STUDENT EXERCISES

The aim of the exercises is to:

  • provide a brief introduction into the organization and content of EcoCyc
  • provide insight regarding E. coli metabolism and gene regulation
  • introduce basic bioinformatics tools

For a full and exhaustive description of EcoCyc, please go to “TUTORIALS”. For background on the individual exercises, go to “Cell Processes” in “MICROBE”.

View a sample exercise, see the correct answers, and learn how it is graded.

SAMPLE EXERCISE

A. Introduction: Go to the EcoCyc Home page.

  1. Familiarize yourself with the different information “page types” in EcoCyc
  2. Repeat the Navigation Tutorial (go to TUTORIALS)
    (Note: it helps to keep all searches open in separate tabs and review the material on each “page type”)
  3. Perform the following actions:
    1. type “TyrR” into Quick Search, click on “Gene” page
    2. type “tyrB” into Quick Search, click on “Transcription Units” page for tyrB
    3. go back to the “TyrB “Gene/Protein” page and click on the first reaction (below “Enzymatic reaction of: leucine aminotransferase tyrosine aminotransferase”)
    4. click on “Leucine Biosynthesis”
    5. click on the “More Details” button

B. Exercise: XylR is a transcriptional activator of the xylose operon.

  1. Identify the specific proteins (6 in total) that are encoded by genes in this operon.
  2. List their individual functions. (Hint: Do a quick search for “XylR” on the EcoCyc main page. Follow the link for “XylR transcriptional activator”. Then, click on the boxed, individual genes to figure out their functions by following the “products” links of each gene).

COMPARE YOUR ANSWER WITH THE FOLLOWING STUDENT ANSWERS:

Student #1 Answer:

  • xylA, xylB, xylF, xylG, xylH, xylR.
  • Functions include xylose

Grade for Student #1 Answer: On a scale of 0-12 (0 = no pts, 12 = full credit)
I would give the student a score of 2.
The student made the mistake of listing the genes and not the proteins: XylA is the protein, xylA stands for the gene. While, the student stated the overall function, he/she did not list the individual functions of the proteins.

Student #2 Answer:

  • XylA, XylB, XylF, XylG, XylH, XylR.
  • Functions include xylose, isomerase, kinase, ABC Transporter, activator.

Grade for Student #2 Answer: On a scale of 0-12 (0 = no pts, 12 = full credit)
I would give the student a score of 6.
This student listed all proteins correctly but was not specific enough in stating the individual functions.

Student #3 Answer:

  • The six proteins are XylA, XylB, XylF, XylG, XylH, XylR
  • The function of XylA is an isomerase that breaks down xylose. XylB’s function is to phosphorylate D-xylulose. XylF, G, and H are subunits of an ABC Transporter. XylR is an activator.

Grade for Student #3 Answer: On a scale of 0-12 (0 = no pts, 12 = full credit)
I would give the student a score of 10.
The student listed the six proteins and identified each one’s function, but he was not very specific about each one’s function. Yes, XylF, G, and H comprise an ABC Transporter, but he/she should have pointed out that F is the substrate binding component, G binds and hydrolyses ATP and H is the membrane channel. He/she also pointed out that XylR is an activator. However, since there are many different kinds of activators in E. coli, the additional term “transcriptional” should have been included. Without this key work, the answer is incomplete.

As you can see, a short but concise answer is all that is needed. It is easier to generate a short reply than a long exposition. Your TA will be favorably impressed.