1. Molecular Biology of the Gene
Chapter 10
Molecular Biology of the Gene

2. Introduction Viruses infect organisms by
Viruses infect organisms by
binding to receptors on a host’s target cell,
injecting viral genetic material into the cell, and
hijacking the cell’s own molecules and organelles to produce new copies of the virus.
The host cell is destroyed, and newly replicated viruses are released to continue the infection.
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3. Introduction Viruses are not generally considered alive because they
Viruses are not generally considered alive because they
are not cellular and
cannot reproduce on their own.
Because viruses have much less complex structures than cells, they are relatively easy to study at the molecular level.
For this reason, viruses are used to study the functions of DNA.
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4. The Structure of the Genetic Material DNA Replication
Figure 10.0_1
Chapter 10: Big Ideas
The Structure of the Genetic Material
DNA Replication
Figure 10.0_1 Chapter 10: Big Ideas
The Flow of Genetic Information from DNA to RNA to Protein
The Genetics of Viruses and Bacteria 4

5. Figure 10.0_2
Figure 10.0_2 Herpesvirus 5

6. THE STRUCTURE OF THE GENETIC MATERIAL
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7. 10.1 SCIENTIFIC DISCOVERY: Experiments showed that DNA is the genetic material
Until the 1940s, the case for proteins serving as the genetic material was stronger than the case for DNA.
Proteins are made from 20 different amino acids.
DNA was known to be made from just four kinds of nucleotides.
Studies of bacteria and viruses
ushered in the field of molecular biology, the study of heredity at the molecular level, and
revealed the role of DNA in heredity.
Student Misconceptions and Concerns
1. Understanding bacteriophage replication can be difficult for students with limited knowledge of cell biology or genetics. Therefore, understanding the methods, results, and significance of the Hershey and Chase experiments is even more problematic. Considerable time and attention to these details will be required for many of your students.
2. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
Teaching Tips
1. A phage functions like a needle and syringe, injecting a drug. The needle and syringe are analogous to the protein components of the phage. The drug to be injected is analogous to the phage DNA.
2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
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8. 10.1 SCIENTIFIC DISCOVERY: Experiments showed that DNA is the genetic material
In 1928, Frederick Griffith discovered that a “transforming factor” could be transferred into a bacterial cell. He found that
when he exposed heat-killed pathogenic bacteria to harmless bacteria, some harmless bacteria were converted to disease-causing bacteria and
the disease-causing characteristic was inherited by descendants of the transformed cells.
Student Misconceptions and Concerns
1. Understanding bacteriophage replication can be difficult for students with limited knowledge of cell biology or genetics. Therefore, understanding the methods, results, and significance of the Hershey and Chase experiments is even more problematic. Considerable time and attention to these details will be required for many of your students.
2. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
Teaching Tips
1. A phage functions like a needle and syringe, injecting a drug. The needle and syringe are analogous to the protein components of the phage. The drug to be injected is analogous to the phage DNA.
2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
© 2012 Pearson Education, Inc. 8

9. 10.1 SCIENTIFIC DISCOVERY: Experiments showed that DNA is the genetic material
In 1952, Alfred Hershey and Martha Chase used bacteriophages to show that DNA is the genetic material of T2, a virus that infects the bacterium Escherichia coli (E. coli).
Bacteriophages (or phages for short) are viruses that infect bacterial cells.
Phages were labeled with radioactive sulfur to detect proteins or radioactive phosphorus to detect DNA.
Bacteria were infected with either type of labeled phage to determine which substance was injected into cells and which remained outside the infected cell.
Student Misconceptions and Concerns
1. Understanding bacteriophage replication can be difficult for students with limited knowledge of cell biology or genetics. Therefore, understanding the methods, results, and significance of the Hershey and Chase experiments is even more problematic. Considerable time and attention to these details will be required for many of your students.
2. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
Teaching Tips
1. A phage functions like a needle and syringe, injecting a drug. The needle and syringe are analogous to the protein components of the phage. The drug to be injected is analogous to the phage DNA.
2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
© 2012 Pearson Education, Inc. 9

10. 10.1 SCIENTIFIC DISCOVERY: Experiments showed that DNA is the genetic material
The sulfur-labeled protein stayed with the phages outside the bacterial cell, while the phosphorus-labeled DNA was detected inside cells.
Cells with phosphorus-labeled DNA produced new bacteriophages with radioactivity in DNA but not in protein.
Student Misconceptions and Concerns
1. Understanding bacteriophage replication can be difficult for students with limited knowledge of cell biology or genetics. Therefore, understanding the methods, results, and significance of the Hershey and Chase experiments is even more problematic. Considerable time and attention to these details will be required for many of your students.
2. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
Teaching Tips
1. A phage functions like a needle and syringe, injecting a drug. The needle and syringe are analogous to the protein components of the phage. The drug to be injected is analogous to the phage DNA.
2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
Animation: Hershey-Chase Experiment
Animation: Phage T2 Reproductive Cycle
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11. Figure 10.1A
Head
DNA
Tail
Tail fiber
Figure 10.1A Phage T2 11

12. Figure 10.1A_1
Head
Tail
Tail fiber
Figure 10.1A_1 Phage T2 (TEM) 12

13. The radioactivity is in the liquid.
Figure 10.1B
Radioactive protein
Empty protein shell
Phage
The radioactivity is in the liquid.
Bacterium
Phage DNA
Batch 1: Radioactive protein labeled in yellow
DNA
Centrifuge
Pellet 1 2 3 4
Figure 10.1B The Hershey-Chase experiment
Batch 2: Radioactive DNA labeled in green
Radioactive DNA
Centrifuge
The radioactivity is in the pellet.
Pellet 13

14. Batch 1: Radioactive protein labeled in yellow
Figure 10.1B_1
Empty protein shell
Radioactive protein
Phage
Bacterium
Phage DNA
DNA
Batch 1: Radioactive protein labeled in yellow 1 2
Figure 10.1B_1 The Hershey-Chase experiment (part 1)
Batch 2: Radioactive DNA labeled in green
Radioactive DNA 14

15. The radioactivity is in the liquid.
Figure 10.1B_2
Empty protein shell
The radioactivity is in the liquid.
Phage DNA
Centrifuge
Pellet 3 4
Figure 10.1B_2 The Hershey-Chase experiment (part 2)
Centrifuge
The radioactivity is in the pellet.
Pellet 15

16. A phage attaches itself to a bacterial cell.
Figure 10.1C 1
A phage attaches itself to a bacterial cell. 2
The phage injects its DNA into the bacterium. 3
The phage DNA directs the host cell to make more phage DNA and proteins; new phages assemble. 4
The cell lyses and releases the new phages.
Figure 10.1C A phage replication cycle 16

17. A phage attaches itself to a bacterial cell.
Figure 10.1C_1 1
A phage attaches itself to a bacterial cell.
The phage injects its DNA into the bacterium. 2
Figure 10.1C_1 A phage replication cycle (part 1) 17

18. The cell lyses and releases the new phages.
Figure 10.1C_2
The phage DNA directs the host cell to make more phage DNA and proteins; new phages assemble. 3 3
Figure 10.1C_2 A phage replication cycle (part 2)
The cell lyses and releases the new phages. 4 18

19. 10.2 DNA and RNA are polymers of nucleotides
DNA and RNA are nucleic acids.
One of the two strands of DNA is a DNA polynucleotide, a nucleotide polymer (chain).
A nucleotide is composed of a
nitrogenous base,
five-carbon sugar, and
phosphate group.
The nucleotides are joined to one another by a sugar-phosphate backbone.
Student Misconceptions and Concerns
1. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
2. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars.
© 2012 Pearson Education, Inc. 19

20. Animation: DNA and RNA Structure
10.2 DNA and RNA are polymers of nucleotides
Each type of DNA nucleotide has a different nitrogen-containing base:
adenine (A),
cytosine (C),
thymine (T), and
guanine (G).
Student Misconceptions and Concerns
1. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
2. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars.
Animation: DNA and RNA Structure
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21. Sugar-phosphate backbone
Figure 10.2A A T C G T A
Sugar-phosphate backbone C G
Phosphate group A T G C A G A
Nitrogenous base
Nitrogenous base (can be A, G, C, or T)
Covalent bond joining nucleotides A T G C
Sugar T A T A C C C C C G T A
DNA nucleotide
Thymine (T)
A DNA double helix T T T
Phosphate group
Figure 10.2A The structure of a DNA polynucleotide G G
Sugar (deoxyribose)
DNA nucleotide G G
Two representations of a DNA polynucleotide 21

22. A DNA double helix Figure 10.2A_1 A T C G T A C G A T G C G A T G C T
Figure 10.2A_1 The structure of a DNA polynucleotide (part 1) C G T A
A DNA double helix 22

23. Sugar-phosphate backbone
Figure 10.2A_2
Sugar-phosphate backbone
Phosphate group A A
Nitrogenous base
Covalent bond joining nucleotides
Sugar C C
DNA nucleotide T T G G
Figure 10.2A_2 The structure of a DNA polynucleotide (part 2) G G
Two representations of a DNA polynucleotide 23

24. Thymine (T) Phosphate group
Figure 10.2A_3
Nitrogenous base (can be A, G, C, or T)
Thymine (T)
Phosphate group
Figure 10.2A_3 The structure of a DNA polynucleotide (part 3)
Sugar (deoxyribose)
DNA nucleotide 24

25. Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Pyrimidines Purines
Figure 10.2B
Thymine (T)
Cytosine (C)
Adenine (A)
Guanine (G)
Pyrimidines
Purines
Figure 10.2B The nitrogenous bases of DNA 25

26. Thymine (T) Cytosine (C) Pyrimidines Figure 10.2B_1
Figure 10.2B_1 The nitrogenous bases of DNA (part 1)
Thymine (T)
Cytosine (C)
Pyrimidines 26

27. Adenine (A) Guanine (G) Purines Figure 10.2B_2
Figure 10.2B_2 The nitrogenous bases of DNA (part 2)
Adenine (A)
Guanine (G)
Purines 27

28. 10.2 DNA and RNA are Polymers of Nucleotides
RNA (ribonucleic acid) is unlike DNA in that it
uses the sugar ribose (instead of deoxyribose in DNA) and
RNA has the nitrogenous base uracil (U) instead of thymine.
Student Misconceptions and Concerns
1. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
2. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars.
© 2012 Pearson Education, Inc. 28

29. Nitrogenous base (can be A, G, C, or U)
Figure 10.2C
Nitrogenous base (can be A, G, C, or U)
Phosphate group
Uracil (U)
Figure 10.2C An RNA nucleotide
Sugar (ribose) 29

30. Cytosine Uracil Adenine Guanine Ribose Phosphate Figure 10.2D
Figure 10.2D A computer model showing part of an RNA polynucleotide 30

31. 10.3 SCIENTIFIC DISCOVERY: DNA is a double-stranded helix
In 1952, after the Hershey-Chase experiment demonstrated that the genetic material was most likely DNA, a race was on to
describe the structure of DNA and
explain how the structure and properties of DNA can account for its role in heredity.
Student Misconceptions and Concerns
Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent pairs of nitrogenous bases joined by hydrogen bonds. Each rope represents a sugar-phosphate backbone.
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32. Figure 10.3A
Figure 10.3A Rosalind Franklin and her X-ray image of DNA 32

33. Figure 10.3A_1
Figure 10.3A_1 Rosalind Franklin and her X-ray image of DNA (part 1) 33

34. Figure 10.3A_2
Figure 10.3A_2 Rosalind Franklin and her X-ray image of DNA (part 2) 34

35. 10.3 SCIENTIFIC DISCOVERY: DNA is a double-stranded helix
In 1953, James D. Watson and Francis Crick deduced the secondary structure of DNA, using
X-ray crystallography data of DNA from the work of Rosalind Franklin and Maurice Wilkins and
Chargaff’s observation that in DNA,
the amount of adenine was equal to the amount of thymine and
the amount of guanine was equal to that of cytosine.
Student Misconceptions and Concerns
Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent pairs of nitrogenous bases joined by hydrogen bonds. Each rope represents a sugar-phosphate backbone.
© 2012 Pearson Education, Inc. 35

36. 10.3 SCIENTIFIC DISCOVERY: DNA is a double-stranded helix
Watson and Crick reported that DNA consisted of two polynucleotide strands wrapped into a double helix.
The sugar-phosphate backbone is on the outside.
The nitrogenous bases are perpendicular to the backbone in the interior.
Specific pairs of bases give the helix a uniform shape.
A pairs with T, forming two hydrogen bonds, and
G pairs with C, forming three hydrogen bonds.
Student Misconceptions and Concerns
Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent pairs of nitrogenous bases joined by hydrogen bonds. Each rope represents a sugar-phosphate backbone.
Animation: DNA Double Helix
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37. Figure 10.3B
Figure 10.3B Watson and Crick in 1953 with their model of the DNA double helix 37

38. Figure 10.3C
Figure 10.3C A rope ladder model for the double helix
Twist 38

39. Partial chemical structure
Figure 10.3D
Hydrogen bond
Base pair
Figure 10.3D Three representations of DNA
Ribbon model
Partial chemical structure
Computer model 39

40. Base pair Ribbon model C G C G G C G C T A A T C G A T T A C G G C C G
Figure 10.3D_1
C G
C G
G C
G C
Base pair
T A
A T
C G
A T
T A
C G
G C
Figure 10.3D_1 Three representations of DNA (part 1)
C G
A T
A T
T A
Ribbon model 40

41. Partial chemical structure
Figure 10.3D_2
Hydrogen bond
G C
T A
A T
Figure 10.3D_2 Three representations of DNA (part 2)
C G
Partial chemical structure 41

42. Computer model Figure 10.3D_3
Figure 10.3D_3 Three representations of DNA (part 3)
Computer model 42

43. 10.3 SCIENTIFIC DISCOVERY: DNA is a double-stranded helix
In 1962, the Nobel Prize was awarded to
James D. Watson, Francis Crick, and Maurice Wilkins.
Rosalind Franklin probably would have received the prize as well but for her death from cancer in Nobel Prizes are never awarded posthumously.
The Watson-Crick model gave new meaning to the words genes and chromosomes. The genetic information in a chromosome is encoded in the nucleotide sequence of DNA.
Student Misconceptions and Concerns
Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent pairs of nitrogenous bases joined by hydrogen bonds. Each rope represents a sugar-phosphate backbone.
© 2012 Pearson Education, Inc. 43

44. DNA REPLICATION
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45. 10.4 DNA replication depends on specific base pairing
In their description of the structure of DNA, Watson and Crick noted that the structure of DNA suggests a possible copying mechanism.
DNA replication follows a semiconservative model.
The two DNA strands separate.
Each strand is used as a pattern to produce a complementary strand, using specific base pairing.
Each new DNA helix has one old strand with one new strand.
Student Misconceptions and Concerns
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. Demonstrate the complementary base pairing within DNA. Present students with the base sequence to one side of a DNA molecule and have them work quickly at their seats to determine the sequence of the complimentary strand. For some students, these sorts of quick practice are necessary to reinforce a concept and break up a lecture.
2. The semiconservative model of DNA replication is like making a photo from a negative and then a new negative from the photo. In each new negative and photo pair, the new item was made from an old item.
Animation: DNA Replication Overview
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46. A parental molecule of DNA
Figure 10.4A_s1
A T
C G
G C
A T
T A
A parental molecule of DNA
Figure 10.4A_s1 A template model for DNA replication (step 1) 46

47. A parental molecule of DNA
Figure 10.4A_s2
A T T A A T
C G C G G C
G C G C C A
A T A T
Free nucleotides
T A T A
A parental molecule of DNA
The parental strands separate and serve as templates
Figure 10.4A_s2 A template model for DNA replication (step 2) 47

48. A parental molecule of DNA
Figure 10.4A_s3
A T T A A T
A T
A T
C G C G G
C G
C G C
G C G C C
G C
G C A
A T A T
A T
A T
Free nucleotides
T A T A
T A
T A
A parental molecule of DNA
The parental strands separate and serve as templates
Two identical daughter molecules of DNA are formed
Figure 10.4A-s3 A template model for DNA replication (step 3) 48

49. Daughter DNA molecules
Figure 10.4B
A T
G C
A T
Parental DNA molecule
A T
T A C G C G T
Daughter strand A
C G
C G
C G
Parental strand T
C G A
Figure 10.4B The untwisting and replication of DNA
C G
A T
T A
A T
C G
G C
A T T
A T A
A T
G C
Daughter DNA molecules 49

50. 10.5 DNA replication proceeds in two directions at many sites simultaneously
DNA replication begins at the origins of replication where
DNA unwinds at the origin to produce a “bubble,”
replication proceeds in both directions from the origin, and
replication ends when products from the bubbles merge with each other.
Student Misconceptions and Concerns
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask the students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter.
2. There are about 500,000 words in the Biology: Concepts & Connections textbook. The accuracy of DNA replication would be like copying every word in this textbook by hand 2,000 times and writing just one word incorrectly, making one error in every 1 billion words.
© 2012 Pearson Education, Inc. 50

51. 10.5 DNA replication proceeds in two directions at many sites simultaneously
DNA replication occurs in the 5 to 3 direction.
Replication is continuous on the 3 to 5 template.
Replication is discontinuous on the 5 to 3 template, forming short segments.
Student Misconceptions and Concerns
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask the students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter.
2. There are about 500,000 words in the Biology: Concepts & Connections textbook. The accuracy of DNA replication would be like copying every word in this textbook by hand 2,000 times and writing just one word incorrectly, making one error in every 1 billion words.
© 2012 Pearson Education, Inc. 51

52. 10.5 DNA replication proceeds in two directions at many sites simultaneously
Two key proteins are involved in DNA replication.
DNA ligase joins small fragments into a continuous chain.
DNA polymerase
adds nucleotides to a growing chain and
proofreads and corrects improper base pairings.
Animation: Origins of Replication
Student Misconceptions and Concerns
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask the students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter.
2. There are about 500,000 words in the Biology: Concepts & Connections textbook. The accuracy of DNA replication would be like copying every word in this textbook by hand 2,000 times and writing just one word incorrectly, making one error in every 1 billion words.
Animation: Leading Strand
Animation: Lagging Strand
Animation: DNA Replication Review
© 2012 Pearson Education, Inc. 52

53. 10.5 DNA replication proceeds in two directions at many sites simultaneously
DNA polymerases and DNA ligase also repair DNA damaged by harmful radiation and toxic chemicals.
DNA replication ensures that all the somatic cells in a multicellular organism carry the same genetic information.
Student Misconceptions and Concerns
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask the students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter.
2. There are about 500,000 words in the Biology: Concepts & Connections textbook. The accuracy of DNA replication would be like copying every word in this textbook by hand 2,000 times and writing just one word incorrectly, making one error in every 1 billion words.
© 2012 Pearson Education, Inc. 53

54. Two daughter DNA molecules
Figure 10.5A
Parental DNA molecule
Origin of replication
Parental strand
Daughter strand
“Bubble”
Figure 10.5A Multiple bubbles in replicating DNA
Two daughter DNA molecules 54

55. 5 end 3 end P HO A T P P C G P P G C P P T A OH P 3 end 5 end 5
Figure 10.5B
5 end
3 end P HO 5 2 4 A T 3 3 1 1 2 4 P 5 P C G P P G C
Figure 10.5B The opposite orientations of DNA strands P P T A OH P
3 end
5 end 55

56. DNA polymerase molecule
Figure 10.5C 3
DNA polymerase molecule
This daughter strand is synthesized continuously 5
Parental DNA 5 3
Replication fork
This daughter strand is synthesized in pieces 3 5
Figure 10.5C How daughter DNA strands are synthesized 5 3
DNA ligase
Overall direction of replication 56

57. THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN
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58. 10.6 The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits
DNA specifies traits by dictating protein synthesis.
The molecular chain of command is from
DNA in the nucleus to RNA and
RNA in the cytoplasm to protein.
Transcription is the synthesis of RNA under the direction of DNA.
Translation is the synthesis of proteins under the direction of RNA.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. Consider placing the basic content from Figure 10.6A on the board, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail.
Teaching Tips
1. It has been said that everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to evaluate the validity of this statement.
2. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
© 2012 Pearson Education, Inc. 58

59. DNA NUCLEUS CYTOPLASM Figure 10.6A_s1
Figure 10.6A_s1 The flow of genetic information in a eukaryotic cell (step 1) 59

60. DNA Transcription RNA NUCLEUS CYTOPLASM Figure 10.6A_s2
Figure 10.6A_s2 The flow of genetic information in a eukaryotic cell (step 2) 60

61. DNA Transcription RNA NUCLEUS CYTOPLASM Translation Protein
Figure 10.6A_s3
DNA
Transcription
RNA
NUCLEUS
CYTOPLASM
Translation
Figure 10.6A_s3 The flow of genetic information in a eukaryotic cell (step 3)
Protein 61

62. 10.6 The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits
The connections between genes and proteins
The initial one gene–one enzyme hypothesis was based on studies of inherited metabolic diseases.
The one gene–one enzyme hypothesis was expanded to include all proteins.
Most recently, the one gene–one polypeptide hypothesis recognizes that some proteins are composed of multiple polypeptides.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. Consider placing the basic content from Figure 10.6A on the board, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail.
Teaching Tips
1. It has been said that everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to evaluate the validity of this statement.
2. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
© 2012 Pearson Education, Inc. 62

63. Figure 10.6B
Figure 10.6B The bread mold Neurospora crassa growing in a culture dish 63

64. 10.7 Genetic information written in codons is translated into amino acid sequences
The sequence of nucleotides in DNA provides a code for constructing a protein.
Protein construction requires a conversion of a nucleotide sequence to an amino acid sequence.
Transcription rewrites the DNA code into RNA, using the same nucleotide “language.”
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. The transcription of DNA into RNA is like a reporter’s transcription of a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written language.
2. The sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame (see Module 10.16).
© 2012 Pearson Education, Inc. 64

65. 10.7 Genetic information written in codons is translated into amino acid sequences
The flow of information from gene to protein is based on a triplet code: the genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of nonoverlapping three-base “words” called codons.
Translation involves switching from the nucleotide “language” to the amino acid “language.”
Each amino acid is specified by a codon.
64 codons are possible.
Some amino acids have more than one possible codon.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. The transcription of DNA into RNA is like a reporter’s transcription of a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written language.
2. The sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame (see Module 10.16).
© 2012 Pearson Education, Inc. 65

66. Figure 10.7 Transcription and translation of codons DNA
DNA molecule
Gene 1
Gene 2
Gene 3
Figure 10.7 Transcription and translation of codons
DNA A A A C C G G C A A A A
Transcription
RNA U U U G G C C G U U U U
Translation
Codon
Polypeptide
Amino acid 66

67. DNA Transcription RNA Codon Translation Polypeptide Amino acid A A A C
Figure 10.7_1
DNA A A A C C G G C A A A A
Transcription U U U G G C C G U U U U
RNA
Codon
Translation
Figure 10.7_1 Transcription and translation of codons (partial)
Polypeptide
Amino acid 67

68. 10.8 The genetic code dictates how codons are translated into amino acids
Characteristics of the genetic code
Three nucleotides specify one amino acid.
61 codons correspond to amino acids.
AUG codes for methionine and signals the start of transcription.
3 “stop” codons signal the end of translation.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. You may want to note the parallel between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups.
2. The authors note the universal use of the genetic code in all forms of life. The evolutionary significance of this fundamental, universal language is a reminder of the shared ancestry of all life. The universal genetic code is part of the overwhelming evidence for evolution.
© 2012 Pearson Education, Inc. 68

69. 10.8 The genetic code dictates how codons are translated into amino acids
The genetic code is
redundant, with more than one codon for some amino acids,
unambiguous in that any codon for one amino acid does not code for any other amino acid,
nearly universal—the genetic code is shared by organisms from the simplest bacteria to the most complex plants and animals, and
without punctuation in that codons are adjacent to each other with no gaps in between.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. You may want to note the parallel between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups.
2. The authors note the universal use of the genetic code in all forms of life. The evolutionary significance of this fundamental, universal language is a reminder of the shared ancestry of all life. The universal genetic code is part of the overwhelming evidence for evolution.
© 2012 Pearson Education, Inc. 69

70. Second base First base Third base Figure 10.8A
Figure 10.8A Dictionary of the genetic code (RNA codons) 70

71. T A C T T C A A A A T C A T G A A G T T T T A G
Figure 10.8B_s1
Strand to be transcribed T A C T T C A A A A T C
DNA A T G A A G T T T T A G
Figure 10.8B_s1 Deciphering the genetic information in DNA (step 1) 71

72. T A C T T C A A A A T C A T G A A G T T T T A G A U G A A G U U U U A
Figure 10.8B_s2
Strand to be transcribed T A C T T C A A A A T C
DNA A T G A A G T T T T A G
Transcription
RNA A U G A A G U U U U A G
Figure 10.8B_s2 Deciphering the genetic information in DNA (step 2) 72

73. T A C T T C A A A A T C A T G A A G T T T T A G A U G A A G U U U U A
Figure 10.8B_s3
Strand to be transcribed T A C T T C A A A A T C
DNA A T G A A G T T T T A G
Transcription
RNA A U G A A G U U U U A G
Figure 10.8B_s3 Deciphering the genetic information in DNA (step 3)
Start codon
Stop codon
Translation
Polypeptide
Met
Lys
Phe 73

74. Figure 10.8C
Figure 10.8C The mice to the left and right are engineered to express a green fluorescence protein obtained from a jelly (jellyfish) 74

75. 10.9 Transcription produces genetic messages in the form of RNA
Overview of transcription
An RNA molecule is transcribed from a DNA template by a process that resembles the synthesis of a DNA strand during DNA replication.
RNA nucleotides are linked by the transcription enzyme RNA polymerase.
Specific sequences of nucleotides along the DNA mark where transcription begins and ends.
The “start transcribing” signal is a nucleotide sequence called a promoter.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. As students learn about transcription, they might wonder which of the two strands of DNA is read. This uncertainty may add to the confusion about the details of the process, and students might not even think to ask. As noted in Module 10.9, the location of the promoter, a specific binding site for RNA polymerase, determines which strand is read.
Teaching Tips
Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away.
© 2012 Pearson Education, Inc. 75

76. 10.9 Transcription produces genetic messages in the form of RNA
Transcription begins with initiation, as the RNA polymerase attaches to the promoter.
During the second phase, elongation, the RNA grows longer.
As the RNA peels away, the DNA strands rejoin.
Finally, in the third phase, termination, the RNA polymerase reaches a sequence of bases in the DNA template called a terminator, which signals the end of the gene.
The polymerase molecule now detaches from the RNA molecule and the gene.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. As students learn about transcription, they might wonder which of the two strands of DNA is read. This uncertainty may add to the confusion about the details of the process, and students might not even think to ask. As noted in Module 10.9, the location of the promoter, a specific binding site for RNA polymerase, determines which strand is read.
Teaching Tips
Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away.
Animation: Transcription
© 2012 Pearson Education, Inc. 76

77. Direction of transcription Template strand of DNA
Figure 10.9A
Free RNA nucleotides
RNA polymerase T C C A A T A U T C T G U G A C C A U C C A C A G T A G G T T A
Figure 10.9A A close-up view of transcription
Direction of transcription
Template strand of DNA
Newly made RNA 77

78. Terminator DNA RNA polymerase DNA of gene Promoter DNA Initiation
Figure 10.9B
RNA polymerase
Terminator DNA
DNA of gene
Promoter DNA 1
Initiation 2
Elongation
Area shown in Figure 10.9A
Figure 10.9B The transcription of a gene
Growing RNA 3
Termination
Completed RNA
RNA polymerase 78

79. RNA polymerase Terminator DNA DNA of gene Promoter DNA 1 Initiation
Figure 10.9B_1
RNA polymerase
Terminator DNA
DNA of gene
Promoter DNA 1
Initiation
Figure 10.9B_1 The transcription of a gene (part 1) 79

80. 2 Elongation Area shown in Figure 10.9A Growing RNA Figure 10.9B_2
Figure 10.9B_2 The transcription of a gene (part 2)
Growing RNA 80