Take Home Quiz: to Think, Synthesize and Explore

BIO 315 BIOINFORMATICSQUIZ #2

Name ______

TAKE HOME QUIZ: TO THINK, SYNTHESIZE AND EXPLORE

Please insert your answers into this electronic file inblueand send me the file with the name: YourLastName_Quiz2

For parts of this quiz, you should refer tothe articles under Quiz #2 on the Quizzes page of the website. Information on that page indicates what you should read or review in the articles. You should be able to obtain answers for the questions from the articles, but you may useadditional resources, if you would like. For each question, indicate the source(s) you use for answer. For articles on the webpage, you may simply refer to the name on the link, but provide citations and URLs for any additional references you use.

Summarizing what you know…

1. What does the abbreviation ORF stand for? What is an ORF? How do some define an ORF differently and why? Look at optional parameters in NCBI’s ORF Finder for a clue.

2. Based on the article“Defining Genes”, list the different types of ORF’s. Give more than simply their abbreviation. How are they distinguished, i.e. based on what criteria? Using any of the sources, briefly explain why ORFs are not always easy to identify.

3. Various sources will talk about annotation as a broader or more limited task depending on their focus. Based on Figure 1 of “Genome Annotation 01”, describe what it means to annotate a genome? In your description, indicate what tasks are required for annotation. Describe at least four tasks. Use your own words in the description.

4. Prepare an outline that describes how genomes are annotated. The article “Genome Annotation 12” should be helpful to answer this question. Be sure to summarize using your own words.

Data Interpretation and Discovery…

Look at the article describing the annotation of Trichodermaharzianumand answer the following questions.

1. On what basis were Quality ESTs chosen for Table 2? Explain what method is used and the criteria.

2. Which group of organisms (fungi, plants or animals) appears to have more closely related genes to Trichodermaharzianum? Support your answer with data from Table 5.

3. Would you expect the answer you found for #2? If so, why? Go to NCBI’s Taxonomy database to find out what organism it is. Follow the links and you will find three strains. Follow the link to the first one. What is the Genbank synonym name? Formerly, this organism was found under this alternate name which is an anamorph. What is an anamorph? You will need to go to a general source on the web to answer this last question.

Exploring protein structure…

1. Use NCBI’s Structure database to pull up the 3D structure for 1XND. Complete the following related to this entry.

a. What type of enzyme is this?

b. The International Union of Biochemistry and Molecular Biology has developed enzyme nomenclature that includes an EC number. What is the enzyme number for this protein (i.e E.C.#.#.#.#)? Where did you find this information?

c. From what organism is this protein?

d. View the 3D structure. What secondary structures do you see? Which type predominates?

e. Do a screen shot of the 3D Structure Summary page and attach a printout of the shot to your quiz.

2. Now use NCBI’s Structure database to pull up the 3D structure for 2IY2. Complete the following related to this entry.

Note: Only answer the question asked. Including the entire line of information will indicate a lack of understanding and result in point deductions.

a. What is the name of the protein as indicated in the MMDB entry and publication?

b. Briefly describe what type of protein this is? Your description should be able to answer the questions: what category of protein; what functions it has, how does it accomplish this? Where did you find this information and what is the original source?

c. Are we observing the entire protein in this crystal structure? If no, what are you observing?

d. From what organism is this protein?

e. What is the ligand? Hint: If you are having trouble, you can find this info at NCBI or PDB

Extra Credit:

Pull up the 3D structure for 2IEM. In the Sequence/Alignment Viewer window, highlight amino acid 51 and 198.

a. Which amino acid at these two positions have you highlighted?

b. Look at where these amino acids appear in the 3D structure. Are they close or far apart in the 3D structure? What might you predict is holding them in this position?

Submit a screen shot (attach a printout) to demonstrate the highlighted amino acids and how you reached your answer.