Guidelines I want you to follow when producing web pages for this course.
Your first home page assignment
Your task is to create a web page that describes a protein and its structure. I suggest you begin by searching Protein Data Bank, your favorite textbook, or PubMed. The key is to indentify a protein whose structure has been determined. I highly recommend that you NOT choose a structure/protein whose information is based on multiple NMR structures. You want to find a protein that has each amino acid identified. The second criteria will be gaining access to the paper that describes your chosen protein. Many papers are freely available, but some publishers never make papers freely available. Therefore, you will want to plan ahead enough to secure the papers via the library (either online or via Inter-Library Loan which can take 2 weeks).
The main point is to link structure to function. Use the one paper that determine the protein's structure as you only journal source unless you want general background such as that found in textbooks.
You may start with the template I have created. As a part of this assignment, you must include the following:
I will be reading the content to look for accuracy and clarity. I will be looking at your references to make sure you have used proper CBE style citation. I will be testing your links (including the email link) to make sure they are all functional. I want you to target an audience that has completed Bio111 and Genetics. You can see previous pages, but they had different assignments.
To capture an image from the screen, create a Snapz Pro file or save the image file from your browser.
Your second home page assignment
Your second assignment is to identify orthologs (genes evolved from a common ancestral gene) of your chosen protein. You will want to consult sources such as BLAST, Entrez, OMIM, PDB, etc. to find these orthologs. I have created a help page for those of you new to DNA databases. If your original protein's structure was determined from a prokaryote, then you survey should include orthologs from metazoans. If your protein crystal was produced from a vertebrate, then be sure to survey other vertebrates but also prokaryotes. You should specifically look for orthologs in the "big seven" and any others species that prove helpful in understanding your proteins cellular roles.
Human |
Mouse |
C. elegans |
Drosophila |
|---|---|---|---|
Arabidopsis |
Yeast |
E. coli |
Others of interest |
For Genomics
alumni, this is not meant
to be an all out genomics blockbuster assignment.
The main point is to provide sequences and information obained through orthologs of the species from which your structure was determined.
For this assignment, focus on phenotypes, mutations, diseases, drug binding sites, virus binding sites, similar proteins, etc. Since your first assignment focused on structure/function, this assignment should widen the circle of information about your chosen protein. Keep in mind you are trying to identify critical amino acids and evolution often retains those amino acids that are required for protein function.
1) Your third assignment will no doubt stretch you into uncomfortable territory. The structure of a protein is becoming increasingly important and increasingly, biologists need to learn more about computer science. Therefore, it would would be good for you to create a chime tutorial for your chosen protein. You must use the same protein from assignment 1. A chime tutorial is one where you, the author, determine what you want the viewer to see. You write a script that creates buttons to provide viewers with the appropriate views. I will be looking for tutorials that tell me something functionally significant, not just secondary and quaternary structures.
In order to run chime, you must have the chime plugin installed and use either Internet Explorer (on Windows) or Netscape 4.7x and Classic OS (on Macs). Chime is a proprietary plugin and the community has created a free, Java-based substitution called Jmol. However, Jmol is too new for us to use at this time. We hope to switch in the coming year. If you would like to develop a Jmol script instead of Chime, you are encouraged to do so, but it will be harder since there is little documentation for creating buttons, etc.
How do you create a link from a framed web page back to a non-framed page so the new page fills the entire browser and not just the tiny button frame? Highlight the text that will make the link and in the properties window (se below), find the place that says "Target". Click and hold and choose "parent". See the image below to see an example.
You have already seen some of my chime tuturials, like the one for dsDNA. Go to this template to see your starting place and read these directions. John Kogoy helped me write the direcitons on how to create chime scripts. In your folder on the BioServer, you will find a chime file that contains all these files so you can begin with them. In addition, we will have an in-class workshop when you turn in your second exam.
Your last home page assignment
(due April 29; posted by class time) will be your review paper. The
goals of this assignment are: 1) each student to choose a paper from the three
I have selected; 2) summarize the results of the paper; 3) critique the paper
(Do the results support the authors' claims? Are the figures adequate?); and
4) suggest future experiments to do to learn more about the topic. When you
make suggestions about future work, indicate what question you want to ask,
what method(s) you would use, and what kind of results might you expect.
For this assignment, you do not have to reproduce any figures (keeping in mind
that figures from the original paper being reviewed will be copy right protected).
Here are your choices for 2005 (PDF Files):
I will grade your paper with the following weights:
You can see some papers from the past.
