Welcome to Introduction to Bioinformatics Monday, 15 September

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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
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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)

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Regulatory Protein and their Binding Sites
Palindromic sequences
What is it?
What about with DNA?
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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

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Regulatory Protein and their Binding Sites
Palindromic sequences
5-
-3 3-
-5
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

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Regulatory Protein and their Binding Sites
Palindromic sequences
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
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Regulatory Protein and their Binding Sites
Palindromic sequences
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
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Regulatory Protein and their Binding Sites
Palindromic sequences
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
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Regulatory Protein and their Binding Sites
Palindromic sequences
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
Palindromes Serve as binding sites for dimeric
protein
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Regulatory Protein and their Binding Sites
SQ7 Is the binding site of NtcA palindromic?
GTA ..(8).. TAC
GTA ..(8).. TAC
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Regulatory Protein and their Binding Sites
SQ7 How does NtcA bind to its binding site?
GTA ..(8).. TAC
GTA ..(8).. TAC
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Regulatory Protein and their Binding Sites
SQ8 What if NtcA site were attached to lacZ?
GTA ..(8).. TAC
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Regulatory Protein and their Binding Sites
SQ8 What if NtcA site were attached to lacZ?
hetQ
5-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNN
NNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3-CAT
..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNN
NNNNNNNNNNTACNNNNNNNNNNNNNNNN
NtcA
GTA ..(8).. TAC
lacZ
5-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNN
NNNNNNNNNNNATGNNNNNNNNNNNNNNNN3-CACTCAATCGAGTGNN
NNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNN
NNNNNNNNNN
Operator
Crp
GTA ..(8).. TAC
RNA Polymerase
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Regulatory Protein and their Binding Sites
SQ8 What if NtcA site were attached to lacZ?
hetQ
5-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNN
NNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3-CAT
..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNN
NNNNNNNNNNTACNNNNNNNNNNNNNNNN
GTA ..(8).. TAC
lacZ
5-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNN
NNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3-CAT
..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNN
NNNNNNNNNNTACNNNNNNNNNNNNNNNN
Operator
NtcA
GTA ..(8).. TAC
RNA Polymerase
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Regulatory Protein and their Binding Sites
SQ5 How many genes have promoters? CRP sites?
lacZ
5-GTGAGTTAGCTCACNNTTTACANTANNNNTATGTTNNNNNNNNNNNN
NNNNNNNNNNNATGNNNNNNNNNNNNNNNN3-CACTCAATCGAGTGNN
AAATGTANNNNNNATACAANNNNNNNNNNNNNNNNNNNNNNNTACNNNNN
NNNNNNNNNNN
Operator
Crp
GTA ..(8).. TAC
RNA Polymerase
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Regulatory Protein and their Binding Sites
SQ10 Issues when modeling genomic DNA?