The Internet Workbook: Question 3

Net Problem #3

Metabolism and Metabolic Regulation

Now we'll use the net to learn about the regulation of metabolic processes. We'll be using a database called PUMA, which stands for "Phylogeny, Metabolism, Alignments." This is a database of pathways and regulatory circuits that exist in a variety of different cell types.

As with other exercises, you may want to read through this one completely or print it out before starting.

Go to PUMA (http://www.mcs.anl.gov/home/compbio/PUMA/Production/puma.html). Depending on what machine you are using you may wish to use PUMA with or without graphics. If you're on a slower machine or have a tenuous net connection, without graphics may be better.
To get an idea of the enormous amount of information in PUMA, go to the "functional overview." This contains most of the pathways that you have so far studied in biochemistry.
To get an idea of how difficult it can sometimes be to understand the information in PUMA, click on any one of these pathways.
Now back up and go to Access to PUMA objects. This is a searchable index. Look for the glycolytic enzyme 'pyruvate kinase'.
This inquiry should return hot keys for the pathway, compound, and enzyme. Let's look at the pathway, as represented in PUMA. Click on either of the hot keys, they go to the same place.
This is a schematic representation of the pyruvate kinase reaction, including regulatory features. Click on 2.7.1.40, pyruvate kinase itself. You'll get a page that will show you the names of some of the pathways this enzyme is involved in. However, continue to click on the enzyme number itself, listed at the top of the page. This page tells you a little something about the enzyme itself, and some of the reactions it is involved in.
Now back out and do the same thing for enzyme 2.7.1.37. If you look at the pathway, you'll see this is a protein kinase that is phosphorylating pyruate kinase. Remember not to dwell on the large list of reactions that 2.7.1.37 participates in, but continue on to facts about the enzyme itself. Does anything in the enzyme description immediately tell you about what is happening with pyruvate kinase, other than that it can be phosphorylated (hint: no). 2.7.1.37 is the general designation for a variety of protein kinases, just as 3.1.3.16 is the general designation for a variety of protein phosphatases.
The great thing about databases is that you can continue to mine them for information almost indefinitely. Now let's try backing out a bit more, back to the original level you obtained after your keyword search, the level that contained hot keys to pathways, compounds, and enzymes. Note that there is a different phosphatase listed here: 3.1.3.49. Click on this; now we get to a set of information that is specific enough to use.
Based on the information you obtain here and the structure of the pyruvate kinase regulatory pathway you've accessed, answer the following questions:
1. What does 3.1.3.49 do?
2. Does phosphorylation increase or decrease the activity of pyruvate kinase?
3. Which form of pyruvate kinase is active, 'a' or 'b'?
4. What cellular compartment does the pyruvate kinase reaction take place in?
5. What compound increases the activity of the protein kinase that phosphorylates pyruvate kinase?

Last updated: July 18, 1998
URL: http://biotech.icmb.utexas.edu/glycolysis/wwwquest3.html
Questions or Comments: feedback@biotech.icmb.utexas.edu
BioTech Resources Web Project
Indiana Institute for Molecular and Cellular Biology
©, 1995-1998 The Trustees of Indiana University