Chapter 14: Biotechnology and Genomics

Transcription

1 Chapter 14: Biotechnology and Genomics AP Curriculum Alignment Biotechnology is extremely important to humans. Human desires for improvements in our food, environment and health have driven this field of science. Biotechnology makes it possible to directly engineer heritable changes in cells to yield novel protein products that will produce these improvements. Big Idea 1 stresses that evolution is a change in genetic makeup over time. The procedures of biotechnology, including the amplification of a sample of DNA (PCR) and the ability to determine the nucleotide sequence of DNA, have empowered us with the ability to compare fossil DNA with extant species. Chapter 14 mentions this process but we actually put this information to use in Chapter 19 when the comparison of molecular traits is explained in detail. Big Idea 3 explains that genetic information is the repository of instructions that enable survival, growth, and reproduction of organisms. The human desire for knowledge and improved living conditions drove the development of biotechnology and genetic engineering. Chapter 14 explains in detail many of the genetic processes and resulting products. The curriculum framework requires that students be able to justify the claim that humans can manipulate heritable information through the knowledge of at least two genetic engineering techniques. ALIGNMENT OF CONTENT TO THE CURRICULUM FRAMEWORK Big Idea 1: The process of evolution drives the diversity and unity of life. Enduring understanding (EU) 1.A: Change in the genetic makeup of a population over time is evolution. Essential knowledge (EK) 1.A.4: Biological evolution is supported by scientific evidence from many disciplines, including mathematics. b. Molecular, morphological and genetic information of existing and extinct organisms add to our understanding of evolution. Evidence of student learning is a demonstrated understanding of each of the following: 3. Biochemical and genetic similarities, in particular DNA nucleotide and protein sequences, provide evidence for evolution and ancestry. Big Idea 3: Living systems store, retrieve, transmit, and respond to information essential to life processes. Enduring understanding (EU) 3.A: Heritable information provides for continuity of life. Essential knowledge (EK) 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information. e. Genetic engineering techniques can manipulate the heritable information of DNA and, in special cases, RNA. To foster student understanding of this concept, instructors can choose an Mader, Biology, 12 th Edition Chapter

2 illustrative example such as: Electrophoresis Plasmid-based transformation Restriction enzyme analysis of DNA Polymerase Chain Reaction (PCR) f. Illustrative examples of products of genetic engineering include: Genetically modified foods Transgenic animals Cloned animals Pharmaceuticals, such as human insulin or factor X Concepts covered in Chapter 14 also align to the learning objectives that provide a foundation for the course, an inquiry-based laboratory experience, class activities, and AP exam questions. Each learning objective (LO) merges required content with one or more of the seven science practices (SP), and one activity or lab can encompass several learning objectives. The learning objectives and science practices from the Curriculum Framework that pertain to biotechnology and genomics are shown in the table below. Note that other learning objectives may apply as well. LO 1.11 The student is able to design a plan to answer scientific questions regarding how organisms have changed over time using information from morphology, biochemistry and geology LO 3.5 The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies. Key Concepts Summary Cloning Cloning is the production of genetically identical copies of DNA, cells, or organisms through some asexual means. Examples are plants growing shoots that form a new plant and a bacterium using binary fission to produce an exact copy of itself. Gene therapy is when cloned genes are used to modify a human. Recombinant DNA Recombinant DNA (rdna) contains DNA from two or more different sources, such as a human cell and a bacterial cell. rdna is made using restriction enzymes, which are found naturally in bacteria. o Scientists use restriction enzymes to isolate and cut specific sequences of DNA. o Human DNA is placed into a plasmid, circular accessory DNA found in some bacteria, and sealed using the enzyme DNA ligase. o The plasmid is then taken up by a living bacterium where the gene functions normally and is copied when the bacterium undergoes binary fission 220 Mader, Biology, 12 th Edition, Chapter 14

3 Polymerase Chain Reaction (PCR) Polymerase chain reaction (PCR) is a process of quickly making many copies of a piece of DNA and mimics DNA replication. PCR uses DNA polymerase extracted from thermophilic bacteria and thus can withstand high temperatures. PCR can amplify, or make many hundreds of copies, of a small amount of initial sample DNA, allowing scientists to do greater analysis. PCR has been used to amplify DNA extracted from ancient specimens so that it can be compared to that of living organisms or by comparing DNA of two living species to study their genetic relatedness. Genetically modified organisms (GMOs), which have had a foreign gene inserted into them. DNA analysis Cut DNA can be run through a process called gel electrophoresis, which separates DNA fragments according to their size with the resulting distinctive bands that can be used to identified the person and is a method of DNA finger printing Short tandem repeat sequences (STRs) of DNA can be fluorescently labeled. A laser excites the fluorescent STRs, and a detector records the amount of emission for each DNA fragment in terms of peaks and valleys. This printout produces the newest method of DNA finger printing. Comparative genomics The human genome has 3 billion known base pairs but only 2% of the genome codes for proteins DNA information that was once considered junk DNA may be active in genome evolution. Comparative genomics and proteomics shows that little difference exists between the DNA sequence of our bases and those of many other organisms, increasing our knowledge of evolutionary relationships among species. Key Terms bioinformatics biotechnology products cloning comparative genomics DNA fingerprinting DNA ligase DNA microarrays DNA profiling ex vivo gene therapy functional genomics Gel electrophoresis gene cloning gene pharming gene therapy genetic profile genomics GMOs Human Genome Project in vivo gene therapy intergenic sequences interspersed repeat polymerase chain reaction proteome proteomics recombinant DNA restriction enzyme short tandem repeat structural genomics tandem repeat transgenic organisms transposons vector Mader, Biology, 12 th Edition Chapter

4 Teaching Strategies An important note: Investigation 8 from the AP Biology lab manual requires several days of preparation before students can conduct their investigations. Students are generally fascinated by biotechnology. Investigation 8: Bacterial Transformation and Investigation 9: Biotechnology: Restriction Enzyme Analysis of DNA are both centered on genetics and the transfer of information. The College Board estimates between 7-9 class periods for these two labs but I feel that they can be conducted in far less time. You can order kits for transformation from biological supply houses and the most fascinating kits are using the pglo gene. Kits can also be ordered that are crime scene analysis for Investigation 9. Class time: Seven 45 minute class periods (45 minutes each) Day 1: Lecture on the basic procedures in biotechnology, restriction enzymes and the use of plasmids as vector 25 minutes Video such as HHMI s about genetic engineering 5 minutes Activity 1: modeling restriction enzymes 20 minutes Day 2: Lecture on remaining biotechnology techniques not discussed on Day 1 10 minutes Activity 2: biotechnology group research 25 minutes Group presentations on Activity 2 10 minutes Day 3: College Board Investigation 8: Bacterial Transformation 45 minutes Day 4: Continuation of Investigation 8: counting and analyzing the transformation efficiency 25 minutes Preparation for Investigation 9: pouring gels for gel electrophoresis, cutting DNA using restriction enzymes 20 minutes Day 5: Investigation 9: Biotechnology: Restriction Enzyme Analysis 45 minutes Day 6: Continuation of Investigation 9: analysis of DNA fragments and graphing results 45 minutes. Day 7: Summative assessment. 222 Mader, Biology, 12 th Edition, Chapter 14

5 Suggested Approaches One approach to the lengthy labs about biotechnology is to request an in-school field trip for your students and a substitute for yourself. In that way you have condensed the time necessary for the labs. Start the transformation activity before the field trip and include the analysis potion during your in-school field trip. You can make the transformation protocol more of an inquiry based lab by setting up a research scenario. Students will pretend to be working in a biotech firm who has financial problems. They are asked to research the various stages in the transformation protocol to see where steps could be changes to save money. Students get their revised protocols approved by the teacher and proceed with Investigation 8. Make sure that one group is the control group and follows the protocol as it is written in the lab. Student Misconceptions and Pitfalls The simplest misconception is that many students do not understand how restriction enzymes function and believe that they only cut through half of the DNA. Students generally think of science as having a body of knowledge that is unchanging. The Human Genome Project completion and its effect on our understanding of human DNA is a great place to show the dynamics of changing knowledge. There are many ethical questions about GMO and their possible effects on humans. Most students initially think that GMOs are harmful and this is a great time to talk about their benefits to humans. Mader, Biology, 12 th Edition Chapter

6 Suggested Activities Activity 1: Modeling Restriction Enzymes The purpose of this demonstration is to show the process of gene splicing through an analogy. Materials: several lengths of 16mm film, scissors, tape Procedure: Take a long piece of film which you have previously taped into a loop. Now take another length of film and cut a "scene" from it. Cut open the loop and, using tape, splice the new scene into it. Make the analogy that films and tapes are made by splicing scenes together just as a gene sequence (new scene) is spliced into an existing plasmid or chromosome (original loop), using restriction enzymes (scissors) and ligases (tape). (From information by Robert Lord on Access Excellence). Note that construction paper can be used instead on 16mm film. Activity 2: Biotechnology Research Students, working in groups of 3 or 4, conduct Internet-based research on their assigned biotechnology topic. Remind students about responsible web searching, and how to determine whether a site is a legitimate source. Biotechnology topics to research: 1. Electrophoresis 2. Plasmid-based transformation 3. Restriction enzyme analysis of DNA 4. Polymerase Chain Reaction (PCR) 5. Genetically modified foods 6. Transgenic animals 7. Cloned animals 8. Pharmaceuticals, such as human insulin or factor X They will present their findings to the class describing the technologies that are used and how humans have manipulated the genetic material in order to produce a desired product. 224 Mader, Biology, 12 th Edition, Chapter 14

7 Student Edition Chapter Review Answers Answers to Assess Questions 1. c; 2. c; 3. c; 4. d; 5. d; 6. d; 7. b; 8. d; 9. d; 10. d; 11. c; 12. d; 13. d; 14. d Answers to Applying the Big Ideas Questions 1. The field of comparative genomics is yielding valuable new insights into the relationships between species, impacting taxonomy and evolutionary biology. a) Describe TWO kinds of data that could be collected by scientists to provide a direct answer to the question, how is the concept of biological evolution supported by genomics? b) Explain how the data you suggested in part (a) would provide a direct answer to the question. Essential Knowledge Science Practice Learning Objective 1.A.4: Biological evolution is supported by scientific evidence from many disciplines, including mathematics. 5.3: The student can evaluate the evidence provided by data sets in relation to a particular scientific question. 1.9: The student is able to evaluate evidence provided by data from many scientific disciplines that support biological evolution. 4 points maximum. Description of the appropriate kind of data and the appropriately linked explanation of its selection may include: Descriptions of kind of data (1 point each) The human genome has many small regions of DNA that vary among individuals and may vary by only one nucleotide. Prokaryotes typically possess a singular chromosome with genes that are packed together very closely. Eukaryotic chromosomes are more complex and the genes are seemingly randomly distributed along the length of a chromosome and are more Explanations (1 point each) Genetic variation provides a mechanism for natural selection to act upon. Many SNPs have no effect, while others may contribute to enzymatic differences affecting phenotype. Similar organisims have similar genome structure. In general, the more complex an organism is, the more complex the genome of that organism 0 with more and larger introns. Mader, Biology, 12 th Edition Chapter

8 fragmented into exons with more intervening introns scattered throughout. Because of genomics, we now know that there are repetitive DNA elements that include tandem repeats (repeats next to each other on the chromosome). Because of genomics, we now know that there are repetitive DNA elements that include interspersed repeats (repeats that occur intermittently on a single chromosome or across multiple chromosomes). The true significance of transposons has only begun to come to light with genomics. Transposons have been found across multiple domains of life: they have been found in bacteria, fruit flies, humans, and many other organisms. Comparative genomics offers a way to study changes in a genome over time, because the model organisms have a shorter generation time than humans. The number and types of tandem repeats may vary significantly from one individual to another, making them invaluable as indicators of heritage. Because of their common occurrence, interspersed repeats are thought to play a role in the evolution of new genes. These moving DNA sequences can sometimes alter neighboring genes, particularly decreasing their expression. The movement of transposons throughout the genome is thought to be a driving force in the evolution of living organisms. Many scientists now think that many repetitive DNA elements were originally derived from transposons. Comparing genomes can help us understand the evolutionary relationships between organisms (e.g. it was found that the genomes of all vertebrates are highly similar). Modern technology allows comparisons of genomes of organisms from every domain, revealing interesting and sometimes unexpected relationships. 226 Mader, Biology, 12 th Edition, Chapter 14

9 2. Identify and describe at least TWO commonly used genetic engineering technologies used by scientists to manipulate heritable information. Essential Knowledge Science Practice Learning Objective 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information. 6.4: The student can make claims and predictions about natural phenomena based on scientific theories and models. 3.5: The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies. 2 points maximum. Descriptions of technologies employed to manipulate heritable information may include (1 point each): Gel electrophoresis (now being replaced by fluorescently-labeled DNA fragments excited by lasers and resulting transmissions detected and recorded): Used in DNA fingerprinting or DNA profiling, this method separates DNA fragments according to their size; the result of fragment sorting was a pattern of distinctive bands that can identify a person due to each person having their own restriction enzyme sites. Plasmid-based transformation makes use of recombinant DNA technology: Plasmids are small accessory rings of DNA found in bacteria that are not part of the main chromosome but can instead replicate on its own and can be easily removed from or introduced into a bacterial cell (vector DNA). Using restriction enzymes to cleave DNA and DNA ligase to seal DNA, foreign DNA can be introduced into bacteria and be replicated, cloning the introduced DNA. Restriction enzyme analysis of DNA: Restriction enzymes cut DNA at specific locations. Each restriction enzyme recognizes a specific sequence of nucleotides. After the enzyme cuts the DNA, sticky ends may be formed that are useful in the cloning of DNA sequences. Polymerase Chain Reaction (PCR) quickly creates many clones of a piece of DNA without first inserting it into a plasmid. The process mimics DNA replication in the cell, except that PCR is very specific it amplifies only a targeted DNA sequence. PCR is a chain reaction because the targeted DNA is repeatedly replicated as long as the process continues. Illustrative examples of products of genetic engineering include: genetically modified foods, transgenic animals, cloned animals, and pharmaceuticals. Mader, Biology, 12 th Edition Chapter

10 Answers to Applying the Science Practices Questions Think Critically 1. Of the 253 dots, 48 are red (19 percent), 32 are yellow (13 percent), and 173 are green (68 percent). 2. Black spots occur where there was no expression of a particular gene in either the normal or the cancer cell. For example, this could be a gene that is only expressed during embryogenesis. 3. Based on a micro array chip, genes could be selected that had either higher expression in prostate cancer cells or higher expression in normal cells. One of these genes could then be studied as a potential cause of prostate cancer. 228 Mader, Biology, 12 th Edition, Chapter 14

11 Additional Questions for AP Practice 1. Develop a question about evolution that could be answered by biochemical evaluation. Design a plan to research your question. 2. Which of the following biotechnology procedures has created the greatest impact on DNA analysis of small samples of DNA? A) PCR B) Gel electrophoresis C) DNA fingerprinting D) Short tandem repeat profiling 3. Explain the difference between Golden Rice and normal rice. Predict what effect this rice would have on the human population. 4. A knockout mouse could provide scientists with A) A model organism that contains too many copies of a gene as so produces a great deal of proteins B) A model organism that can only be male C) A model organism that lacks a gene that is mutated in a particular human disease D) A much larger mouse to study. 5. What is correct about the human genome? A) 95% of our genes code for proteins B) Our genome does not contain any coding regions C) Protein coding regions account for only 85% of the human genome D) Only 2% of the human genome are protein coding regions. Mader, Biology, 12 th Edition Chapter

12 Grid-In Question 1. The sequencing of the human genome revealed many surprising things about our DNA, including the number of intergenic versus protein-coding sequences. What percent of our DNA is made up of noncoding sequences? 230 Mader, Biology, 12 th Edition, Chapter 14

13 Answers to Additional Questions for AP Practice 1. Answers will vary, but questions will likely ask which of a group of organisms are more closely related (lists should include at least three organisms). The research plan would be to compare DNA or protein sequences in a protein found in all organisms such as cytochrome c. The organisms with the fewest differences would be the most closely related. 2. A is the correct answer because PCR is the only procedure that is capable of making enough copies of a small sample of DNA so that it can actually be analyzed. 3. Golden Rice has been genetically modified so that it produces higher amounts of vitamin A. The prediction should include knowledge that humans whose diet is primarily rice would be healthier if they ate this genetically modified rice instead of normal rice. 4. C is the correct answer. 5. D is the correct answer. Answers to Grid-In Questions 1. Chapter: 14 Biotechnology and Genomics Answer: 98% 24%+59%+15%= 98% Mader, Biology, 12 th Edition Chapter