#StandardsGoals for 2024: What’s new for BISAC - Tech Forum 2024
DNA and RNA Polymerization
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3. 0 Sugar-phosphate backbone DNA nucleotide Phosphate group Nitrogenous base Sugar DNA polynucleotide DNA nucleotide Sugar (deoxyribose) Thymine (T) Nitrogenous base (A, G, C, or T) Phosphate group
19. 0 Polypeptide Translation Transcription Gene 1 DNA molecule DNA strand Codon Amino acid Gene 2 Gene 3 RNA
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24. 0 Examples of gene use Recombinant DNA plasmid E. coli bacterium Plasmid Bacterial chromosome Gene of interest DNA Gene of interest Cell with DNA containing gene of interest Recombinant bacterium Clone of cells Genes may be inserted into other organisms Genes or proteins are isolated from the cloned bacterium Harvested proteins may be used directly Examples of protein use Gene of interest Isolate plasmid 1 Isolate DNA 2 Cut plasmid with enzyme 3 Cut cell’s DNA with same enzyme 4 Combine targeted fragment and plasmid DNA 5 Add DNA ligase, which closes the circle with covalent bonds 6 Put plasmid into bacterium by transformation 7 Allow bacterium to reproduce 8 9
25. 0 E. coli bacterium Plasmid Bacterial chromosome Gene of interest DNA Cell with DNA containing gene of interest Isolate plasmid Isolate DNA 1 2
26. 0 E. coli bacterium Plasmid Bacterial chromosome Gene of interest DNA Cell with DNA containing gene of interest Gene of interest Isolate plasmid Isolate DNA Cut plasmid with enzyme Cut cell’s DNA with same enzyme 1 2 3 4
27. 0 E. coli bacterium Plasmid Bacterial chromosome Gene of interest DNA Cell with DNA containing gene of interest Gene of interest Isolate plasmid Isolate DNA Cut plasmid with enzyme Cut cell’s DNA with same enzyme 1 2 3 4 Combine targeted fragment and plasmid DNA 5
28. 0 E. coli bacterium Plasmid Bacterial chromosome Gene of interest DNA Cell with DNA containing gene of interest Gene of interest Isolate plasmid Isolate DNA Cut plasmid with enzyme Cut cell’s DNA with same enzyme 1 2 3 4 Recombinant DNA plasmid Gene of interest Combine targeted fragment and plasmid DNA Add DNA ligase, which closes the circle with covalent bonds 5 6
29. 0 Recombinant DNA plasmid Gene of interest Recombinant bacterium Put plasmid into bacterium by transformation 7
30. 0 Recombinant DNA plasmid Gene of interest Recombinant bacterium Clone of cells Put plasmid into bacterium by transformation Allow bacterium to reproduce 8 7
31. 0 Recombinant DNA plasmid Gene of interest Recombinant bacterium Clone of cells Genes or proteins are isolated from the cloned bacterium Harvested proteins may be used directly Examples of protein use Put plasmid into bacterium by transformation Allow bacterium to reproduce 8 7 Genes may be inserted into other organisms Examples of gene use 9
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33. 0 Agrobacterium tumefaciens DNA containing gene for desired trait Ti plasmid Insertion of gene into plasmid Recombinant Ti plasmid 1 Restriction site
34. Agrobacterium tumefaciens DNA containing gene for desired trait Ti plasmid Insertion of gene into plasmid Recombinant Ti plasmid 1 Restriction site Plant cell Introduction into plant cells 2 DNA carrying new gene
35. Agrobacterium tumefaciens DNA containing gene for desired trait Ti plasmid Insertion of gene into plasmid Recombinant Ti plasmid 1 Restriction site Plant cell Introduction into plant cells 2 DNA carrying new gene Regeneration of plant 3 Plant with new trait
39. 0 Cycle 1 yields 2 molecules 2 1 3 Genomic DNA Cycle 3 yields 8 molecules Cycle 2 yields 4 molecules 3 5 3 5 3 5 Target sequence Heat to separate DNA strands Cool to allow primers to form hydrogen bonds with ends of target sequences 3 5 3 5 3 5 3 5 3 5 Primer New DNA 5 DNA polymerase adds nucleotides to the 3 end of each primer 5
40. 0 Cycle 1 yields 2 molecules Genomic DNA 3 5 3 5 3 5 Target sequence Heat to separate DNA strands Cool to allow primers to form hydrogen bonds with ends of target sequences 3 5 3 5 3 5 3 5 3 5 Primer New DNA 5 DNA polymerase adds nucleotides to the 3 end of each primer 2 1 5 3
43. 0 Mixture of DNA fragments of different sizes Completed gel Longer (slower) molecules Gel Power source Shorter (faster) molecules
Editor's Notes
Student Misconceptions and Concerns 1. If your class has not yet studied Chapter 3, consider assigning module 3.16 on “Nucleic Acids” before addressing the contents of Chapter 10. 2. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases. Teaching Tips 1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Griffith, Hershey, Chase, Franklin, and Chargaff). 2. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars.
Figure 10.2A The structure of a DNA polynucleotide. This figure shows a short stretch of DNA. The nucleotides can theoretically be arranged in any order, since all nucleotides have a phosphate group that can be joined to the sugar of any other nucleotide. The order of nucleotides within a gene, however, is what provides the information for producing a specific protein.
Figure 10.2A The structure of a DNA polynucleotide. This figure shows a short stretch of DNA. The nucleotides can theoretically be arranged in any order, since all nucleotides have a phosphate group that can be joined to the sugar of any other nucleotide. The order of nucleotides within a gene, however, is what provides the information for producing a specific protein.
Figure 10.2B Nitrogenous bases of DNA. Nitrogenous bases are of two types. The pyrimidines, cytosine and thymine, consist of a single ring. The purines, adenine and guanine, are double-ringed structures.
Figure 10.2C An RNA nucleotide. This figure shows an RNA nucleotide, with the pyrimidine uracil as the nitrogenous base. At this point it would be useful to compare and contrast the nucleotides of DNA and RNA. Similarities: Purines are A and G, Pyrimidine is C. Both types of nucleotides have a phosphate group. Nucleotides are covalently linked to form polynucleotides. (This could be related back to the dehydration synthesis reaction producing polysaccharides, triglycerides, and proteins.) Differences: DNA nucleotides have T; RNA nucleotides have U. DNA nucleotides have deoxyribose sugar; RNA nucleotides have ribose sugar.
Figure 10.2D Part of an RNA polynucleotide. This figure emphasizes that RNA is a polymer of nucleotides and that the arrangement of the nucleotides can have many variations.
Figure 10.3D Three representations of DNA. Hydrogen bonding between bases can be seen in the partial chemical structure in the center. This figure can also be used to point out the opposite polarity of the DNA chains as emphasized in Module 10.5. From top to bottom, the chain on the left is oriented 5 3 while the chain on the right is oriented 3 5 . A 5 end has a free phosphate group attached to the 5 carbon of the sugar and a 3 end has a free –OH group attached to the 3 carbon of the sugar.
Figure 10.3D Three representations of DNA.
Figure 10.3D Three representations of DNA.
The role of proteins in expression of a genotype can be connected to the experiments that established the foundations of genetics. The round-wrinkled phenotypes of Mendel’s pea plants were due to differences in the production of a Starch Branching Enzyme (SBEI). The round-seeded plants had a functional version of the SBEI enzyme, allowing the formation of amylopectin, a highly branched form of starch, from sucrose. The wrinkled-seeded plants stored excess sucrose due to their lack of a functional SBEI enzyme and accumulated excess water as a result. When both types of seeds completed a natural dehydration process in seed maturation, the round seeds retained their shape, while the wrinkled seeds shriveled from water loss. Student Misconceptions and Concerns 1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing the basic content from Figure 10.6 on the board, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. Teaching Tips 1. It has been said that everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the validity of this statement. 2. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
Due to alternative splicing scenarios (see Module 11.6), in which transcripts of the same gene can be used to produce different proteins, the one gene–one polypeptide hypothesis needs to be updated. Estimates suggest that at least a third of human genes are subject to alternative splicing events. Neurexins are a family of cell surface proteins involved in cell-cell adhesion and recognition in neurons. There are three neurexin genes and multiple alternative splicing sites for the transcripts from these genes, leading to the potential for more than a thousand different protein variants. Student Misconceptions and Concerns 1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing the basic content from Figure 10.6 on the board, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. Teaching Tips 1. It has been said that everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the validity of this statement. 2. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
Figure 10.6A Flow of genetic information in a eukaryotic cell. Transcription is the production of RNA using DNA as a template. In eukaryotic cells, transcription occurs in the nucleus, and the resulting RNA (mRNA) enters the cytoplasm. Translation is the production of protein, using the sequence of nucleotides in RNA. Translation occurs in the cytoplasm for both prokaryotic and eukaryotic cells.
Figure 10.6A Flow of genetic information in a eukaryotic cell. Transcription is the production of RNA using DNA as a template. In eukaryotic cells, transcription occurs in the nucleus, and the resulting RNA (mRNA) enters the cytoplasm. Translation is the production of protein, using the sequence of nucleotides in RNA. Translation occurs in the cytoplasm for both prokaryotic and eukaryotic cells.
Figure 10.6A Flow of genetic information in a eukaryotic cell. Transcription is the production of RNA using DNA as a template. In eukaryotic cells, transcription occurs in the nucleus, and the resulting RNA (mRNA) enters the cytoplasm. Translation is the production of protein, using the sequence of nucleotides in RNA. Translation occurs in the cytoplasm for both prokaryotic and eukaryotic cells.
Comparing the linguistic meaning of transcription and translation is a useful analogy for the biochemical processes. Transcription involves staying in the nucleic acid language, while translation involves converting nucleotide codes into the amino acid language of proteins. I suggest that a student whose native language is not English may transcribe the words of an instructor during the lecture presentation, and then translate those words into his or her native language for better understanding. I also relate a story about purchasing a recipe book in French and not being able to make any of the dishes without translating the information into English! Student Misconceptions and Concerns 1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. Teaching Tips 1. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written language. 2. The sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame (see Module 10.16).
Figure 10.7 Transcription and translation of codons.
Figure 10.7 Transcription and translation of codons.
Student Misconceptions and Concerns 1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. Teaching Tips 1. Figure 12.1 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. Referring to this figure in class helps students relate the text to your lecture. 2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to cut and remove the minute of film and a way to cut the new film apart and 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 relationship.
At step 6, there are actually three types of products that include plasmid DNA: (1) The ends of the plasmid can rejoin so that its original sequence is restored. (2) A recombinant DNA molecule can be formed containing part or all of the gene of interest. (3) Recombinant DNA molecules form that contain sequences unrelated to the gene of interest, representing the largest percentage of recombinant molecules. This mixture of products is typically used to transform bacteria under conditions where each cell is likely to take up only one plasmid. The cells are grown to form colonies, and properties of the plasmid and target DNA are used to detect the colony containing the recombinant plasmid carrying the gene of interest. Plasmids usually contain marker genes whose products indicate the presence of the plasmid within a bacterial host. A common approach is to use a plasmid with two markers, genes whose products indicate the presence of the plasmid within a bacterial cell. The site at which the plasmid is cut to add the target DNA is within one of the marker genes. Bacterial cells that show the action of both marker genes are not carrying target DNA and can be eliminated from the population. Bacterial cells expressing only the intact marker gene carry a recombinant plasmid. If the whole genome from the target organism is represented, this collection of clones is called a gene library (see Module 12.3). DNA from cells in this library can be tested for hybridization to a probe (see Module 12.5), to identify the cell carrying the gene of interest. Student Misconceptions and Concerns 1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. Teaching Tips 1. Figure 12.1 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. Referring to this figure in class helps students relate the text to your lecture. 2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to cut and remove the minute of film and a way to cut the new film apart and 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 relationship.
At step 6, there are actually three types of products that include plasmid DNA: (1) The ends of the plasmid can rejoin so that its original sequence is restored. (2) A recombinant DNA molecule can be formed containing part or all of the gene of interest. (3) Recombinant DNA molecules form that contain sequences unrelated to the gene of interest, representing the largest percentage of recombinant molecules. This mixture of products is typically used to transform bacteria under conditions where each cell is likely to take up only one plasmid. The cells are grown to form colonies, and properties of the plasmid and target DNA are used to detect the colony containing the recombinant plasmid carrying the gene of interest. Plasmids usually contain marker genes whose products indicate the presence of the plasmid within a bacterial host. A common approach is to use a plasmid with two markers, genes whose products indicate the presence of the plasmid within a bacterial cell. The site at which the plasmid is cut to add the target DNA is within one of the marker genes. Bacterial cells that show the action of both marker genes are not carrying target DNA and can be eliminated from the population. Bacterial cells expressing only the intact marker gene carry a recombinant plasmid. If the whole genome from the target organism is represented, this collection of clones is called a gene library (see Module 12.3). DNA from cells in this library can be tested for hybridization to a probe (see Module 12.5), to identify the cell carrying the gene of interest. Student Misconceptions and Concerns 1. Student comprehension of restriction enzymes, nucleic acid probes, and many other aspects of recombinant DNA techniques depends upon a comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that covers the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, in their reactions to the controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. Teaching Tips 1. Figure 12.1 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. Referring to this figure in class helps students relate the text to your lecture. 2. The general genetic engineering challenge discussed in Module 12.1 begins with the need to insert a gene of choice into a plasmid. This process is very similar to film or video editing. What do we need to do to insert a minute of one film into another? We will need techniques to cut and remove the minute of film and a way to cut the new film apart and 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 relationship.
Figure 12.1 An overview of gene cloning. This figure shows steps 1–8 as detailed on the previous two slides.
Figure 12.1 An overview of gene cloning.
Figure 12.1 An overview of gene cloning.
Figure 12.1 An overview of gene cloning.
Figure 12.1 An overview of gene cloning.
Figure 12.1 An overview of gene cloning.
Figure 12.1 An overview of gene cloning.
Figure 12.1 An overview of gene cloning.
GM plants: Resistance to herbicides: Roundup Ready Soybeans contain a bacterial version of an amino acid synthesis enzyme that is less sensitive to glyphosate (Roundup). Resistance to pests: Bt corn produces an insect toxin, derived from the bacterium Bacillus thuringiensis. Improved nutritional profile: “Golden rice” has increased beta-carotene due to the presence of daffodil genes. GM animals: Improved qualities: Sheep with an extra copy of a growth hormone gene grow larger and faster and produce more milk and wool. Production of proteins or therapeutics: “Pharm” animals (see Module 12.6). The first GM organism approved for sale as food was the Flavr-Savr tomato. The modification was intended to prolong the shelf life of the tomato by keeping it from softening when ripe. Softening is caused by an enzyme called polygalacturonase that breaks down pectins in fruit. In the Flavr-Savr tomato, production of polygalacturonase was blocked by an antisense RNA molecule complementary to the enzyme’s mRNA. The shelf life of the tomato was indeed prolonged, but ultimately there was little flavor to savor as consumers found the fruit to have a bland taste! For Discovery Video Transgenics, go to Animation and Video Files. Student Misconceptions and Concerns 1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms. 2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent provides proof of evolution that may be missed by your students. Teaching Tips 1. Roundup Ready Corn, a product of the agricultural biotechnology corporation Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. Module 12.9 discusses some of the issues related to the concerns over the use of GM organisms.
Figure 12.8A Using the Ti plasmid as a vector for genetically engineering plants. A modified form of the Ti (tumor inducing) plasmid is used in plant genetic engineering. The tumor inducing genes have been removed from the plasmid but genes required for insertion into plant chromosomes have been retained. The gene of interest has been inserted into the plasmid under the control of a bacterial promoter.
Figure 12.8A Using the Ti plasmid as a vector for genetically engineering plants. A modified form of the Ti (tumor inducing) plasmid is used in plant genetic engineering. The tumor inducing genes have been removed from the plasmid but genes required for insertion into plant chromosomes have been retained. The gene of interest has been inserted into the plasmid under the control of a bacterial promoter.
Figure 12.8A Using the Ti plasmid as a vector for genetically engineering plants. A modified form of the Ti (tumor inducing) plasmid is used in plant genetic engineering. The tumor inducing genes have been removed from the plasmid but genes required for insertion into plant chromosomes have been retained. The gene of interest has been inserted into the plasmid under the control of a bacterial promoter.
Figure 12.8B A mix of “golden rice” and standard rice.
Bt corn (see notes for Module 12.8) has been the focus of two ecological concerns. The first is related to the development of resistance to Bt toxin by the European corn borer. Those insects that can survive the levels of Bt toxin produced by the corn will reproduce, and the level of resistance to the toxin will increase among their offspring. Bt corn has been formulated to provide a high dose of the toxin to eliminate the majority of corn borers that come into contact with it. In addition, farmers are required to provide a “refuge,” a field planted with non- Bt corn where susceptible corn borers can survive. The rationale is that these susceptible corn borers will interbreed with resistant ones that survive the Bt toxin, and the resulting offspring with lowered resistance will be subject to the high toxin levels from Bt corn. Farmers are concerned that the cost of planting a field where corn borers damage the crop will not be offset by the gains of planting Bt corn on the remaining fields. A second possible cause for concern is related to the spread of Bt corn pollen beyond the edges of a cornfield. A laboratory study showed 50% mortality for larvae of the monarch butterfly feeding on leaves of milkweed plants dusted with Bt corn pollen. A field study using potted milkweed plants at various distances from a Bt corn field showed 19% mortality for monarch larvae feeding on plants closest to the field. The extent to which monarch larvae encounter Bt pollen under natural conditions is not known, and studies of this phenomenon are continuing. Student Misconceptions and Concerns 1. The genetic engineering of organisms can be controversial, creating various degrees of social unease and resistance. Yet, many debates about scientific issues are confused by misinformation. This provides an opportunity for you to assign students to take a position on such issues and support their arguments with accurate research. Students might debate whether a food or drug made from GM/transgenic organisms should be labeled as such, or discuss the risks and advantages of producing GM organisms. 2. The fact that the technologies described in this chapter can be used to swap genes between prokaryotes and eukaryotes reveals the fundamental similarities in genetic mechanisms shared by all forms of life. This very strong evidence of common descent provides proof of evolution that may be missed by your students. Teaching Tips 1. Roundup Ready Corn, a product of the agricultural biotechnology corporation Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. Module 12.9 discusses some of the issues related to the concerns over the use of GM organisms.
Since PCR will amplify any DNA sequence with ends matching the primers, contamination by even a small amount of DNA that may contain primer-matching sites can be a concern. Stringent conditions are used for collecting and handling samples to guard against contamination. Critics of PCR point to possible contamination when questioning the accuracy of the method. The developer of PCR, Kary Mullis, was retained as an expert witness for the defense in the O. J. Simpson murder trial. While he was never called to testify, it was reported that he would cite contamination as one reason to discount the DNA evidence used in the trial. Student Misconceptions and Concerns 1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete. 2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest. Teaching Tips 1. 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!
Figure 12.12 DNA amplification by PCR. This figure shows several cycles of the PCR process, emphasizing that the number of templates doubles with each cycle.
Figure 12.12 DNA amplification by PCR. This figure shows several cycles of the PCR process, emphasizing that the number of templates doubles with each cycle.
Figure 12.12 DNA amplification by PCR. This figure shows several cycles of the PCR process, emphasizing that the number of templates doubles with each cycle.
For BLAST Animation Gel Electrophoresis, go to Animation and Video Files. Student Misconceptions and Concerns 1. Television programs might lead some students to expect DNA profiling to be quick and easy. Ask students to consider why DNA profiling actually takes many days or weeks to complete. 2. Students might expect DNA profiling for criminal investigations to involve an analysis of the entire human genome. Consider explaining why such an analysis is unrealistic and unnecessary. Modules 12.12–12.16 describe methods used to describe specific portions of the genome of particular interest. Teaching Tips 1. 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 the 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, since these colors are often made by color combinations.
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