1. 16.2 DNA Replication

2. Layout of the Eukaryote DNA
Two DNA strands are antiparallel
Run in opposite directions
3’ (three prime) – 5’ (five prime)
5’ (five prime) – 3’ (three prime)

3. DNA Replication
Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material

4. DNA Replication
Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication
In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules

5. Fig. 16-9-1 A T C G T A A T G C (a) Parent molecule
Figure 16.9 A model for DNA replication: the basic concept

6. (b) Separation of strands
Fig 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

7. (b) Separation of strands
Fig 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

8. Semiconservative Model
Each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand

9. (a) Conservative model
Fig
First replication
Second replication
Parent cell
(a) Conservative model
(b) Semiconserva- tive model
Figure Three alternative models of DNA replication
(c) Dispersive model

10. Matthew Meselson and Franklin Stahl

11. DNA in Prokaryotes and Eukaryotes
ring of chromosome
holds nearly all of the cell’s genetic material

12. Prokaryote DNA Replication
DNA replication begins at a single point and continues to replicate whole circular strand
Replication goes in both directions around the DNA (begins with replication fork)

13. Fig. 16-12 Origin of replication Parental (template) strand
Daughter (new) strand
Replication fork
Double-
stranded
DNA molecule
Replication bubble
0.5 µm
Two daughter DNA molecules
(a) Origins of replication in E. coli
Origin of replication
Double-stranded DNA molecule
Parental (template) strand
Figure Origins of replication in E. coli and eukaryotes
Daughter (new) strand
0.25 µm
Bubble
Replication fork
Two daughter DNA molecules
(b) Origins of replication in eukaryotes

14. DNA Replication Overview
DNA splits into two strands
Complementary base pairs fill in (A with T, C with G)
Left with two DNA molecules
Semiconservative model
Identical

15. Eukaryote DNA Replication
Begins in hundreds of locations along the chromosome
Origins of replication

16. Initiation of DNA Replication
Begins when the DNA molecule “unzips”
Replication fork
Replication “bubble”
Hydrogen bonds between base pairs breaks
Helicase
Single-strand binding proteins
Topoisomerase – relieves pressure of DNA ahead of replication fork

17. 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

18. Synthesis of a New DNA Strand
Each strand serves as a template for a new strand to form
Primer of RNA
The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand
Complimentary bases will attach
DNA polymerase
E. coli – DNA polymerase III and DNA polymerase I
Humans – 11 different DNA polymerase molecules

19. Synthesis of a New DNA Strand
RNA primer
Nucleoside triphosphate
As each nucleotide is added to the new strand, 2 phosphates are lost
Hydrolysis releases energy to drive reaction

20. Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate
dATP supplies adenine to DNA and is similar to the ATP of energy metabolism
The difference is in their sugars: dATP has deoxyribose while ATP has ribose
As each monomer of dATP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

21. Synthesis of a New DNA Strand
Antiparallel Elongation
Remember 3’ – 5’ and 5’ – 3’
Replication in the 3’ to 5’ direction ONLY
MEANING the NEW strand of DNA will form starting with the 5’ end
Leading strand (only 1 primer needed – moves toward the replication fork)
Lagging strand (many primers needed – moves away from replication fork)

22. Fig. 16-16b1 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand
Figure 16.6 Synthesis of the lagging strand

23. Fig. 16-16b2 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5
RNA primer 3 1 5
Figure 16.6 Synthesis of the lagging strand

24. Fig. 16-16b3 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5
RNA primer 3 1 5 3
Okazaki fragment 5 3 1 5
Figure 16.6 Synthesis of the lagging strand

25. Fig. 16-16b4 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5
RNA primer 3 1 5 3
Okazaki fragment 5 3 5 1 3 5 3 2 1 5
Figure 16.6 Synthesis of the lagging strand

26. Fig. 16-16b5 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5
RNA primer 3 1 5 3
Okazaki fragment 5 3 5 1 3 5 3 2 1 5 5 3
Figure 16.6 Synthesis of the lagging strand 3 5 2 1

27. Fig. 16-16b6 Figure 16.6 Synthesis of the lagging strand 3 5 5 3
Template strand 3 5
RNA primer 3 1 5 3
Okazaki fragment 5 3 5 1 3 5 3 2 1 5 5 3
Figure 16.6 Synthesis of the lagging strand 3 5 2 1 5 3 3 1 5 2
Overall direction of replication

30. Important Enzymes
Helicase, single-strand binding protein, topoisomerase
Primase
Synthesis of RNA primer
DNA polymerase III (DNA pol III)
Add new bases to DNA strand
DNA polymerase I (DNA pol I)
Removes and replaces RNA primer from 5’ end
DNA ligase
Links Okazaki fragments and replaces RNA primer from 3’ end

31. Topoisomerase Video

32. The Finished Product
Each DNA molecule has one original strand and one new strand
Molecules are identical

33. DNA Replication Video

34. Fig. 16-UN5

35. Repair of DNA DNA polymerase Nuclease
Proofreads and repairs damaged/mismatched DNA
Nuclease
Removes section of DNA that is damaged
DNA polymerase and DNA ligase replace missing portion

36. Telomeres Found at the ends of each chromosome Contain no genes
Sequence that can be cut short and will not affect normal functioning
TTAGGG
Telomerase lengthens telomeres in gametes
Aging? Cancer? As telomeres get shorter, aging may be triggered. Telomeres shorten and may start affecting replication (cancer cells) – trigger cell death - apoptosis

37. Telomeres
The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions
There is evidence of telomerase activity in cancer cells, which may allow cancer cells to persist

38. 16.3 A chromosome consists of a DNA molecule packed together with proteins

39. Chromosomes

40. Chromosome Structure Bacterial chromosome Eukaryotic chromosomes
double-stranded
circular
small amount of protein
Eukaryotic chromosomes
Linear DNA molecules
large amount of protein
DNA in bacteria is “supercoiled” and found in a region of the cell called the nucleoid

41. Chromatin and Histones
Chromatin is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells
Histones are proteins that are responsible for the first level of DNA packing in chromatin
Form a tight bond because DNA is negatively charged and the histones have a positive charge

42. Nucleosomes, or “beads on a string” (10-nm fiber)
Fig a
Nucleosome
(10 nm in diameter)
DNA double helix (2 nm in diameter) H1
Histone tail
Histones
Figure 16.21a Chromatin packing in a eukaryotic chromosome
DNA, the double helix
Histones
Nucleosomes, or “beads on a string” (10-nm fiber)

43. Looped domains (300-nm fiber) Metaphase chromosome
Fig b
Chromatid
(700 nm)
30-nm fiber
Loops
Scaffold
300-nm fiber
Figure 16.21b Chromatin packing in a eukaryotic chromosome
Replicated chromosome (1,400 nm)
30-nm fiber
Looped domains (300-nm fiber)
Metaphase chromosome

44. Chromosome Organization
Chromatin is organized into fibers
10-nm fiber
DNA winds around histones to form nucleosome “beads”
Nucleosomes are strung together
30-nm fiber
Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber

45. Chromosome Organization
300-nm fiber
The 30-nm fiber forms looped domains that attach to proteins
Metaphase chromosome
The looped domains coil further
The width of a chromatid is 700 nm

47. Euchromatin
Most chromatin is loosely packed in the nucleus during interphase
Condenses prior to mitosis
Euchromatin

48. Heterochromatin
During interphase, a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin
Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions