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Tuesday, 18 September 2012DNA Structure / Sanger & Tuppy

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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 ...

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DNA Structure

Biology Today and Tomorrow

 Starr, Evers, and Starr (2010)

DNA Structure

Biology: Understanding

Life

Alters (2000)

DNA StructureE. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?

DNA StructureE. How can the helical structure of DNA and internucleotide distance be discerned from Franklin and Gosling's x-ray photograph?

DNA Structure

It's necessary to be slightly underemployed if you are

to do something significant.

- Jim Watson

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

-

DNA Directionality & PalindromesSQ10. If one strand of DNA had the sequence 5'-GGACT-3', what would be the sequence of the second strand?

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.

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,

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

Sanger and Tuppy (1951)

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.

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.

Sanger and Tuppy (1951)

1. Cys-Gly B1a.1

Sanger and Tuppy (1951)

1. Cys-Gly B1a.1

Sanger and Tuppy (1951)

1. Cys-Gly B1a.12. Leu-Cys B1a.6

Sanger and Tuppy (1951)

1. Cys-Gly B1a.12. Leu-Cys B1a.63. Leu-Cys-Gly #1 & #2

Sanger and Tuppy (1951)

Sanger and Tuppy (1951)

1. Cys-Gly B1a.12. Leu-Cys B1a.63. Leu-Cys-Gly #1 & #2

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

Sanger and Tuppy (1951)

Coming Attractions

Benzer (1959)

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