1. Fig. 16-1
Figure 16.1 How was the structure of DNA determined?

2. Building a Structural Model of DNA: Scientific Inquiry
After most biologists became convinced that DNA was the genetic material, the challenge was to determine how its structure accounts for its role
Maurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structure
Franklin produced a picture of the DNA molecule using this technique
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3. (a) Rosalind Franklin Fig. 16-6a
Figure 16.6 Rosalind Franklin and her X-ray diffraction photo of DNA
(a) Rosalind Franklin

4. (b) Franklin’s X-ray diffraction photograph of DNA
Fig. 16-6b
Figure 16.6 Rosalind Franklin and her X-ray diffraction photo of DNA
(b) Franklin’s X-ray diffraction photograph of DNA

5. Animation: DNA Double Helix
Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce that DNA was helical
The X-ray images also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous bases
The width suggested that the DNA molecule was made up of two strands, forming a double helix
Animation: DNA Double Helix
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6. 5 end Hydrogen bond 3 end 1 nm 3.4 nm 3 end 0.34 nm 5 end
Fig. 16-7a
5 end
Hydrogen bond
3 end
1 nm
3.4 nm
Figure 16.7 The double helix
3 end
0.34 nm
5 end
(a) Key features of DNA structure
(b) Partial chemical structure

7. 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 antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior
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8. 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
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9. Purine + purine: too wide
Fig. 16-UN1
Purine + purine: too wide
Pyrimidine + pyrimidine: too narrow
Purine + pyrimidine: width consistent with X-ray data

10. 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
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11. Adenine (A) Thymine (T) Guanine (G) Cytosine (C) Fig. 16-8
Figure 16.8 Base pairing in DNA
Guanine (G)
Cytosine (C)

12. Concept 16.2: Many proteins work together in DNA replication and repair
The relationship between structure and function is manifest in the double helix
Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material
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13. The Basic Principle: Base Pairing to a Template Strand
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
Animation: DNA Replication Overview
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14. A T C G T A A T G C (a) Parent molecule Fig. 16-9-1
Figure 16.9 A model for DNA replication: the basic concept

15. (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

16. (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

17. 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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18. 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
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19. 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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20. 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

21. 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
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22. 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
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23. 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
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24. 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
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25. 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

26. 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
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27. 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
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28. 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

29. 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

30. 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
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31. Figure 16.6 Synthesis of the lagging strand
Fig b6 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

32. Table 16-1

33. 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