<p> Biotechnology worksheet Note: the following questions follow the order of the animations.</p><p>DNA Sequencing the human genome Go to http://www.genome.gov/25019885 and watch the ten short segments on DNA sequencing. Summarize this process by answering the questions below. 1. How many base pairs does the haploid human genome contain (approximately)?</p><p>2. In which year was the first draft of the human genome project finished?</p><p>3. In which year was it started?</p><p>4. What was the goal of the human genome project?</p><p>5. What was the purpose of creating a genomic map?</p><p>6. Fragments of ______(length in bp) were stored in BACs. What is a BAC?</p><p>7. How did the genetic map allow to put the BAC fragments in the correct order.</p><p>8. Each fragment contained in a BAC was then cut into smaller fragment of approximately ______(length in bp). These fragments were stored in</p><p>______(vector) and used to transform ______.</p><p>9. E. coli cells were used as copy machines for the human DNA fragments. Explain</p><p>10.What are the four main ingredients of a sequencing reaction?</p><p>11.Which end (3’ or 5’) of the new strand will have the dideoxynucleotide? 12.How do dideoxynucleotides differ from normal nucleotides?</p><p>13.What is the effect of incorporating a dideoxynucleotide?</p><p>14.Which products does a completed sequencing reaction contain?</p><p>15.How do the following processes/equipments contribute to obtaining the DNA sequence?</p><p> gel electrophoresis</p><p> laser</p><p> camera</p><p> computer</p><p>16.How long are the read-outs (in bp)?</p><p>17.How were all the different read-outs put in the correct order?</p><p>DNA Fingerprinting 1. Go to http://www.dnai.org/d/index.html and click on “Human Identification” and then on “Profiling” and answer the following questions: Click on the button “DNA variations and fingerprints. Then click on button A DNA variation. What does VNTR stand for?</p><p>2. What does STR stand for?</p><p>3. A certain locus is described as 3/10. What does that mean?</p><p>4. What is special about the markers used in DNA typing? 5. Now click on the button “The first DNA “fingerprints”” (next to the DNA variation button) . What did Jeffreys restrict?</p><p>6. Assuming that Jeffreys used the same restriction enzymes to restrict the genomes of different people, what would cause differences in length of the fragments?</p><p>7. What does Southern blotting accomplish?</p><p>8. The first gel that you see in the animation has a full smear going down both lanes. Why is that?</p><p>9. How did Jeffreys identify the location of polymorphic VNTRs in the smear?</p><p>10. What do you need to do to visualize the results?</p><p>11. What is the advantage of using single-locus probes?</p><p>12. When looking at the lanes in the D1S80 locus gel, lane A has two radioactive probes bound, while lane B has only one. Explain.</p><p>13. Summarize the steps in making a VNTR profile from a tissue sample.</p><p>14. Now click on “Today’s DNA profile”. Where are STRs located?</p><p>15. How many STRs does the FBI test?</p><p>16. Are those STRs linked or inherited independently from each other?</p><p>17. How does PCR help detect STR differences?</p><p>18. Do you need to run your amplified STRs through a gel?</p><p>19. Do you need to do Southern blotting?</p><p>20. Interpret the computer output for the “blue” channel.</p><p>21. What is a random match probability?</p><p>22. Calculate the probability of a person of Asian descent inheriting 10/11 for D8S1179. 23. Summarize the steps in making a FBI DNA fingerprint, starting from a tissue sample.</p><p>DNA arrays ( = microarray assay of gene expression levels, Fig. 20.15) Watch the animation at http://www.dnalc.org/ddnalc/resources/dnaarray.html and list the steps Pat Brown used when comparing growth stage-specific gene expression. Fill in the blanks and answer the questions. To create an expression profile, you have to - Isolate ______</p><p> ______to create cDNA</p><p> embed onto ______</p><p> Incubate with ______</p><p> ______color pattern</p><p>24. What did the lymphochip contain?</p><p>25. How did he distinguish between cDNA from the different cancer types?</p><p>26. What happened when he incubated the arrays with the tagged cDNA?</p><p>27. What does it mean if a square is yellow?</p>