NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 1 of 11 Cherri Church Unit 9: DNA Fingerprinting Unit Time Frame: five 50 minute periods Unit Outline: Lesson 1: Introduction to DNA fingerprinting Lesson 2: Review of Homework Assignment & Interpretation of DNA Fingerprints Lesson 3: Preparing DNA Samples Using Restriction Endonuclease EcoRI/Pstl & Agarose Gel Lesson 4 & 5: Agarose Gel Electrophoresis Lesson 1: Day - Introduction to DNA fingerprinting Time: (50 minutes) Prior Knowledge: Students will have read section 13-2 (pgs. 322-326) Manipulating DNA in the PrenticeHall Biology (Miller,K. and Levine, J.) book to insure that they have a general idea of how DNA can be extracted, cut, and separated as well as how gel electrophoresis is used to create the actual DNA fingerprint. General Concepts: * All living organisms contain their own unique DNA code * The DNA code of an individual can be used for identification of that individual or for placement within a larger group * Synthetic DNA “codes” can be used as a means of tagging inanimate objects * DNA fingerprinting has many real world applications and can be used in a variety of fields/professions. Standards:NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientificinquiries.” “Scientific explanations must adhere to criteria such as a proposed explanation must be logically consistent, it must abide by the rules of evidence, it must be open to questions and possible modification, and it must be based on historical and current scientific knowledge.” (NSES pg. 176) Content Stand C: Life Science The Molecular Basis of Heredity “Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organisms whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring.” (NSES, pg. 185). AZ State Standards Strand 1: Concept 4: PO 4 Strand 4: Concept 2: PO 1 NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 2 of 11 Common Misconceptions: “Though students are usually familiar with the base pairs, they often do not understand the antiparallel orientation of the two DNA strands and usually have not thought about the fact that 5’ and 3’ ends of the strands are different…” (Kreuzer, pg. 118). Essential Questions: 1) What type of biotechnology do all of the excerpts have in common? 2) What type of training (skills/academic) might be required in biotechnology? 3) How is DNA fingerprinting useful across a broad range of fields? 4) How can a DNA fingerprint determine an organism’s relationship to others? 5) Are DNA fingerprints more similar/more different within a given species? 6) Do all living organisms on the planet share some commonalities in their DNA? Behavioral Objectives (SWBAT): * Describe some of the ways in which DNA fingerprinting can be used in our world * Explain what kind of education/skills might be necessary in the field of biotechnology, specifically, that of DNA fingerprinting * Analyze, interpret, and match a given DNA fingerprint with another * Discuss how DNA is similar/different among species on our planet Lesson Description: This lesson will give students an overview of how DNA fingerprinting is used in the real world by introducing them to the basics of DNA fingerprinting. A variety of real world uses of DNA fingerprinting is given to pique student interest. Students are then given the opportunity to interpret actual or teachergenerated DNA fingerprints. The homework assignment helps to prepare students for creating their own DNA fingerprint later in the week. Using information contained in the DNA Forensics site at www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml create several excerpts to show examples of the various ways in which DNA fingerprints can be used in the real world and hand these out to student groups. Students read their own excerpt and those of other groups to try to find what they all have in common. Students are given paper examples of DNA fingerprints to analyze/interpret. A matching set versus a mismatched set would work well to illustrate key differences. Each student is given an actual DNA fingerprint and must find his/her “parents” among those distributed throughout the room (or within smaller groups). Level of Inquiry: This is a level 2. Students are using a scenario and pre-determined procedures. Materials: Paper examples of DNA fingerprints Computer with internet access Safety: None NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 3 of 11 Homework Assignment: Refer to BIO-RAD Biotechnology Explorer DNA Fingerprinting Kit Instruction Manual: • Students read Lesson 1: Introduction to DNA Fingerprinting (pp. 21-22) and Lesson 2: Restriction Digestion of DNA Samples (pp. 23-24) and answer questions. Conceptual Understandings (Homework): *DNA is composed of nucleotides connected via hydrogen bonds at two complimentary nitrogenous bases *The DNA “backbone” is made up of a sugar (deoxyribose) and a phosphate *DNA is similar across all life forms *Restriction endonucleases act as molecular “scissors” to cut DNA into fragments *Restriction enzymes differentially cut DNA based on a recognition site, which results in DNA fragments of different sizes Real world connections: DNA fingerprinting has almost unlimited real-world applications. It can be used to identify individuals, indicate guilt or innocence, identify evolutionary linage, establish paternity, and detect genetically modified organisms and pathogenic organisms. Lesson 2: Day 2 - Review of Homework Assignment & Interpretation of DNA Fingerprints Time: (50 minutes) Prior Knowledge: Students will have participated in the previous day’s activities and assessment to make sure they are confident with matching DNA fingerprints of individuals. They will also have had the chance to clarify their general knowledge regarding the lab process thus far. General Concepts: *DNA fingerprints can be used in both criminal and civil court proceedings *DNA can be found in hair, nails, bones, and blood cells (except RBCs) *DNA can be amplified in cases where there is only trace evidence available *Databases of DNA can make analysis and matching much quicker *The use of DNA fingerprints has applications in fields other than forensics Standards: NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientific inquiries.” “Scientific explanations must adhere to criteria such as a proposed explanation must be logically consistent, it must abide by the rules of evidence, it must be open to questions and possible modification, and it must be based on historical and current scientific knowledge” (NSES, pg. 176). Content Standard C: Life Science The Molecular Basis of Heredity “Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring” (NSES, pg. 185). NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 4 of 11 AZ State Standards Strand 1: Concept 2: PO 5 Concept 3: PO 2 Concept 4: PO 3 & PO 4 Common Misconceptions: “Though students are usually familiar with the base pairs, they often do not understand the antiparallel orientation of the two DNA strands and usually have not thought about the fact that 5’ and 3’ ends of the strands are different…” (Kreuzer, pg. 118). Essential Questions: 1) How can DNA evidence be used to pinpoint a suspect or parent? 2) How is the use of DNA a more accurate way of determining guilt or paternity? 3) If DNA is scant, how can it be magnified for use in the lab? 4) Can DNA be used to determine the probability of disease? 5) What problems might the use of DNA fingerprinting potentially cause? Behavioral Objectives (SWBAT): *Propose a future use for DNA fingerprints *Determine the most likely ‘suspect’ or ‘father’ using DNA fingerprinting *Explain how DNA fingerprinting might be useful to doctors or other medical professionals Lesson Description: This lesson gives students the opportunity to clarify any lingering misconceptions or have any questions regarding the homework or DNA fingerprinting answered before they actually have to create and subsequently interpret a real DNA fingerprint using gel electrophoresis. It also gives them a good idea of how DNA can be used in real world criminal and civil court cases. Students access the ‘How Stuff Works’ website at www.howstuffworks.com and enter DNA Fingerprinting into the search bar. This will take them to the main page where they will click on the ‘Introduction to How DNA Evidence Works’ section. From here, students click on the small red PRINT icon (upper right hand portion of the page) to access full article. • Students copy down the pictures of the gels in the ‘Sexual Assault Case’ and the ‘Paternity Exclusion/Inclusion’ on graph paper (they will use these pictures to answer the following Essential Questions) • For the ‘Sexual Assault Case’ gel have students decide which suspect is guilty of the crime and use a colored pen or pencil to circle the fragments of DNA which link him to the evidence (sperm DNA) ~ Explain the following: - How did you determine which suspect was guilty of the crime? - Could the boyfriend of the victim be excluded without a doubt? - What is the point of using the K526 Controls? • For the ‘Paternity Exclusion/Paternity Inclusion’ gel have students use a colored pen or pencil to circle the fragments of DNA which link the father and child (they may use a different color to the child to the mother as well) ~ Explain the following: - How did you decide which alleged father was the child’s? - Does the child also show similarities to its mother? NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 5 of 11 Level of Inquiry: Level 2. If students us a pre-determined scenario and procedures. Level 3 if students develop their own scenario and procedures. Materials: BIORAD DNA Fingerprinting Kit Safety: Wear gloves and lab coats to avoid staining. Goggles should be worn at all times. Any chemical splashes should be flushed, especially of the eyes, for a minimum of 15 minutes. Wash hands before and after lab. Food and drink should never be in the lab area. Homework Assignment: Refer to BIO-RAD Biotechnology Explorer DNA Fingerprinting Kit Instruction Manual: • Students read Lesson 2: Restriction Digestion of DNA Samples (Laboratory Procedure) (pp.26-28) to prepare for their upcoming lab. Conceptual Understandings (Homework): *Sterile lab technique must be followed to avoid cross contamination of DNA samples *Enzymes must always be added to micro test tubes last to insure accuracy *Proper handling and correct temperature of reagents and DNA samples is crucial for good results Real world connections: DNA fingerprinting has almost unlimited real-world applications. It can be used to identify individuals, indicate guilt or innocence, identify evolutionary linage, establish paternity, and detect genetically modified organisms and pathogenic organisms. Lesson 3: Day 3 - Preparing DNA Samples Using Restriction Endonuclease EcoRI/Pstl & Agarose Gel Time: (50 minutes) Prior Knowledge: Students will need to have prior experience using the micropipette, as well as a clear understanding of the importance of sterile lab technique to avoid cross contamination between samples or enzyme. They must also be able to follow lab protocols and maintain a clear, concise lab notebook. General concepts: *Correct micropipette technique is crucial to accurate measurement *Adherence to protocol is necessary to insure steps are followed in the prescribed order *Sterile technique must be observed to insure purity and accuracy in DNA samples *Reading the lab protocol prior to the actual lab activity and answering questions will aid in understanding as well as help in correct procedure during class *The enzyme EcoRI/Pstl cuts the DNA into fragments for analysis using gel electrophoresis *Casting an agarose gel requires correct preparation of the gel tray to obtain a uniform gel *Keeping detailed, accurate records will aid in later analyses and conclusions NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 6 of 11 Standards: NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientific inquiries.” “Scientific explanations must adhere to criteria such as a proposed explanation must be logically consistent, it must abide by the rules of evidence, it must be open to questions and possible modification, and it must be based on historical and current scientific knowledge” (NSES, pg. 176). Content Standard C: Life Science The Molecular Basis of Heredity “Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring” (NSES, pg. 185). AZ State Standards Strand1: Concept 2: PO1 & PO 5 Concept 4: PO 3 Common misconceptions: “Though students are usually familiar with the base pairs, they often do not understand the antiparallel orientation of the two DNA strands and usually have not thought about the fact that 5’ and 3’ ends of the strands are different…” (Kreuzer, pg. 118). Essential Questions: 1) How does a restriction endonuclease work to prepare DNA fragments for gel electrophoresis? 2) Why is the enzyme (EcoRI/Pstl) added to each of the DNA samples last? 3) What modifications can be made if a centrifuge is not available? 4) What might happen to the enzyme (EcoRI/Pstl) if the temperature is too hot/too cold? 5) An agarose gel cast should be how full for the best results? Behavioral Objectives (SWBAT): *Demonstrate correct and sterile lab techniques as they use the various reagents and apparatus *Record neatly and accurately all materials, methods, and observations during the lab procedure *Explain the role of EcoRI/Pstl in DNA fingerprinting *Cast an agarose gel (if required by instructor) Lesson Description: This lesson gives students the opportunity to set up their own DNA samples with a restriction enzyme and pour the agarose gel they will need to perform the actual DNA fingerprinting using gel electrophoresis. In addition, they have the opportunity to practice sterile lab technique and good micropipette skills. Assessment: The laboratory procedure itself acts as an assessment of laboratory skills and technique. Each student should also have a lab notebook, which contains all information pertinent to carrying out the lab protocols. Homework Assignment: (begin in class if time allows) Refer to BIO-RAD Biotechnology Explorer DNA Fingerprinting Kit Instruction Manual: • Students read Lesson 3: Electrophoresis and Staining of DNA Samples (pp. 30-40) and answer questions (p.30) NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 7 of 11 Conceptual Understandings: (Homework) *Reading the lab protocol prior to the actual lab activity and answering questions will aid in understanding as well as help in correct procedure during class *The use of inference to determine EcoRI/Pstl restriction sites is useful Days 4 and 5: Agarose Gel Electrophoresis Time: two 50 minute periods Prior Knowledge: Students will need to be familiar with loading an agarose gel and carrying out the electrophoresis process (including the addition of buffer solution). They must also know how to stain a finished gel and interpret the results. Correctly following lab protocols and maintenance of a clear, concise lab notebook is also necessary. General Concepts: *Correct micropipette technique is crucial to accurate measurement *Adherence to protocol is necessary to insure steps are followed in the prescribed order *Careful loading of agarose gel is necessary to avoid puncturing the gel *Attention to detail when adding buffer, setting time, and setting current for the electrophoresis is vital *Proper handling of the gel while staining will insure more visible results *DNA is negatively charged at one end (this allows the various DNA fragments to move through the gel) *Each band in the gel contains the DNA sample of a different suspect or the crime scene *DNA samples may exhibit different patterns based on their respective restriction sites *DNA samples will move at different rates based on their size *Keeping detailed, accurate records will aid in later analyses and conclusions Standards: NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientific inquiries.” “Scientific explanations must adhere to criteria such as a proposed explanation must be logically consistent, it must abide by the rules of evidence, it must be open to questions and possible modification, and it must be based on historical and current scientific knowledge” (NSES, pg. 176). Content Standard C: Life Science The Molecular Basis of Heredity “Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring” (NSES, pg. 185). AZ State Standards Strand 1: Concept 2: PO 1& PO 5 Concept 3: PO 2 Concept 4: PO 3 & PO 4 NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 8 of 11 Common Misconceptions: “Though students are usually familiar with the base pairs, they often do not understand the antiparallel orientation of the two DNA strands and usually have not thought about the fact that 5’ and 3’ ends of the strands are different…” (Kreuzer, pg. 118). Essential Questions: 1) What is the purpose of the loading dye and the buffer solution? 2) What might happen to the samples in the various lanes of the gel if they are allowed to run too long? 3) How would an increase/decrease in the current applied to the gel change your results? 4) Can you determine which fragments (large vs. small) will move the furthest from the loading wells? 5) In order to obtain the maximum contrast for your stained gel, what should you do during the rinsing process? Behavioral Objectives (SWBAT): *Demonstrate correct and sterile lab techniques as they use the various reagents and apparatus *Record neatly and accurately all materials, methods, and observations during the lab procedure *Load an agarose gel and run an electrophoresis using the correct amount of buffer *Follow the prescribed time and current requirements to generate a DNA fingerprint using gel electrophoresis *Correctly stain and dry an agarose gel for interpretation Lesson Description: This lesson requires students to prepare their DNA samples for loading into the prepared agarose gel. It also allows them to use an electrophoresis apparatus to separate the DNA fragments for later analysis. They also practice staining of the agarose gel once the electrophoresis is complete and use this final gel to create their hypothesis as to the most likely ‘suspect’. Inquiry: Level 2 if students use a pre-determined scenario and procedures. Level 3 if students develop their own scenario and procedures. Materials: BIORAD DNA Fingerprinting Kit Safety: Wear gloves and lab coats to avoid staining. Goggles should be worn at all times. Any chemical splash in the eyes should be flushed with water for a minimum of 15 minutes. Wash hands before and after lab. Food and drink should never be in the lab area. Assessment: The laboratory procedure itself acts as an assessment of laboratory skills and technique. Each student should also have a lab notebook, which contains all information pertinent to carrying out the lab protocols. In addition, students should answer questions on (pp. 34 and 36) of the lab protocol. Real world connections: DNA fingerprinting has almost unlimited real-world applications. It can be used to identify individuals, indicate guilt or innocence of a crime, identify evolutionary linage, establish paternity, and detect genetically modified organisms and pathogenic organisms. NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 9 of 11 Extension Exercise I: Prior Knowledge: Students will have to use the information gathered during their laboratory exercises to generate both linear and semi-log graphs for the DNA of the suspects and the crime scene. They should understand the concept of a best-fit line as this is the key method of determining a correct DNA match. Careful attention to detail, skill and accuracy of measurement, and calculation are also crucial. General Concepts: *Data must be neat to allow easier transference from lab notebook to graph form *Careful measurement is necessary to accurate results *Quantitative analyses provide a higher level of confidence than qualitative observation alone *Accuracy and correct graphic representation provide greater support for a given conclusion Standards: NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientific inquiries.” “Scientific explanations must adhere to criteria such as a proposed explanation must be logically consistent, it must abide by the rules of evidence, it must be open to questions and possible modification, and it must be based on historical and current scientific knowledge” (NSES, pg. 176). Content Standard C: Life Science The Molecular Basis of Heredity “Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring” (NSES, pg. 185). AZ State Standards Strand 1: Concept 2: PO 1& PO 5 Concept 3: PO 2 Concept 4: PO 3 & PO 4 Essential Questions: 1) Does a linear or semilog graph work better for estimating DNA fragment sizes? 2) How do the DNA fragment sizes compare with that of the crime scene? 3) Which DNA samples have been cut at similar Eco/RI or Pstl recognition sites? 4) How does a best-fit line allow further interpretation of the DNA evidence at the crime scene when compared with the DNA of the suspects? 5) How does graphic representation of quantitative data increase your confidence in determining a likely suspect? Behavioral Objectives (SWBAT): *Use recorded data to generate usable graphic representations of results *Justify the use of linear or semi-log graph paper *Draw conclusions based on analysis of quantitative data *Explain the importance of accuracy in accumulation and interpretation of data NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 10 of 11 Lesson Description: This lesson gives students experiential practice at integrating mathematical and logical reasoning into their laboratory technique. This allows them to understand the importance of recording data accurately and professionally in their lab notebooks; they also learn how to display more convincing representations of their data using quantitative analyses rather than just qualitative observations. In addition, students can use their findings to formulate their own views of which methods are more accurate and effective when the results of crime scene evidence will determine the outcome of a case or be used to decide a suspect’s guilt or innocence. Assessment: The creation of graphs to show quantitative data of DNA fragments for comparison acts as an assessment tool. In addition, the questions on (pp. 42 & 46) of the lab protocol should be answered by individual students. Extension Exercise II: Prior Knowledge: Awareness that information contained in DNA fingerprints may be used for the determination of susceptibility to disease or to show the presence of certain genotypes specific to racial/ethnic groups is necessary. Historical uses for good or ill of science and technology presented in conjunction with current ELSI to insure students all have a comprehensive understanding of the ELSI of genetic research. Students are presented with information gleaned from the presentation of TGen representative, Stephanie Buchholtz, who specializes in ELSI of genomic research to insure this goal. General concepts: *New advances in biotechnology occur at a much faster rate than our ability to create regulations for them *Responsibility for maintaining the integrity of research in the field of genomics is personal, national, and global *Religious and cultural views play a role in how genetic research may be applied or utilized by all *Personal/public rights must be protected while allowing for the continuation of much needed genetic research Standards: NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientific inquiries.” “Scientific explanations must adhere to criteria such as a proposed explanation must be logically consistent, it must abide by the rules of evidence, it must be open to questions and possible modification, and it must be based on historical and current scientific knowledge” (NSES, pg. 176). Content Standard G: History and Nature of Science Historical Perspectives “Usually, changes in science occur as small modifications in extant knowledge” (NSES, pg. 201). AZ State Standard Strand 1: Concept 4: PO 4 Essential Questions: 1) Is one set of ethical, legal, and social regulations enough to protect the rights of all people? 2) What are some of the most important reasons for the continuation of genetic research? NAU BIOTECH © 2009 Cherri Church NAU BIOTECH Unit 9 of 12: DNA Fingerprinting Page 11 of 11 3) Should the regulation of scientific and technological advances be of concern to every person? 4) Do scientists/physicians have an obligation to their public in terms of disclosure where genetic issues are concerned? 5) Who should have access to genetic findings and research results? Behavioral Objectives (SWBAT): *Argue a viewpoint on a specific ELSI of genetic research using research to back up key ideas *Decide the roles of individuals in the regulation and application of scientific research *Explain what ‘informed consent’ means for all those involved in a given scenario *Distinguish between the responsibilities of each of the following in terms of genetic research: individual, scientist/researcher, doctor, corporations, governments, funding sources Lesson Description: This lesson focuses on the ethical, legal, and social implications of such procedures as DNA fingerprinting as well as the use of or cataloging of this data by government entities. Students gain practice at integrating research into their written responses. This allows them to understand the importance of formulating their own views of certain biotechnology processes and the information they generate as it pertains to their personal lives or the lives of those with whom they come into contact. Assessment: • Students access information on-line regarding mitochondrial DNA to answer the following… ~ American culture uses paternal affiliation to trace a child’s lineage. However, many indigenous cultures trace their lineage using maternal connections. What are the advantages/disadvantages of each system? • Students search on-line sources for information on inherited diseases/disorders then answer the following… ~ What are some common human diseases that can be predicted using an individual’s DNA fingerprint? (at least three examples should be given) ~ Would you want to know if information contained in your DNA fingerprint predicted the possibility or inevitability of your inheriting a given disease? What about your children? What are the pros and cons of having this type of knowledge? • Students go to the ‘How Stuff Works’ website at www.howstuffworks.com and scroll down to the More Great Links section to access the article Marines reprimanded for refusing DNA test to respond to the following… ~ Are the concerns expressed by Cpl. Mayfield and Cpl. Vlacovsky valid or are they in violation of following the direct orders of the U.S. military? ~ Should organizations such as the U.S. military be allowed to maintain genetic samples of its enrollees? Why or why not? References: Mardigian,R. Biotechnology Explorer DNA Fingerprinting Kit, Instruction Manual-Catalog # 1660007EDU, California: BIO-RAD Life Science Group Miller, K., Levine, J. (2006). Biology. New Jersey: Pearson / Prentice Hall. National Research Council. (1996). National Science Education Standards, Washington DC : National Academy Press Online: How Stuff Works www.howstuffworks.com Human Genome Project www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml Kits: BIORAD DNA Fingerprinting Kit NAU BIOTECH © 2009 Cherri Church
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