Download Quiz #2

BIO 315 BIOINFORMATICS
QUIZ #2
Name _______________________________________________________
TAKE HOME QUIZ: TO THINK, SYNTHESIZE AND EXPLORE
Please insert your answers into this electronic file in blue and send me the file with the name:
YourLastName_Quiz2
For parts of this quiz, you should refer to the 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 use additional
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 Trichoderma harzianum and 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 Trichoderma harzianum? 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.