1. Chapter 16-Molecular Genetics
You must know:
The structure of DNA
The history of the discovery of DNA gained from the work of
Replication
Replication, transcription and translation
Differences between bacterial vs. eukaryotic chromosomes
How DNA packaging affects gene expression

2. Life’s Operating Instructions
In 1953, James Watson and Francis Crick introduced an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA
DNA, the substance of inheritance, is the most celebrated molecule of our time
Hereditary information is encoded in DNA and reproduced in all cells of the body
This DNA program directs the development of biochemical, anatomical, physiological, and (to some extent) behavioral traits

3. How do we know DNA the genetic material?
Scientific Inquiry
Early in the 20th century
ID of inheritance was a major challenge
Morgan showed that genes are located on chromosomes
DNA and protein are candidates for the genetic material
Bacterial and viruses helped with this

4. Evidence that DNA can Transform Bacteria
Griffith in 1928 showed the genetic role
2 strains of bacterium
One pathogenic, other was not
Mixed heat-killed remains with pathogenic with the living, living became pathogenic
Transformation

5. Mixture of heat-killed S cells and living R cells
Figure 16.2
EXPERIMENT
Mixture of heat-killed S cells and living R cells
Heat-killed S cells (control)
Living S cells (control)
Living R cells (control)
RESULTS
Figure 16.2 Inquiry: Can a genetic trait be transferred between different bacterial strains?
Mouse dies
Mouse healthy
Mouse healthy
Mouse dies
Living S cells

6. More evidence
In 1944, Oswald Avery, Maclyn McCarty, and Colin MacLeod announced that the transforming substance was DNA
Their conclusion was based on experimental evidence that only DNA worked in transforming harmless bacteria into pathogenic bacteria
Many biologists remained skeptical, mainly because little was known about DNA
More evidence for DNA as the genetic material came from studies of viruses that infect bacteria
Such viruses, called bacteriophages (or phages), are widely used in molecular genetics research

7. Phage head Tail sheath Tail fiber DNA 100 nm Bacterial cell
Figure 16.3
Phage head
Tail sheath
Tail fiber
Figure 16.3 Viruses infecting a bacterial cell.
DNA
100 nm
Bacterial cell

8. Do you need more?
In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA is the genetic material of a phage known as T2
To determine this, they designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection
They concluded that the injected DNA of the phage provides the genetic information

9. Additional Evidence
It was known that DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group
In 1950, Erwin Chargaff reported that DNA composition varies from one species to the next
This evidence of diversity made DNA a more credible candidate for the genetic material

10. Chargaff’s Rules Base composition of DNA varies between species
A and T are equal in number, G and C are equal
Basis for these rules was not understood until the discovery of the double helix

11. Sugar–phosphate backbone
Figure 16.5
Sugar–phosphate backbone
Nitrogenous bases
5 end
Thymine (T)
Adenine (A)
Cytosine (C)
Figure 16.5 The structure of a DNA strand.
Phosphate
Guanine (G)
Sugar (deoxyribose)
DNA nucleotide
Nitrogenous base
3 end

12. The Race to discover the structure of DNA
DNA was accepted as the genetic matrial
But how?
Maurice Wilkins and Rosalind Franklin were using x-ray crystallography
Rosalind produced the famous plate 51

13. Franklin’s X-ray diffraction photograph of DNA
Figure 16.6
Figure 16.6 Rosalind Franklin and her X-ray diffraction photo of DNA.
(a) Rosalind Franklin
(b)
Franklin’s X-ray diffraction photograph of DNA

14. Franklin’s work
Enabled Watson to deduce the helical structure of the molecule
Width and spacing was calculated
The pattern in the photo confirmed that DNA is double helix
Thought that Maurice Wilkins “borrowed” Rosie’s plate to show Watson- returned it

15. 5 end 3 end 3 end 5 end Hydrogen bond 3.4 nm 1 nm 0.34 nm (a)
Figure 16.7
5 end C G
Hydrogen bond C G
3 end G C G C T A
3.4 nm T A G C G C C G A T
1 nm C G T A C G G C C G A T
Figure 16.7 The double helix. A T
3 end A T
0.34 nm
5 end T A
(a)
Key features of DNA structure
(b) Partial chemical structure
Space-filling model
(c)

16. The proof
Watson and Crick built models of a double helix to conform to the X-rays and chemistry of DNA
Franklin had concluded that there were two outer sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior
Watson built a model in which the backbones were antiparallel (their subunits run in opposite directions
At first, Watson and Crick thought the bases paired like with like (A with A, and so on), but such pairings did not result in a uniform width
Instead, pairing a purine with a pyrimidine resulted in a uniform width consistent with the X-ray data

17. Purine  purine: too wide
Figure 16.UN01
Purine  purine: too wide
Pyrimidine  pyrimidine: too narrow
Figure 16.UN01 In-text figure, p. 310
Purine  pyrimidine: width consistent with X-ray data

18. And there is more
Watson and Crick reasoned that the pairing was more specific, dictated by the base structures
They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C)
The Watson-Crick model explains Chargaff’s rules: in any organism the amount of A = T, and the amount of G = C

19. Sugar Sugar Adenine (A) Thymine (T) Sugar Sugar Guanine (G)
Figure 16.8
Sugar
Sugar
Adenine (A)
Thymine (T)
Figure 16.8 Base pairing in DNA.
Sugar
Sugar
Guanine (G)
Cytosine (C)

20. Form fits function Relationship between structure and function
Copying mechanism for genetic material

21. Base pairing to a Template Strand
Each strand acts as a template for building a new strand in replication
Parent molecule unwinds
Two daughter strands built
Base pairing rules

22. (a) Parent molecule A T C G T A A T G C Figure 16.9-1
Figure 16.9 A model for DNA replication: the basic concept.

23. (a) Parent molecule (b) Separation of strands A T A T C G C G T A T A
Figure A T A T C G C G T A T A A T A T G C G C
(a) Parent molecule
(b)
Separation of strands
Figure 16.9 A model for DNA replication: the basic concept.

24. (a) Parent molecule (b) Separation of strands (c)
Figure A T A T A T A T C G C G C G C G T A T A T A T A A T A T A T A T G C G C G C G C
(a) Parent molecule
(b)
Separation of strands
(c)
“Daughter” DNA molecules, each consisting of one parental strand and one new strand
Figure 16.9 A model for DNA replication: the basic concept.

25. Semiconservative Model
Watson and Crick’s semiconservative model
predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand

26. Meselson and Stahl Supported the semiconservative model
Labeled nucleotides of old strands with heavy isotopes of nitrogen
New nucleotides labeled with a lighter isotope

27. Bacteria cultured in medium with 15N (heavy isotope) 2
Figure 16.11
EXPERIMENT 1
Bacteria cultured in medium with 15N (heavy isotope) 2
Bacteria transferred to medium with 14N (lighter isotope)
RESULTS 3
DNA sample centrifuged after first replication 4
DNA sample centrifuged after second replication
Less dense
More dense
CONCLUSION
Predictions:
First replication
Second replication
Conservative model
Figure Inquiry: Does DNA replication follow the conservative, semiconservative, or dispersive model?
Semiconservative model
Dispersive model

28. Structure of DNA
Prokaryotic DNA
Eukaryotic DNA
One double stranded circular DNA molecule Small amount of protein
Linear DNA
Protein packaged as chromatin
4 levels of packaging

29. Nucleosome- packaging- 1
10-nm fiber, basic unit
DNA histone form beads on a string
8 histone molecules with the aa tail projecting outward
Histone H1 (different from the rest) binds DNA to the next histone

30. Why do we need all this packaging?
1. more tightly packaged, less accessible to transcription enzymes
2. reduces gene expression
3. Interphase- chromatin is the highly extended form or euchromatin which can undergo transcription
4. More condensed is heterochromatin- generally not transcribed
5. Barr bodies are heterochromatin

31. Packaging nm fiber
String of nucleosomes coils to form chromatin fiber that is 30 nm
Interphase is when this occurs
Histone 3 &4

32. Packaging -3 300 nm fiber Looped domains
Formed to a scaffold of non histone proteins

33. Packaging -4 1,400nm Maximally folding compact chromosome Metaphase
2 chromatids

34. Chromosome with Euchromatin and Heterochromatin

35. DNA Replication S phase Mitosis/Meiosis Fast and accurate
More than a dozen enzymes are involved

36. 6 points of DNA Replication
1. Begins at sites-Origins of Replication
Bubbles will eventually fuse

37. Replication Fork or bubble
2. Initiation proteins bind
Separate strands
DNA replication proceeds in both directions along the DNA strand until molecule is copied
DNA strand is short RNA called primer, enzymes primase does this
Enzymes
Helicase
SS binding proteins
Topoisomerase
Relieves strand by breaking, swiveling and rewind the DNA

38. DNA Polymerase
3. Catalyzes elongation of new DNA at the replication Fork
Bacterial uses different polymerases, III and I
Adds DNA nucleotide to primer which is RNA, done by dATP, exergonic reaction

39. Adding nucleotides
4. DNA polymerase adds nucleotides to the strand one at a time in the 5’-3’ direction Bonding of A-T, C-G
Basically purine to pyrimidine
Keeps the symmetry to the molecule

40. Antiparallel elongation
5 Leading and Lagging strands
5. leading toward fork is continuous
Lagging 3’-5’-away from fork is discontinuous
Antiparallel
A-T
C-G
Purine to pyrimidine

41. Okazaki Fragments 6.Lagging is in pieces Starts as discontinous
Sealed by DNA ligase
Forms continuous strand

42. DNA Accuracy Dependent on the specificity of base pairing
A-T, C-G
Mismatch Repair
Enzymes that cut out nuclease
New sequence is DNA poly and DNA ligase
Cancer cells accumulate errors
Nucleotide excision repair system

43. Of importance DNA repair enzymes on skin after exposure to UV rays
Thymine bases, or thymine dimers cause DNA to buckle, interferes with replication
Xeroderma pigmentosum

44. Telomeres- ase-Blackburn
Replicating the ends
TTAGGG- does not code for anything noncoding repeating sequence
x repeated
Telomerase
Enzyme that stimulates ends to lengthen in germ cells
Zygotes only have maximum
Somatic cells do not have this at birth

45. Lagging strand template 3 5 DNA pol III Lagging strand 3 5
Figure 16.18
DNA pol III
Parental DNA
Leading strand 5 5 3 3 3 5 3 5
Connecting protein
Helicase
Lagging strand template 3 5
Figure A current model of the DNA replication complex.
DNA pol III
Lagging strand 3 5

46. Bozeman Links Structure of DNA
Replication