PowerPoint Presentation Materials
to accompany
Genetics: Analysis and Principles
Robert J. Brooker
CHAPTER 9
MOLECULAR STRUCTURE
OF DNA AND RNA
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INTRODUCTION

In this chapter we will shift our attention to
molecular genetics

The study of DNA structure and function at the
molecular level
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9-2
9.1 IDENTIFICATION OF DNA AS
THE GENETIC MATERIAL
Frederick Griffith
the first widely accepted demonstrations
of bacterial transformation
He found something in the lab but no in
hurry for publication. This is his line.
“Almighty God is in no hurry, why should I be? “
“Disappointment is my daily bread, but I thrive on
it“
Frederick Griffith
Born
1879
Died
1941
Griffith’s Experiment, 1927
Figure 9.2
9-8
Frederick Griffith Experiments
with Streptococcus pneumoniae


Griffith studied a bacterium (pneumococci) now
known as Streptococcus pneumoniae (ZATÜRE)
S. pneumoniae comes in two strains
 S  Smooth

Secrete a polysaccharide capsule



Protects bacterium from the immune system of animals
Produce smooth colonies on solid media
R  Rough


Unable to secrete a capsule
Produce colonies with a rough appearance
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9-5

In addition, the capsules of two smooth strains can differ
significantly in their chemical composition
Figure 9.1

Rare mutations can convert a smooth strain into a rough
strain, and vice versa

However, mutations do not change the type of the strain
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9-6
Oswald Theodore Avery
(1877-1955)
He is best known for his discovery that
deoxyribonucleic acid (DNA) serves as genetic
material
For many years, genetic information was
thought to be contained in cell protein.
The Experiments of Avery,
MacLeod and McCarty


Avery, MacLeod and McCarty realized that
Griffith’s observations could be used to identify
the genetic material
They carried out their experiments in the 1940s


At that time, it was known that DNA, RNA, proteins and
carbohydrates are major constituents of living cells
They prepared cell extracts from type IIIS cells
containing each of these macromolecules



Only the extract that contained purified DNA was able
to convert type IIR into type IIIS
Treatment of the extract with RNase or protease did not
eliminate transformation
Treatment with DNase did
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
Figure 9.3
Avery et al also conducted the following experiments

To further verify that DNA, and not a contaminant (RNA
or protein), is the genetic material
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9-11
RNA Functions as the Genetic
Material in Some Viruses

In 1956, A. Gierer and G. Schramm isolated RNA
from the tobacco mosaic virus (TMV), a plant virus

Purified RNA caused the same lesions as intact TMV
viruses


Therefore, the viral genome is composed of RNA
Since that time, many RNA viruses have been
found

Refer to Table 9.1
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9-20
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9.2 NUCLEIC ACID
STRUCTURE

DNA and RNA are large macromolecules with
several levels of complexity




1. Nucleotides form the repeating units
2. Nucleotides are linked to form a strand
3. Two strands can interact to form a double helix
4. The double helix folds, bends and interacts with
proteins resulting in 3-D structures in the form of
chromosomes
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9-22
Figure 9.7
9-23
Nucleotides

The nucleotide is the repeating structural unit of
DNA and RNA

It has three components




A phosphate group
A pentose sugar
A nitrogenous base
Refer to Figure 9.8
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9-24
Figure 9.8
9-25

These atoms are found within individual nucleotides

However, they are removed when nucleotides join together to make
strands of DNA or RNA
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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9-26

Base + sugar  nucleoside


Base + sugar + phosphate(s)  nucleotide


Example
 Adenine + ribose = Adenosine
 Adenine + deoxyribose = Deoxyadenosine
Example
 Adenosine monophosphate (AMP)
 Adenosine diphosphate (ADP)
 Adenosine triphosphate (ATP)
Refer to Figure 9.10
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9-27
Base always
attached here
Phosphates are
attached there
Figure 9.10
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9-28

Nucleotides are covalently linked together by
phosphodiester bonds


A phosphate connects the 5’ carbon of one nucleotide to
the 3’ carbon of another
Therefore the strand has directionality

5’ to 3’
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9-29
Figure 9.11
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Discovery of the Structure of DNA

In 1953, James Watson and Francis Crick
discovered the double helical structure of DNA

The scientific framework for their breakthrough was
provided by other scientists including



Linus Pauling
Rosalind Franklin and Maurice Wilkins
Erwin Chargaff
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9-31
Linus Pauling
Linus Pauling (1901-1994)
the only person to win two Nobel prizes
1954 Nobel Prize in Chemistry
1962 Nobel Peace Prize


He elucidated a-helix structure,
and he built ball-and-stick models
Linus Pauling

In the early 1950s, he
proposed that regions of
protein can fold into a
secondary structure


a-helix
To elucidate this structure,
he built ball-and-stick
models
Figure 9.12
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9-32
Rosalind Elsie Franklin
(1920-1958)
a British chemist and crystallographer who
is best known for her role in the discovery
of the structure of DNA
It was her x-ray diffraction photos of DNA
and her analysis of that data--provided to
Francis Crick and James Watson without
her knowledge--that gave them clues
crucial to building their correct theoretical
model of the molecule in 1953
Rosalind Franklin

She used X-ray
diffraction to study
wet fibers of DNA
The diffraction pattern is interpreted
(using mathematical theory)
This can ultimately provide
information concerning the
structure of the molecule
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9-33
Rosalind Franklin

She made marked advances in X-ray diffraction
techniques with DNA

The diffraction pattern she obtained suggested
several structural features of DNA



Helical
More than one strand
10 base pairs per complete turn
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9-34
Erwin Chargaff
(1905 – 2002)
Chargaff discovered two rules that helped lead
to the discovery of the double helix structure
of DNA
Erwin Chargaff’s Experiment
1- DNA the number of guanine units equals the number of
cytosine units, and the number of adenine units equals the
number of thymine units.
2- The relative amounts of guanine, cytosine, adenine and
thymine bases varies from one species to another. This
hinted that DNA rather than protein could be the genetic
material.
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9-35
Watson and Crick

Familiar with all of these key observations, Watson
and Crick set out to solve the structure of DNA


They tried to build ball-and-stick models that incorporated
all known experimental observations
A critical question was how the two (or more strands)
would interact


An early hypothesis proposed that the strands interact
through phosphate-Mg++ crosslinks
Refer to Figure 9.15
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9-41
Figure 9.15

This hypothesis was, of course, incorrect!
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9-42
Watson and Crick


They went back to the ball-and-stick units
They then built models with the



They first considered a structure in which bases form
H bonds with identical bases in the opposite strand


Sugar-phosphate backbone on the outside
Bases projecting toward each other
ie., A to A, T to T, C to C, and G to G
Model building revealed that this also was incorrect
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9-43
Watson and Crick

They then realized that the hydrogen bonding of A
and T resembled that between C and G

So they built ball-and-stick models with AT and CG
interactions



These were consistent with all known data about DNA structure
Refer to Figure 9.16
Watson, Crick and Maurice Wilkins were awarded
the Nobel Prize in 1962

Rosalind Franklin died in 1958, and Nobel prizes are not
awarded posthumously
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9-44
The DNA Double Helix

General structural features (Figures 9.17 & 9.18)



Two strands are twisted together around a
common axis
There are 10 bases and 3.4 nm per complete twist
The two strands are antiparallel


One runs in the 5’ to 3’ direction and the other 3’ to 5’
The helix is right-handed

As it spirals away from you, the helix turns in a
clockwise direction
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9-45
Figure 9.17
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9-48
The DNA Double Helix

General structural features (Figures 9.17 & 9.18)

There are two asymmetrical grooves on the
outside of the helix

1. Major groove

2. Minor groove

Certain proteins can bind within these grooves

They can thus interact with a particular sequence of bases
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9-47
Figure 9.17
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9-48
Figure 9.18
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9-49
DNA Can Form Alternative Types
of Double Helices

The DNA double helix can form different
types of secondary structure

The predominant form found in living cells is
B-DNA

However, under certain in vitro conditions,
A-DNA and Z-DNA double helices can form
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9-50

A-DNA





Right-handed helix
11 bp per turn
Occurs under conditions of low humidity
Little evidence to suggest that it is biologically important
Z-DNA



Left-handed helix
12 bp per turn
Its formation is favored by



GG-rich sequences, at high salt concentrations
Cytosine methylation, at low salt concentrations
Evidence from yeast suggests that it may play a role in
transcription and recombination
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9-51
Bases
substantially
tilted relative
to the central
axis
Bases
substantially
tilted relative
to the central
axis
Bases relatively
perpendicular to the
central axis
Sugar-phosphate
backbone follows a
zigzag pattern
Figure 9.19
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DNA Can Form a Triple Helix
Edirne Selimiye Mosque
DNA Can Form a Triple Helix

In the late 1950s, Alexander Rich et al discovered
triplex DNA


It was formed in vitro using DNA pieces that were made
synthetically
In the 1980s, it was discovered that natural doublestranded DNA can join with a synthetic strand of
DNA to form triplex DNA

The synthetic strand binds to the major groove of the
naturally-occurring double-stranded DNA

Refer to Figure 9.20
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9-53

T binds to an
AT pair in
biological DNA


C binds to a
CG pair in
biological DNA
Triplex DNA has been
implicated in several
cellular processes


Figure 9.20
Triplex DNA formation
is sequence specific
The pairing rules are
Replication,
transcription,
recombination
Cellular proteins that
specifically recognize
triplex DNA have been
recently discovered
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stabilized by the presence of a cation, especially potassium
Model for quadruplex-mediated down-regulation of gene expression
DNA wound
around histone
proteins
Figure 9.21
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RNA Structure

The primary structure of an RNA strand is much
like that of a DNA strand

Refer to Figure 9.22 vs. 9.11

RNA strands are typically several hundred to
several thousand nucleotides in length

In RNA synthesis, only one of the two strands of
DNA is used as a template
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9-57
Figure 9.22
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
Although usually single-stranded, RNA molecules
can form short double-stranded regions

This secondary structure is due to complementary basepairing



This allows short regions to form a double helix
RNA double helices typically



A to U and C to G
Are right-handed
Have the A form with 11 to 12 base pairs per turn
Different types of RNA secondary structures are
possible

Refer to Figure 9.23
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9-59
Complementary regions
Held together by
hydrogen bonds
Figure 9.23
Noncomplementary regions
Have bases projecting away
from double stranded regions
Also called
hair-pin
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9-60

Many factors
contribute to the
tertiary structure of
RNA

Molecule contains
single- and doublestranded regions
For example


Base-pairing and
base stacking within
the RNA itself
These spontaneously
interact to produce
this 3-D structure
Interactions with
ions, small
molecules and large
proteins
Figure 9.24

Figure 9.24 depicts the tertiary structure of tRNAphe

The transfer RNA that carries phenylalanine
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9-61