Shelf fungus.
Photo©CLCase

Biology 230

Biosurfing

The purpose of this assignment is to help you
1) to help you locate web sites that have useful information for biology students.
2) to introduce you to cell biology

  BIOL 230 lab contents   BIOL 230   My home page
 

Type your answers (1, 2, 3...). Do not rewrite the questions.

Look at the apoptosis movie to answer questions 1-3 below (http://www.cellsalive.com/apop.htm)
1. Describe in your own words the physical change you see in cell undergoing apoptosis.
2. Why would you want to control apoptosis in cancer?
3. Why would you want to control apoptosis in strokes?

Look at (the 1 MB movie of) Dictyostelium and use your text book to answer questions 4-6.
4. Is the cytoskeleton rigid like the vertebrate skeleton?
5. What is Dictyostelium (See Lab 1 help page)?
6. You used a slime mold (Physarum) in Lab Experiment 1. Which life cycle represents the life cycle of Dictyostelium? (The other one must be Physarum.)
Life cycle drawings

7. PubMed is an index to articles published in medical and scientific journals maintained by the National Library for Medicine. Check out PubMed (choose the PubMed database) by looking for an article on a disease associated with the cytoskeleton. Give the article citation in the proper format. Note, that PubMed is an index--the articles are published in peer-reviewed journals, not in PubMed.

For questions 8-12. Information science has been applied to biology in the field of bioinformatics. The National Center for Biotechnology Information (NCBI) creates public databases for storage and organization of the vast amount of informtion available on proteins and genes. Genomic maps are published in a database called BLAST (Basic Local Alignment Search Tool). Go to the Map View for Homo sapiens in BLAST
8. What is the longest chromosome?
9. How many different human nuclear chromosomes are there?
10. What's mt?
11. Remember bey1, bey2, and gey; for what do they code? Type each in the Search box. What chromosomes are they on?
12 The protein 53 (p53) gene is a tumor suppressor gene, i.e., its activity stops the formation of tumors. If a person inherits only one functional copy of the p53 gene from their parents, they are predisposed to cancer and usually develop several independent tumors in a variety of tissues in early adulthood. However, mutations in p53 are found in most tumor types, and so contribute to the complex network of molecular events leading to tumor formation. type ' 53 gene' in the Search Box. On what chromosome is the p53 gene located?

13. The protein encoded by p53 has 393 amino acids. Mutations would change one or more amino acids. A DNA array can be used to detect the specific mutation in a patient. What is the value of knowing the specific mutation in a patient's cancer cells?

For questions 14-16. Assume you have isolated a protein and sequenced the amino acids in that protein. The amino acids are abbreviated by single letters (Amino acid code). (FASTA is a way of writing proteins and nucleic acids in one letter codes that work in any language. FASTA stands for Fast All.) Use BLAST to see if this protein is known and what its function is. Go to BLAST home. Select Protein BLAST. Copy and paste the following into the FASTA Search box. Then click the blue BLAST button at the bottom of the page.

ETLMEYLENPKKYIPGTKMIFAG

When the results are tabulated,

14. What is the protein?
15. Provide a one-sentence description of the function of this protein.
16. Click on Taxonomy Reports. What other types of organisms have this protein?

For questions 17-19. Return to Protein BLAST, Copy and paste the following into the Search box. Then click the BLAST! button at the bottom of the page.

VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST
PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVD
PENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

17. What is the protein?

Now paste the following into the Search box.

VHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST
PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVD
PENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

18. How does this amino acid sequence differ from the one above?
19. What disease is caused by this protein?

20.You isolated this oligonucleotide (short piece of DNA) in your milk: cacaccaccgcagcgaatct Use Nucleotide BLAST to identify the organism that left it there?

21. Look at the sporangia in the video <Sporangia> In your own words describe what the zoospores do when released from the sporangium?

22. Browse the sites on careers in biology. What new career(s) did you learn about?

23. Identify (or come as close as you can to) this cell.

24. Identify (or come as close as you can to) this cell.

25. Identify (or come as close as you can to) this cell.