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DNA Structure/Composition
Taryono
Faculty of Agriculture
Gadjah Mada University
Flow of Genetic Information
RNA
Transcription
DNA
Replication
Protein
Translation
DNA

Discovery of the DNA double helix
A. 1950’s
B. Rosalind Franklin - X-ray photo of DNA.
C. Watson and Crick - described the
DNA molecule from Franklin’s X-ray.
DNA is the Genetic Material




DNA encodes all the information in the cell
The composition of the DNA is the same in all cells
within an organism
 Variation among different cells is achieved by
reading the DNA differently
DNA contains four bases that encode all the
information to make a bacteria or a human
In some viruses the genetic material is RNA
How is Information Encoded in
DNA?



DNA Consists of four kinds of
bases (A,C,G,T) joined to a
sugar phosphate backbone
Bases carry the genetic
information while the phosphate
backbone is structural
Two complementary strands of
bases (C-G) and (A-T)
DNA is a Polymer of
Deoxyribonucleotide Units
DEOXYRIBONUCLEOTIDE
DEOXY RIBO NUCLEOTIDE
Deoxyribonucleic Acid (DNA)
Nucleotide:
1. Phosphate group
2. 5-carbon sugar
3. Nitrogenous base

~2 nm wide
DNA Nucleotide
Phosphate
Group
O
O=P-O
O
5
CH2
O
N
C1
C4
Sugar
(deoxyribose)
C3
C2
Nitrogenous base
(A, G, C, or T)
DNA Double Helix
“Rungs of ladder”
Nitrogenous
Base (A,T,G or C)
“Legs of ladder”
Phosphate &
Sugar Backbone
DNA Double Helix
5
O
3
3
O
P
5
O
C
G
1
P
5
3
2
4
4
2
3
1
P
T
5
A
P
3
O
O
P
5
O
3
5
P
Nitrogenous Bases

PURINES
1. Adenine (A)
2. Guanine (G)

A or G
PYRIMIDINES
3. Thymine (T)
4. Cytosine (C)
T or C
BASE-PAIRINGS
Purines
Pyrimidines
Base
Pairs
Adenine (A)
Thymine (T)
A=T
Guanine (G)
Cytosine (C)
C G
3 H-bonds
G
C
# of
H-Bonds
2
3
BASE-PAIRINGS
H-bonds
G
C
T
A
Chargaff’s Rule

Adenine must pair with Thymine

Guanine must pair with Cytosine

Their amounts in a given DNA molecule will be
about the same.
T
A
G
C
Deoxy ribo nucleotide
Ribose= Five Carbon Sugar Molecule
HOCH2
5´
H
4´
H
3´
HO
OH
O
H
1´
2´ H
OH
Ribose (RNA)
HOCH2
5´
H
4´
H
3´
HO
OH
O
H
1´
2´ H
H
Deoxyribose (DNA)
Backbone Sugar Molecules
O
O P O
O
H2 C 5´
H
H
The DNA Backbone is a
OH
Deoxyribose Polymer
O
H
3´ 2´
1´
H
O
H
O P O
O
H2 C 5´ O OH
H
H 1´
H
3´ 2´
Deoxyribose sugars
are linked by
Phosphodiester Bonds
H
O
H
O P O
O
-
H2 C 5´ O OH
H
H 1´
H 3´ 2´ H
HO
H
5´-p
5´
3´-OH
3´
O
O P O
-
5´
O
5´
3´
H2 C 5´ O OH
H H
1´
H
-
3´ 2´
O
H
H
O P O
O
H2 C 5´ O OH
H H
1´
H
-
O3´ 2´
H
H
O P O
O
H2 C 5´ O OH
H H
1´
H
H
3´ 2´
HO H
3´
3´
5´
O
O P O
O
O P O
O
O
H2 C 5´ O OH
H
H 1´
H
3´ 2´
H
H
O
H
O P O
O
3´ 2´
3´ 2´
H
O
H
O P O
O
H2 C 5´ O OH
H
H 1´
H
OH
H2 C 5´ O Base
H
H 1´
H
O
H
O P O
O
-
H2 C 5´ O OH
H
H 1´
H 3´ 2´ H
HO
H
OH
H2 C 5´ O Base
H
H 1´
H
3´ 2´
O
H
O P O
O
H
-
OH
H2 C 5´ O Base
H
H 1´
H 3´ 2´ H
HO
H
DeoxyRibonucleotide NH2
N
HC
O-
NH2
N
HC
N
CH
N
O
O
O
N
P O P O P OCH2 O
H
H
OOOH
H
HO
H
CH
N
N
HOCH2 O
H
H
H
HO
N
Deoxyadenosine
5´-triphosphate
(dATP)
H
H
DeoxyRibonucleoside Deoxyadenosine
DNA is Composed of Four
Different Ribonucleotides
NH2
C
N
C
N
CH
9
C C N
H N
H
Adenine
HN
O C
O
C
1
N
H
C
C
O
C
Two
Purines
N
H N
C
CH
9
C C N
N
H2 N
H
Guanine
CH3
H
Thymine
Two
Pyrimidines
O
NH2
C
H
N
C
C 1 C
N
H
H
Cytosine
O
O P O
O
C
CH3
HN
C
O
O C
C
N
H
H2 C
O
H
H
H
T
A
C
G
5´
3´
H
O
H NH2
O P O
C
H
N
C
O
O C
C
N
H
H2 C O
H
H
H
H
O
H O
O P O
C
CH3
HN
C
O
O C
C
H
H2 C O N
H
H
-
H
HO
H
H
T
A
3´
5´
Base Pairing Follows:
Chargaff’s Rule:

DNA has equal numbers of thiamines
and adenines (A=T) and equal numbers
of guanines and cytosines (G=C)
Note that in each pair there is one purine and one pyrimidine
A-T
G-C
Base Pairing Occurs Through
Hydrogen Bonds
G-C
A-T
G
C
=
A
T
Advantages of Double-Stranded
Nature of DNA

Forms a stable structure
 Hydrophobic
bases stack on top of one
another away from solvent
 Charged phosphate backbone is on the
outside accessible to solvent

Each strand can serve as the template
 For
a new strand of DNA (replication)
 For an RNA molecule (transcription)
Double-stranded DNA Forms a
Double Helix
Native DNA Forms a B-DNA
Helix



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Two strands wind about each
other in a right-handed manner
Diameter: ~20Å
Bases per turn: 10 (~34Å)
A major and a minor groove
Major
Minor
20Å
DNA is Highly Packaged within
the Cell

If the DNA from a single human cell were
stretched out end to end, it would be ~2 meters in
length
DNA
2M
Cell Nucleus (magnified
lots of times)
-8
5 x 10 M
Mechanisms of Packaging

Has to be Organized so that DNA can be
Untangled for Replication and Transcription
 Supercoiling
 Wrapping

around Proteins to Create Chromatin
Enzymes that Modulate the Packaging of
DNA are called Topoisomerases
Supercoiling

Most native DNA exists in a negatively
supercoiled state
 This
means that it is slightly unwound and it is a bit
easier to pull the two strands apart
More supercoiling
Topoisomerases Modulate
Supercoiling

Topoisomerases act as Molecular Scissors
 They
can make a cut in the DNA and pass second strand
through that break to untangle the DNA
DNA is Coiled Around Histone
Proteins

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DNA is wrapped
around abundant
nuclear proteins
called Histones
This forms a
complex called a
Nucleosome
Histones are H1,
H2A, H2B, H3, H4
DNA is Further Packaged
Take Home Message
DNA is a double helix composed of a sugarphosphate backbone and base pairs (a
polymer of deoxyribonucleotides)
 Composition/Structure
 DNA is compacted to fit into the cell through:

 Supercoiling
 Extensive

interactions with proteins
These factors all contribute to how the DNA
is Read