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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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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Base always attached here

Phosphates are attached there

Figure 9.10

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dNMP
A, G, C or T

NMP
A, G, C or U

Figure 9.9

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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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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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 Chargaffs Data

% A = % T & %G = %C However %AT DID NOT = %GC This observation became known as Chargaffs rule

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Watson & Crick Model DNA Structure

Base Pairing Key to DNA Structure

Features of the DNA Double Helix

2 nm P 5end
H HO

3end
HH

H HH N

One complete turn 3.4 nm

A S P S P S G C P S P 5phosphate 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 3hydroxyl 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

H2N O H N O P O CH2 O O HH HH H O N N N H

O H HH

O CH2 O P O O

NH NH2 2 N

HH O H

H2N H N

N N H

O CH2 O P O O

O O N O O P O CH2 O N NH2 O HH HH H H H H N N O O P O CH2 O N O HH HH H OH H

HH N
N O H

HH

O CH2 O P O O

H N O CH3

H2N

3end

5 end

Features of the DNA Double Helix

Minor groove Minor groove

Major groove

Major groove

Ball-and-stick model of DNA

Space-filling model of DNA

Major Helical Conformations of DNA

A-DNA B-DNA

Melting Point Curve: Tm is Proportional to %GC

A260

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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