Note: the Following Questions Follow the Order of the Animations

Biotechnology worksheet Note: the following questions follow the order of the animations.

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)?

2. In which year was the first draft of the human genome project finished?

3. In which year was it started?

4. What was the goal of the human genome project?

5. What was the purpose of creating a genomic map?

6. Fragments of ______(length in bp) were stored in BACs. What is a BAC?

7. How did the genetic map allow to put the BAC fragments in the correct order.

8. Each fragment contained in a BAC was then cut into smaller fragment of approximately ______(length in bp). These fragments were stored in

______(vector) and used to transform ______.

9. E. coli cells were used as copy machines for the human DNA fragments. Explain

10.What are the four main ingredients of a sequencing reaction?

11.Which end (3’ or 5’) of the new strand will have the dideoxynucleotide? 12.How do dideoxynucleotides differ from normal nucleotides?

13.What is the effect of incorporating a dideoxynucleotide?

14.Which products does a completed sequencing reaction contain?

15.How do the following processes/equipments contribute to obtaining the DNA sequence?

gel electrophoresis

camera

computer

16.How long are the read-outs (in bp)?

17.How were all the different read-outs put in the correct order?

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?

2. What does STR stand for?

3. A certain locus is described as 3/10. What does that mean?

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?

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?

7. What does Southern blotting accomplish?

8. The first gel that you see in the animation has a full smear going down both lanes. Why is that?

9. How did Jeffreys identify the location of polymorphic VNTRs in the smear?

10. What do you need to do to visualize the results?

11. What is the advantage of using single-locus probes?

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.

13. Summarize the steps in making a VNTR profile from a tissue sample.

14. Now click on “Today’s DNA profile”. Where are STRs located?

15. How many STRs does the FBI test?

16. Are those STRs linked or inherited independently from each other?

17. How does PCR help detect STR differences?

18. Do you need to run your amplified STRs through a gel?

19. Do you need to do Southern blotting?

20. Interpret the computer output for the “blue” channel.

21. What is a random match probability?

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.

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 ______

 ______to create cDNA

 embed onto ______

 Incubate with ______

 ______color pattern

24. What did the lymphochip contain?

25. How did he distinguish between cDNA from the different cancer types?

26. What happened when he incubated the arrays with the tagged cDNA?

27. What does it mean if a square is yellow?