NUCLEIC ACID STRUCTURE
• DNA and RNA are large macromolecules with
several levels of complexity
• Nucleotides form the repeating units
• Phosphodiester bonds link
nucleotides to form a strand
• Two strands interact to form
a double helix
• The double helix interacts with
proteins resulting in 3-D structures
in the form of chromatin
3D structure
Nucleotide Components
Figure 9.8
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9-25
Combining all the parts
• Base + sugar  nucleoside
– Example
• Adenine + ribose = Adenosine
• Adenine + deoxyribose = Deoxyadenosine
• Base + sugar + phosphate(s)  nucleotide
– Example
• Adenosine monophosphate (AMP)
• Adenosine diphosphate (ADP)
• Adenosine triphosphate (ATP)
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9-27
Base always
attached here
Phosphates are
attached there
Figure 9.10
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dNMP
NMP
A, G, C or T
Figure 9.9
A, G, C or U
The structure of nucleotides found in (a) DNA and (b) RNA
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Nucleotide Polymerization Reaction:
Phosphodiester Bond Formation
Figure 9.11
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9-30
•
Events Leading to DNA Structure
1953, James Watson
and Francis Crick discovered
Determination
the double helical structure of DNA
• The scientific framework for their breakthrough was
provided by other scientists including
– Linus Pauling
– Rosalind Franklin
– Erwin Chargaff
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9-31
Linus Pauling
Rosalind Franklin
• Helical
• Double stranded
• 10 base pairs per turn
X-ray Diffraction Pattern of DNA
Experiment
• It was assumed the four bases: A, G, C and T
were in a repeating, tetranucleotide configuration
• Therefore, there should be the same amount of A,
G, C & T in any molecule of DNA form any source
• Chargaff carefully determined the exact
percentages of nuceotides in DNA from several
sources
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Erwin Chargaff’s Data
• % A = % T & %G = %C
• However %AT DID NOT = %GC
• This observation became known as Chargaff’s rule
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Watson & Crick
Model DNA
Structure
Base Pairing Key to DNA
Structure
Features of the DNA Double
Helix
2 nm
5end
P
One complete
turn 3.4 nm
H2N
N
N
O–
N
H
N
O P O CH2
O
–
O
HH
HH
O
H
HH
H
H2N
H
N
N
O
O
N
O
O P O CH2 O
N
NH2
O–
HH
HH
H
H
H
H N
N
O
O
O P O CH2 O
N
O–
HH
HH
H
OH H
3end
H
N
O–
CH2 O P O
O
H
NH
NH22
N
HH
O
N
O
HO
H HH
H
A S
P S
P
S
G C
P
S
P
5phosphate
S
G C
P S
SC P S
P S
P
S P
S
A T S P
G C S P
S
P
C G S
S P
T A P
S
P S
P
3hydroxyl
S
P
G
P S
C G P
S
P
T A
S
P
S G C
P S
One nucleotide
A T
S
S
P
0.34 nm
S
P
P
SC G
S P
S C G
P
3end
H
HH
O
N
H
N
O–
CH2 O P O
O
H
HH
N
N
HH
O
H
O–
CH2 O P O
O–
H2N
O
CH3
5 end
Features of the DNA Double
Helix
Minor
groove
Major
groove
Minor
groove
Major
groove
Ball-and-stick model of DNA
Space-filling
model of DNA
Major Helical Conformations of
DNA
A-DNA
B-DNA
A260
Melting Point Curve:
Tm is Proportional to %GC
Tm= 68.9 + (0.41)(%GC)
The Three-Dimensional Structure
of DNA
Figure 9.21
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RNA Structure
• The primary structure of an RNA strand is much
like that of a DNA strand
• RNA is made as a single strand only, however it
may form a double stranded structures
• RNA strands can be a 10s to1000s of nt in length
• RNA is made from a DNA template - only one of
the two strands of a DNA helix is used as the
template
• RNA contains uracil rather than thymine
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Figure 9.22
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RNA Secondary Structures
Figure 9.23
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RNA Tertiary Structure – a tRNA
Figure 9.24
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