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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). - PowerPoint PPT Presentation
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Welcome toIntroduction to Bioinformatics
Wednesday, 25 JanuaryIntroduction to Molecular Biology
Part 2: DNA to protein
• Coming attractions!• Significance• Palindromes (SQ4)• Why introns? (SQ8)• Types of mutation (SQ12)
These discussion groups may be useful if they are utilized by others in the class.
I think the Blackboard discussions can be really helpful with using peers
as resources
i am pretty certain it will if people
actively read and use it.
little understanding of what the big picture is.
when explaining the concepts please
also mention the practical
applications
200820121993
E. coli: What makes it kill?
Escherichia coli . . .
. . . very small lab rats
Courtesy of Kent State University Microbiology
E. coli: What makes it kill?
Escherichia coli . . .
haemorrhagic colitis
E. coli: What makes it kill?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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 AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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
E. coli: What makes it kill?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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 AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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
E. coli: What makes it kill?
Similarity finder
Killer proteinMembrane protein, sodium transporter
Iron responsive transcriptional regulator
Calcium dependent protein kinase
Unknown protein
Unknown protein
Unknown protein
. . .
Killer functions
ideas for new antibiotics
How to find set of O157:H7-specific protein?
How to find set of O157:H7-specific protein?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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 AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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
How to sift through thousands of proteins?
How to find set of O157:H7-specific protein?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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 AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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
How to sift through thousands of proteins?
How to find set of O157:H7-specific protein?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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 AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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
DEFINE K12-set AS Genes-of K12-DNA
DEFINE O157-set AS Genes-of O157-DNA
FOR EACH protein IN O157-set
WHEN Constituent-of (K12-set, protein) = FALSE
COLLECT protein
"Constituent-of"? "Same"?
How to find basis of drought resistance?
Wild-type crops Drought-resistant
Gene finder Gene finder
DEFINE K12-set AS Genes-of K12-DNA
DEFINE O157-set AS Genes-of O157-DNA
FOR EACH protein IN O157-set
WHEN Constituent-of (K12-set, protein) = FALSE
COLLECT protein
"Constituent-of"? "Same"?
Ray Wu, Cornell Univ.
How to find basis of human traits?
Great apes Humans
Gene finder Gene finder
DEFINE K12-set AS Genes-of K12-DNA
DEFINE O157-set AS Genes-of O157-DNA
FOR EACH protein IN O157-set
WHEN Constituent-of (K12-set, protein) = FALSE
COLLECT protein
"Constituent-of"? "Same"?
How to find set of O157:H7-specific protein?
E. coli K12 E. coli O157:H7
Gene finder Gene finder
TCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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 AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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
DEFINE K12-set AS Genes-of K12-DNA
DEFINE O157-set AS Genes-of O157-DNA
FOR EACH protein IN O157-set
WHEN Constituent-of (K12-set, protein) = FALSE
COLLECT protein
"Constituent-of"? "Same"?
>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
>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
>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
Information+
Self-assembly
Structure+
Function
ProteinDNA
CGACCATCGCCTTAGTAC
Study Question 11
How do genes exert control over cellular processes?
Structure
TranscriptomicsSystems
GenomicsTCTACTTATA TTCAATCCAC AGGGCTACACAAGAGTCTGT TGAATGAACA CATACATGGTTTCTGTCTGC 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
Metabolomics
Proteomics
What does this have to do withbioinformatics?
Michael MontagueJ Craig Venter Institute
Wednesday, January 26, 12:30(12:15 food)
Engineering West Building, Room 401
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
Are there any programs that predict the
conformation/chemical properties of proteins?
Study Question 12
Information+
Self-assembly
Structure+
Function
ProteinDNA
CGACCATCGCCTTAGTAC
Study Question 11
How do genes exert control over cellular processes?
when explaining the concepts please
also mention the practical
applications
Important applications?
What have we gotten from…
Michael Faraday
Unity of electricity and magnetism
Inst Chem, Hebrew Univ Jerusalem
What have we gotten from…
William Roentgen
Behavior of electricity in a vacuum
http://www.wired.com/science/discoveries/news/2007/11/dayintech_1108
Welcome toIntroduction to Bioinformatics
Wednesday, 25 JanuaryIntroduction to Molecular Biology
Part 2: DNA to protein
• Coming attractions!• Significance• Palindromes (SQ4)• Why introns? (SQ8)• Types of mutation (SQ12)
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.
Palindromic Sequences
What is it?
What about with DNA? GCTATCG
Backwards = forwards ROTATOR
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
• DNA is double stranded
What is it?
What about with DNA? GCTATCG
Backwards = forwards ROTATOR
• DNA is redundant
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
• DNA is double stranded
Palindromic Sequences
What is it?
What about with DNA? GCTATCG
Backwards = forwards ROTATOR
• DNA is redundant
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
• DNA is double stranded
TTAATGTGAGTTAGCTCACTCATTAATGAGTGAGCTAACTCACATTAA
• DNA has direction (read 5’->3’)
5’- -3’3’- -5’
Palindromic Sequences
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
5’- -3’3’- -5’
TAT GGCATGCTAGC
TTAAT TCATTAATTA AGTAA
CGTACGATCGG TAT
DNA: cruciform
RNA: stem/loop
Palindromic SequencesPalindromic sequences as structural RNA
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
5’- -3’3’- -5’
tRNA
UAU GGCAUGCUAGC
UUAAU UCAUU
DNA: cruciform
RNA: stem/loop
Palindromic SequencesPalindromic sequences as structural RNA
Palindromic SequencesPalindromic sequences as protein binding sites
why palindromes are targeted by DNA-binding proteins
why [are] palindromes… targeted by DNA-binding
proteins
recognizes GTGAGTT
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA
Palindromic SequencesPalindromic sequences as protein binding sites
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA
Palindromic SequencesPalindromic sequences as protein binding sites
Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTG
AGCTAACT
CACATTAA
Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNN
NNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT
AATGAGTGAGCTAACTCACATTAA
Palindrom
ic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNN
NNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT
AATGAGTGAGCTAACTCACATTAA
recognizes GTGAGTT
Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATTAATGAGTGAGCTAACTCACATTAA
Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNN
NNNNNNN
NNNNNNNN
NNNNNNN
NNNNNNNN
NNNNN
NNNNNNNN
NNNNN
TTAATGTG
AGTTAGCT
CACTCATT
AATGAGTGAGCTAACTCACATTAA
Palin
drom
ic Se
quen
ces
Palin
drom
ic se
quen
ces a
s pro
tein
bind
ing
sites
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNN
NNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT
AATGAGTGAGCTAACTCACATTAA
Palindromes: Serve as binding sites for dimeric protein
Palindromic SequencesPalindromic sequences as protein binding sites
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA
GTA ..(8).. TAC
5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
gene
Palindromic SequencesPalindromic sequences as protein binding sites
GTA ..(8).. TAC
5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
gene
Transcription factor
RNA Polymerase
Palindromic SequencesPalindromic sequences as protein binding sites
RNA
Is the promoter a beginning string of nucleotides for RNA,
GTA ..(8).. TAC
5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
gene
Transcription factor
RNA Polymerase
Palindromic SequencesPalindromic sequences as protein binding sites
RNA
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?
Structure of DNA5' 3'
Structure of DNA
ATG GAG CCT …
Which strand determines the
codons of the gene?
5’
3’
3’
5’
Structure of DNA
Structure of DNA
Structure of DNA
Structure of DNA
ATG GAG CCT …
Which strand determines the
codons of the gene?
5’
3’
3’
5’
Structure of DNAStructure of the Genome
GGCAGAATGTGAAGCTAGGCATTGTACCTAGCCGTCTTACACTTCGATCCGTAACATGGATC
Where might be a start codon? (presume ATG)
10 20 30
Structure of DNAStructure of the Genome
GGCAGAATGTGAAGCTAGGCATTGTACCTAGCCGTCTTACACTTCGATCCGTAACATGGATC
Where might be a start codon? (presume ATG)
10 20 30
Structure of DNAStructure of the Genome
GGCAGAATGTGAAGCTAGGCATTGTACCTAGCCGTCTTACACTTCGATCCGTAACATGGATC
Where might be a start codon? (presume ATG)
10 20 30
Structure of DNAStructure of the Genome
GGCAGAATGTGAAGCTAGGCATTGTACCTAGCCGTCTTACACTTCGATCCGTAACATGGATC
Where might be a start codon? (presume ATG)
10 20 30
Structure of DNAStructure of the Genome
GGCAGAATGTGAAGCTAGGCATTGTACCTAGCCGTCTTACACTTCGATCCGTAACATGGATC
Where might be a start codon? (presume ATG)
10 20 30
Structure of DNAStructure of the Genome
GGCAGAATGTGAAGCTAGGCATTGTACCTAGCCGTCTTACACTTCGATCCGTAACATGGATC
1 2
43
Where might be a start codon? (presume ATG)
5’5’3’
3’
I think it could be easier if we spoke with the students near us first (ex.in little groups) for a minute or two,
then ask for comments from the whole class.
Structure of DNAStructure of the Genome
5’5’3’
3’