2. Cell Cycle, Cancer, and the Biology Student Workbench An intro to what BSW can do 2002 Steve Moore & Kathy Gabric

3. p53 p53 is a tumor suppressor gene. It turns on other genes that inhibit the cell cycle. If p53 is mutated, the mutant form results in a protein that cannot perform its function. Its disruption is associated with approximately 50 to 55 percent of human cancers As a result, the cell cycle has no “brakes” to slow it down, and it proceeds at a reckless speed.

4. p53 p53 can tell the cell to commit suicide. This is called apoptosis or programmed cell death. If p53 is mutated, the cell looses its ability to have cancer cells kill themselves. A mutated p53 can be inherited from one generation to the next. The mutation may cause cancer, or may make it more susceptible to tumor causing viruses attaching and inactivating the gene.

5. p53: Keeping Cancer in Check The p53 tumor suppressor and its surrounding molecules are now the focus of thousands of studies in laboratories around the world. These studies may one day lead to new treatments for the most frequent and life-threatening of cancers.

6. This is what p53 looks like.

7. How can a scientist studying p53 find its amino acid sequence?

8. BSW is a tool to search databases for protein and DNA sequences.

9. Lets Begin! Go to Just click on the words above to begin. We suggest you keep this window open and have BSW open in another.

10. Biology Student Workbench Click on – Student Interface to the Biology Workbench (SIB) You may have to do this through several pages. Type in username and password and then submit PS. You will have to register first if you have not yet done so. Its Free!

11. Create a New Session You have numerous options that are self explanatory. BSW will save all of your work sessions for you. Today, we will create a new session and call it cancer.

12. Choose Protein Tools The tools available to you and a description of their use is provided for you. First use: Multiple database search for protein sequences Type in p53 and select the GenBank Primate sequence. Click Ndjinn to activate the tool.

13. Hard Part! Look for Human p53 (TP53) gene, complete cds. (Complete DNA Sequence) Lots of other partial sequences, DNA fragments, exons and introns, and other animal DNA are given. Place a check next to it and import the sequence. The sequence will be saved at the bottom of the page.

14. Amino Acid Sequences Compare a Protein sequence to a protein sequence database Choose GenBank Primate Sequences Check your imported sequence Activate the tool by clicking on BLASTP

15. Find a similar protein The higher the score, the more closely related the proteins will be. In looking for a mutation, they should be very similar with only a few changes. For this activity choose tumor protein p53 (Li-Fraumeni syndrome)... Check it and import the sequence.

16. Compare the Sequences Align multiple protein sequences with each other. Select the 2 proteins you have saved. Activate the tool by clicking on CLUSTALW

17. Compare the Sequences The letters in blue mean that the amino acids are highly conserved. In real people terms, it means they are the same. Notice the change from proline in the normal p53 gene to alanine in the Li Fraumeni p53 gene. This means that the DNA was mutated and as a result it coded for the wrong amino acid. Import this alignment to save it.

18. So what’s the big problem with 1 wrong amino acid? Really how different are proline and alanine anyway?

19. Proline vs. Alanine Proline

20. I still don’t see what the big problem is! What does this little switch actually do to the person?

21. Li Fraumeni Syndrome Li-Fraumeni syndrome is a cancer prone disease. Prognosis: most common cancer in Li-Fraumeni children are : soft tissues sarcoma before the age of 5 yrs and osteosarcoma afterwards, and breast cancer in young adults; other frequent cancers: brain tumors, leukemias, adrenocortical carcinoma; 1/3 of patients have developed more than one primary cancer, which is quite characteristic of Li- Fraumeni syndrome. Cancers in this disease, as in other cancer-prone diseases, often occur early in life: 50% of patients aged 30 yrs have had a cancer and 90% have had cancer by age 60 yrs.

22. So what about the DNA that resulted in this?

23. Choose Nucleic Tools The tools available to you and a description of their use is provided for you. First use: Multiple database search for nucleic sequences Type in p53 and select the GenBank Primate sequence. Click Ndjinn to activate the tool.

24. Hard Part! Look for Human p53 (TP53) gene, complete cds. (Complete DNA Sequence) Lots of other partial sequences, DNA fragments, exons and introns, and other animal dna are given. Place a check next to it and import the sequence. The sequence will be saved at the bottom of the page.

25. Find a similar, but mutated sequence. Do Ndjinn search for Li-Fraumeni Syndrome An odd quirk is that you must enter it as li-fraumeni exactly. Choose the GenBank Primate sequences & click on Ndjinn Import this nucleic sequence. Select both sequences and align them by clicking on ClustalW Compare the sequences.

26. What’s Up? How does this compare to what we saw in the protein sequence? How can we explain the differences?

27. BSW is a tool to analyze databases for protein and DNA sequences. This tool can be used for research into proteins and the important jobs they do. Or to find out why an alteration in the protein results in a disease state. The problem may ultimately lie in the DNA, and BSW can be used to determine its sequences to.

28. How could you use Biology Student Workbench? Any ideas for projects you’d like to try?