BCH 4053--General Biochemistry I--Spring 2003

Extra Credit Problem No. 3

This extra credit problem is an exercise developed by Dr. Charles Sackerson , Department of Biology, Iona College.  It should help you to begin to understand the relationship between a nucleotide sequence in a gene, an amino acid sequence in a protein, and the three dimensional structure of the protein dictated by the amino acid sequence. It gives you an introduction to web resources for comparing gene sequences, matching gene sequences with protein sequences, and visualizing proteins in three-dimensions. Of course, it only touches the surface of these resources, but it points a way you can follow up on with any protein or sequence of interest to you.

This problem is optional, and is to be done individually.  (I decided against making it a group activity in that everyone should go through the total exercise).  You may help each other, but you must obtain the pages for the report yourself and not rely on copying another students pages.

Follow Sackerson's instructions except skip items 1 and 2 (pasting of the sequence into Word and printing a copy).

The problem is worth four points, one each for each of the following pages.

1. First two pages of your Blastn search (genes)
2. First two pages of your Blastx search (proteins)
3. Abstract of most recent article on disease of the protein
4. Printout of page showing chime structure of protein

The problem is given at the URL:

 http://www.iona.edu/faculty/csackerson/sequence.htm

Report is due on Friday, March 21..

Added Note:

If the computer you are using does not have Chime version 2.0.3 or later, you will have a problem with the last step of loading a protein structure from the PDB databank into protein explorer because of the URL length. In that case, get a structure by clicking here, then save the file (called pdb1A01.ent) to your hard drive. Then return to Protein Explorer,  click on "Explore More", then "load a different molecule", then browse your hard drive to the file you just saved. This will load the structure into Protein Explorer. When you are ready to print the structure, click on the frame with the structure before choosing "file--print".