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1-Nucleotides and Nucleic Acids
1-Nucleotides and Nucleic Acids
DNA
dNTPs
transcription
rNTPs
RNA
Protein
salvage
synthesis
catabolism
Breakdown products
De novo
synthesis
Metabolites
(amino acids, HCOO-, etc.)
Last ~3 Lectures
iClicker Question
To which of the following things is the
red arrow NOT pointing?
A) A purine residue
B) An adenine residue
C) A 5 end residue
D) A deoxyadenosine residue
E) None of the above
Base
Phosphates
Purine or Pyrimidine
1, 2, or 3
Sugar
Ribose or Deoxyribose
Nucleoside
Nucleotide
C
Furanose rings
Fischer
Projection
D-ribose
-D-ribose
(this anomer found in some
nucleotide precursors)
Linear aldehyde
-D-2-deoxyribose
(found in deoxynucleotides
and DNA)
:
:
pyrimidine
:
:
purine
They are classical Bronsted bases, because N1 and N3 of pyrimidine, and N1, N3, and
N7 of purine have pairs of non-bonding electrons that can be used to form covalent bonds to
protons. pKas are in the 4-5 range.
Questions:
1) Will the nitrogens be protonated at physiological pH? Why or why not?
2) Why isnt N9 of purine basic?
iClicker Question
Which of the following statements describes the
state of the N1, N3, and N7 nitrogen atoms in purine
and pyrimidine at physiological pH?
A. They will not be protonated because their pKas are too high.
B. They will not be protonated because their pKas are too low.
C. They will all be protonated.
D. Only N7 will be protonated.
E. I dont know.
iClicker Question
Why isnt N9 of the purine ring basic?
A. N9 is sp3 hybridized and therefore cannot accept a proton
B. The non-bonding electrons on N9 are delocalized
C. Protonation of N9 would lead to a loss of resonance
stabilization
D. Both B and C
E. All of the above
:
:
NH2
3
2
5
6
1
2
8
4
N
X
X
O
H
O
H
O
N
CH3
O
N
X
N
X
H2N
N
N
Idiosyncratic nomenclature
Bases
Nucleosides Nucleotides
Cytosine
Uracil
Thymine
Adenine
Guanine
Cytidine
Uridine
Thymidine
Adenosine
Guanosine
Cytidylic acid
Uridylic acid
Thymidylic acid
Adenylic acid
Guanylic acid
1.10) Tautomerism
The bases can exist in multiple tautomeric forms.
H
O
H
H2N
Keto tautomer
(>99.9%)
N
X
H2N
Enol tautomer X
<0.1%)
O
H
keto
H2N
enol
N
X
H2N
N
X
iClicker Question
In the above equilibrium, why does the keto
tautomer predominate over the enol tautomer?
A. The standard free energy of the keto tautomer is greater than
the standard free energy of the enol tautomer.
B. The standard free energy of the keto tautomer is less than the
standard free energy of the enol tautomer.
C. The O-H bond is more polarized than the N-H bond.
D. The keto tautomer is better able to form a Watson-Crick
basepair than is the enol tautomer.
E. Both B and C.
pKa = 7
pKa = 12
pyrophosphate
pKas of pyrophosphoric acid = 1, 2.5, 6.1, 8.5
(e.g., 2, 3, or 5 O of ribose)
Monoester pKas 1, 6
Diester pKa 1
II.
III.
B.
Nitrogen basicity
B.
In phase
Out of phase
n
2sin B
Helical Pitch = 34
2)
3)
4)
O
H
H2N
N
X
H2N
N
X
Presumably you could measure the equilibrium ratio by NMR or some other
spectroscopic technique, but I was unable to find such measurements in the
literature.
Watson and Crick relied on quantum mechanical calculations to which they were
referred by Cavendish laboratory colleague Jerry Donahue.
The keto tautomeric state has since been verified by countless crystallographic
and NMR studies.
iClicker Question
To calculate the distance (d) associated with a
spot in a fiber diffraction pattern, which of the
following things do we NOT need to know?
A. The distance of the spot from the center of the diffraction
pattern.
B. The distance of the X-ray source from the specimen.
C. The distance of the film from the specimen.
D. The wavelength of the radiation.
E. None of the above.
2.
Strands are linked by complementary sets of Hbond donors and acceptors on the bases!!
Watson and Crick (1953): It has not escaped our
notice that the specific pairing we have postulated
immediately suggests a possible copying mechanism
for the genetic material.
iClicker Question
Why does the DNA double helix only
contain AT and GC basepairs?
A. These are the only pairs of bases that have
complementary arrays of H-bonding groups.
B. These are the only pairs of bases that fit into the double
helix without leaving any unsatisfied H-bond donors or
acceptors.
C. These are the only basepairs that exhibit perfect symmetry.
D. Both A and B.
E. All of the above.
B.
II.
2.
Chargaffs rules
3.
Watson/Crick basepairs
A.
B.
C.
A-DNA
Reversible transition
B-DNA
H2O
Implies that B-form is stabilized by an interaction with water.
Rosalind Franklin was the first to recognize that there were two different
forms of DNA and to coin the terms A- and B-DNA.
Because she recognized this, she was able to look at one form at a time
explaining the high quality of her fiber diffraction data
Experimental Method
X-ray structures 102,151
NMR structures 11,214
EM structures 922
Hybrid 89
Other 193
PDB ID (year)
Sequence
1BNA (1981)
3BSE (2009)
3V9D (2012)
1ZF1 (2005)
CGCGAATTCGCG*
ACTACAATGTTGCAAT
CCCCGGTACCGGGG
CCGGGCCCGG
Helical
axis
150
A-DNA
26
2.9
31
11.6 bp
34
20
12
C3-endo
Important differences
1)
A-DNA has less rise than B-DNA due, in part, to the different sugar puckers
2)
3)
a)
b)
Results in 6 hole
80 (close to g-)
Butane
(Newman projection)
Voet, Voet, and Pratt: Figures 24-5 and 24-7
3BSE
iClicker Question
What is this basepair?
5-me O4 N6 N7
N7
O6 N4
A) TA
B) AT
C) CG
D) GC
E) None of the above
3BSE
iClicker Question
What is this basepair?
N3
O2
N2 O2
N3
A) TA
B) AT
C) CG
D) GC
E) None of the above
G
N
NH2
2
HN
O
NH2
2
HN
HN
HN
T
Dickerson, R.E. (1983)
Scientific American 249,
94-111
NH2
HN
N
W
NH2
NHW
2
iClicker Question
Why does water stablize
B-DNA relative to A-DNA?
A) Only the B-DNA minor groove has appropriate H-bonding
groups for H-bonding to water.
B) The narrow minor groove of A-DNA excludes water while the
broader minor groove of B-DNA admits water.
C) Both A and B.
D) None of the above.
Z-DNA
B-DNA
2DCG
3BSE
anti
syn
?
C2 endo
anti
anti
2DCG
1BNA
estions:
Why do bulky substituents (e.g., Br) at 8 position of purine ring favor Z-DNA?
Why does high salt favor Z-DNA?
II.
III.
B.
How do the overall shape of A- and B-form helices differ and how
do the different sugar puckers contribute to this?
C.
D.
E.
Z-form helices
A.
B.