Welcome to
Molecular Biology Through Discovery
Tuesday, 17 September 2013
DNA Structure
DNA Structure
Biology Today
and Tomorrow
Starr, Evers, and
Starr (2010)
DNA Structure
Biology:
Understanding
Life
Alters (2000)
DNA Structure
E. How can the helical structure of DNA and
internucleotide distance be discerned from
Franklin and Gosling's x-ray photograph?
DNA Structure
E. How can the helical structure of DNA and
internucleotide distance be discerned from
Franklin and Gosling's x-ray photograph?
DNA Structure
http://h2physics.org/?cat=48
DNA Structure
http://h2physics.org/?cat=48
DNA Structure
http://h2physics.org/?cat=48
DNA Structure
1 Å = 10-8 cm
1 cm
http://h2physics.org/?cat=48
DNA Structure
~D
~D + nλ
a
D
a = f (D, λ, Δx) = λ D / Δx
Would like to be able to do the math.
http://h2physics.org/?cat=48
Δx
DNA Structure
http://h2physics.org/?cat=48
DNA Structure
SQ7. 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 Structure
SQ7. 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 Structure
SQ7. 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?
angle?
?
?
DNA Structure
SQ7. 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 Structure
SQ7. 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?
angle?
?
DNA Structure
DNA Structure
It's necessary to be slightly
underemployed if you are
to do something significant.
- Jim Watson
O
NH
N
N
P
NH
N
N
N
-O
O
2
N
O
O
N
O
O
O
-O
O
P
O
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.
N
NH
NH
N
O
2
O
-O
P
N
N
O
O
O
-O
O
P
O
NH
2
DNA Directionality & Palindromes
SQ10. If one strand of DNA had
the sequence 5'-GGACT-3',
what would be the sequence
of the second strand?
DNA Directionality & Palindromes
I 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?
Backwards = forwards
ROTATOR
What about with DNA?
GCTATCG
• DNA is double stranded
TTAATGTGAGTTAGCTCACTCATT
AATTACACTCAATCGAGTGAGTAA
Palindromic Sequences
What is it?
Backwards = forwards
ROTATOR
What about with DNA?
GCTATCG
• DNA is double stranded
• DNA is redundant
TTAATGTGAGTTAGCTCACTCATT
AATTACACTCAATCGAGTGAGTAA
Palindromic Sequences
What is it?
Backwards = forwards
ROTATOR
What about with DNA?
GCTATCG
• DNA is double stranded
• DNA is redundant
• DNA has direction (read 5’->3’)
5’- TTAATGTGAGTTAGCTCACTCATT -3’
3’- AATTACACTCAATCGAGTGAGTAA -5’
AATGAGTGAGCTAACTCACATTAA
Palindromic Sequences
5’- TTAATGTGAGTTAGCTCACTCATT -3’
3’- AATTACACTCAATCGAGTGAGTAA -5’
TA
T G
GC
AT
GC
TA
GC
TTAAT TCATT
AATTA AGTAA
CG
TA
CG
DNA: cruciform
AT
CG
RNA: stem/loop
G T
AT
Palindromic Sequences
5’- TTAATGTGAGTTAGCTCACTCATT -3’
3’- AATTACACTCAATCGAGTGAGTAA -5’
UA
U G
GC
AU
GC
UA
GC
UUAAU UCAUU
DNA: cruciform
RNA: stem/loop
tRNA
Palindromic Sequences
why [are] palindromes…
targeted by DNA-binding proteins
why palindromes are targeted by DNA-binding proteins
Palindromic Sequences
NNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTNNNNNNNNNNNNN
NNNNNNNNNNNNNN
NNNNNNNNNNNNN
AATGAGTGAGCTAACTCACATTAA
recognizes GTGAGTT
Palindromic Sequences
NNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTNNNNNNNNNNNNN
NNNNNNNNNNNNNN
NNNNNNNNNNNNN
AATGAGTGAGCTAACTCACATTAA
recognizes GTGAGTT
Palindromes: Serve as binding sites for dimeric protein
gene
5’-GTA
3’-CAT
GTA
..(8)..
TAC
..(8)..
..(8)..
TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN
ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
gene
5’-GTA
3’-CAT
GTA
..(8)..
..(8)..
TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN
ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
Transcription
RNA
factor
RNA Polymerase
..(8)..
TAC
Reading articles
Reading articles
• Read through (Highlight problems)
• Reread (Put words to problems)
• Plan solution to problems
(What do you need to know?)
• Solve problems
(Find what you need to know)
Problem Set 5
Problem Set 5
Goodbye from
Molecular Biology Through Discovery
Tuesday, 17 September 2013