Welcome toMolecular Biology Through Discovery
Tuesday, 17 September 2013DNA Structure / Benzer (1959)Finally found a mentor!
Is there anything that we should physically or
electronically be turning in as proof?
DNA Structure
ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ...
A class discussion on the tetranucleotide
hypothesis might help.
DNA Structure
ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ...TAGGCCACTGCCCAACCCTCCATCATAAAACTTGGGCTTGGGAGGCAGAGCCTAACCTCTCTCACTCTAGACAGGTCTAAGATGATTGGGAACGAAATGAGCCGTCTCGACTTTTTCGCGAAGTGGCTAA ...
#1: Hello!
#2: Complete description of our civilization
DNA StructureSQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid?
DNA Directionality & Palindromes
…would like to go into deeper discussion about palindromic sequences
Palindromic Sequences
What is it?
What about with DNA? AGTTGA
Backwards = forwards ROTATOR
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
• DNA is double stranded
SQ16. … why is AGTTGA not a DNA palindrome?
What is it?
What about with DNA? AGTTGA
Backwards = forwards ROTATOR
• DNA is redundant
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
• DNA is double stranded
Palindromic Sequences
What is it?
What about with DNA? AGTTGA
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 RNAThe full biological roles of palindromic
sequences is still a bit unclear to me
SQ18. What is the relationship between a palindromic sequence and a potential hairpin structure?
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
5’- -3’3’- -5’
tRNA
UAU GGCAUGCUAGC
UUAAU UCAUU
DNA: cruciform
RNA: stem/loop
Palindromic SequencesPalindromic sequences as structural RNA
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
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
5’- -3’3’- -5’
How many 12-nt palindromes would you expect at random in the genome of Anabaena variabilis?
GTA ..(8).. TAC
5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
gene
Transcription factor
Palindromic SequencesPalindromic sequences as protein binding sites
RNA
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
5’- -3’3’- -5’
How many 12-nt palindromes would you expect at random in the genome of Anabaena variabilis?
Welcome toMolecular Biology Through Discovery
Tuesday, 17 September 2013DNA Structure / Benzer (1959)
Fermi Problems
• Focus on what is being asked
• Estimate what can be estimated
• Set limits on what can't
How many piano tuners are there in Chicago?
Fermi Problems
• Focus on what is being asked
• Estimate what can be estimated
• Set limits on what can't
What fraction of the cells in your body are bacterial?
Benzer (1959)
Hoping you will go over the experiment. It is so hard to
visualize what goes down in a lab without actually laying on hands.
Wrinch (1936) – What is a Gene?
Morgan T (1934) Nobel Lecture
Drosophilachromosome
What are genes?... There is no consensus of opinion amongst
geneticists as to what the genes are – whether they are
real or purely fictitious...
Benzer (1959)
Whatis a
Gene?
SQ2. Is there any reason to believe from classical genetics that genes have internal structure?
Benzer (1959)I still have trouble connecting recombination with the distance b/w genetic markers.
Richard Twyman, University of Warwick
Benzer (1959)I still have trouble connecting recombination with the distance b/w genetic markers.
Elizabeth Ellis University of Strathclyde