What would you like discussed in class, on any subject that has already come up?
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Transcript of What would you like discussed in class, on any subject that has already come up?
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Welcome toMolecular Biology Through Discovery
Tuesday, 18 September 2012DNA Structure / Sanger & Tuppy
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What would you like discussed in class, on any subject that has already come up?
General Questions
The mentor list and clarification on who,
what, when, etc.
Who can we pick, how many can we choose from?
What are we turning in exactly on Thursday???
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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
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DNA Structure
Biology Today and Tomorrow
Starr, Evers, and Starr (2010)
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DNA Structure
Biology: Understanding
Life
Alters (2000)
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DNA StructureE. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?
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DNA StructureE. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?
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DNA Structure
It's necessary to be slightly underemployed if you are
to do something significant.
- Jim Watson
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From the nucleotides shown above, construct a double-stranded DNA fragment with the sequence ACTG.
You may: duplicate (Ctrl-d) horizontal flip (Alt-hgoh) vertical flip (Alt-hgov) and/or rotate (Alt-hgor)the nucleotides, but you may not change the relative positions of their atoms.
NH
2
N
N
N
N
PO
OO
O
-
NH
2
NN
N
O
PO
OO
O
-
O
NNH
O
PO
OO
O
-
NH
2
N
N
N
NH
O
PO
OO
O
-
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DNA Directionality & PalindromesSQ10. If one strand of DNA had the sequence 5'-GGACT-3', what would be the sequence of the second strand?
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DNA Directionality & PalindromesI understand what a
palindrome is in English but when it comes to DNA how come 5'-AGTTGA-3' isn't a palindrome when it's anti-parallel strand is
3'-TCAACT-5' which is also a palindrome.
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Palindromic Sequences
What is it?
What about with DNA? GCTATCG
Backwards = forwards ROTATOR
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
• DNA is double stranded
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What is it?
What about with DNA? GCTATCG
Backwards = forwards ROTATOR
• DNA is redundant
TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
• DNA is double stranded
Palindromic Sequences
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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
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TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
5’- -3’3’- -5’
TAT GGCATGCTAGC
TTAAT TCATTAATTA AGTAA
CGTACGATCGG TAT
DNA: cruciform
RNA: stem/loop
Palindromic SequencesPalindromic sequences as structural RNA
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TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA
5’- -3’3’- -5’
tRNA
UAU GGCAUGCUAGC
UUAAU UCAUU
DNA: cruciform
RNA: stem/loop
Palindromic SequencesPalindromic sequences as structural RNA
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Palindromic SequencesPalindromic sequences as protein binding sites
why palindromes are targeted by DNA-binding proteins
why [are] palindromes… targeted by DNA-binding
proteins
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recognizes GTGAGTT
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA
Palindromic SequencesPalindromic sequences as protein binding sites
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NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA
Palindromic SequencesPalindromic sequences as protein binding sites
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Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTG
AGCTAACT
CACATTAA
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Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNN
NNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT
AATGAGTGAGCTAACTCACATTAA
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Palindrom
ic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNN
NNNNNNNNNNNNNNN
NNNNNNNNNNNNN
NNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT
AATGAGTGAGCTAACTCACATTAA
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recognizes GTGAGTT
Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATTAATGAGTGAGCTAACTCACATTAA
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Palindromic Sequences
Palindromic sequences as protein binding sites
NNNNNNNN
NNNNNNN
NNNNNNNN
NNNNNNN
NNNNNNNN
NNNNN
NNNNNNNN
NNNNN
TTAATGTG
AGTTAGCT
CACTCATT
AATGAGTGAGCTAACTCACATTAA
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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
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Palindromes: Serve as binding sites for dimeric protein
Palindromic SequencesPalindromic sequences as protein binding sites
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNN
TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA
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GTA ..(8).. TAC
5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
gene
Palindromic SequencesPalindromic sequences as protein binding sites
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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,
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Sanger and Tuppy (1951)
Phe-Val-Asp-Glu-His-Leu-Cys-Gly
Thr-Pro-Lys-Ala
Gly-Glu-Arg-Gly-Tyr-Leu-Val-Cys-Gly
Ser-His-Leu-Val-Glu-Ala
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Sanger and Tuppy (1951)
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Sanger and Tuppy (1951)
Insulin is a dimer, composed of one A chain (fraction A) and a B chain (fraction B). Sanger and Tuppy determined this experimentally by oxidizing insulin with performic acid. The sequence of fraction B was determined experimentally as being at least composed of phenylalanine, valine, aspartic acid, and glutamic acid, and well as threonine, proline, lysine, and alanine. This was done using a prepared sample of polypeptide fragments, which were separated through a process known as paper chromatography. A similar process was done for fraction A. From all the studies perform, the overall structure and cross linking between chains can be deduced. Cross-linking can occur on cysteine residues, because they contain sulfur atoms, capable of dimerizing with one another and forming stable covalent bonds. Overall, two phenylalanine and two glcyl chains were determined to be the subunits of this particular form of insulin.
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Sanger and Tuppy (1951)
Now, how this was deduced was through a number of chromatography tests where different chemicals were used in order to split insulin at different bond points and then examine the fragments. In the first section we can see Phe.Val.Asp.Glu.His.Leu.CySO3H.Gly which has been determined by the following: B4β2, B1α2, B2γ8, B1α1, B1β8, B1γ1, B1α6, B1β13, B1γ4, B1β10, B1α5, B1γ7, B1β12, B4β1, B1γ6, B1β5. Where B1α1 refers to the test number and type, then spot number.
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Sanger and Tuppy (1951)
1. Cys-Gly B1a.1
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Sanger and Tuppy (1951)
1. Cys-Gly B1a.1
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Sanger and Tuppy (1951)
1. Cys-Gly B1a.12. Leu-Cys B1a.6
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Sanger and Tuppy (1951)
1. Cys-Gly B1a.12. Leu-Cys B1a.63. Leu-Cys-Gly #1 & #2
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Sanger and Tuppy (1951)
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Sanger and Tuppy (1951)
1. Cys-Gly B1a.12. Leu-Cys B1a.63. Leu-Cys-Gly #1 & #2
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Results vs Conclusions
Shahroze Mandi Shaun
Bobby Supriya Tayab
Kaleigh Jonathan Michael Colleen
AbdulCailin Sue Kristen
Abdallah Celeste Neda Yordanos
Me And go to CyanoBIKE
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Sanger and Tuppy (1951)
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Coming Attractions
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Benzer (1959)
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Goodbye fromMolecular Biology Through Discovery
Tuesday, 18 September 2012
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 ...G-O-O-D-B-Y-E