Introduction DNA technologies affect our lives in many ways.

Introduction DNA technologies affect our lives in many ways.
Gene cloning is used to produce medical and industrial products. GMOs have become a regular part of our diet and have other types of commercial uses. DNA profiling has changed the field of forensic science. New technologies produce valuable data for biological research. DNA can be used to investigate historical questions. Many GMOs have become a natural part of our environment.

Big Ideas Gene Cloning Genetically Modified Organisms DNA Profiling
Figure Chapter 12: Big Ideas DNA Profiling Genomics

Gene Cloning

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 laboratory techniques used to study and manipulate genetic material. Genetic engineering involves manipulating genes for practical purposes. Student Misconceptions and Concerns  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.  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  Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1 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.  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) cut cut the new film apart, and (c) 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. Active Lecture Tips  As you begin to address genetic engineering and GMO foods, ask students to work in small groups to brainstorm about what they know about genetically engineered foods. Have each group create a list of statements that can be short or long, reflecting their impressions. The results may surprise you, and help you address some common misunderstandings and concerns.

Fish that have been genetically engineered to make a jellyfish protein that fluoresces under UV light. Figure 12.1a Glowing angelfish produced by transferring a gene originally obtained from a jelly (cnidarian)

Gene cloning leads to the production of multiple, identical copies of a gene-carrying piece of DNA in vitro (in a test tube) to form a single DNA molecule.

Recombinant DNA is formed by joining nucleotide sequences from two different sources and often different species. One source contains the gene that will be cloned. Another source is a gene carrier, called a vector. Plasmids are small, circular DNA molecules that replicate separately from the much larger bacterial chromosome; they are often used as vectors. Student Misconceptions and Concerns  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.  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  Figure 12.1B is a synthesis of the techniques discussed in further detail in Modules 12.2–12.5. Figure 12.1 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.  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) cut the new film apart, and (c) 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. Active Lecture Tips  As you begin to address genetic engineering and GMO foods, ask students to work in small groups to brainstorm about what they know about genetically engineered foods. Have each group create a list of statements that can be short or long, reflecting their impressions. The results may surprise you, and help you address some common misunderstandings and concerns.

Figure 12.1b-0 An overview of gene cloning
E. coli bacterium A cell with DNA containing the gene of interest 1 A plasmid is isolated. 2 The cell’s DNA is isolated. Bacterial chromosome Plasmid Examples of gene use Gene of interest (gene V) 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. 6 DNA ligase is added, which joins the two DNA molecules. Genes may be inserted into other organisms. Recombinant DNA plasmid Gene of interest Examples of protein use The recombinant plasmid is taken up by a bacterium through trans- formation Figure 12.1b-0 An overview of gene cloning 7 9 Recombinant bacterium Harvested proteins may be used directly. The bacterium reproduces. 8 Clone of cells

A gene is used to alter bacteria for cleaning up toxic waste.
A gene for pest resistance is inserted into plants. A protein is used to make “stone-washed” blue jeans. Figure 12.1b-3 An overview of gene cloning (Bt corn) A protein is used to dissolve blood clots in heart attack therapy.

Restriction site Sticky end
Figure Every restriction enzyme recognizes one specific nucleotide sequence (its restriction site). Restriction site DNA GAATTC CTTAAG A restriction enzyme always cuts DNA sequences at its restriction site in an identical manner. Restriction enzyme G AATTC CTTAA G Sticky end A piece of DNA from another source (the gene of interest) is cut by the same restriction enzyme. Gene of interest AATTC G G CTTAA Sticky end The DNA fragments from the two sources stick together by hydrogen bonding of base pairs. Figure Creating recombinant DNA using a restriction enzyme and DNA ligase (step 5) G AATT C G AATT C C TTAA G C TTAA G The enzyme DNA ligase creates new covalent bonds that join the backbones of the DNA strands. The result is a piece of recombinant DNA. DNA ligase Recombinant DNA

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. In a plasmid library, genomic DNA is carried by plasmids. In a bacteriophage (phage) library, genomic DNA is incorporated into bacteriophage DNA. Student Misconceptions and Concerns  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.  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. Active Lecture Tips  As you begin to address genetic engineering and GMO foods, ask students to work in small groups to brainstorm about what they know about genetically engineered foods. Have each group create a list of statements that can be short or long, reflecting their impressions. The results may surprise you, and help you address some common misunderstandings and concerns.

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

Reverse transcriptase can help make genes for cloning Enzyme from HTLVs!
A researcher can focus on the genes expressed in a particular kind of cell by using its mRNA as the starting material for cloning. 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, and the DNA that results from such a procedure, called complementary DNA (cDNA), represents only the subset of genes that had been transcribed into mRNA in the starting cells. Student Misconceptions and Concerns  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.  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 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).  Reverse transcriptase is introduced in Module 10.20, where HIV is discussed. Even if students were not assigned Chapter 10, Module provides a meaningful background for the natural and significant roles of this enzyme. Active Lecture Tips  As you begin to address genetic engineering and GMO foods, ask students to work in small groups to brainstorm about what they know about genetically engineered foods. Have each group create a list of statements that can be short or long, reflecting their impressions. The results may surprise you, and help you address some common misunderstandings and concerns.

Reverse transcriptase can help make genes for cloning
Advantages of cloning with cDNA include the ability to study genes responsible for specialized functions 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  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.  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 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).  Reverse transcriptase is introduced in Module 10.20, where HIV is discussed. Even if students were not assigned Chapter 10, Module provides a meaningful background for the natural and significant roles of this enzyme. Active Lecture Tips  As you begin to address genetic engineering and GMO foods, ask students to work in small groups to brainstorm about what they know about genetically engineered foods. Have each group create a list of statements that can be short or long, reflecting their impressions. The results may surprise you, and help you address some common misunderstandings and concerns.

Figure 12.4-0 Making an intron-lacking gene from eukaryotic mRNA
Cell nucleus Exon Intron Exon Intron Exon DNA of a eukaryotic gene Transcription 1 Test tube Addition of reverse transcriptase; synthesis of new DNA strand RNA transcript 4 Reverse transcriptase RNA splicing (removes introns and joins exons) 2 cDNA strand being synthesized mRNA Breakdown of RNA 5 Direction of synthesis Synthesis of second DNA strand 6 Figure Making an intron-lacking gene from eukaryotic mRNA cDNA of gene (no introns) Isolation of mRNA from the cell 3

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  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.  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  Google and other 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. Active Lecture Tips  As you begin to address genetic engineering and GMO foods, ask students to work in small groups to brainstorm about what they know about genetically engineered foods. Have each group create a list of statements that can be short or long, reflecting their impressions. The results may surprise you, and help you address some common misunderstandings and concerns.

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.

Genetically Modified Organisms
“GMO” s

Table 12.6-0 Some Protein Products of Recombinant DNA Technology

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 may be cloned to produce more animals with the same traits. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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. Active Lecture Tips  If you have already addressed basic transcription and translation in your course, consider asking small groups of students in your class to explain the following. DNA technology is primarily used to produce proteins. Why aren’t lipids and carbohydrates typically produced by these processes?

Goat’s milk contains antithrombin – a protein that prevents blood clots and blocked arteries.
Figure 12.6a-0 A goat carrying a gene for human blood protein that is secreted in the milk

Sheep produces AAT protein that fights hereditary emphysema.
Figure 12.6b Sheep that have been genetically modified to produce a useful human protein

DNA technology has changed the pharmaceutical industry and medicine
DNA technology, including gene cloning, is widely used to produce medicines and to diagnose diseases. Therapeutic hormones produced by DNA technology include insulin to treat diabetes, human growth hormone to treat dwarfism, and tissue plasminogen activator (TPA), a protein that helps dissolve blood clots and reduces the risk of subsequent heart attacks. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 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.

Therapeutic hormones In 1982, humulin, human insulin produced by bacteria Became the first recombinant drug approved by the Food and Drug Administration

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

DNA technology has changed the pharmaceutical industry and medicine
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 to mount a lasting defense against that pathogen, thereby preventing disease. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 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.

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 called the Ti plasmid. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

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

GMO crops may be able to help a great many hungry people by improving food production, shelf life, pest resistance, and the nutritional value of crops. Golden Rice, a transgenic variety created in with a few daffodil genes, produces yellow grains containing beta-carotene, which our body uses to make vitamin A. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Figure 12.8b Golden Rice

Genetic engineers are now creating plants that make human proteins for medical use. Pharmaceutical trials currently under way involve using modified rice to treat infant diarrhea, corn to treat cystic fibrosis, safflower to treat diabetes, and duckweed to treat hepatitis. Although promising, no plant-made drugs intended for use by humans have been approved or sold. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Agricultural researchers are producing transgenic animals by injecting cloned genes directly into the nuclei of fertilized eggs. Genetically modified pigs convert less healthy fatty acids to omega-3 fatty acids, producing meat with four to five times as much healthy omega-3 fat as regular pork. Atlantic salmon have been genetically modified to mature in half the time of conventional salmon and grow to twice the size. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Hawaiian papayas Yummy!
Figure Are genetically modified organisms safe? (photo: papaya fruit)

Damage caused by PRS in a Puna papaya field

Benefits of agricultural genetic engineering
Hawaii’s papaya industry seemed doomed just a few decades ago. A deadly pathogen called the papaya ringspot virus (PRV) had spread throughout the islands. Virus a problem in 1950-’60’s, but could not be contained in 1992. It appeared poised to completely decimate the papaya plant population. 11/19/2014:

Benefits of agricultural engineering
Scientists from the University of Hawaii were able to rescue the industry by creating new, genetically engineered PRV-resistant strains of papaya c. 1998 Today, the papaya industry is once again vibrant, and the vast majority of Hawaii’s papayas are genetically modified organisms (GMOs).

Possible hazards of GMOs?
Some critics have raised safety concerns about GMOs for the people who eat them and A GMOs impact on the environment. (ecosystem) Should we in fact be concerned about the safety of GMO crops? This question continues to foster considerable debate and disagreement.

Genetically modified organisms raise health concerns
Scientists use safety measures to guard against production and release of new pathogens and competitive species. To guard against rogue microbes, scientists developed a set of guidelines, including strict laboratory safety and containment procedures, the genetic crippling of transgenic organisms to ensure that they cannot survive outside the laboratory, and a prohibition on certain obviously dangerous experiments. Today, most public concern centers on whether GMOs are safe for humans and the environment. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Genetically modified organisms are used in crop production because they are more nutritious or cheaper to produce. But do these advantages come at a cost to the health of people consuming GMOs? Especially consumption over many years? Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

A 2012 animal study involved 104 pigs that were divided into two groups. One group was fed a diet containing 39% GMO corn. Another group was fed a closely related non-GMO corn. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

The health of the pigs—in terms of growth, organ structure, and immune response against foreign DNA—was measured in the short term (31 days), in the medium term (110 days), and over the normal generational life span. The researchers reported no significant differences between the two groups and no traces of foreign DNA in the slaughtered pig. At least, for a two-year consumption of that particular GMO . . . Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Although pigs are a good model organism for human digestion, critics argue that human data are required to draw conclusions about the safety of dietary GMOs in people. A human study of Golden Rice was conducted jointly by Chinese and American scientists and published in 2012 and concluded that GMO rice can indeed be effective in preventing vitamin A deficiency among children who rely on rice as a staple food. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Percentage absorbed and converted to vitamin A
75 50 Percentage absorbed and converted to vitamin A 25 Figure 12.9 Vitamin A production after consumption of different sources of beta carotene Capsule of pure beta-carotene Golden rice Spinach

To date, no study has documented health risks in humans from GMO foods and there is general agreement among scientists that the GMO foods on the market are safe. On the other hand, because they are new, it is not yet possible to know, and we haven’t yet measured the long-term effects (if any) of GMOs on human health. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Concerns remain that transgenic plants might pass their new genes to related species in nearby wild areas and disturb the composition of the natural ecosystem. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

In the case of GMO crops, zero risk is probably unattainable. Scientists and the public need to weigh the possible benefits versus risks on a case-by-case basis. The best scenario would be to proceed with caution, basing our decisions on sound scientific information rather than on either irrational fear or blind optimism. Student Misconceptions and Concerns  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 ask students to research an issue before taking firm positions. 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. 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 (GMOs), 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.

Gene therapy may someday help treat a variety of diseases
Gene therapy is the alteration of a diseased individual’s genes for therapeutic purposes. One possible procedure is the following: A gene from a healthy person is cloned, converted to an RNA version, and then inserted into the RNA genome of a harmless virus. Bone marrow cells are taken from the patient and infected with the recombinant virus. The virus inserts a DNA version of its genome, including the normal human gene, into the cells’ DNA. The engineered cells are then injected back into the patient. Teaching Tips  In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law. The following link to a related U.S. government website 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 website can be found at  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, may face the potential of directed human evolution.

Cloned gene (normal allele)
1 An RNA version of a healthy human gene is inserted into a retrovirus. RNA genome of virus Healthy person 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 Bone marrow 4 The engineered cells are injected into the patient.

The promise of gene therapy thus far exceeds actual results, but there have been some successes in the treatment of severe combined immunodeficiency (SCID) and Leber’s congenital amaurosis (LCA). Teaching Tips  In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law. The following link to a related U.S. government website 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 website can be found at  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, may face the potential of directed human evolution.

The use of gene therapy raises ethical questions. Some critics suggest that tampering with human genes in any way will inevitably lead to the practice of eugenics, the deliberate effort to control the genetic makeup of human populations. Other observers see no fundamental difference between the transplantation of genes into somatic cells and the transplantation of organs. Teaching Tips  In 2008, the Genetic Information Nondiscrimination Act (GINA) was signed into law. The following link to a related U.S. government website 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 website can be found at  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, may face the potential of directed human evolution.

Identifying organisms using their unique dna/rna base sequences
DNA Profiling Identifying organisms using their unique dna/rna base sequences

The analysis of genetic markers can produce a DNA profile
DNA profiling is the analysis of DNA samples to determine whether they came from the same individual. In a typical investigation involving a DNA profile: DNA samples are isolated from the crime scene, suspects, victims, or other evidence, selected markers from each DNA sample are amplified (copied many times), producing a large sample of DNA fragments, and the amplified DNA markers are compared, providing data about which samples are from the same individual. 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.  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  Figure describes the general steps of DNA profiling. This overview is a useful reference to employ while the details of each step are discussed. Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

The PCR method is used to amplify DNA sequences
Cycle 1 yields two molecules Cycle 2 yields four molecules Cycle 3 yields eight molecules Additional Cycles… Sample 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′ Primer New DNA Figure DNA amplification by PCR Polymerase chain reaction (PCR) is a technique by which a specific segment of a DNA molecule can be targeted and quickly amplified in the laboratory.

The advantages of PCR include the ability to amplify DNA from a small sample, rapid results, and a reaction that is highly sensitive, copying only the target sequence. 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.  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! Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Devised in 1985, PCR has had a major impact on biological research and biotechnology. PCR has been used to amplify DNA from fragments of ancient DNA from a mummified human, a 40,000-year-old frozen woolly mammoth, a 30-million-year-old plant fossil, and DNA from fingerprints or from tiny amounts of blood, tissue, or semen found at crime scenes. 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.  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! Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Gel electrophoresis sorts DNA molecules by size
Many DNA technology applications rely on gel electrophoresis, a method that separates macromolecules, usually proteins or nucleic acids, on the basis of size, electrical charge, or other physical properties. 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.  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. Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

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

Short tandem repeat 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, that are used in DNA profiling. STR analysis compares the lengths of STR sequences at specific sites in the genome and typically analyzes 13 sites scattered in the genome. 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.  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. Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

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

Amplified crime scene DNA Amplified suspect’s DNA
Longer STR fragments Figure 12.14b DNA profiles generated from the STRs in Figure 12.14a Shorter STR fragments

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, and probe the origin of nonhuman materials. 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.  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. Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology MasteringBiology instructor resource area for a description of this activity.

DNA profiling has provided evidence in many forensic investigations
One of the strangest cases of DNA profiling is that of Cheddar Man, a 9,000-year-old skeleton found in a cave near Cheddar, England. DNA was extracted from his tooth and analyzed. The DNA profile showed that Cheddar Man was a direct ancestor—through approximately 300 generations—of a present-day schoolteacher who lived only a half mile from the cave! 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.  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. Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

RFLPs can be used to detect differences in DNA sequences
Geneticists have cataloged many single-base-pair variations in the genome. Such a variation found in at least 1% of the population is called a single nucleotide polymorphism (SNP, pronounced “snip”). SNPs occur on average about once in 100 to 300 base pairs in the human genome, in the coding sequences of genes and in noncoding sequences between genes. 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.  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) Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

RFLPs can be used to detect differences in DNA sequences
SNPs may alter a restriction site—the sequence recognized by a restriction enzyme. Such alterations change the lengths of the restriction fragments formed by that enzyme when it cuts the DNA. A sequence variation of this type is called a restriction fragment length polymorphism (RFLP, pronounced “rif-lip”). Thus, RFLPs can serve as genetic markers for particular loci in the genome. 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.  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) Active Lecture Tips • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Restriction enzymes added
DNA sample 1 DNA sample 2 w Cut C C G G G G C C A C G G T G C C z x Cut C C G G G G C C Cut C C G G G G C C y y Sample 1 Sample 2 Figure RFLP analysis Longer fragments z x w Shorter fragments y y

Genomics

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. As of 2013, the genomes of nearly 7,000 species have been completed, and thousands more are in progress. 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. Genomics provides significant support of 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. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Table 12.17 Some important completed genomes

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. Genomics provides significant support of 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. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

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  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. Genomics provides significant support of the other types of evidence for evolution.  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.  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  The main U.S. Department of Energy Office website in support of the Human Genome Project is found at  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.  The authors note that there are 3 billion nucleotide pairs in the human genome. There are about 3 billion seconds in 95 years. This simple reference can add meaning to the significance of these large numbers.  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.)  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. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Results of the Human Genome Project indicate that humans have about 21,000 genes in 3 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. 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. Genomics provides significant support of the other types of evidence for evolution.  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.  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  The main U.S. Department of Energy Office website in support of the Human Genome Project is found at  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.  The authors note that there are 3 billion nucleotide pairs in the human genome. There are about 3 billion seconds in 95 years. This simple reference can add meaning to the significance of these large numbers.  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.)  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. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Much of the DNA between genes consists of repetitive DNA, nucleotide sequences present in many copies in the genome. Stretches of DNA with thousands of short repetitions are also prominent at the centromeres and ends of chromosomes—called telomeres. 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. Genomics provides significant support of the other types of evidence for evolution.  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.  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  The main U.S. Department of Energy Office website in support of the Human Genome Project is found at  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.  The authors note that there are 3 billion nucleotide pairs in the human genome. There are about 3 billion seconds in 95 years. This simple reference can add meaning to the significance of these large numbers.  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.)  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. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

In a second main type of repetitive DNA, each repeated unit is hundreds of nucleotides long, and the copies are scattered around the genome. Most of these sequences seem to be associated with transposable elements (“jumping genes”), DNA segments that can move or be copied from one location to another in a chromosome and even between chromosomes. 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. Genomics provides significant support of the other types of evidence for evolution.  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.  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  The main U.S. Department of Energy Office website in support of the Human Genome Project is found at  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.  The authors note that there are 3 billion nucleotide pairs in the human genome. There are about 3 billion seconds in 95 years. This simple reference can add meaning to the significance of these large numbers.  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.)  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. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Proteomics is the scientific study of the full set of proteins encoded by a genome
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. Teaching Tips  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.)  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. 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. Genomics provides significant support of the other types of evidence for evolution. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

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, which is involved with speech and vocalization. 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. 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. Genomics provides significant support of the other types of evidence for evolution. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Genomes hold clues to human evolution
Neanderthals first appeared at least 300,000 years ago, were humans’ closest relatives, were a separate species, also had the FOXP2 gene, may have had pale skin and red hair, and were lactose intolerant. 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. 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. Genomics provides significant support of the other types of evidence for evolution. Active Lecture Tips • See the Activity Personal Genomics: Would You Give Your DNA Away on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity instructor resource area for a description of this activity . • See the Media Review: “Learn.Genetics” Genetic Science Learning Center from the University of Utah on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

Introduction DNA technologies affect our lives in many ways.

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Introduction DNA technologies affect our lives in many ways.

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Presentation on theme: "Introduction DNA technologies affect our lives in many ways."— Presentation transcript:

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