1. Animation: Origins of Replication
Getting Started
Replication begins at special sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble”
A eukaryotic chromosome may have hundreds or even thousands of origins of replication
Replication proceeds in both directions from each origin, until the entire molecule is copied
Animation: Origins of Replication
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

2. Parental (template) strand Daughter (new) strand
Fig
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
Daughter (new) strand
Figure Origins of replication in E. coli and eukaryotes
0.25 µm
Bubble
Replication fork
Two daughter DNA molecules
(b) Origins of replication in eukaryotes

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

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

5. 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
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

6. 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

7. The initial nucleotide strand is a short RNA primer
DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end
The initial nucleotide strand is a short RNA primer
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

8. An enzyme called primase can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template
The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

9. Synthesizing a New DNA Strand
Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork
Most DNA polymerases require a primer and a DNA template strand
The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

10. 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

11. Nucleoside triphosphate
Fig
New strand 5 end
Template strand 3 end
5 end
3 end
Sugar A T A T
Base
Phosphate C G C G G C G C
DNA polymerase
3 end A T A
Figure Incorporation of a nucleotide into a DNA strand T
3 end C
Pyrophosphate C
Nucleoside triphosphate
5 end
5 end

12. Antiparallel Elongation
The antiparallel structure of the double helix (two strands oriented in opposite directions) affects replication
DNA polymerases add nucleotides only to the free 3end of a growing strand; therefore, a new DNA strand can elongate only in the 5 to 3direction
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

13. Animation: Leading Strand
Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork
Animation: Leading Strand
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

14. Overall directions of replication
Fig
Overview
Origin of replication
Leading strand
Lagging strand
Primer
Lagging strand
Leading strand
Overall directions of replication
Origin of replication 3 5
RNA primer 5
“Sliding clamp” 3 5
DNA poll III
Parental DNA
Figure Synthesis of the leading strand during DNA replication 3 5 5 3 5

15. Overall directions of replication
Fig a
Overview
Origin of replication
Leading strand
Lagging strand
Primer
Lagging strand
Leading strand
Figure Synthesis of the leading strand during DNA replication
Overall directions of replication

16. Origin of replication 3 5 RNA primer 5 “Sliding clamp” 3 5
Fig b
Origin of replication 3 5
RNA primer 5
“Sliding clamp” 3 5
DNA pol III
Parental DNA 3 5
Figure Synthesis of the leading strand during DNA replication 5 3 5

17. Animation: Lagging Strand
To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork
The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase
Animation: Lagging Strand
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

18. 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

19. Overall directions of replication
Fig a
Overview
Origin of replication
Leading strand
Lagging strand
Lagging strand 2 1
Leading strand
Figure 16.6 Synthesis of the lagging strand
Overall directions of replication

20. 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

21. 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

22. 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

23. 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

24. 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

25. 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

26. Table 16-1

27. Single-strand binding protein Overall directions of replication
Fig
Overview
Origin of replication
Leading strand
Lagging strand
Leading strand
Lagging strand
Single-strand binding protein
Overall directions of replication
Helicase
Leading strand 5
DNA pol III 3 3
Primer
Primase 5
Parental DNA 3
Figure A summary of bacterial DNA replication
DNA pol III
Lagging strand 5
DNA pol I
DNA ligase 4 3 5 3 2 1 3 5

28. The DNA Replication Complex
The proteins that participate in DNA replication form a large complex, a “DNA replication machine”
The DNA replication machine is probably stationary during the replication process
Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and “extrude” newly made daughter DNA molecules
Animation: DNA Replication Review
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

29. Proofreading and Repairing DNA
DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides
In mismatch repair of DNA, repair enzymes correct errors in base pairing
DNA can be damaged by chemicals, radioactive emissions, X-rays, UV light, and certain molecules (in cigarette smoke for example)
In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

30. Fig. 16-18 Nuclease DNA polymerase DNA ligase
Figure Nucleotide excision repair of DNA damage
DNA ligase

31. 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
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

32. 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

33. Eukaryotic chromosomal DNA molecules have at their ends nucleotide sequences called telomeres
Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules
It has been proposed that the shortening of telomeres is connected to aging
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

34. Fig
Figure Telomeres
1 µm

35. 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
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

36. 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
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

37. Concept 16.3 A chromosome consists of a DNA molecule packed together with proteins
The bacterial chromosome is a double-stranded, circular DNA molecule associated with a small amount of protein
Eukaryotic chromosomes have linear DNA molecules associated with a large amount of protein
In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

38. Animation: DNA Packing
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
For the Cell Biology Video Cartoon and Stick Model of a Nucleosomal Particle, go to Animation and Video Files.
Animation: DNA Packing
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

39. 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)

40. 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

41. Chromatin is organized into fibers 10-nm fiber
DNA winds around histones to form nucleosome “beads”
Nucleosomes are strung together like beads on a string by linker DNA
30-nm fiber
Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

42. 300-nm fiber Metaphase chromosome
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
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

43. Loosely packed chromatin is called euchromatin
Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis
Loosely packed chromatin is called euchromatin
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
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

44. Histones can undergo chemical modifications that result in changes in chromatin organization
For example, phosphorylation of a specific amino acid on a histone tail affects chromosomal behavior during meiosis
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

45. Condensin and DNA (yellow) Outline of nucleus Condensin (green)
Fig
RESULTS
Condensin and DNA (yellow)
Outline of nucleus
Condensin (green)
DNA (red at periphery)
Figure What role does histone phosphorylation play in chromosomal behavior during meiosis?
Normal cell nucleus
Mutant cell nucleus

46. Sugar-phosphate backbone
Fig. 16-UN2 G C A T T A
Nitrogenous bases G C
Sugar-phosphate backbone C G A T C G
Hydrogen bond T A

47. DNA pol III synthesizes leading strand continuously
Fig. 16-UN3
DNA pol III synthesizes leading strand continuously 3 5
Parental DNA
DNA pol III starts DNA synthesis at 3 end of primer, continues in 5  3 direction 5 3 5
Lagging strand synthesized in short Okazaki fragments, later joined by DNA ligase
Primase synthesizes a short RNA primer 3 5

48. Fig. 16-UN4

49. Fig. 16-UN5

50. You should now be able to:
Describe the contributions of the following people: Griffith; Avery, McCary, and MacLeod; Hershey and Chase; Chargaff; Watson and Crick; Franklin; Meselson and Stahl
Describe the structure of DNA
Describe the process of DNA replication; include the following terms: antiparallel structure, DNA polymerase, leading strand, lagging strand, Okazaki fragments, DNA ligase, primer, primase, helicase, topoisomerase, single-strand binding proteins
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

51. Describe the function of telomeres
Compare a bacterial chromosome and a eukaryotic chromosome
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings