Changing the living world

How we change the living world… Selective breeding: crossing organisms with desired traits to produce the next generation.

How we change the living world… Hybridization: crossing dissimilar organisms to get the best of both.

How we change the living world… Inbreeding: continually breeding individuals with similar characteristics.

GENETIC ENGINEERING

Genetic engineering vocab Recombinant DNA- nucleotide sequences from two different sources to form a single DNA molecule. Transgenic organism – contains a gene from another organism, typically a different species Genetically modified organisms (GMOs)- organisms that have acquired one or more genes by artificial means. Student Misconceptions and Concerns 1. The roles of restriction enzymes and nucleic acid probes, as well as many other aspects of recombinant DNA techniques, rely upon a firm and comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that addresses the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, 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. Teaching Tips 1. Annual flu vaccinations are a common example of using vaccines to prevent diseases that cannot be easily cured. 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. 2. Genetically engineered organisms are controversial, creating various degrees and directions of social resistance. Yet, many debates around issues of science are confused by misinformation. This may be an opportunity for you to make an extra credit or regular assignment for students to take a position, one side or the other, on some aspect of this or related issues. The science would need to be accurate. Students might debate whether a food product made from GM/transgenic organisms should be labeled as such, or students can discuss the risks or advantages of producing GM organisms. 3. The origin of the name “restriction enzymes” may be of interest. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material. 4. The ability to swap genes between prokaryotes and eukaryotes using the technologies described in this chapter reveal the fundamental genetic mechanisms shared by all forms of life. This very strong evidence of common descent is a lesson about evolution that may be missed by your students. 5. Students might think you are just making a bad joke by noting that laboratory-synthesized genes are “designer genes,” but this is a common term. Search the Internet using the keywords “designer genes,” and many scientific (and unscientific) sites will be found. 6. A genomic library of the sentence you are now reading would be all of the sentence fragments that make 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 an “e” is followed by the letter “n” The resulting fragments of this original sentence would look like this, and would be like a type of “genomic library.” Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce. 7. 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 you do not know the song title or artist, you might search the Internet using a unique phrase from the song. (For example, search using “yellow submarine”.) 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 would search using a sequence complementary to the desired sequence. 8. Roundup Ready Corn, a product of 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. 9. As gene therapy technology expands, our ability to modify the genome in human embryos, created 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.

Figure 12.1 Glowing fish Figure 12.1

Genetic Engineering Genetic engineering: The process of manipulating genes for practical purposes. Genetic engineering may involve building recombinant DNA DNA made from two or more different organisms.

Steps in a Genetic Engineering Experiment Step 1 Isolate Target DNA and plasmid and cut with restriction enzymes Step 2 Recombinant DNA is produced. Step 3 Gene cloning: the process by which many copies of the gene of interest are made each time the host cell reproduces. Step 4 Cells undergo selection and then are screened.

Steps in a Genetic Engineering Experiment Step 1 The DNA from the organism containing the gene of interest and the vector are cut by restriction enzymes. A vector is an agent that is used to carry the gene of interest into another cell Commonly used vectors: viruses, yeast, and plasmids. circular bacterial DNA

Plasmids Bacterial chromosome Remnant of bacterium Figure 12.7 Figure 12.7 Bacterial plasmids Bacterial chromosome Remnant of bacterium Colorized TEM Figure 12.7

Isolate plasmids. Bacterial cell Plasmid Figure 12.8 Using recombinant DNA technology to produce useful products (Step 1) Figure 12.8-1

Isolate DNA. Isolate plasmids. Cell containing the gene of interest Bacterial cell Plasmid DNA Figure 12.8 Using recombinant DNA technology to produce useful products (Step 2) Figure 12.8-2

Cut both DNAs with same enzyme. DNA fragments from cell Isolate DNA. Gene of interest Other genes Isolate plasmids. Cell containing the gene of interest Bacterial cell Plasmid DNA Figure 12.8 Using recombinant DNA technology to produce useful products (Step 3) Figure 12.8-3

Cut both DNAs with same enzyme. DNA fragments from cell Isolate DNA. Gene of interest Other genes Mix the DNAs and join them together. Gene of interest Isolate plasmids. Cell containing the gene of interest Bacterial cell Recombinant DNA plasmids Plasmid DNA Figure 12.8 Using recombinant DNA technology to produce useful products (Step 4) Figure 12.8-4

Cut both DNAs with same enzyme. DNA fragments from cell Isolate DNA. Gene of interest Other genes Mix the DNAs and join them together. Gene of interest Isolate plasmids. Cell containing the gene of interest Bacterial cell Recombinant DNA plasmids Bacteria take up recombinant plasmids. Plasmid DNA Recombinant bacteria Figure 12.8 Using recombinant DNA technology to produce useful products (Step 5) Figure 12.8-5

Cut both DNAs with same enzyme. DNA fragments from cell Isolate DNA. Gene of interest Other genes Mix the DNAs and join them together. Gene of interest Isolate plasmids. Cell containing the gene of interest Bacterial cell Recombinant DNA plasmids Bacteria take up recombinant plasmids. Plasmid DNA Bacterial clone Recombinant bacteria Clone the bacteria. Figure 12.8 Using recombinant DNA technology to produce useful products (Step 6) Figure 12.8-6

Cut both DNAs with same enzyme. DNA fragments from cell Isolate DNA. Gene of interest Other genes Mix the DNAs and join them together. Gene of interest Isolate plasmids. Cell containing the gene of interest Bacterial cell Recombinant DNA plasmids Bacteria take up recombinant plasmids. Plasmid DNA Bacterial clone Recombinant bacteria Clone the bacteria. Figure 12.8 Using recombinant DNA technology to produce useful products (Step 7) Find the clone with the gene of interest. Figure 12.8-7

Cut both DNAs with same enzyme. DNA fragments from cell Isolate DNA. Gene of interest Other genes Mix the DNAs and join them together. Gene of interest Isolate plasmids. Cell containing the gene of interest Bacterial cell Recombinant DNA plasmids Bacteria take up recombinant plasmids. Plasmid DNA Bacterial clone Recombinant bacteria Clone the bacteria. Figure 12.8 Using recombinant DNA technology to produce useful products (Step 8) Find the clone with the gene of interest. Some uses of genes Some uses of proteins Gene for pest resistance Protein for dissolving clots Protein for “stone-washing” jeans Gene for toxic-cleanup bacteria The gene and protein of interest are isolated from the bacteria. Genes may be inserted into other organisms. Harvested proteins may be used directly. Figure 12.8-8

RESTRICTION ENZYMES molecular scissors

A Closer Look: Cutting and Pasting DNA with Restriction Enzymes Recombinant DNA is produced by combining two ingredients: A bacterial plasmid The gene of interest How do we cut them? Using restriction enzymes: bacterial enzymes which cut DNA at specific nucleotide sequences produce pieces of DNA called restriction fragments. Why do you think bacteria contain restriction enzymes? Student Misconceptions and Concerns 1. The roles of restriction enzymes and nucleic acid probes, as well as many other aspects of recombinant DNA techniques, rely upon a firm and comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that addresses the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, 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. Teaching Tips 1. Annual flu vaccinations are a common example of using vaccines to prevent diseases that cannot be easily cured. 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. 2. Genetically engineered organisms are controversial, creating various degrees and directions of social resistance. Yet, many debates around issues of science are confused by misinformation. This may be an opportunity for you to make an extra credit or regular assignment for students to take a position, one side or the other, on some aspect of this or related issues. The science would need to be accurate. Students might debate whether a food product made from GM/transgenic organisms should be labeled as such, or students can discuss the risks or advantages of producing GM organisms. 3. The origin of the name “restriction enzymes” may be of interest. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material. 4. The ability to swap genes between prokaryotes and eukaryotes using the technologies described in this chapter reveal the fundamental genetic mechanisms shared by all forms of life. This very strong evidence of common descent is a lesson about evolution that may be missed by your students. 5. Students might think you are just making a bad joke by noting that laboratory-synthesized genes are “designer genes,” but this is a common term. Search the Internet using the keywords “designer genes,” and many scientific (and unscientific) sites will be found. 6. A genomic library of the sentence you are now reading would be all of the sentence fragments that make 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 an “e” is followed by the letter “n” The resulting fragments of this original sentence would look like this, and would be like a type of “genomic library.” Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce. 7. 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 you do not know the song title or artist, you might search the Internet using a unique phrase from the song. (For example, search using “yellow submarine”.) 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 would search using a sequence complementary to the desired sequence. 8. Roundup Ready Corn, a product of 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. 9. As gene therapy technology expands, our ability to modify the genome in human embryos, created 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.

Restriction Enzymes are palindromes: the same forward as backwards, like RACECAR. Examples: GAATTC CCCGGG AAGCTT CTTAAG GGGCCC TTCGAA G AATTC CCC GGG A AGCTT CTTAA G GGG CCC TTCGA A Sticky Ends Blunt End

for a restriction enzyme Recognition sequence for a restriction enzyme DNA A restriction enzyme cuts the DNA into fragments. Restriction enzyme Sticky end Sticky end Figure 12.9 Cutting and pasting DNA (Step 1) Figure 12.9-1

for a restriction enzyme Recognition sequence for a restriction enzyme DNA A restriction enzyme cuts the DNA into fragments. Restriction enzyme Sticky end Sticky end A DNA fragment is added from another source. Figure 12.9 Cutting and pasting DNA (Step 2) Figure 12.9-2

for a restriction enzyme Recognition sequence for a restriction enzyme DNA A restriction enzyme cuts the DNA into fragments. Restriction enzyme Sticky end Sticky end A DNA fragment is added from another source. Fragments stick together by base pairing. Figure 12.9 Cutting and pasting DNA (Step 3) Figure 12.9-3

DNA LIGASE DNA ligase connects the DNA fragments into one continuous strand (DNA Glue or tape) Student Misconceptions and Concerns 1. The roles of restriction enzymes and nucleic acid probes, as well as many other aspects of recombinant DNA techniques, rely upon a firm and comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that addresses the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, 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. Teaching Tips 1. Annual flu vaccinations are a common example of using vaccines to prevent diseases that cannot be easily cured. 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. 2. Genetically engineered organisms are controversial, creating various degrees and directions of social resistance. Yet, many debates around issues of science are confused by misinformation. This may be an opportunity for you to make an extra credit or regular assignment for students to take a position, one side or the other, on some aspect of this or related issues. The science would need to be accurate. Students might debate whether a food product made from GM/transgenic organisms should be labeled as such, or students can discuss the risks or advantages of producing GM organisms. 3. The origin of the name “restriction enzymes” may be of interest. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material. 4. The ability to swap genes between prokaryotes and eukaryotes using the technologies described in this chapter reveal the fundamental genetic mechanisms shared by all forms of life. This very strong evidence of common descent is a lesson about evolution that may be missed by your students. 5. Students might think you are just making a bad joke by noting that laboratory-synthesized genes are “designer genes,” but this is a common term. Search the Internet using the keywords “designer genes,” and many scientific (and unscientific) sites will be found. 6. A genomic library of the sentence you are now reading would be all of the sentence fragments that make 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 an “e” is followed by the letter “n” The resulting fragments of this original sentence would look like this, and would be like a type of “genomic library.” Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce. 7. 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 you do not know the song title or artist, you might search the Internet using a unique phrase from the song. (For example, search using “yellow submarine”.) 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 would search using a sequence complementary to the desired sequence. 8. Roundup Ready Corn, a product of 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. 9. As gene therapy technology expands, our ability to modify the genome in human embryos, created 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.

for a restriction enzyme Recognition sequence for a restriction enzyme DNA A restriction enzyme cuts the DNA into fragments. Restriction enzyme Sticky end Sticky end A DNA fragment is added from another source. Fragments stick together by base pairing. Figure 12.9 Cutting and pasting DNA (Step 4) DNA ligase DNA ligase joins the fragments into strands. Recombinant DNA molecule Figure 12.9-4

Recognition sequences DNA sequence Restriction enzyme EcoRI cuts the DNA into fragments. Sticky end

Your turn to try!!

Plasmids: Can easily incorporate foreign DNA Are readily taken up by bacterial cells Can act as vectors, DNA carriers that move genes from one cell to another Are ideal for gene cloning, the production of multiple identical copies of a gene-carrying piece of DNA Student Misconceptions and Concerns 1. The roles of restriction enzymes and nucleic acid probes, as well as many other aspects of recombinant DNA techniques, rely upon a firm and comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that addresses the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, 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. Teaching Tips 1. Annual flu vaccinations are a common example of using vaccines to prevent diseases that cannot be easily cured. 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. 2. Genetically engineered organisms are controversial, creating various degrees and directions of social resistance. Yet, many debates around issues of science are confused by misinformation. This may be an opportunity for you to make an extra credit or regular assignment for students to take a position, one side or the other, on some aspect of this or related issues. The science would need to be accurate. Students might debate whether a food product made from GM/transgenic organisms should be labeled as such, or students can discuss the risks or advantages of producing GM organisms. 3. The origin of the name “restriction enzymes” may be of interest. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material. 4. The ability to swap genes between prokaryotes and eukaryotes using the technologies described in this chapter reveal the fundamental genetic mechanisms shared by all forms of life. This very strong evidence of common descent is a lesson about evolution that may be missed by your students. 5. Students might think you are just making a bad joke by noting that laboratory-synthesized genes are “designer genes,” but this is a common term. Search the Internet using the keywords “designer genes,” and many scientific (and unscientific) sites will be found. 6. A genomic library of the sentence you are now reading would be all of the sentence fragments that make 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 an “e” is followed by the letter “n” The resulting fragments of this original sentence would look like this, and would be like a type of “genomic library.” Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce. 7. 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 you do not know the song title or artist, you might search the Internet using a unique phrase from the song. (For example, search using “yellow submarine”.) 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 would search using a sequence complementary to the desired sequence. 8. Roundup Ready Corn, a product of 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. 9. As gene therapy technology expands, our ability to modify the genome in human embryos, created 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.

Bacterial cells don’t edit the RNA, so how can they make the correct protein? Genetic Engineers can eliminate the introns from mRNA and reverse the process, producing a DNA strand that is only the instructions for the protein. Use Reverse Transcriptase

Figure 12.11-1 Cell nucleus Exon Intron Exon Intron Exon DNA of eukaryotic gene Transcription Test tube Figure 12.11 Making a gene from eukaryotic mRNA (Step 1) Figure 12.11-1

Figure 12.11-2 Cell nucleus Exon Intron Exon Intron Exon DNA of eukaryotic gene Transcription RNA transcript Introns removed and exons spliced together mRNA Test tube Figure 12.11 Making a gene from eukaryotic mRNA (Step 2) Figure 12.11-2

Figure 12.11-3 Cell nucleus Exon Intron Exon Intron Exon DNA of eukaryotic gene Transcription RNA transcript Introns removed and exons spliced together mRNA Test tube Isolation of mRNA from cell and addition of reverse transcriptase Reverse transcriptase Figure 12.11 Making a gene from eukaryotic mRNA (Step 3) Figure 12.11-3

Figure 12.11-4 Cell nucleus Exon Intron Exon Intron Exon DNA of eukaryotic gene Transcription RNA transcript Introns removed and exons spliced together mRNA Test tube Isolation of mRNA from cell and addition of reverse transcriptase Reverse transcriptase Figure 12.11 Making a gene from eukaryotic mRNA (Step 4) Synthesis of cDNA strand cDNA strand being synthesized Figure 12.11-4

Figure 12.11-5 Cell nucleus Exon Intron Exon Intron Exon DNA of eukaryotic gene Transcription RNA transcript Introns removed and exons spliced together mRNA Test tube Isolation of mRNA from cell and addition of reverse transcriptase Reverse transcriptase Figure 12.11 Making a gene from eukaryotic mRNA (Step 5) Synthesis of cDNA strand cDNA strand being synthesized Synthesis of second DNA strand by DNA polymerase cDNA of gene without introns Figure 12.11-5