1. DNA Technology and Genomics
Chapter 12
DNA Technology and Genomics

2. Introduction DNA technology
DNA technology
has rapidly revolutionized the field of forensics,
permits the use of gene cloning to produce medical and industrial products,
allows for the development of genetically modified organisms for agriculture,
permits the investigation of historical questions about human family and evolutionary relationships, and
is invaluable in many areas of biological research.
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3. Genetically Modified Organisms Genomics
Figure 12.0_1
Chapter 12: Big Ideas
Gene Cloning
Genetically Modified
Organisms
Figure 12.0_1 Chapter 12: Big Ideas
DNA Profiling
Genomics 3

4. Figure 12.0_2
Figure 12.0_2 DNA analysis and profile 4

5. GENE CLONING
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6. 12.1 Genes can be cloned in recombinant plasmids
Biotechnology is the manipulation of organisms or their components to make useful products.
For thousands of years, humans have
used microbes to make wine and cheese and
selectively bred stock, dogs, and other animals.
DNA technology is the set of modern techniques used to study and manipulate genetic material.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1B is therefore an important integrative piece that lays the foundation of most of the biotechnology discussion. Repeatedly referring to this figure in class helps students relate the text to your lecture.
2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to (a) cut and remove the minute of film to be inserted, (b) a way to cut the new film apart, and (c) a way to insert the new minute. In general, this is also like removing one boxcar from one train, and transferring the boxcar to another train. Students can become confused by the details of gene cloning through misunderstanding this basic editing relationship.
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7. Figure 12.1A
Figure 12.1A Glowing fish produced by transferring a gene originally obtained from a jelly (cnidarian) 7

8. 12.1 Genes can be cloned in recombinant plasmids
Genetic engineering involves manipulating genes for practical purposes.
Gene cloning leads to the production of multiple, identical copies of a gene-carrying piece of DNA.
Recombinant DNA is formed by joining nucleotide sequences from two different sources.
One source contains the gene that will be cloned.
Another source is a gene carrier, called a vector.
Plasmids (small, circular DNA molecules independent of the bacterial chromosome) are often used as vectors.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1B is therefore an important integrative piece that lays the foundation of most of the biotechnology discussion. Repeatedly referring to this figure in class helps students relate the text to your lecture.
2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to (a) cut and remove the minute of film to be inserted, (b) a way to cut the new film apart, and (c) a way to insert the new minute. In general, this is also like removing one boxcar from one train, and transferring the boxcar to another train. Students can become confused by the details of gene cloning through misunderstanding this basic editing relationship.
© 2012 Pearson Education, Inc. 8

9. 12.1 Genes can be cloned in recombinant plasmids
Steps in cloning a gene
Plasmid DNA is isolated.
DNA containing the gene of interest is isolated.
Plasmid DNA is treated with a restriction enzyme that cuts in one place, opening the circle.
DNA with the target gene is treated with the same enzyme and many fragments are produced.
Plasmid and target DNA are mixed and associate with each other.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1B is therefore an important integrative piece that lays the foundation of most of the biotechnology discussion. Repeatedly referring to this figure in class helps students relate the text to your lecture.
2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to (a) cut and remove the minute of film to be inserted, (b) a way to cut the new film apart, and (c) a way to insert the new minute. In general, this is also like removing one boxcar from one train, and transferring the boxcar to another train. Students can become confused by the details of gene cloning through misunderstanding this basic editing relationship.
© 2012 Pearson Education, Inc. 9

10. 12.1 Genes can be cloned in recombinant plasmids
Recombinant DNA molecules are produced when DNA ligase joins plasmid and target segments together.
The recombinant plasmid containing the target gene is taken up by a bacterial cell.
The bacterial cell reproduces to form a clone, a group of genetically identical cells descended from a single ancestral cell.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1B is therefore an important integrative piece that lays the foundation of most of the biotechnology discussion. Repeatedly referring to this figure in class helps students relate the text to your lecture.
2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to (a) cut and remove the minute of film to be inserted, (b) a way to cut the new film apart, and (c) a way to insert the new minute. In general, this is also like removing one boxcar from one train, and transferring the boxcar to another train. Students can become confused by the details of gene cloning through misunderstanding this basic editing relationship.
© 2012 Pearson Education, Inc. 10

11. Animation: Cloning a Gene
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1B is therefore an important integrative piece that lays the foundation of most of the biotechnology discussion. Repeatedly referring to this figure in class helps students relate the text to your lecture.
2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to (a) cut and remove the minute of film to be inserted, (b) a way to cut the new film apart, and (c) a way to insert the new minute. In general, this is also like removing one boxcar from one train, and transferring the boxcar to another train. Students can become confused by the details of gene cloning through misunderstanding this basic editing relationship.
Animation: Cloning a Gene
Right click on animation / Click play
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12. Figure 12.1B An overview of gene cloning
E. coli bacterium
Plasmid
A cell with DNA
containing the gene
of interest
Bacterial
chromosome
A plasmid
is isolated. 2
The cell’s DNA
is isolated. 1
Gene of
interest
DNA 3
The plasmid is cut
with an enzyme.
Examples of gene use 4
The cell’s DNA is cut
with the same enzyme.
Gene
of interest 5
The targeted fragment
and plasmid DNA
are combined. 6
DNA ligase is added,
which joins the two
DNA molecules.
Genes may be inserted
into other organisms.
Recombinant
DNA
plasmid
Examples of protein use
Gene
of interest
Figure 12.1B An overview of gene cloning 7
The recombinant plasmid
is taken up by a bacterium
through transformation. 9
Recombinant
bacterium
Harvested
proteins
may be
used
directly. 8
The bacterium
reproduces.
Clone
of cells 12

13. A cell with DNA Plasmid containing the gene of interest E. coli
Figure 12.1B_s1
A cell with DNA
containing the gene
of interest
Plasmid
E. coli
bacterium 2
The cell’s DNA
is isolated.
Bacterial
chromosome 1
A plasmid
is isolated.
Gene of
interest
DNA
Figure 12.1B_s1 An overview of gene cloning (part 1, step 1) 13

14. A cell with DNA Plasmid containing the gene of interest E. coli
Figure 12.1B_s2
A cell with DNA
containing the gene
of interest
Plasmid
E. coli
bacterium 2
The cell’s DNA
is isolated.
Bacterial
chromosome 1
A plasmid
is isolated.
Gene of
interest
DNA 3
The plasmid is cut
with an enzyme. 4
The cell’s DNA is cut
with the same enzyme.
Gene
of interest
Figure 12.1B_s2 An overview of gene cloning (part 1, step 2) 14

15. A cell with DNA Plasmid containing the gene of interest E. coli
Figure 12.1B_s3
A cell with DNA
containing the gene
of interest
Plasmid
E. coli
bacterium 2
The cell’s DNA
is isolated.
Bacterial
chromosome 1
A plasmid
is isolated.
Gene of
interest
DNA 3
The plasmid is cut
with an enzyme. 4
The cell’s DNA is cut
with the same enzyme.
Gene
of interest 5
The targeted fragment
and plasmid DNA
are combined.
Figure 12.1B_s3 An overview of gene cloning (part 1, step 3) 15

16. A cell with DNA Plasmid containing the gene of interest E. coli
Figure 12.1B_s4
A cell with DNA
containing the gene
of interest
Plasmid
E. coli
bacterium 2
The cell’s DNA
is isolated.
Bacterial
chromosome 1
A plasmid
is isolated.
Gene of
interest
DNA 3
The plasmid is cut
with an enzyme. 4
The cell’s DNA is cut
with the same enzyme.
Gene
of interest 5
The targeted fragment
and plasmid DNA
are combined.
Figure 12.1B_s4 An overview of gene cloning (part 1, step 4) 6
DNA ligase is added,
which joins the two
DNA molecules.
Recombinant
DNA
plasmid
Gene
of interest 16

17. The recombinant plasmid is taken up by a bacterium
Figure 12.1B_s5
Recombinant
DNA
plasmid
Gene
of interest 7
The recombinant plasmid
is taken up by a bacterium
through transformation.
Recombinant
bacterium
Figure 12.1B_s5 An overview of gene cloning (part 2, step 1) 17

18. The recombinant plasmid is taken up by a bacterium
Figure 12.1B_s6
Recombinant
DNA
plasmid
Gene
of interest 7
The recombinant plasmid
is taken up by a bacterium
through transformation.
Recombinant
bacterium 8
The bacterium
reproduces.
Figure 12.1B_s6 An overview of gene cloning (part 2, step 2)
Clone
of cells 18

19. The recombinant plasmid is taken up by a bacterium
Figure 12.1B_s7
Genes may be inserted
into other organisms.
Recombinant
DNA
plasmid
Gene
of interest 7
The recombinant plasmid
is taken up by a bacterium
through transformation. 9
Recombinant
bacterium
Harvested
proteins
may be
used
directly. 8
The bacterium
reproduces.
Figure 12.1B_s7 An overview of gene cloning (part 2, step 3)
Clone
of cells 19

20. Figure 12.1B_8
Figure 12.1B_8 An overview of gene cloning (Bt corn) 20

21. Figure 12.1B_9
Figure 12.1B_9 An overview of gene cloning (oil spill) 21

22. Figure 12.1B_10
Figure 12.1B_10 An overview of gene cloning (stonewashed jeans) 22

23. Figure 12.1B_11
Figure 12.1B_11 An overview of gene cloning (heart attack) 23

24. 12.2 Enzymes are used to “cut and paste” DNA
Restriction enzymes cut DNA at specific sequences.
Each enzyme binds to DNA at a different restriction site.
Many restriction enzymes make staggered cuts that produce restriction fragments with single-stranded ends called “sticky ends.”
Fragments with complementary sticky ends can associate with each other, forming recombinant DNA.
DNA ligase joins DNA fragments together.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. The authors note the origin of the name restriction enzymes. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material.
2. A genomic library of the sentence you are now reading would be all of the sentence fragments that made up the sentence. One could string together all of the words of this first sentence, without spaces between letters, and then conduct a word processing edit, placing a space between any place where the letter “e” is followed by the letter “n.” The resulting fragments of this original sentence would look like this and would be similar to a genomic library.
Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce.
© 2012 Pearson Education, Inc. 24

25. Animation: Restriction Enzymes
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. The authors note the origin of the name restriction enzymes. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material.
2. A genomic library of the sentence you are now reading would be all of the sentence fragments that made up the sentence. One could string together all of the words of this first sentence, without spaces between letters, and then conduct a word processing edit, placing a space between any place where the letter “e” is followed by the letter “n.” The resulting fragments of this original sentence would look like this and would be similar to a genomic library.
Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce.
Animation: Restriction Enzymes
Right click on animation / Click play
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26. DNA Restriction enzyme recognition sequence A restriction enzyme cuts
Figure 12.2_s1 1
DNA
Restriction enzyme
recognition sequence
A restriction
enzyme cuts
the DNA into
fragments.
Restriction
enzyme 2
Sticky
end
Sticky
end
Figure 12.2_s1 Creating recombinant DNA using a restriction enzyme and DNA ligase (step 1) 26

27. DNA Restriction enzyme recognition sequence A restriction enzyme cuts
Figure 12.2_s2 1
DNA
Restriction enzyme
recognition sequence
A restriction
enzyme cuts
the DNA into
fragments.
Restriction
enzyme 2
Sticky
end
Sticky
end
Gene of
interest
A DNA fragment
from another
source is added. 3
Figure 12.2_s2 Creating recombinant DNA using a restriction enzyme and DNA ligase (step 2) 27

28. DNA Restriction enzyme recognition sequence A restriction enzyme cuts
Figure 12.2_s3 1
DNA
Restriction enzyme
recognition sequence
A restriction
enzyme cuts
the DNA into
fragments.
Restriction
enzyme 2
Sticky
end
Sticky
end
Gene of
interest
A DNA fragment
from another
source is added. 3
Two (or more)
fragments stick
together by
base pairing.
Figure 12.2_s3 Creating recombinant DNA using a restriction enzyme and DNA ligase (step 3) 4 28

29. DNA Restriction enzyme recognition sequence A restriction enzyme cuts
Figure 12.2_s4 1
DNA
Restriction enzyme
recognition sequence
A restriction
enzyme cuts
the DNA into
fragments.
Restriction
enzyme 2
Sticky
end
Sticky
end
Gene of
interest
A DNA fragment
from another
source is added. 3
Two (or more)
fragments stick
together by
base pairing.
Figure 12.2_s4 Creating recombinant DNA using a restriction enzyme and DNA ligase (step 4) 4
DNA ligase
DNA ligase
pastes the
strands together.
Recombinant
DNA molecule 5 29

30. 12.3 Cloned genes can be stored in genomic libraries
A genomic library is a collection of all of the cloned DNA fragments from a target genome.
Genomic libraries can be constructed with different types of vectors:
plasmid library: genomic DNA is carried by plasmids,
bacteriophage (phage) library: genomic DNA is incorporated into bacteriophage DNA,
bacterial artificial chromosome (BAC) library: specialized plasmids that can carry large DNA sequences.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
A genomic library of the sentence you are now reading would be all of the sentence fragments that made up the sentence. One could string together all of the words of this first sentence, without spaces between letters, and then conduct a word processing edit, placing a space between any place where the letter “e” is followed by the letter “n.” The resulting fragments of this original sentence would look like this and would be similar to a genomic library.
Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce.
© 2012 Pearson Education, Inc. 30

31. A genome is cut up with a restriction enzyme or Recombinant plasmid
Figure 12.3
A genome is cut up with
a restriction enzyme or
Recombinant
plasmid
Recombinant
phage DNA
Figure 12.3 Genomic libraries
Bacterial
clone
Phage
clone
Plasmid library
Phage library 31

32. 12.4 Reverse transcriptase can help make genes for cloning
Complementary DNA (cDNA) can be used to clone eukaryotic genes.
In this process, mRNA from a specific cell type is the template.
Reverse transcriptase produces a DNA strand from mRNA.
DNA polymerase produces the second DNA strand.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. A cDNA library is a way to learn what portion of the genome is active at any given time in a cell’s life. In a very general way, it is like looking at the list of books checked out at a school library (assuming that the checked-out books are being used).
2. Reverse transcriptase is introduced in Module 10.20, where HIV is discussed. Even if students were not assigned this chapter, Module provides a meaningful background for the natural and significant roles of this enzyme.
© 2012 Pearson Education, Inc. 32

33. 12.4 Reverse transcriptase can help make genes for cloning
Advantages of cloning with cDNA include the ability to
study genes responsible for specialized characteristics of a particular cell type and
obtain gene sequences
that are smaller in size,
easier to handle, and
do not have introns.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
1. A cDNA library is a way to learn what portion of the genome is active at any given time in a cell’s life. In a very general way, it is like looking at the list of books checked out at a school library (assuming that the checked-out books are being used).
2. Reverse transcriptase is introduced in Module 10.20, where HIV is discussed. Even if students were not assigned this chapter, Module provides a meaningful background for the natural and significant roles of this enzyme.
© 2012 Pearson Education, Inc. 33

34. introns and joins exons)
Figure 12.4
CELL NUCLEUS
Exon
Intron
Exon
Intron
Exon
DNA of a
eukaryotic
gene 1
Transcription
RNA
transcript 2
RNA splicing (removes
introns and joins exons)
mRNA 3
Isolation of mRNA from
the cell and the addition
of reverse transcriptase;
synthesis of a DNA strand
TEST TUBE
Reverse transcriptase
Figure 12.4 Making an intron-lacking gene from eukaryotic mRNA
cDNA strand
being synthesized 4
Breakdown of RNA
Direction
of synthesis 5
Synthesis of second
DNA strand
cDNA of gene
(no introns) 34

35. introns and joins exons)
Figure 12.4_1
CELL NUCLEUS
Exon
Intron
Exon
Intron
Exon
DNA of a
eukaryotic
gene 1
Transcription
RNA
transcript 2
RNA splicing (removes
introns and joins exons)
mRNA
Figure 12.4_1 Making an intron-lacking gene from eukaryotic mRNA (part 1) 35

36. the cell and the addition of reverse transcriptase;
Figure 12.4_2 3
Isolation of mRNA from
the cell and the addition
of reverse transcriptase;
synthesis of a DNA strand
TEST TUBE
Reverse transcriptase
cDNA strand
being synthesized 4
Breakdown of RNA
Direction
of synthesis
Figure 12.4_2 Making an intron-lacking gene from eukaryotic mRNA (part 2) 5
Synthesis of second
DNA strand
cDNA of gene
(no introns) 36

37. 12.5 Nucleic acid probes identify clones carrying specific genes
Nucleic acid probes bind very selectively to cloned DNA.
Probes can be DNA or RNA sequences complementary to a portion of the gene of interest.
A probe binds to a gene of interest by base pairing.
Probes are labeled with a radioactive isotope or fluorescent tag for detection.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
Some Internet search programs rely upon a methodology similar in one way to the use of a nucleic acid probe. For example, if you want to find the lyrics to a particular song, but do not know the song title or artist, you might search the Internet using a unique phrase from the song. The search engine will scan millions of web pages to identify those sites containing that particular phrase. However, unlike a nucleic acid probe, you would search for the song by using a few of the lyrics. A nucleic acid probe search uses a sequence complementary to the desired sequence.
© 2012 Pearson Education, Inc. 37

38. 12.5 Nucleic acid probes identify clones carrying specific genes
One way to screen a gene library is as follows:
Bacterial clones are transferred to filter paper.
Cells are broken apart and the DNA is separated into single strands.
A probe solution is added and any bacterial colonies carrying the gene of interest will be tagged on the filter paper.
The clone carrying the gene of interest is grown for further study.
Student Misconceptions and Concerns
1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. The recent process of FDA approval for genetically engineered salmon raised for food might be particularly useful and relevant.
Teaching Tips
Some Internet search programs rely upon a methodology similar in one way to the use of a nucleic acid probe. For example, if you want to find the lyrics to a particular song, but do not know the song title or artist, you might search the Internet using a unique phrase from the song. The search engine will scan millions of web pages to identify those sites containing that particular phrase. However, unlike a nucleic acid probe, you would search for the song by using a few of the lyrics. A nucleic acid probe search uses a sequence complementary to the desired sequence.
© 2012 Pearson Education, Inc. 38

39. (single-stranded DNA)
Figure 12.5
Radioactive
nucleic acid probe
(single-stranded DNA)
The probe is mixed with
single-stranded DNA
from a genomic library.
Single-stranded
DNA
Figure 12.5 How a DNA probe tags a gene by base pairing
Base pairing
highlights the
gene of interest. 39

40. GENETICALLY MODIFIED ORGANISMS
© 2012 Pearson Education, Inc. 40

41. 12.6 Recombinant cells and organisms can mass-produce gene products
Recombinant cells and organisms constructed by DNA technologies are used to manufacture many useful products, chiefly proteins.
Bacteria are often the best organisms for manufacturing a protein product because bacteria
have plasmids and phages available for use as gene- cloning vectors,
can be grown rapidly and cheaply,
can be engineered to produce large amounts of a particular protein, and
often secrete the proteins directly into their growth medium.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
As noted in Module 12.6, DNA technology is primarily used to produce proteins. Challenge your students to explain why lipids and carbohydrates are not typically produced by these processes.
© 2012 Pearson Education, Inc. 41

42. 12.6 Recombinant cells and organisms can mass-produce gene products
Yeast cells
are eukaryotes,
have long been used to make bread and beer,
can take up foreign DNA and integrate it into their genomes,
have plasmids that can be used as gene vectors, and
are often better than bacteria at synthesizing and secreting eukaryotic proteins.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
As noted in Module 12.6, DNA technology is primarily used to produce proteins. Challenge your students to explain why lipids and carbohydrates are not typically produced by these processes.
© 2012 Pearson Education, Inc. 42

43. 12.6 Recombinant cells and organisms can mass-produce gene products
Mammalian cells must be used to produce proteins with chains of sugars. Examples include
human erythropoietin (EPO), which stimulates the production of red blood cells,
factor VIII to treat hemophilia, and
tissue plasminogen activator (TPA) used to treat heart attacks and strokes.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
As noted in Module 12.6, DNA technology is primarily used to produce proteins. Challenge your students to explain why lipids and carbohydrates are not typically produced by these processes.
© 2012 Pearson Education, Inc. 43

44. Table 12.6
Table 12.6 Some Protein Products of Recombinant DNA Technology 44

45. Table 12.6_1
Table 12.6_1 Some Protein Products of Recombinant DNA Technology (part 1) 45

46. Table 12.6_2
Table 12.6_2 Some Protein Products of Recombinant DNA Technology (part 2) 46

47. 12.6 Recombinant cells and organisms can mass-produce gene products
Pharmaceutical researchers are currently exploring the mass production of gene products by
whole animals or
plants.
Recombinant animals
are difficult and costly to produce and
must be cloned to produce more animals with the same traits.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
As noted in Module 12.6, DNA technology is primarily used to produce proteins. Challenge your students to explain why lipids and carbohydrates are not typically produced by these processes.
© 2012 Pearson Education, Inc. 47

48. Figure 12.6A
Figure 12.6A A goat carrying a gene for a human blood protein that is secreted in the milk 48

49. Figure 12.6A_1
Figure 12.6A_1 A goat carrying a gene for a human blood protein that is secreted in the milk (part 1) 49

50. Figure 12.6A_2
Figure 12.6A_2 A goat carrying a gene for a human blood protein that is secreted in the milk (part 2) 50

51. Figure 12.6B
Figure 12.6B A pig that has been genetically modified to produce a useful human protein 51

52. 12.7 CONNECTION: DNA technology has changed the pharmaceutical industry and medicine
Products of DNA technology are already in use.
Therapeutic hormones produced by DNA technology include
insulin to treat diabetes and
human growth hormone to treat dwarfism.
DNA technology is used to
test for inherited diseases,
detect infectious agents such as HIV, and
produce vaccines, harmless variants (mutants) or derivatives of a pathogen that stimulate the immune system.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
Annual flu vaccinations are a common way to prevent diseases that cannot be easily treated. However, students might not understand why many people receive the vaccine every year. A new annual vaccine is necessary because the flu viruses keep evolving, another lesson in evolution that may be missed by your students.
© 2012 Pearson Education, Inc. 52

53. Figure 12.7A
Figure 12.7A Human insulin produced by bacteria 53

54. Figure 12.7B
Figure 12.7B Equipment used in the production of a vaccine against hepatitis B 54

55. 12.8 CONNECTION: Genetically modified organisms are transforming agriculture
Genetically modified (GM) organisms contain one or more genes introduced by artificial means.
Transgenic organisms contain at least one gene from another species.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
Roundup Ready Corn, a product of the agricultural biotechnology corporation Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. Module 12.9 discusses some of the issues related to the concerns over the use of GM organisms.
© 2012 Pearson Education, Inc. 55

56. 12.8 CONNECTION: Genetically modified organisms are transforming agriculture
The most common vector used to introduce new genes into plant cells is
a plasmid from the soil bacterium Agrobacterium tumefaciens and
called the Ti plasmid.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
Roundup Ready Corn, a product of the agricultural biotechnology corporation Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. Module 12.9 discusses some of the issues related to the concerns over the use of GM organisms.
© 2012 Pearson Education, Inc. 56

57. Agrobacterium tumefaciens Restriction site
Figure 12.8A_s1
Agrobacterium
tumefaciens
DNA containing the
gene for a desired trait 1 Ti
plasmid
Recombinant
Ti plasmid
The gene is
inserted into
the plasmid.
Restriction
site
Figure 12.8A_s1 Using the Ti plasmid to genetically engineer plants (step 1) 57

58. gene for a desired trait Plant cell
Figure 12.8A_s2
Agrobacterium
tumefaciens
DNA containing the
gene for a desired trait
Plant cell 1 2 Ti
plasmid
Recombinant
Ti plasmid
The gene is
inserted into
the plasmid.
The recombinant
plasmid is
introduced into
a plant cell.
DNA carrying
the new gene
Restriction
site
Figure 12.8A_s2 Using the Ti plasmid to genetically engineer plants (step 2) 58

59. gene for a desired trait Plant cell
Figure 12.8A_s3
Agrobacterium
tumefaciens
DNA containing the
gene for a desired trait
Plant cell 1 2 Ti
plasmid
Recombinant
Ti plasmid
The gene is
inserted into
the plasmid.
The recombinant
plasmid is
introduced into
a plant cell.
DNA carrying
the new gene
Restriction
site
Figure 12.8A_s3 Using the Ti plasmid to genetically engineer plants (step 3) 3
The plant cell
grows into
a plant.
A plant
with the
new trait 59

60. 12.8 CONNECTION: Genetically modified organisms are transforming agriculture
GM plants are being produced that
are more resistant to herbicides and pests and
provide nutrients that help address malnutrition.
GM animals are being produced with improved nutritional or other qualities.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
Roundup Ready Corn, a product of the agricultural biotechnology corporation Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. Module 12.9 discusses some of the issues related to the concerns over the use of GM organisms.
© 2012 Pearson Education, Inc. 60

61. Figure 12.8B
Figure 12.8B A mix of conventional rice (white), the original Golden Rice (light gold), and Golden Rice 2 (dark gold) 61

62. 12.9 Genetically modified organisms raise concerns about human and environmental health
Scientists use safety measures to guard against production and release of new pathogens.
Concerns related to GM organisms include the potential
introduction of allergens into the food supply and
spread of genes to closely related organisms.
Regulatory agencies are trying to address the
safety of GM products,
labeling of GM produced foods, and
safe use of biotechnology.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
Roundup Ready Corn, a product of the agricultural biotechnology corporation Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. Module 12.9 discusses some of the issues related to the concerns over the use of GM organisms.
© 2012 Pearson Education, Inc. 62

63. Figure 12.9A
Figure 12.9A A maximum-security laboratory at the Pasteur Institute in Paris 63

64. Figure 12.9B
Figure 12.9B Genetically engineered crop plants growing near their wild relatives 64

65. 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases
Gene therapy aims to treat a disease by supplying a functional allele.
One possible procedure is the following:
Clone the functional allele and insert it in a retroviral vector.
Use the virus to deliver the gene to an affected cell type from the patient, such as a bone marrow cell.
Viral DNA and the functional allele will insert into the patient’s chromosome.
Return the cells to the patient for growth and division.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
1. In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law.
The following link to a related US government web site characterizes the effect of the act as follows. GINA “… prohibits U.S. insurance companies and employers from discriminating on the basis of information derived from genetic tests.” The web site can be found at
2. As gene therapy technology expands, our ability to modify the genome in human embryos through in vitro fertilization permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution.
© 2012 Pearson Education, Inc. 65

66. 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases
Gene therapy is an
alteration of an afflicted individual’s genes and
attempt to treat disease.
Gene therapy may be best used to treat disorders traceable to a single defective gene.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
1. In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law.
The following link to a related US government web site characterizes the effect of the act as follows. GINA “… prohibits U.S. insurance companies and employers from discriminating on the basis of information derived from genetic tests.” The web site can be found at
2. As gene therapy technology expands, our ability to modify the genome in human embryos through in vitro fertilization permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution.
© 2012 Pearson Education, Inc. 66

67. human gene inserts into the cell’s chromosome.
Figure 12.10
Cloned gene
(normal allele) 1
An RNA version of
a normal human
gene is inserted
into a retrovirus.
RNA genome of virus
Retrovirus 2
Bone marrow cells
are infected with
the virus. 3
Viral DNA carrying the
human gene inserts into
the cell’s chromosome.
Figure One type of gene therapy procedure
Bone marrow
cell from the patient 4
The engineered
cells are injected
into the patient.
Bone
marrow 67

68. Cloned gene (normal allele) An RNA version of a normal human
Figure 12.10_1
Cloned gene
(normal allele)
An RNA version of
a normal human
gene is inserted
into a retrovirus. 1
RNA genome of virus
Figure 12.10_1 One type of gene therapy procedure (part 1)
Retrovirus 68

69. human gene inserts into the cell’s chromosome.
Figure 12.10_2 2
Bone marrow cells
are infected with
the virus. 3
Viral DNA carrying the
human gene inserts into
the cell’s chromosome.
Bone marrow
cell from the patient 4
The engineered
cells are injected
into the patient.
Figure 12.10_2 One type of gene therapy procedure (part 2)
Bone
marrow 69

70. 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases
The first successful human gene therapy trial in 2000
tried to treat ten children with SCID (severe combined immune deficiency),
helped nine of these patients, but
caused leukemia in three of the patients, and
resulted in one death.
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
1. In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law.
The following link to a related US government web site characterizes the effect of the act as follows. GINA “… prohibits U.S. insurance companies and employers from discriminating on the basis of information derived from genetic tests.” The web site can be found at
2. As gene therapy technology expands, our ability to modify the genome in human embryos through in vitro fertilization permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution.
© 2012 Pearson Education, Inc. 70

71. 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases
The use of gene therapy raises many questions.
How can we build in gene control mechanisms that make appropriate amounts of the product at the right time and place?
How can gene insertion be performed without harming other cell functions?
Will gene therapy lead to efforts to control the genetic makeup of human populations?
Should we try to eliminate genetic defects in our children and descendants when genetic variety is a necessary ingredient for the survival of a species?
Student Misconceptions and Concerns
1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms.
2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent is evidence of evolution that may be missed by your students.
Teaching Tips
1. In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law.
The following link to a related US government web site characterizes the effect of the act as follows. GINA “… prohibits U.S. insurance companies and employers from discriminating on the basis of information derived from genetic tests.” The web site can be found at
2. As gene therapy technology expands, our ability to modify the genome in human embryos through in vitro fertilization permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution.
© 2012 Pearson Education, Inc. 71

72. DNA PROFILING
© 2012 Pearson Education, Inc. 72

73. 12.11 The analysis of genetic markers can produce a DNA profile
Student Misconceptions and Concerns
Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
Teaching Tips
Figure describes the general steps of DNA profiling. This overview is a useful reference to employ while the details of each step are discussed.
12.11 The analysis of genetic markers can produce a DNA profile
DNA profiling is the analysis of DNA fragments to determine whether they come from the same individual. DNA profiling
compares genetic markers from noncoding regions that show variation between individuals and
involves amplifying (copying) of markers for analysis.
© 2012 Pearson Education, Inc. 73

74. Crime scene Suspect 1 Suspect 2 DNA is isolated. The DNA of selected
Figure 12.11
Crime scene
Suspect 1
Suspect 2 1
DNA is
isolated. 2
The DNA of
selected
markers is
amplified.
Figure An overview of DNA profiling 3
The amplified
DNA is
compared. 74

75. 12.12 The PCR method is used to amplify DNA sequences
Polymerase chain reaction (PCR) is a method of amplifying a specific segment of a DNA molecule.
PCR relies upon a pair of primers that are
short,
chemically synthesized, single-stranded DNA molecules, and
complementary to sequences at each end of the target sequence.
PCR
is a three-step cycle that
doubles the amount of DNA in each turn of the cycle.
Student Misconceptions and Concerns
1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest.
Teaching Tips
In PCR, the product becomes another master copy. Imagine that while you are photocopying, every copy is used as a master at another copy machine. This would require many copy machines. However, it would be very productive!
© 2012 Pearson Education, Inc. 75

76. yields eight molecules
Figure 12.12
Cycle 1
yields two molecules
Cycle 2
yields four molecules
Cycle 3
yields eight molecules
Genomic
DNA 3 5 3 5 3 5 5 5 3 1
Heat
separates
DNA
strands. 2
Primers bond
with ends
of target
sequences. 3
DNA
polymerase
adds
nucleotides. 3 5 5 3
Target
sequence 5 3 5 5 3 5 3 5 3
Figure DNA amplification by PCR
Primer
New DNA 76

77. Cycle 1 yields two molecules Genomic DNA 3 5 3 5 3 5 5 5 3
Figure 12.12_1
Cycle 1
yields two molecules
Genomic
DNA 3 5 3 5 3 5 5 5 3 1
Heat
separates
DNA
strands. 2
Primers bond
with ends
of target
sequences. 3
DNA
polymerase
adds
nucleotides. 3 5 5 3
Target
sequence
Figure 12.12_1 DNA amplification by PCR (part 1) 5 3 5 5 3 5 3 5 3
Primer
New DNA 77

78. yields eight molecules
Figure 12.12_2
Cycle 2
yields four molecules
Cycle 3
yields eight molecules
Figure 12.12_2 DNA amplification by PCR (part 2) 78

79. 12.12 The PCR method is used to amplify DNA sequences
The advantages of PCR include
the ability to amplify DNA from a small sample,
obtaining results rapidly, and
a reaction that is highly sensitive, copying only the target sequence.
Student Misconceptions and Concerns
1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest.
Teaching Tips
In PCR, the product becomes another master copy. Imagine that while you are photocopying, every copy is used as a master at another copy machine. This would require many copy machines. However, it would be very productive!
© 2012 Pearson Education, Inc. 79

80. 12.13 Gel electrophoresis sorts DNA molecules by size
Gel electrophoresis can be used to separate DNA molecules based on size as follows:
A DNA sample is placed at one end of a porous gel.
Current is applied and DNA molecules move from the negative electrode toward the positive electrode.
Shorter DNA fragments move through the gel matrix more quickly and travel farther through the gel.
DNA fragments appear as bands, visualized through staining or detecting radioactivity or fluorescence.
Each band is a collection of DNA molecules of the same length.
Student Misconceptions and Concerns
1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest.
Teaching Tips
Separating ink using paper chromatography is a simple experiment that approximates some of what occurs in gel electrophoresis. Consider doing this as a class demonstration while addressing electrophoresis. Cut a large piece of filter paper into a rectangle or square. Use markers to color large dots about 2 cm away from one edge of the paper. Separate the dots from each other by 3–4 cm. Place the paper on edge, dots down, into a beaker containing about 1 cm of ethanol or isopropyl alcohol (50% or higher will do). The dots should not be in contact with the pool of alcohol in the bottom of the beaker. As the alcohol is drawn up the filter paper by capillary action, the alcohol will dissolve the ink dots. As the alcohol continues up the paper, the ink follows. Not all of the ink components move at the same speed, based upon their size and chemical properties. If you begin the process at the start of class, you should have some degree of separation by the end of a 50-minute period. Experiment with the technique a day or two before class to fine-tune the demonstration. (Save and air-dry these samples for your class.) Consider using brown, green, and black markers, because these colors are often made by color combinations.
© 2012 Pearson Education, Inc. 80

81. Video: Biotechnology Lab
Student Misconceptions and Concerns
1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest.
Teaching Tips
Separating ink using paper chromatography is a simple experiment that approximates some of what occurs in gel electrophoresis. Consider doing this as a class demonstration while addressing electrophoresis. Cut a large piece of filter paper into a rectangle or square. Use markers to color large dots about 2 cm away from one edge of the paper. Separate the dots from each other by 3–4 cm. Place the paper on edge, dots down, into a beaker containing about 1 cm of ethanol or isopropyl alcohol (50% or higher will do). The dots should not be in contact with the pool of alcohol in the bottom of the beaker. As the alcohol is drawn up the filter paper by capillary action, the alcohol will dissolve the ink dots. As the alcohol continues up the paper, the ink follows. Not all of the ink components move at the same speed, based upon their size and chemical properties. If you begin the process at the start of class, you should have some degree of separation by the end of a 50-minute period. Experiment with the technique a day or two before class to fine-tune the demonstration. (Save and air-dry these samples for your class.) Consider using brown, green, and black markers, because these colors are often made by color combinations.
Video: Biotechnology Lab
Use window controls to play
© 2012 Pearson Education, Inc. 81

82. Power source Completed gel
Figure 12.13
A mixture of DNA
fragments of
different sizes
Longer
(slower)
molecules
Power
source
Shorter
(faster)
molecules
Gel
Figure Gel electrophoresis of DNA
Completed
gel 82

83. Power source Completed gel
Figure 12.13_1
A mixture of DNA
fragments of
different sizes
Longer
(slower)
molecules
Power
source
Shorter
(faster)
molecules
Gel
Figure 12.13_1 Gel electrophoresis of DNA (part 1)
Completed
gel 83

84. Figure 12.13_2
Figure 12.13_2 Gel electrophoresis of DNA (part 2) 84

85. 12.14 STR analysis is commonly used for DNA profiling
Repetitive DNA consists of nucleotide sequences that are present in multiple copies in the genome.
Short tandem repeats (STRs) are short nucleotide sequences that are repeated in tandem,
composed of different numbers of repeating units in individuals and
used in DNA profiling.
STR analysis
compares the lengths of STR sequences at specific sites in the genome and
typically analyzes 13 different STR sites.
Student Misconceptions and Concerns
1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest.
Teaching Tips
In most legal cases, the probability of two people having identical DNA profiles can be one in 10 billion or more. However, eyewitness testimony has been a standard part of the justice system. If you want to make the point about the unreliability of eyewitnesses in a trial, compared to techniques such as genetic profiling, consider this exercise. Arrange for a person who is not well known to the class to run into your classroom, take something you have placed near you (perhaps a bag, stack of papers, or box), and leave quickly. You need to take care that no one in the class is so alarmed as to do something dangerous. Once the “thief” is gone, tell the class that this was planned and do not speak. Have them each write a description of the person, including height, hair color, clothing, facial hair, behavior, etc. Many students will be accurate, but some will likely get details wrong. This is also an effective exercise to demonstrate the need for large sample sizes and accurate recording devices for good scientific technique.
© 2012 Pearson Education, Inc. 85

86. The number of short tandem repeats do not match
Figure 12.14A
STR site 1
STR site 2
Crime scene
DNA
The number of short
tandem repeats match
The number of short tandem
repeats do not match
Figure 12.14A Two representative STR sites from crime scene DNA samples
Suspect’s
DNA 86

87. Crime Suspect’s scene DNA DNA Longer STR fragments
Figure 12.14B
Crime
scene
DNA
Suspect’s
DNA
Longer STR fragments
Figure 12.14B DNA profiles generated from the STRs in Figure 12.14A
Shorter STR fragments 87

88. 12.15 CONNECTION: DNA profiling has provided evidence in many forensic investigations
DNA profiling is used to
determine guilt or innocence in a crime,
settle questions of paternity,
identify victims of accidents, and
probe the origin of nonhuman materials.
Student Misconceptions and Concerns
1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest.
Teaching Tips
Although the statistical odds of a DNA-profiling match can exceed one in 10 billion, the odds of a mistake in the collecting and testing procedures can be much greater. This is an important distinction. An error as simple as mislabeling a sample can confuse the results. Unfortunately, the odds of human error will vary and are difficult to determine.
© 2012 Pearson Education, Inc. 88

89. Figure 12.15A
Figure 12.15A STR analysis proved that convicted murderer Earl Washington was innocent, freeing him after 17 years in prison. 89

90. Figure 12.15B
Figure 12.15B Cheddar Man and one of his modern-day descendants 90

91. 12.16 RFLPs can be used to detect differences in DNA sequences
A single nucleotide polymorphism (SNP) is a variation at a single base pair within a genome.
Restriction fragment length polymorphism (RFLP) is a change in the length of restriction fragments due to a SNP that alters a restriction site.
RFLP analysis involves
producing DNA fragments by restriction enzymes and
sorting these fragments by gel electrophoresis.
Student Misconceptions and Concerns
1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete.
2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest.
Teaching Tips
Here is another way to explain restriction fragment analysis. Consider these two words, equilibrium and equalibrium. Imagine that a mutation produced the spelling error of the second word. If we used a “restriction enzyme” that splits these words between u and i, how will the fragments compare in size and number?
equilibrium = equ ilibri um (three fragments of three, six, and two letters)
equalibrium = equalibri um (two fragments of nine and two letters)
© 2012 Pearson Education, Inc. 91

92. Restriction enzymes added DNA sample 1 DNA sample 2 Sample 1 Sample 2
Figure 12.16
Restriction
enzymes
added
DNA sample 1
DNA sample 2 w
Cut z x
Cut
Cut y y
Figure RFLP analysis
Sample 1
Sample 2
Longer
fragments z x w
Shorter
fragments y y 92

93. Restriction enzymes added
Figure 12.16_1
Restriction
enzymes
added
DNA sample 1
DNA sample 2 w
Cut z x
Figure 12.16_1 RFLP analysis (part 1)
Cut
Cut y y 93

94. Sample 1 Sample 2 Longer fragments z x w Shorter fragments y y
Figure 12.16_2
Sample 1
Sample 2
Longer
fragments z x
Figure 12.16_2 RFLP analysis (part 2) w
Shorter
fragments y y 94

95. GENOMICS
© 2012 Pearson Education, Inc. 95

96. 12.17 Genomics is the scientific study of whole genomes
Genomics is the study of an organism’s complete set of genes and their interactions.
Initial studies focused on prokaryotic genomes.
Many eukaryotic genomes have since been investigated.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support for the other types of evidence for evolution.
Teaching Tips
The first targets of genomics were prokaryotic pathogenic organisms. Consider asking your students in class to suggest why this was a good choice. Students may note that the genomes of these organisms are smaller than eukaryotes and that many of these organisms are of great medical significance.
© 2012 Pearson Education, Inc. 96

97. Table 12.17
Table Some Important Completed Genomes 97

98. 12.17 Genomics is the scientific study of whole genomes
Genomics allows another way to examine evolutionary relationships.
Genomic studies showed a 96% similarity in DNA sequences between chimpanzees and humans.
Functions of human disease-causing genes have been determined by comparing human genes to similar genes in yeast.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support for the other types of evidence for evolution.
Teaching Tips
The first targets of genomics were prokaryotic pathogenic organisms. Consider asking your students in class to suggest why this was a good choice. Students may note that the genomes of these organisms are smaller than eukaryotes and that many of these organisms are of great medical significance.
© 2012 Pearson Education, Inc. 98

99. 12.18 CONNECTION: The Human Genome Project revealed that most of the human genome does not consist of genes
The goals of the Human Genome Project (HGP) included
determining the nucleotide sequence of all DNA in the human genome and
identifying the location and sequence of every human gene.
Student Misconceptions and Concerns
1. The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support for the other types of evidence for evolution.
2. Students might assume that the term junk DNA implies that these noncoding regions of DNA are useless. This might be a good time to note the old saying, absence of evidence is not evidence of absence. Our current inability to understand the role(s) of noncoding DNA does not mean that these regions have no significance.
3. Students might know that humans have 23 pairs of chromosomes. Consider asking them how many different types of chromosomes are found in humans. Some will not have realized that there are 24 types, 22 autosomes plus X and Y sex chromosomes.
Teaching Tips
1. The main U.S. Department of Energy Office website in support of the human genome project is found at
2. The website for the National Center for Biotechnology Information is The center, established in 1988, serves as a national resource for biomedical information related to genomic data.
3. The authors note that there are 3.2 billion nucleotide pairs in the human genome. There are about 3.2 billion seconds in years. This simple reference can add meaning to the significance of these large numbers.
4. Challenge students to explain why a complete understanding of an organism’s genome and proteomes is still not enough to understand the full biology of an organism. Ask them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by the inheritance of certain chromosomes, but by incubation temperature.)
5. Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc. 99

100. 12.18 CONNECTION: The Human Genome Project revealed that most of the human genome does not consist of genes
Results of the Human Genome Project indicate that
humans have about 20,000 genes in 3.2 billion nucleotide pairs,
only 1.5% of the DNA codes for proteins, tRNAs, or rRNAs, and
the remaining 98.5% of the DNA is noncoding DNA including
telomeres, stretches of noncoding DNA at the ends of chromosomes, and
transposable elements, DNA segments that can move or be copied from one location to another within or between chromosomes.
Student Misconceptions and Concerns
1. The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support for the other types of evidence for evolution.
2. Students might assume that the term junk DNA implies that these noncoding regions of DNA are useless. This might be a good time to note the old saying, absence of evidence is not evidence of absence. Our current inability to understand the role(s) of noncoding DNA does not mean that these regions have no significance.
3. Students might know that humans have 23 pairs of chromosomes. Consider asking them how many different types of chromosomes are found in humans. Some will not have realized that there are 24 types, 22 autosomes plus X and Y sex chromosomes.
Teaching Tips
1. The main U.S. Department of Energy Office website in support of the human genome project is found at
2. The website for the National Center for Biotechnology Information is The center, established in 1988, serves as a national resource for biomedical information related to genomic data.
3. The authors note that there are 3.2 billion nucleotide pairs in the human genome. There are about 3.2 billion seconds in years. This simple reference can add meaning to the significance of these large numbers.
4. Challenge students to explain why a complete understanding of an organism’s genome and proteomes is still not enough to understand the full biology of an organism. Ask them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by the inheritance of certain chromosomes, but by incubation temperature.)
5. Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc.
100

101. Exons (regions of genes coding for protein
Figure 12.18
Exons (regions of genes coding for protein
or giving rise to rRNA or tRNA) (1.5%)
Introns and
regulatory
sequences
(24%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Unique
noncoding
DNA (15%)
Figure Composition of the human genome
Repetitive
DNA
unrelated to
transposable
elements
(15%)
101

102. 12.19 The whole-genome shotgun method of sequencing a genome can provide a wealth of data quickly
The Human Genome Project proceeded through three stages that provided progressively more detailed views of the human genome.
A low-resolution linkage map was developed using RFLP analysis of 5,000 genetic markers.
A physical map was constructed from nucleotide distances between the linkage-map markers.
DNA sequences for the mapped fragments were determined.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support of the other types of evidence for evolution.
Teaching Tips
1. Challenge students to explain why a complete understanding of an organism’s genome and proteomes is still not enough to understand the full biology of an organism. Ask them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by the inheritance of certain chromosomes, but by incubation temperature.)
2. Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc.
102

103. 12.19 The whole-genome shotgun method of sequencing a genome can provide a wealth of data quickly
The whole-genome shotgun method
was proposed in 1992 by molecular biologist J. Craig Venter, who
used restriction enzymes to produce fragments that were cloned and sequenced in just one stage and
ran high-performance computer analyses to assemble the sequence by aligning overlapping regions.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support of the other types of evidence for evolution.
Teaching Tips
1. Challenge students to explain why a complete understanding of an organism’s genome and proteomes is still not enough to understand the full biology of an organism. Ask them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by the inheritance of certain chromosomes, but by incubation temperature.)
2. Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc.
103

104. 12.19 The whole-genome shotgun method of sequencing a genome can provide a wealth of data quickly
Today, this whole-genome shotgun approach is the method of choice for genomic researchers because it is
relatively fast and
inexpensive.
However, limitations of the whole-genome shotgun method suggest that a hybrid approach using genome shotgunning and physical maps may prove to be the most useful.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support of the other types of evidence for evolution.
Teaching Tips
1. Challenge students to explain why a complete understanding of an organism’s genome and proteomes is still not enough to understand the full biology of an organism. Ask them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by the inheritance of certain chromosomes, but by incubation temperature.)
2. Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc.
104

105. Chop up each chromosome with restriction enzymes
Figure 12.19
Chromosome
Chop up each chromosome
with restriction enzymes
DNA fragments
Sequence the fragments
Figure The whole-genome shotgun method
Align the fragments
Reassemble the full
sequence
105

106. 12.20 Proteomics is the scientific study of the full set of proteins encoded by a genome
Proteomics
is the study of the full protein sets encoded by genomes and
investigates protein functions and interactions.
The human proteome includes about 100,000 proteins.
Genomics and proteomics are helping biologists study life from an increasingly holistic approach.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support of the other types of evidence for evolution.
Teaching Tips
1. Challenge students to explain why a complete understanding of an organism’s genome and proteomes is still not enough to understand the full biology of an organism. Ask them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by the inheritance of certain chromosomes, but by incubation temperature.)
2. Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc.
106

107. 12.21 EVOLUTION CONNECTION: Genomes hold clues to human evolution
Human and chimp genomes differ by
1.2% in single-base substitutions and
2.7% in insertions and deletions of larger DNA sequences.
Genes showing rapid evolution in humans include
genes for defense against malaria and tuberculosis,
a gene regulating brain size, and
the FOXP2 gene involved with speech and vocalization.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support of the other types of evidence for evolution.
Teaching Tips
Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc.
107

108. 12.21 EVOLUTION CONNECTION: Genomes hold clues to human evolution
Neanderthals
were close human relatives,
were a separate species,
also had the FOXP2 gene,
may have had pale skin and red hair, and
were lactose intolerant.
Student Misconceptions and Concerns
The similarities in genotypes and phenotypes among members of a human family are expected and understood by most students. Yet many students have a difficult time extrapolating this knowledge and applying it to the phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool for modern systematics and genomics provides significant support of the other types of evidence for evolution.
Teaching Tips
Students may enter your course with little appreciation of the scientific questions that remain unanswered. Struggling with the details of what we now know can overwhelm our students, leaving little room to wonder about what is not yet understood. The surprises and questions noted in Modules 12.18–12.21 reveal broad challenges that await the work of our next generation of scientists. Emphasize the many opportunities that exist to resolve unanswered questions, here and throughout your course, as an invitation to future adventures for students.
© 2012 Pearson Education, Inc.
108

109. Figure 12.21
Figure Reconstruction of a Neanderthal female, based on a 36,000-year-old skull
109

110. You should now be able to
Explain how plasmids are used in gene cloning.
Explain how restriction enzymes are used to “cut and paste” DNA into plasmids.
Explain how plasmids, phages, and BACs are used to construct genomic libraries.
Explain how a cDNA library is constructed and how it is different from genomic libraries constructed using plasmids or phages.
Explain how a nucleic acid probe can be used to identify a specific gene.
© 2012 Pearson Education, Inc.
110

111. You should now be able to
Explain how different organisms are used to mass-produce proteins of human interest.
Explain how DNA technology has helped to produce insulin, growth hormone, and vaccines.
Explain how genetically modified (GM) organisms are transforming agriculture.
Describe the risks posed by the creation and culturing of GM organisms and the safeguards that have been developed to minimize these risks.
© 2012 Pearson Education, Inc.
111

112. You should now be able to
Describe the benefits and risks of gene therapy in humans. Discuss the ethical issues that these techniques present.
Describe the basic steps of DNA profiling.
Explain how PCR is used to amplify DNA sequences.
Explain how gel electrophoresis is used to sort DNA and proteins.
Explain how short tandem repeats are used in DNA profiling.
© 2012 Pearson Education, Inc.
112

113. You should now be able to
Describe the diverse applications of DNA profiling.
Explain how restriction fragment analysis is used to detect differences in DNA sequences.
Explain why it is important to sequence the genomes of humans and other organisms.
Describe the structure and possible functions of the noncoding sections of the human genome.
Explain how the human genome was mapped.
© 2012 Pearson Education, Inc.
113

114. You should now be able to
Compare the fields of genomics and proteomics.
Describe the significance of genomics to the study of evolutionary relationships and our understanding of the special characteristics of humans.
© 2012 Pearson Education, Inc.
114

115. DNA fragments Recombinant DNA plasmids Recombinant bacteria
Figure 12.UN01
Bacterial
clone
Cut
Bacterium
DNA
fragments
Recombinant
DNA
plasmids
Cut
Recombinant
bacteria
Figure 12.UN01 Reviewing the Concepts, 12.3
Plasmids
Genomic library
115

116. Power source DNA is attracted to  pole due to PO4 groups
Figure 12.UN02
A mixture of DNA
fragments
Longer
fragments
move slower
A “band” is a
collection of DNA
fragments of one
particular length
Power
source
Shorter
fragments
move faster
Figure 12.UN02 Reviewing the Concepts, 12.13
DNA is attracted to 
pole due to PO4 groups
116

117. Figure 12.UN03 Connecting the Concepts, question 1
DNA
amplified
via
(a)
Bacterial
plasmids
DNA
sample
treated with
treated with
(b)
DNA
fragments
sorted by size via
(c)
Recombinant plasmids
are inserted
into bacteria
Figure 12.UN03 Connecting the Concepts, question 1
Add
(d)
Particular
DNA
sequence
highlighted
are copied via
(e)
117

118. DNA amplified via (a) Bacterial plasmids DNA sample treated with
Figure 12.UN03_1
DNA
amplified
via
(a)
Bacterial
plasmids
DNA
sample
treated with
treated with
(b)
Figure 12.UN03_1 Connecting the Concepts, question 1 (part 1)
118

119. DNA fragments sorted by size via (c) Recombinant plasmids are inserted
Figure 12.UN03_2
DNA
fragments
sorted by size via
(c)
Recombinant plasmids
are inserted
into bacteria
Add
(d)
Figure 12.UN03_2 Connecting the Concepts, question 1 (part 2)
Particular
DNA
sequence
highlighted
are copied via
(e)
119