Welcome to Molecular Biology Through Discovery Tuesday, 17 September 2013 DNA Structure / Benzer...

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 Structure

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?



• DNA is redundant




What is it?



• DNA is redundant



TTAATGTGAGTTAGCTCACTCATTAATGAGTGAGCTAACTCACATTAA

• DNA has direction (read 5’->3’)

5’- -3’3’- -5’



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?


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


Palindromic sequences as protein binding sites

NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN


TTAATGTGAGTTAGCTCACTCATT AATGAGTG

AGCTAACT

CACATTAA



NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN

NNNNNNNNNNNNN

NNNNNNNNNNNNN

TTAATGTGAGTTAGCTCACTCATT

AATGAGTGAGCTAACTCACATTAA

Palindrom

ic Sequences


NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN

NNNNNNNNNNNNN

NNNNNNNNNNNNN



recognizes GTGAGTT





TTAATGTGAGTTAGCTCACTCATTAATGAGTGAGCTAACTCACATTAA



NNNNNNNN

NNNNNNN

NNNNNNNN

NNNNNNN

NNNNNNNN

NNNNN

NNNNNNNN

NNNNN

TTAATGTG

AGTTAGCT

CACTCATT


Palin

drom

ic Se

quen

ces

Palin

drom

ic se

quen

ces a

s pro

tein

bind

ing

sites

NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN

NNNNNNNNNNNNN

NNNNNNNNNNNNN



Palindromes: Serve as binding sites for dimeric protein





GTA ..(8).. TAC

5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN

gene


GTA ..(8).. TAC


gene

Transcription factor

RNA Polymerase


RNA


5’- -3’3’- -5’

How many 12-nt palindromes would you expect at random in the genome of Anabaena variabilis?

Probability

How often A-A-A-A-A-A?

Probability

How often 1-1-1-1-1-1?

Probability


Probability

How often 1-1-1-1-1-1?

Probability

How often 1-2-1-1-1-1?

Probability

How often 1-1-1-1-1-1?

Probability


Probability

How often A-T-G-G-T-A?

Probability

How often A-T-G-G-T-A?

Counting

GTA ..(8).. TAC


gene

Transcription factor


RNA


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

What is the question?

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?

Fermi Problems

What is the question?What do you need?

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)

Benzer (1959)

Complementation Test

Benzer (1959)

Complementation Test

Phage

E. coli

Benzer (1959)

Benzer (1959)

Recomination Test

Phage

E. coli

(Cis-Trans Test)

Measuredistance

Benzer (1959)

Complementation Test?

Phage

E. coli

Recombination Test?

Benzer (1959)

Whatis a

Gene?

SQ2. Is there any reason to believe from classical genetics that genes have internal structure?

Benzer (1959)

rII region of bacteriophage T4

What do you need for the experiment?

Benzer (1959)


mutation

Benzer (1959) experiment

Problem Set 5

Benzer (1959)


Benzer (1959)Determine distances between markers by

Recombination

Benzer (1959)I still have trouble connecting recombination with the distance b/w genetic markers.


Richard Twyman, University of Warwick


Elizabeth Ellis University of Strathclyde

Goodbye fromMolecular Biology Through Discovery

Thursday, 19 September 2013

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Welcome to Molecular Biology Through Discovery Tuesday, 17 September 2013 DNA Structure / Benzer...

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