1. PowerPoint Presentation Materials to accompany
Genetics: Analysis and Principles
Robert J. Brooker
CHAPTER 9
MOLECULAR STRUCTURE OF DNA AND RNA
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2. 9.1 IDENTIFICATION OF DNA AS THE GENETIC MATERIAL
To fulfill its role, the genetic material must meet several criteria
1. Information: It must contain the information necessary to make an entire organism
2. Transmission: It must be passed from parent to offspring
3. Replication: It must be copied
In order to be passed from parent to offspring
4. Variation: It must be capable of changes
To account for the known phenotypic variation in each species
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3. 9.1 IDENTIFICATION OF DNA AS THE GENETIC MATERIAL
The data of many geneticists, including Mendel, were consistent with these four properties
However, the chemical nature of the genetic material cannot be identified solely by genetic crosses
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4. Frederick Griffith Experiments with Streptococcus pneumoniae
Griffith studied a bacterium (Diplococcus pneumoniae) now known as Streptococcus pneumoniae
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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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
9-6
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6. In 1928, Griffith conducted experiments using two strains of S
In 1928, Griffith conducted experiments using two strains of S. pneumoniae: type IIIS and type IIR
1. Inject mouse with live type IIIS bacteria
Mouse died
Type IIIS bacteria recovered from the mouse’s blood
2. Inject mouse with live type IIR bacteria
Mouse survived
No living bacteria isolated from the mouse’s blood
3. Inject mouse with heat-killed type IIIS bacteria
4. Inject mouse with live type IIR + heat-killed type IIIS cells
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7. Figure 9.2
9-8
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8. Griffith concluded that something from the dead type IIIS was transforming type IIR into type IIIS
He called this process transformation
The substance that allowed this to happen was termed the transformation principle
Griffith did not know what it was
The nature of the transforming principle was determined using experimental approaches that incorporated various biochemical techniques
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9. 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
9-10
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10. 9-11 Avery et al also conducted the following experiments Figure 9.3
To further verify that DNA, and not a contaminant (RNA or protein), is the genetic material
Figure 9.3
9-11
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11. Hershey and Chase Experiment with Bacteriophage T2
In 1952, Alfred Hershey and Marsha Chase provided further evidence that DNA is the genetic material
Figure 9.4
Inside the capsid
They studied the bacteriophage T2
It is relatively simple since its composed of only two macromolecules
DNA and protein
Made up of protein
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12. Figure 9.5 Life cycle of the T2 bacteriophage
Figure 10-5 Reproductive cycle of a T-even bacteriophage, as known in The electron micrograph shows an E. coli cell during infection by numerous phages.

13. The Hershey and Chase experiment can be summarized as such:
Used radioisotopes to distinguish DNA from proteins
32P labels DNA specifically
35S labels protein specifically
Radioactively-labeled phages were used to infect nonradioactive Escherichia coli cells
After allowing sufficient time for infection to proceed, the residual phage particles were sheared off the cells
=> Phage ghosts and E. coli cells were separated
Radioactivity was monitored using a scintillation counter
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14. Testing the Hypothesis
Only the genetic material of the phage is injected into the bacterium
Isotope labeling will reveal if it is DNA or protein
Testing the Hypothesis
Refer to Figure 9.6
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15. Testing the Hypothesis
Figure 9.6
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16. Figure 9.6
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17. The Data
9-18
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18. Interpreting the Data 9-19
Most of the 35S was found in the supernatant
But only a small percentage of 32P
These results suggest that DNA is injected into the bacterial cytoplasm during infection
This is the expected result if DNA is the genetic material
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19. Figure 10-6 Summary of the Hershey–Chase experiment demonstrating that DNA, and not protein, is responsible for directing the reproduction of phage T2 during the infection of E. coli.

20. 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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21. Figure 10-8 Reconstitution of hybrid tobacco mosaic viruses
Figure 10-8 Reconstitution of hybrid tobacco mosaic viruses. In the hybrid, RNA is derived from the wild-type TMV virus, while the protein subunits are derived from the HR strain. Following infection, viruses are produced with protein subunits characteristic of the wild-type TMV strain and not those of the HR strain. The top photograph shows TMV lesions on a tobacco leaf compared with an uninfected leaf. At the bottom is an electron micrograph of mature viruses.

22. 9-21
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23. 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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24. 9-23 Figure 9.7 Three-dimensional structure
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25. 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
9-24
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26. Figure 9.8
9-25
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27. 9-26 These atoms are found within individual nucleotides Figure 9.9
However, they are removed when nucleotides join together to make strands of DNA or RNA
A, G, C or T
A, G, C or U
Figure 9.9
The structure of nucleotides found in (a) DNA and (b) RNA
9-26
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28. Base + sugar  nucleoside
Example
Adenine + ribose = Adenosine
Adenine + deoxyribose = Deoxyadenosine
Base + sugar + phosphate(s)  nucleotide
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
Refer to Figure 9.10
9-27
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29. 9-28 Figure 9.10 Base always attached here
Phosphates are attached there
Figure 9.10
9-28
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30. 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’
The phosphates and sugar molecules form the backbone of the nucleic acid strand
The bases project from the backbone
9-29
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31. ribonucleic acid (RNA)
Fig. 9.9 (TE Art)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O
Base
Base P O
CH2 P O
CH2 5¢ O 5¢ O O– O – 4¢ 1¢ 4¢ 1¢ H H H H H H H H 3¢ 2¢
Phosphate 3¢ 2¢
Phosphate O H O OH
2¢ Deoxyribose
Ribose
Repeating unit of
deoxyribonucleic
acid (DNA)
Repeating unit of
ribonucleic acid (RNA)

32. Figure 9.11
9-30
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33. Figure 10-12 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure (a) Linkage of two nucleotides by the formation of a – phosphodiester bond, producing a dinucleotide. (b) Shorthand notation for a polynucleotide chain.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.

34. A Few Key Events Led to the 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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35. 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
Refer to Figure 9.12b
Figure 9.12
9-32
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36. Fig. 9.13
Rosalind Franklin

37. Photo 51 x-ray diffraction of wet DNA showing the B form double helix
taken by Rosalind Franklin and Raymond Gosling on Friday, 2nd May, 1952
by long exposure started the previous day

38. 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
9-34
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39. Erwin Chargaff’s Experiment
Chargaff pioneered many of the biochemical techniques for the isolation, purification and measurement of nucleic acids from living cells
It was already known then that DNA contained the four bases: A, G, C and T
9-35
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40. Testing the Hypothesis
An analysis of the base composition of DNA in different species may reveal important features about the structure of DNA
Testing the Hypothesis
Refer to Figure 9.14
9-36
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41. Figure 9.14
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42. Figure 9.14
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43. The Data
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44. Table 10-3 Copyright © 2006 Pearson Prentice Hall, Inc.
Table DNA Base Composition Data
Table Copyright © 2006 Pearson Prentice Hall, Inc.

45. Interpreting the Data The compelling observation was that
Percent of adenine = percent of thymine
Percent of cytosine = percent of guanine
the percentage of C + G does not necessarily equal the percentage of A + T
This observation became known as Chargaff’s rule
It was crucial evidence that Watson and Crick used to elucidate the structure of DNA
9-40
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46. 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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47. This hypothesis was, of course, incorrect!
Figure 9.15
This hypothesis was, of course, incorrect!
9-42
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48. Watson and Crick They went back to the ball-and-stick units
They then built models with the
Sugar-phosphate backbone on the outside
Bases projecting toward each other
They first considered a structure in which bases form H bonds with identical bases in the opposite strand
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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49. 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
9-44
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50. Fig. 9.16

51. 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 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
9-45
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52. Key Features •Two strands of DNA form a •The bases in opposite strands
Fig (TE Art)
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Key Features
2 nm
5¢ end
3¢ end
•Two strands of DNA form a
right-handed double helix. H HO H H H H H H P O– O
•The bases in opposite strands
hydrogen bond according to the
AT/GC rule. A S
H2N N O P O P S O N
CH2 O O S G C P N H P N S O– H S G C P
5¢phosphate O P O
CH2 N O N NH
NH2 2 H
•The 2 strands are antiparallel
with regard to their 5¢to 3¢
directionality. P S O– H H H H H H H H O– C S O S P H
H2N N N
CH2 O P O P S O
•There are ~10.0 nucleotides in
each strand per complete 360°
turn of the helix. P N H H N S P O O N S O H A T S O P O
CH2 O N NH P 2 O– H H H H H H H H G C S H H O– S P O H H N N
CH2 O P O P C G S N H O– S N P O O H T A N
H2N S P O P O
CH2 O N O P S O– P H H H H H
CH3 P S
3¢ hydroxyl OH H G
One complete
turn 3.4 nm P S
3¢ end
5¢ end C G S P P T A S S P G C P S A T
One nucleotide
0.34 nm S P S S P P S C G S P S C G P

53. Ball-and-stick model of DNA Space-filling model of DNA
Fig (TE Art)
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Minor
groove
Minor
groove
Major
groove
Major
groove
Ball-and-stick model of DNA
Space-filling
model of DNA

54. The DNA Double Helix General structural features (Figures 9.17 & 9.18)
The double-bonded structure is stabilized by
1. Hydrogen bonding between complementary bases
A bonded to T by two hydrogen bonds
C bonded to G by three hydrogen bonds
2. Base stacking
Within the DNA, the bases are oriented so that the flattened regions are facing each other
9-46
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55. 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
9-47
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56. Figure 9.17
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57. Figure 9.18
9-49
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58. The Three-Dimensional Structure of DNA
To fit within a living cell, the DNA double helix must be extensively compacted into a 3-D conformation
This is aided by DNA-binding proteins
Refer to 9.21
This topic will be discussed in detail in Chapter 10
9-55
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59. DNA wound around histone proteins
Figure 9.21
9-56

60. 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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61. Figure 9.22
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62. Table 10-4 Copyright © 2006 Pearson Prentice Hall, Inc.
Table RNA Characterization
Table Copyright © 2006 Pearson Prentice Hall, Inc.

63. Different types of RNA secondary structures are possible
Although usually single-stranded, RNA molecules can form short double-stranded regions
This secondary structure is due to complementary base-pairing
A to U and C to G
This allows short regions to form a double helix
Different types of RNA secondary structures are possible
Refer to Figure 9.23
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64. Complementary regions
Held together by hydrogen bonds
Figure 9.23
Noncomplementary regions
Also called hair-pin
Have bases projecting away from double stranded regions
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65. Molecule contains single- and double-stranded regions
Many factors contribute to the tertiary structure of RNA
For example
Base-pairing and base stacking within the RNA itself
Interactions with ions, small molecules and large proteins
Molecule contains single- and double-stranded regions
These spontaneously interact to produce this 3-D structure
Figure 9.24
Figure 9.24 depicts the tertiary structure of tRNAphe
The transfer RNA that carries phenylalanine
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66. Figure 10-1 Copyright © 2006 Pearson Prentice Hall, Inc.
Figure 10-1 Simplified view of the central dogma describing information flow involving DNA, RNA, and proteins within cells.
Figure Copyright © 2006 Pearson Prentice Hall, Inc.