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Welcome to Introduction to Bioinformatics Monday, 15 September

Welcome to Introduction to Bioinformatics Monday, 15 September. Scenario 2: Regulatory protein / Simulations SQ 5, 7, 8, 9, 10. Scenario 1: Genomic comparisons Problem Sets 1M and 1P. Regulatory Protein and their Binding Sites. What do we talk about?.

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Welcome to Introduction to Bioinformatics Monday, 15 September

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  1. Welcome toIntroduction to BioinformaticsMonday, 15 September Scenario 2: Regulatory protein / Simulations SQ 5, 7, 8, 9, 10 Scenario 1: Genomic comparisons Problem Sets 1M and 1P

  2. Regulatory Protein and their Binding Sites What do we talk about? • Palindromic sequences: relationship to protein binding (SQ7) • Gene fusions: e.g. ntcA / lacZ (SQ8) • How many promoters? CRP-binding sites? (SQ5) • How does lac regulation work? • Simulations? • Why do them? (SQ10) • Pitfalls? (SQ9)

  3. Backwards = forwards GCTATCG • DNA is double stranded ROTATOR TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA Regulatory Protein and their Binding Sites Palindromic sequences What is it? What about with DNA?

  4. GCTATCG ROTATOR • DNA has direction (read 5’->3’) 5’- -3’ 3’- -5’ Regulatory Protein and their Binding Sites Palindromic sequences What is it? Backwards = forwards What about with DNA? • DNA is double stranded • DNA is redundant TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  5. TAT GGCATGCTAGCTTAAT TCATTAATTA AGTAACGTACGATCGG TAT tRNA DNA: cruciform RNA: stem/loop Regulatory Protein and their Binding Sites Palindromic sequences 5’- -3’ 3’- -5’ TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  6. recognizes GTGAGTT Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  7. recognizes GTGAGTT Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  8. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  9. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  10. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  11. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  12. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA recognizes GTGAGTT

  13. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  14. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

  15. Regulatory Protein and their Binding Sites Palindromic sequences NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA Palindromes: Serve as binding sites for dimeric protein

  16. 5’-GTA ..(8).. TAC-3’3’-CAT ..(8).. ATG -5’ Regulatory Protein and their Binding Sites SQ7: Is the binding site of NtcA palindromic? GTA ..(8).. TAC GTA ..(8).. TAC

  17. 5’-GTA ..(8).. TAC-3’3’-CAT ..(8).. ATG -5’ Regulatory Protein and their Binding Sites SQ7: How does NtcA bind to its binding site? GTA ..(8).. TAC GTA ..(8).. TAC

  18. hetQ 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN NtcA N RNA Polymerase Regulatory Protein and their Binding Sites SQ8: What if NtcA site were attached to lacZ? GTA ..(8).. TAC

  19. N C Regulatory Protein and their Binding Sites SQ8: What if NtcA site were attached to lacZ? hetQ 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN NtcA GTA ..(8).. TAC lacZ 5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN Operator Crp GTA ..(8).. TAC RNA Polymerase

  20. N Regulatory Protein and their Binding Sites SQ8: What if NtcA site were attached to lacZ? hetQ 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN GTA ..(8).. TAC lacZ 5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN Operator NtcA GTA ..(8).. TAC RNA Polymerase

  21. Transcription How many? How many? Regulatory Protein and their Binding Sites SQ5: How many genes have promoters? CRP sites? lacZ 5’-GTGAGTTAGCTCACNNTTTACANTANNNNTATGTTNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CACTCAATCGAGTGNNAAATGTANNNNNNATACAANNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN Operator Crp GTA ..(8).. TAC RNA Polymerase

  22. Regulatory Protein and their Binding Sites SQ10: Issues when modeling genomic DNA?

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