Unit 4-DNA Analysis Review Guide

Transcription

1 Name: KEY Match the term on the right with the definition on the left. Unit 4-DNA Analysis Review Guide 1. A procedure used to determine the order of the base pairs that make up a DNA molecule E 2. These are proteins that cut the DNA in the lab in order for the DNA to be sorted out by electrophoresis I 3. DNA found in the nucleus of the cell D 4. This type of DNA is passed down from the mother only and is found outside the nucleus of the cell K 5. Check cells B 6. This is a way scientists make more DNA copies from a small sample quickly using a thermocycler G 7. The components of this monomer are: phosphate, sugar, and a nitrogen base C 8. Different length fragments created by cutting a strand of DNA at a specific nucleotide sequence A 9. Locations on a chromosome that contain short sequences of repeating nucleotides within the DNA molecule J 10. Skin cells F 11. This technique is used for sex identification by looking at repeating sequences of nucleotides on the Y chromosome L 12. A technique used to separate out DNA samples by running an electric current through buffer in a chamber with an agarose gel holding the samples H Answer the following questions using complete sentences. A. Restriction Fragment Length Polymorphisms (RFLP s) B. Buccal Cells C. Nucleotide D. Nuclear DNA E. Sequencing F. Epithelial Cells G. Polymerase Chain Reaction (PCR) H. Gel Electrophoresis I. Restriction Enzyme J. Short Tandem Repeat (STR) K. Mitochondrial DNA L. Y-STR 1. DNA a. What is the function of DNA? The function of DNA is to tell our bodies what to do-it is the instructions for life. b. What is an intron? What is an exon? An intron is the part of the DNA that does not code for proteins. An exon is the part of the DNA that does code for proteins. c. Label the parts of a nucleotide below. d. Write the complementary anti-parallel strand for the following strand of DNA: 5 -CAGTTAGCCTCATCGATCGCGCTTAGAGCCCTTTGGCAC-3 3 -GTCAATCGGAGTAGCTAGCGCGAATCTCGGGAAACCGTG-5

2 2. Mitochondrial DNA a. How are mitochondrial DNA and nuclear DNA similar? How are they different? Similarities Differences Both instructions for function Both have complementary base pairing Both can be used in DNA analysis Nuclear DNA in the nucleus while mtdna is in the mitochondria. Mitochondrial DNA is much more prevalent. Nuclear DNA is unique to each individual. mtdna come from the mother only and all siblings share the same mtdna. b. Where does our mtdna come from? The mtdna comes from our mothers. c. Why can t we use mtdna to distinguish between siblings of the same mother? mtdna cannot be used to distinguish between siblings because the DNA is the same since it only comes from our mother. 3. What type of clothing should a forensic scientist wear when collecting biological material at a crime scene? Forensic scientists should wear: latex/nitrile gloves, face mask, boot covers, eye protection, and a lab coat/coveralls. 4. Why should forensic scientists take these precautions when collecting biological material? Forensic scientists should take these precautions for two reasons: to protect the biological sample at the crime scene from contamination and to protect themselves from potential blood borne diseases. 5. Before biological materials are collected at a crime scene, what should forensic scientists do? Forensic scientists should photograph and sketch the biological materials before they collect it at the crime scene. 6. Collection of Biological Materials a. How should biological materials be collected at a crime scene? Biological materials should be collected with clean forceps or Q-tip-a new pair for each sample. b. How should biological materials be packaged for transport? Biological materials should be packaged in a brown bag or swab box that has a lot of air circulation. c. How should dried blood be collected? Dried blood should be swabbed with a q-tip that has been soaked in distilled water. Then the q-tip should go into its own swab box. d. How should blood in soil be collected? Blood in soil should be packaged in an airtight container and immediately frozen. e. Why do scientists want to inhibit the growth of bacteria? Bacteria degrades biological material and makes it unusable for DNA analysis. 7. List some possible sources of DNA. Blood, semen, sweat, skin, saliva, cheek cells (buccal), any other tissue that contain cells. 8. Polymerase Chain Reaction (PCR) a. What do you need to complete PCR? In order to complete PCR, you need: a biological sample, primers, DNA nucleotide bases, and the enzyme Taq polymerase. b. What are the steps of PCR?

3 1. Put DNA sample and master mix into a test tube. 2. Heat it up to break the hydrogen bonds. 3. Cool it down so the primers can bind to the DNA strand at the appropriate place. 4. Heat it up again so that Taq polymerase can add nucleotide bases to the separated strands. 5. Repeat the process many, many times. c. What is the result of PCR? The result of PCR is billions of the original DNA sample to be used in gel electrophoresis. 9. Restriction Fragment Length Polymorphism (RFLP s) a. What is the purpose of restriction enzymes in RFLP? The restriction enzymes cut the DNA stand at specific locations to create different sized fragments. b. How many restriction enzymes are typically used in RFLP? RFLP uses 11 restriction enzymes. c. How big is the sample size needed to complete RFLP? RFLP s need a very large sample size-a stain around the size of a nickel. 10. Gel Electrophoresis a. What is the purpose of gel electrophoresis? The purpose of gel electrophoresis is to separate the DNA fragments by size. b. What is the purpose of the electric current? The purpose of the electrical current is to create a magnetic field that will cause the DNA to move through the gel. c. What causes DNA to move through the gel? The phosphate group in the backbone of DNA is negatively charged and will be attracted to the positive electrode in gel electrophoresis. This causes the DNA to move through the gel. d. Where are smaller fragments found on the results? Where are larger fragments found on the gel? The smaller fragments will be found at the bottom of the ladder because they move faster and therefore farther than the bigger fragments. 11. RFLP Simulation a. Use the restriction enzyme Hind III to cut the DNA sample below. The enzyme will cut the DNA at the following sequence: A AGCT Suspect # A T G C A G T C G A C A G T A A G C T A G G C A G T A A C C A G T A A G C T A G G A C A G T G A C T A C G T C A G C T G T C A T T C G A T C C G T C A T T G G T C A T T C G A T C C T G T C A C T G G C C C G A T A A G C T A G C C G T T A G T C A G T C A A G C T T C T A C C T G A G T C A G T C A C G G G C T A T T C G A T C G G C A A T C A G T C A G T T C G A A G A T G G A C T C A G T C A G T b. How many fragments are in the sample? There are five fragments in the sample. c. Create a DNA ladder for the DNA sample in the gel box below.

4 d. Based on your results, was there a match? Based on my results, there was not a match to the crime scene. 12. Short Tandem Repeats (STR) a. What part of the DNA is used for STR analysis? The non-coding or intron region of the DNA is used for STR analysis because the exons code for our genetic traits and are virtually identical in all humans. b. STR s are usually how many base pairs long? STR s are usually 2-10 base pairs (bp) long. c. What is a loci? A loci is a location on a chromosome where STR s can be found. They are similar for all humans. d. How many loci are used to evaluate DNA using STR s? 13 loci are used to evaluate DNA using STR s. e. Why are STR s reported as two different numbers? STR s are reported as two different numbers because you have two copies of a chromosome-one from mom and one from dad and you are looking at the differences between the two alleles. f. How big is the biological sample needed to complete a STR analysis? You need a very small biological sample to complete STR analysis-only 9 cells. g. What is a Y-STR? A Y-STR is a repeating set of bases located on the Y chromosome. h. What are Y-STR s used for? Y-STR s are used to identify a male in sexual assault cases, to distinguish between multiple males, and in ancestry testing in males. i. What is the importance of the flanking sequences in a DNA profile? The flanking sequence is the location for the primers to bind in PCR. The sequence is the same in human DNA which allows us to create synthetic strands to copy a certain section of DNA. 13. STR Simulation In October 2016, an earthquake rocked central Italy. Several American tourists were among the victims. A mother and father in Miami lost contact with their son, who had been staying in a hotel in the city of Norcia, near the earthquakes epicenter. Italian rescue workers found the remains of several young men among the ruins of the hotel where the son was staying. Rescue workers noticed only one body that had light colored hair. Forensic scientists in Italy isolated DNA from the victim and sent the results to a forensic lab in the United

5 States. The parents in Miami sent blood samples to the same lab so that they could be analyzed and compared to the victim. The partial DNA profiles of the parents are shown below. D5S818 The following is the partial DNA profile of the victim. Allele 1: 5 - CTACA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA TTCGA -3 Allele 2: 5 - CTACA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA TTCGA -3 D16S539 Allele 1: 5 - AATTC GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA CTTAG 3 Allele 2: 5 - AATTC GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA CTTAG 3 D3S1358 Allele 1: 5 - GACCT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CCGTA -3 Allele 2: 5 - GACCT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CAGT CCGTA -3 TH01 Allele 1: 5 - CGATC TAGC TAGC TAGC TAGC TAGC TAGC TAGC TAGC TAGC ATTCG 3 Allele 2: 5 - CGATC TAGC TAGC TAGC TAGC TAGC TAGC TAGC TAGC TAGC TAGC TAGC ATTCG 3

6 Locus a. Complete the following table. Repeat Unit # of repeats (4 pts) on Allele 1 # of repeats on Allele 2 Length of Both Flanking Sequences (bp) Total Fragment Length of Allele 1 (bp) (4 pts) D5S818 GGAA D16S539 GACA D3S1358 CAGT TH01 TAGC b. Determine which of the DNA profiles below matches the victim s DNA profile. Total Fragment Length of Allele 2 (bp) (4 pts) Victim #2 matches the partial DNA fingerprint from the body found in the hotel ruins. c. Is the victim the son of the two parents in Miami? Victim 2 is the son of the two parents in Miami because his partial profile is a mixture of STR s from both of the parents DNA. 14. Use the chart below to compare the newest DNA analysis technique, STR s, with the previous DNA analysis technique, RFLP s. Similarities Differences Non-coding region of DNA PCR and Gel Electrophoresis RFLP-Large fragment sizes STR-2-10 bps that repeat RFLP-large sample STR s-small sample RFLP-very easily degraded STR s-small sample size so it is less susceptible to degradation. RFLP-11 enzymes used STR-13 loci

7 15. CODIS a. What is CODIS? CODIS is the national database of DNA profiles. b. Whose DNA goes into CODIS? The DNA of people who are part of a crime or have committed a serious crime is put into CODIS. 16. Pipetting a. Describe the steps you need to take to pick up and dispense a sample using a micropipette. Make sure you have at least 5 steps. 1. Turn the knob to the desired amount. 2. Put on a new tip. 3. Depress the plunger until it reaches the first point of resistance. 4. Put the pipette into the sample. 5. Let go of the knob to suck up a sample. 6. Remove the pipette from the sample. 7. Put the tip into the well in the gel. 8. Depress the knob until the second point of resistance. 9. Remove the pipette from the well. 10. Let go of the knob. 11. Throw away the tip. b. What unit does the micropipette measure in? The micropipette measures in micro liters.