Evidence from DNA 40- to 1 2 50-minute sessions 69 M O D E L I N G ACTIVITY OVERVIEW SUMMARY Students learn how DNA fingerprinting is done by performing a simulation of the process used to generate different sized pieces of DNA. They compare their simulation to the actual procedures used by scientists to prepare DNA fingerprints. KEY CONCEPTS AND PROCESS SKILLS 1. Blood types can be used as evidence about identity and about family relationships. 2. Blood typing can provide sufficient evidence to rule out relationships, but not enough to prove relationships. 3. DNA fingerprinting is done by using enzymes to cut an individual s DNA into characteristic pieces, and then separating the pieces to generate the individual s unique DNA pattern, or fingerprint. 4. Because each person s DNA sequence differs at many locations, each individual s DNA fingerprint is unique. KEY VOCABULARY DNA DNA fingerprinting MATERIALS AND ADVANCE PREPARATION For the teacher 1 Transparency 69.1, DNA Patterns For each group of four students * 1 tape, transparent For each pair of students 1 Student Sheet 69.1, DNA Person 1 1 Student Sheet 69.2, DNA Person 2 * 2 scissors *Not supplied in kit Teacher s Guide D-199
Activity 69 Evidence from DNA Prepare the Student Sheets for the activities. Photocopy one of the sheets onto a palecolored paper to distinguish it from the other. An option that makes the DNA sequences easier to manage (though harder for students to cut out) is to reduce the two sequences in size and copy them onto a single sheet of paper. TEACHING SUMMARY Getting Started 1. Review the need for more information to identify the lost children. Doing the Activity 2. Students compare simple DNA fingerprints to identify a sample. 3. Students model the cutting of DNA to produce pieces of different lengths. Follow-Up 4. Relate the results of the simulation to the appearance of bands in a DNA fingerprint and discuss the answers to the Analysis Questions. Extension Students research the Human Genome Project on the Internet. BACKGROUND INFORMATION DNA Fingerprinting The DNA fingerprinting process is more complex than implied in the student activity, though many of the details are supplied on page D-84 of the Student Book. Even tiny amounts of DNA, such as might be found in the single cell at the root of a strand of hair, can be amplified by the polymerase chain reaction (PCR) to make many copies of a particular sequence of interest. As simulated in the activity, the DNA is then cut up using restriction endonucleases, enzymes obtained from bacteria which cut at specific sequences of DNA, to give an assortment of lengths of DNA. The cut pieces of DNA from the person in question and one or more reference people are then run onto an electrophoretic gel. The electrical current applied to the solution in which the gel sits causes the negatively charged DNA pieces to move toward the positive electrode. Smaller pieces of DNA move more quickly through the gel. A D-200 Science and Life Issues
Evidence from DNA Activity 69 Southern blot is made from the gel by transferring the DNA fragments to a nylon membrane. Finally, specific radiolabelled DNA sequences are used to probe the membrane; the probes bind to the complementary sites on the DNA fragments. When the blot is covered with X-ray film, the radioactivity darkens the film wherever the probe has bonded with DNA. As suggested by the diversity of individual critters created in Activity 65, Breeding Critters More Traits, the DNA from any individual is bound to be unique. Furthermore, the DNA targeted in the fingerprinting process is some of the DNA between the genes (though, like all DNA, it is inherited as part of the chromosomes). Because most DNA between the genes does not have a vital function (as far as we know), its sequence varies much more among individuals than does the sequence of functioning genes, without affecting our traits. The sequences probed in a DNA fingerprint are usually the repetitive sequences known as variable number tandem repeats, or VNTRs. Since these repeated sequences accumulate mutations through the generations very easily, the exact lengths and numbers of copies vary on each chromosome. Thus, the various bands on each person s DNA fingerprint vary, in both position and intensity. The position of the band on a gel is related to its length: shorter bands migrate farther. The intensity is related to the frequency of pieces of a given length: the more pieces of a given length, the darker the corresponding band. Human Genome Project The Human Genome Project has been an international effort whose goal was to enable us to understand the function of every human gene on the 23 pairs of chromosomes. Groups of scientists and technicians have been working to sequence all the DNA, so that every last gene can be identified. Even though the human genome contains about 30,000 genes, plus a huge amount of extra DNA between the genes, this project has been completed by both the public effort and a private corporation as these materials are published. Direct sequencing is becoming so rapid that some day everyone s unique DNA sequence might become part of a data bank. Even now, ethical and legal issues regarding access and actions in response to genetic information are surfacing. However, even now that the complete sequencing of the human genome has been accomplished, much work is required before scientists will understand the structure and function of the entire human genome. Some of the questions that remain include what each gene encodes and what these products (mostly various proteins) do, and Teacher s Guide D-201
Activity 69 Evidence from DNA how genes are switched on and off during an organism s development and as a response to environmental conditions. (These questions have been partly addressed for a relatively small number of genes.) REFERENCES Collins, Francis S., et al. New Goals for the U.S. Human Genome Project: 1998-2003. Science vol. 282 (October 23, 1998): 682-89. Lowrie, P. and S. Wells. Genetic Fingerprinting. New Scientist,vol. 52 (1991). D-202 Science and Life Issues
Evidence from DNA Activity 69 TEACHING SUGGESTIONS GETTING STARTED 1. Review the need for more information to identify the lost children. Review which children may belong to John and Belinda and which to Mai and Paul, and review students ideas about how to be more certain of the children s identity. Explain that blood typing is only the first step in finding the children; it narrows the field of candidates, but does not provide proof of relationships. Have students read the Introduction and Challenge to the activity on page D-81 in the Student Book. Review the information about the four letters of the genetic code. Encourage students to ask any questions they may have and refer them to the diagrams they constructed for Analysis Question 1 of Activity 63, Show Me the Genes! (which show the hierarchy from DNA to gene to chromosome to cell to person). Explain that the letters of the code provide information just as the letters in a sentence convey information. The regions between genes are what get fingerprinted, and these letters differ more among people than do the genes. DOING THE ACTIVITY 2. Students compare simple DNA fingerprints to identify a sample. Part One of the Procedure allows students to see how DNA fingerprinting can be used to identify a person whose DNA has been found at the scene of a crime. In this case, students will be able to match the DNA fingerprint from the blood at the crime scene with the DNA fingerprint of Suspect 2. A similar approach could be used if the parents in the Namelia story had a baby tooth, for example, from their child that could be used to isolate a sample of the child s DNA. (In the next activity, students will find out that Belinda kept a tooth lost by her daughter. Do not reveal this to students at this time.) 3. Students model the cutting of DNA to produce pieces of different lengths. Distribute Student Sheet 69.1, DNA Person 1, and Student Sheet 69.2, DNA Person 2, to each student pair and explain that each of the two sheets has a DNA sequence from a different person. The activity will help students understand how different fingerprints are produced from these different DNA sequences, even though, at a glance, they have most letters of code in common. Teacher s Note: Before handing out the scissors, emphasize that when cutting out and taping the bands of DNA sequence together, the students are not representing any stage of the DNA fingerprinting process. The simulation really begins at Step 5 of the Procedure. (By cutting out the strands and taping them together they are preparing the simulated DNA strands as they are extracted from cells.) Have students turn to the Procedure on pages D-82 to D-83 in the Student Book. Each student in the pair is responsible for using one of the Student Sheets to prepare a single linear sequence of DNA (each chromosome in our cells contains a single DNA molecule which is far, far longer). Cutting each set of sequences into strips, and then taping them together in numbered order, produces a long ribbon. This ribbon simulates the DNA extracted from cells. Teacher s Guide D-203
Activity 69 Evidence from DNA Teacher s Note: In this activity, double-stranded DNA is represented as a single strand in order to simplify the mechanics of the activity. The simulation begins when each student cuts his or her DNA strand at specific sites (i.e. after every AAG) to simulate the action of an enzyme that cuts DNA at specific sequences. Students will observe that because the two sequences are unique, each is cut at different places, generating different numbers and lengths of pieces. (Person 1 s DNA gets 5 cuts, while Person 2 s gets 3 cuts.) The result is two different patterns of pieces, when sorted by length. Below are the patterns generated from Person 1 and Person 2. Person 1 Person 2 After completing the Procedure, students should read How DNA Fingerprinting Is Performed in the Lab on page D-84 in the Student Book, which illustrates the basic steps of the DNA fingerprinting technique. Review these steps with the students, and then have them complete the Analysis Questions. FOLLOW UP 4. Relate the results of the simulation to the appearance of bands in a DNA fingerprint and discuss the answers to the Analysis Questions. Help students relate the pattern of strips they generated to the patterns of stained bands such as those shown in Part One of the Procedure. Project Transparency 69.1, DNA Patterns. Ask, Which pattern would be generated from Person 1 s DNA, and which from Person 2 s DNA? Pattern C corresponds to Person 1, while Pattern B corresponds to Person 2. Emphasize that the position of each band indicates the relative length of the DNA fragment. The darkness of the band is a function of the number of fragments of that length. In reality (but not in the simulation), dark bands are due to a large number of copies of identical, repeated sequences. Remind the class that the lost children have not been conclusively identified, although blood typing has suggested some candidates. Ask the class how DNA fingerprinting might help provide evidence about the lost children. They may suggest comparing the DNA of the children of Samarra to the DNA of John and Belinda s and Mai and Paul s children. However, the parents are unlikely to have a source of DNA from their children to use for com- D-204 Science and Life Issues
Evidence from DNA Activity 69 parison. Ask students if there is any way they could use the DNA fingerprinting technique, given the fact that they don t have samples from the children from before they were lost. They may suggest comparing the children s DNA to the DNA of the parents. If so, make a note of this suggestion and tell them they will return to this idea in the next activity. If they don t suggest it, then leave the question open until the next activity. Emphasize that when the students cut out the DNA sequence strips for each person and taped them together, they were not simulating anything at all. They were merely assembling a single intact stretch of DNA to use as they modeled selected steps of the fingerprinting process. 2. Look at this DNA fingerprint. Extension Students research the Human Genome Project on the Internet. Have students go to the SALI page of the SEPUP website for links to websites about the Human Genome Project. There they can explore some of the latest research on human genes. SUGGESTED ANSWERS TO ANALYSIS QUESTIONS 1. In your science notebook, create a table like the one below. In the table, match the steps you did in the simulation to the steps scientists use to make DNA fingerprints. DNA added here Band A Band B Band C Band D a. Which single band represents the smallest pieces of DNA? Explain how you can tell. Band D represents the smallest pieces since it moved the farthest in the gel. b. Which single band represents the most common length of DNA for this fingerprint? Explain how you can tell. What scientists do Extract DNA from cells Cut the DNA with enzymes Use an agar gel and electric current to separate DNA pieces Make the DNA visible What we did in the simulation Used sequence from Student Sheet to represent the DNA Cut the paper DNA after a specific sequence Sorted the DNA pieces by hand, by size (not necessary in simulation) Teacher s Guide D-205
Activity 69 Evidence from DNA Band B represents the most common length: it is darkest, and thus contains the greatest amount of material (number of fragments). 3. Why are DNA fingerprints unique to each person? In your explanation, refer to the way that DNA is cut up and sorted, and refer to the DNA of Person 1 and Person 2 from the activity. Each person s DNA is cut at the same sequences (in this case, AAG). Since different individuals have these sequences in different places in the variable regions of the DNA, cuts occur at different places, as in the simulation with Person 1 and Person 2. This produces different lengths of DNA for each person, which appear as bands at different positions in actual DNA fingerprints. D-206 Science and Life Issues
Name Date DNA Person 1 1. First cut along the solid border around the edges. 2. Then cut out each strip of letters along the dotted lines and tape each to the one before, to make a long ribbon of letters. The numbers at the end of each line will help you keep the strips in order. As you tape on each strip, you will cover the previous number. T T G T G G C C C C C C A A T T G T T 1 G T T A G A A A G G A G G G G A A G T 2 A T G A G A T T T T T T T T T A G G C 3 A C A C A C A A G A G A T A T A G A G 4 A A A A A T T G T G G T G T A G A G C 5 C C C C G A A A A A A A A A A A A C A 6 C A C A C A A G A T A G A T G T G T G 7 T G C G C G C G G G G G G G A A T A A 8 2001 The Regents of the University of California C A G T G T T G T A T T A A T T T A T 9 A G A A A A T A A G A T A T A T G G G 10 Science and Life Issues Student Sheet 69.1 D-207
Name Date DNA Person 2 1. First cut along the solid border around the edges. 2. Then cut out each strip of letters along the dotted lines and tape each to the one before, to make a long ribbon of letters. The numbers at the end of each line will help you keep the strips in order. As you tape on each strip, you will cover the previous number. T T G T G G C C C C C C A A T T G T T 1 A T T A G A G G G G A G G G G A A G T 2 A T G A G A T T T T T G T T T A T G C 3 A C A C A C A T G A G A T A T A A A G 4 A A C A A T T G T G G T G T A G A G C 5 C C C C G A A A A C C C C A A A A C A 6 C A C A A A A G A T A G A T G T G T G 7 T G A G C G C G G G G G G G A A T C T 8 C A G T G T T G T A T T A A C C T A T 9 2001 The Regents of the University of California A G A A A A T T T G A T A T A T G G G 10 Science and Life Issues Student Sheet 69.1b D-209
DNA Patterns A B C D 2001 The Regents of the University of California Science and Life Issues Transparency 69.1 D-211