1. Structure and Replication of DNA

2. Outline DNA as the genetic material
(16.2, 16.3, 16.4)
Watson-Crick model of DNA Structure
(16.5, 16.7, 16.6, 16.8,)
Semiconservative model of DNA replication
(16.9, 16.10, 16.11, 16.12, 16.13, 16.14, 16.15, 16.16, 16.17, )
Repair of Damaged DNA
(16.18, 16.19)
Telomerase extension of chromosome ends
(16.20)
Chromatin
(16.21)

3. Are Genes Composed of DNA or Protein?
Only four nucleotides
thought to have monotonous structure
Protein
20 different amino acids – greater potential variation
More protein in chromosomes than DNA

4. Bacterial Transformation Experiments
Fredrick Griffith (1928) –demonstrate the existence of “Transforming Principle,” a substance able to confer a heritable phenotype from one strain of bacteria to another.
Avery MacLeod and McCarty – determine the transforming principle was DNA.

5. Streptococcus Pneumoniae

6. Griffith Experiment

7. Avery Experiment

8. Fig. 16-3
Phage head
Tail sheath
Tail fiber
DNA
100 nm
Bacterial
cell

9. Hershey Chase Experiment

10. Additional Evidence Chargaff Ratios
% A = %T and %G = %C (Complexity in DNA Structure)
A T G C
Arabidopsis 29% 29% 20% 20%
Humans 31% 31% 18% 18%
Staphlococcus 13% 13% 37% 37%
DNA Content of Diploid and Haploid cells
Gametes Somatic Cells
Humans pg pg
Chicken pg pg

11. DNA
Friedrich Meischer (1869) extracted a phosphorous rich material from nuclei of which he named nuclein
DNA – deoxyribonucleic acid
Monomer – Nucleotide
Deoxyribose
Phosphate
Nitrogenous Base (4)
Phosphodiester Bond
DNA has direction - 5’ and 3’ ends
Chromosomes are composed of DNA

12. Purine + purine: too wide
Fig. 16-UN1
Purine + purine: too wide
Pyrimidine + pyrimidine: too narrow
Purine + pyrimidine: width consistent with X-ray data

13. Watson and Crick Model Franklins X-Ray Data Watson and Crick
DNA is Double Helix
2 nm diameter
Phosphates on outside
3.4 nm periodicity
Bases 0.34nm apart
Watson and Crick
Base Pairing

15. DNA Replication
Semiconservative Replication

16. Other Models of Replication
Conservative
Replication
Semi-Conservative
Replication
Dispersive
Replication

17. Density Centrifugation
Culture Bacteria
in 15N isotope
(DNA fully 15N)
One Cell Division
in 14N
2nd Cell Division
in 14N
Less Dense
More Dense
14N DNA
15N/14N DNA
15N/14N DNA
15N DNA
Density Centrifugation

19. DNA Replication: A Closer Look
The copying of DNA is remarkable in its speed and accuracy
More than a dozen enzymes and other proteins participate in DNA replication
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20. Origins of Replication
Video

21. At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating
Helicases are enzymes that untwist the double helix at the replication forks
Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template
Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands
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22. Single-strand binding proteins
Fig
Primase
Single-strand binding proteins 3
Topoisomerase 5 3
RNA primer
Figure Some of the proteins involved in the initiation of DNA replication 5 5 3
Helicase

24. DNA Polymerase 3’ 5’
Pol 3’ 5’

25. Leading and Lagging Strands3’ 5’
Pol
Leading Strand 5’
Lagging Strand 3’
Pol
RNA
Primer 3’
Okazaki Fragments 5’
Video

26. Other Proteins at Replication Fork3’ 5’
DNA Pol III
Single Stranded
Binding Proteins
Pol
Leading Strand 5’
DNA Pol I
Lagging Strand 3’
Pol
Ligase
Helicase
Primase 3’
Okazaki Fragments 5’

27. Overall directions of replication
Fig
Overview
Origin of replication
Leading strand
Lagging strand
Lagging strand 2 1
Leading strand
Overall directions of replication 3 5 5 3
Template strand 3
RNA primer 3 5 1 5
Okazaki fragment 3 5 3 1 5 5 3 3
Figure 16.6 Synthesis of the lagging strand 2 1 5 3 5 3 5 2 1 5 3 3 1 5 2
Overall direction of replication

28. Damaged DNA Nuclease Excision Repair
DNA Polymerase
Ligase

29. Replicating the Ends of DNA Molecules
Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes
The usual replication machinery provides no way to complete the 5 ends, so repeated rounds of replication produce shorter DNA molecules
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30. Replicating Ends of Linear Chromosomes

31. Fig. 16-19 Figure 16.19 Shortening of the ends of linear DNA molecules5
Ends of parental DNA strands
Leading strand
Lagging strand 3
Last fragment
Previous fragment
RNA primer
Lagging strand 5 3
Parental strand
Removal of primers and replacement with DNA where a 3 end is available 5 3
Second round of replication
Figure Shortening of the ends of linear DNA molecules 5
New leading strand 3
New lagging strand 5 3
Further rounds of replication
Shorter and shorter daughter molecules

32. Fig
Figure Telomeres
1 µm

33. If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce
An enzyme called telomerase catalyzes the lengthening of telomeres in germ cells
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34. Telomerase

35. Chromatin Structure DNA, the double helix Histones
Nucleosome
(10 nm in diameter)
DNA double helix (2 nm in diameter) H1
Histone tail
Histones
DNA, the double helix
Histones
Nucleosomes, or “beads on a string” (10-nm fiber)
video

36. Looped domains (300-nm fiber) Metaphase chromosome
Fig b
Chromatid
(700 nm)
30-nm fiber
Loops
Scaffold
300-nm fiber
Replicated chromosome (1,400 nm)
30-nm fiber
Looped domains (300-nm fiber)
Metaphase chromosome

37. 30 nm chromatin fiber
Held together by histone tails interacting with neighboring nucleosomes
Inhibits transcription
Allows DNA replication

38. Gene Expression Beadle and Tatum Exp Transcription Translation
Roles of RNA

39. Beadle and Tatum Isolation of Nutritional Mutants

41. One Gene – One Polypeptide
Intermediates in arginine
biosynthesis
Mutant
Ornithine
Citrulline
Arginine
arg-1 +
arg-2 -
arg-3 - 
Note: A plus sign means growth; a minus sign means no growth.
arg arg arg-3
Percursor Ornithine Citruline Arginine
One Gene – One Enzyme
One Gene – One Polypeptide

42. Central Dogma of Molecular Biology

45. Gene Structure Transcribed Region Promoter Terminator ) ( RNA
Open Reading Frame
5’UTR
3’UTR

47. Three Parts to Transcription
Transcriptional Initiation –
RNA polymerase binds to promoter
DNA strands separate
RNA synthesis begins as ribonucleotides complementary to template strand are linked
Transcriptional Elongation
RNA polymerase moves down DNA unwinding a small window of DNA.
Nucleotides are added to the growing RNA chain
Transcriptional Termination
When the RNA polymerase reaches terminator the RNA and the RNA polymerase are released from the DNA.

49. RNA Processing in Eukaryotes
Pre-mRNA (hnRNA) 5’ 3’
Modification of 5’ and 3’ ends
5’CAP
Poly A tail
Exon Intron1 Exon Intron Exon Intron3 Exon4
Spicing of exons

51. Genetic Code

52. Locate start codon (1st ATG from 5’ end)
Identifying ORF 5’
GACGACGGAUGCGCAAUGCGUCUCUAUGAGACGUAGCUCAC
Locate start codon (1st ATG from 5’ end)
Identify Codons (non overlapping units of three codons including and following start codon)
Stop at stop codon ( remember stop codon doesn’t encode amino acid)
Nucleotides before start codon – 5’UTR
Nucleotides after stop codon -3’UTR
[MetArgAsnAlaSerLeu]

53. (a) Tobacco plant expressing a firefly gene (b) Pig expressing a
Fig. 17-6
Figure 17.6 Expression of genes from different species
(a) Tobacco plant expressing
a firefly gene
(b) Pig expressing a
jellyfish gene

54. Players in Translation
mRNA – Genetic Code
Ribosome – synthesizes protien
tRNA – adaptor molecule
Amino acids
Aminoacyl tRNA synthetases
- attach amino acids to tRNAs

55. GDP GDP Amino end of polypeptide E 3 mRNA Ribosome ready for
Fig
Amino end
of polypeptide E 3
mRNA
Ribosome ready for
next aminoacyl tRNA P
site A
site 5
GTP
GDP E E P A P A
Figure The elongation cycle of translation
GDP
GTP E P A

56. tRNA

58. Ribosomes

59. Three parts to Translation
Initiation
Delivery of Ribosome with first tRNA to start codon.
Elongation Cycle
Three Parts of Elongation Cycle
Delivery of tRNA to A site
Transpeptidase Activity – Amino acids on tRNA in P site cleaved from tRNA and attached to amino acid on tRNA in A site.
Translocation – Ribosome ratchets over on codon. The tRNA that was in the A site is moved to the P site. The uncharged tRNA in the P site exits the ribosome through the E site.
Termination
When ribosome reaches the stop codon a release factor binds to the A site and triggers the release of the polypeptide. The ribosome releases the tRNA and the mRNA.

60. The Functional and Evolutionary Importance of Introns
Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing
Such variations are called alternative RNA splicing
Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes
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61. Gene DNA Exon 1 Intron Exon 2 Intron Exon 3 Transcription
Fig
Gene
DNA
Exon 1
Intron
Exon 2
Intron
Exon 3
Transcription
RNA processing
Translation
Domain 3
Figure Correspondence between exons and protein domains
Domain 2
Domain 1
Polypeptide

62. Polysomes

63. Polypeptide synthesis always begins in the cytosol
Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER
Polypeptides destined for the ER or for secretion are marked by a signal peptide
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64. A signal-recognition particle (SRP) binds to the signal peptide
The SRP brings the signal peptide and its ribosome to the ER
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

65. Proteins targeted to ER

66. Functions of RNA mRNA – genetic code tRNA – adaptor molecules
rRNA- part of ribosome
snRNA – part of splicosome
SRP RNA – part of SRP
siRNA- eukaryotic gene regulation

67. Silent Mutations
Missense Mutations
Nonsense Mutations