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Welcome to Introduction to Bioinformatics Wednesday, 25 January Introduction to Molecular Biology

Welcome to Introduction to Bioinformatics Wednesday, 25 January Introduction to Molecular Biology Part 2: DNA to protein. Coming attractions! Significance Palindromes (SQ4) Why introns? (SQ8) Types of mutation (SQ12).

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Welcome to Introduction to Bioinformatics Wednesday, 25 January Introduction to Molecular Biology

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  1. Welcome toIntroduction to BioinformaticsWednesday, 25 JanuaryIntroduction to Molecular Biology Part 2: DNA to protein • Coming attractions! • Significance • Palindromes (SQ4) • Why introns? (SQ8) • Types of mutation (SQ12)

  2. I think the Blackboard discussions can be really helpful with using peers as resources These discussion groups may be useful if they are utilized by others in the class. i am pretty certain it will if people actively read and use it.

  3. little understanding of what the big picture is. when explaining the concepts please also mention the practical applications

  4. 2008 1993 2012

  5. Escherichia coli . . . . . . very small lab rats Courtesy of Kent State University Microbiology E. coli: What makes it kill?

  6. E. coli: What makes it kill? Escherichia coli . . . haemorrhagic colitis

  7. TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA Gene finder Gene finder E. coli: What makes it kill? E. coli K12 E. coli O157:H7

  8. TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA Gene finder Gene finder E. coli: What makes it kill? E. coli K12 E. coli O157:H7

  9. Killer protein Killer functions Membrane protein, sodium transporter Iron responsive transcriptional regulator Calcium dependent protein kinase Unknown protein Unknown protein Unknown protein . . . Similarity finder ideas for new antibiotics E. coli: What makes it kill? How to find set of O157:H7-specific protein?

  10. TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA Gene finder Gene finder How to find set of O157:H7-specific protein? E. coli K12 E. coli O157:H7 How to sift through thousands of proteins?

  11. TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA Gene finder Gene finder How to find set of O157:H7-specific protein? E. coli K12 E. coli O157:H7 How to sift through thousands of proteins?

  12. TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA Gene finder Gene finder How to find set of O157:H7-specific protein? E. coli K12 E. coli O157:H7 DEFINE K12-set AS Genes-ofK12-DNA DEFINE O157-set AS Genes-ofO157-DNA FOR EACH protein IN O157-set WHEN Constituent-of (K12-set, protein) = FALSE COLLECT protein "Constituent-of"? "Same"?

  13. How to find basis of drought resistance? Wild-type crops Drought-resistant Gene finder Gene finder Ray Wu, Cornell Univ. DEFINE K12-set AS Genes-ofK12-DNA DEFINE O157-set AS Genes-ofO157-DNA FOR EACH protein IN O157-set WHEN Constituent-of (K12-set, protein) = FALSE COLLECT protein "Constituent-of"? "Same"?

  14. How to find basis of human traits? Great apes Humans Gene finder Gene finder DEFINE K12-set AS Genes-ofK12-DNA DEFINE O157-set AS Genes-ofO157-DNA FOR EACH protein IN O157-set WHEN Constituent-of (K12-set, protein) = FALSE COLLECT protein "Constituent-of"? "Same"?

  15. TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA Gene finder Gene finder How to find set of O157:H7-specific protein? E. coli K12 E. coli O157:H7 DEFINE K12-set AS Genes-ofK12-DNA DEFINE O157-set AS Genes-ofO157-DNA FOR EACH protein IN O157-set WHEN Constituent-of (K12-set, protein) = FALSE COLLECT protein "Constituent-of"? "Same"?

  16. >NC_000913 (size:4639221) AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAA AAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATA GCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGG GCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCT GCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTG CCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCT GCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTA GAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCC GCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAA CGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT GTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGAT GGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCC CCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACC GGTCAAGGGCATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTG GTCCGGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCG ATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGA ATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAAC GGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGG TATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCC GCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCA ATCTCTGTCGTGGTAAATAACGATGATGCGACCACTGGCGTGCGCGTTAC TCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAA CTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGC AGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATT

  17. >NC_000913 (size:4639221) AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAA AAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATA GCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGG GCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCT GCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTG CCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCT GCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTA GAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCC GCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAA CGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT GTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCC CCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT

  18. >NC_000913 (size:4639221) AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAA AAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATA GCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGG GCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCT GCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTG CCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCT GCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTA GAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCC GCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAA CGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT GTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCC CCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT

  19. Information +Self-assembly DNA Protein Structure+Function CGACCATCGCCTTAGTAC Study Question 11 How do genes exert control over cellular processes?

  20. Structure Metabolomics Genomics TCTACTTATA TTCAATCCAC AGGGCTACAC AAGAGTCTGT TGAATGAACA CATACATGGT TTCTGTCTGC TCTGACCTCT GGCAGCTTTC TGGATTTCGG AACTCTAGCC TGCCCCACTC GAACCTTAGT GACTTCTGCT ATACCAAAGT CTCCGTAAAC CTCTAACATG ATGTCAGCAA TGAATAAACT TTGTTAAAGG TACAAATGAA AAGAGTTTAA AGTTAAAAAC GAATTGCAGT AAACCTGTAT GGTTACATGA ACTGCCTAAA TTATATATTT TAAGAAATTA ATTGCAATTA CCCCAGCTGT CATTAAAAAG AGGCAAATAC GACAGCACTG ACCCTCAAGA AGGCACCGGC GCTGAAATTC CGCTGAGAGC AGAGTGGTAC CCCTGCACCA GGTCTTTCCT GTGGGCACTG ATGAATGACT GAACGAACGA TTGAATGAAA Proteomics Transcriptomics Systems What does this have to do withbioinformatics?

  21. Science (17 Dec 2010) 330:1605 IV.G. How a greater ability to predict protein function from its primary structure would change the world we live in Michael MontagueJ Craig Venter Institute Wednesday, January 26, 12:30(12:15 food) Engineering West Building, Room 401 Are there any programs that predict the conformation/chemical properties of proteins?

  22. Study Question 12

  23. Information +Self-assembly DNA Protein Structure+Function CGACCATCGCCTTAGTAC Study Question 11 How do genes exert control over cellular processes?

  24. when explaining the concepts please also mention the practical applications Important applications?

  25. What have we gotten from… Michael Faraday Unity of electricity and magnetism Inst Chem, Hebrew Univ Jerusalem

  26. What have we gotten from… William Roentgen Behavior of electricity in a vacuum http://www.wired.com/science/discoveries/news/2007/11/dayintech_1108

  27. Welcome toIntroduction to BioinformaticsWednesday, 25 JanuaryIntroduction to Molecular Biology Part 2: DNA to protein I am hearing the word palindromic DNA for the first time, I was wondering if and example could be given of a palindromic DNA sequence. • Coming attractions! • Significance • Palindromes (SQ4) • Why introns? (SQ8) • Types of mutation (SQ12)

  28. Backwards = forwards GCTATCG • DNA is double stranded ROTATOR TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA Palindromic Sequences What is it? What about with DNA?

  29. Backwards = forwards GCTATCG ROTATOR Palindromic Sequences What is it? What about with DNA? • DNA is double stranded • DNA is redundant TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  30. Backwards = forwards GCTATCG ROTATOR TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences What is it? What about with DNA? • DNA is double stranded • DNA is redundant • DNA has direction (read 5’->3’) 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  31. TAT GGCATGCTAGCTTAAT TCATTAATTA AGTAACGTACGATCGG TAT DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  32. UAU GGCAUGCUAGCUUAAU UCAUU tRNA DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  33. Palindromic Sequences Palindromic sequences as protein binding sites why [are] palindromes… targeted by DNA-binding proteins why palindromes are targeted by DNA-binding proteins

  34. TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA recognizes GTGAGTT Palindromic Sequences Palindromic sequences as protein binding sites

  35. TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

  36. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  37. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  38. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  39. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA recognizes GTGAGTT

  40. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  41. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA

  42. Palindromic Sequences Palindromic sequences as protein binding sites TTAATGTGAGTTAGCTCACTCATT NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN AATGAGTGAGCTAACTCACATTAA Palindromes: Serve as binding sites for dimeric protein

  43. RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites gene 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN GTA ..(8).. TAC

  44. gene 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN Transcription factor RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites RNA GTA ..(8).. TAC Is the promoter a beginning string of nucleotides for RNA,

  45. gene 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN Transcription factor RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites RNA GTA ..(8).. TAC Is the promoter a beginning string of nucleotides for RNA, and if so, can such a beginning string have uses beyond just defining the beginning of the promoter sequence?

  46. Structure of DNA 5' 3'

  47. Structure of DNA 5’ 3’ ATG GAG CCT … Which strand determines the codons of the gene? 3’ 5’

  48. Structure of DNA

  49. Structure of DNA

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