeptides you have been studying? 4. What is the function of this protein? 5. Based on what you learned from the alignment results you analyzed with SIM, the BLAST reports, and a search through PubMed, what human disease is caused by the mutation you identified? Explain your answer and briefly describe the phenotype associated with this disease This is the thing reading or instruction you have to follow Sequence Alignment to Identify a Mutation n this chapter, we examined the causes of different types of mutations and how mutations affect phenotype by altering the structure and function of proteins. The emergence of genomics, bioinformatics, and proteomics as key disciplines in modern genetics has provided geneticists with an unprecedented set of tools for identifying and analyzing mutations in gene and protein sequences. In this exercise we will use the ExPASy (Expert Protein Analysis System) site, which is hosted by the Swiss Institute for Bioinformatics and provides a wealth of resources for studying proteins. Here we will use an ExPASy program called SIM (for “similarity” in sequence) to compare two polypeptide sequences so as to pinpoint a mutation. Once the mutation has been identified, you will learn more about the gene encoding these polypeptides and about a human disease condition associated with this gene. Exercise I  Identifying a Missense Mutation Affecting a Protein in Humans 1. Begin this exercise by accessing the ExPASy site at http://www.expasy.ch/ tools/sim-prot.html. The SIM feature is an algorithm-based software program that allows us to compare multiple polypeptide sequences by looking for amino acid similarity in the sequences. 2. Following are amino acid sequences for polypeptides expressed in two different people. Person A MGAPACALALCVAVAIVAGASSESLGTEQ RVVGRAAEVPGPEPGQQEQLVFGSGDAV ELSCPPPGGGPMGPTVWVKDGTGLVPSE RVLVGPQRLQVLNASHEDSGAYSCRQRLT QRVLCHFSVRVTDAPSSGDDEDGEDEA EDTGVDTGAPYWTRPERMDKKLLAVPA ANTVRFRCPAAGNPTPSISWLKNGREFR GEHRIGGIKLRHQQWSLVMESVVPSDRG NY TCVVENKFGSIRQT Y TLDVLERS PHRPILQAGLPANQTAVLGSDVEFHC KVYSDAQPHIQWLKHVEVNGSKVG PDGTPYVTVLKTAGANTTDKELEVLSLH NVTFEDAGEYTCLAGNSIGFSHHSAWLVV LPAEEELVEADEAGSVYAGILSYGVGFFL FILVVAAVTLCRLRSPPKKGLGSPTVHK ISRFPLKRQVSLESNASMSSNTPLVRIARL SSGEGPTLANVSELELPADPKWELSRARL TLGKPLGEGCFGQVVMAEAIGIDKDRAA KPVTVAVKMLKDDATDKDLSDLVSEMEM MKMIGKHKNIINLLGACTQGGPLYVLVEY AAKGNLREFLRARRPPGLDYSFDTCKPPE EQLTFKDLVSCAYQVARGMEYLASQKCI HRDLAARNVLVTEDNVMKIADFGLARD VHNLDYYKKTTNGRLPVKWMAPEALFD RVYTHQSDVWSFGVLLWEIFTLGGSPYPG IPVEELFKLLKEGHRMDKPANCTHDLYMI MRECWHAAPSQRPTFKQLVEDLDRVLT VTSTDEYLDLSAPFEQYSPGGQDTPSSSS GDDSVFAHDLLPPAPPSSGGSRT Person B MGAPACALALCVAVAIVAGASSESLGTEQ RVVGRAAEVPGPEPGQQEQLVFGSGDAV ELSCPPPGGGPMGPTVWVKDGTGLVPSE RVLVGPQRLQVLNASHEDSGAYSCRQRLT QRVLCHFSVRVTDAPSSGDDEDGEDEAE DTGVDTGAPYWTRPERMDKKLLAVPAA NTVRFRCPAAGNPTPSISWLKNGREFRGE HRIGGIKLRHQQWSLVMESVVPSDRGNY TCVVENKFGSIRQTYTLDVLERSPHRPILQ AGLPANQTAVLGSDVEFHCKVYSDAQPHI QWLKHVEVNGSKVGPDGTPYVTVLKTA GANTTDKELEVLSLHNVTFEDAGEYTCL AGNSIGFSHHSAWLVVLPAEEELVEADEA GSVYAGILSYRVGFFLFILVVAAVTLCRLR SPPKKGLGSPTVHKISRFPLKRQVSLESNA SMSSNTPLVRIARLSSGEGPTLANVSELEL PADPKWELSRARLTLGKPLGEGCFGQVV MAEAIGIDKDRAAKPVTVAVKMLKDDAT DKDLSDLVSEMEMMKMIGKHKNIINLL GACTQGGPLYVLVEYAAKGNLREFLRAR RPPGLDYSFDTCKPPEEQLTFKDLVSCAY QVARGMEYLASQKCIHRDLAARNVLVT EDNVMKIADFGLARDVHNLDYYKKTTN GRLPVKWMAPEALFDRVYTHQSDVWSF GVLLWEIFTLGGSPYPGIPVEELFKLLKEG HRMDKPANCTHDLYMIMRECWHAAPSQ RPTFKQLVEDLDRVLTVTSTDEYLDLSAP FEQYSPGGQDTPSSSSSGDDSVFAHDLLP PAPPSSGGSRT 3. Copy and paste each sequence into the “SEQUENCE” text boxes in SIM. (Hint: Access these sequences from the Companion Web site so that you can copy and paste the sequence into SIM.) Use the Person A sequence for sequence 1 and the Person B sequence for sequence 2. Click the “User-entered sequence” button for each. Name the sequences Person A and Person B as appropriate. Submit the sequences for comparison and then answer the following questions: (a) How many amino acids are in each polypeptide sequence that was analyzed? (b) Look carefully at the alignment results. Can you find any differences in amino acid sequence when comparing these two polypeptides? What did you find? Exercise II  Identifying the Genetic Basis for a Human Genetic Disease Condition 1. Go to the ExPASy home page and find the BLAST link. Run a protein BLAST (blastp) search to identify which polypeptide you have been studying. Explore the BLAST reports for the top three protein sequences that aligned with your query sequence by clicking on the link for each sequence. Pay particular attention to the “Comment” section of each report to help you answer the questions in the following part. 2. Now that you know what gene you are working with, go to PubMed (http:// www.ncbi.nlm.nih.gov/entrez/query. fcgi?db=PubMed) and search for a review article from the authors Vajo, Z., Francomano, C. A., and Wilkin, D. J. Study Area: Exploring Genomics 3. Answer the following questions: (a) What gene codes for the polypeptides have you been studying? (b) What is the function of this protein? (c) Based on what you learned from the alignment results you analyzed in Exercise I, the BLAST reports, and your PubMed search, what human disease is caused by the mutation you identified in Exercise I? Explain your answer and briefly describe phenotypes associated with the disease.

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