Protein Assignment Information and Grading Rubrics:

1) Protein Assignment 1: Due 11 February, 2019

For this assignment, you need to upload to the course Dropbox folder entitled "Protein Assignment" a single page Word document that contains:

1) The name of the protein you intend to study this semester and its PDB ID code.

2) The full name of the organism in which the protein is found.

3) A couple of sentences on why you chose your particular protein.

4) A figure you have created with a drawing program that illustrates the reaction mechanismof your protein.

You must name your file: Lastname_Firstname_ProtAssignment_1.docx, with your actual name in place of "Lastname" and "Firstname".

 

2) Protein Assignment 2: Due 4 March, 2019

For this assignment, you need to upload your work in Microsoft Word format to the subfolder entitled "Protein Assignment 2" in the "Protein Assignment" course Dropbox folder.

For this assignment, you need to perform a literature search of your protein including:

1) Scientific papers in which the structure, function and importance of your chosen protein is discussed.

2) You need to include a minimum of 5 scientific articles in your review. Only one of these articles may be a review article; the others must be peer-reviewed publications in which novel scientific data is presented.

3) For each article, you will need to write a paragraph summary describing the techniques used and the importance of the article to our undertanding of the protein.

You must name your file: Lastname_Firstname_ProtAssignment_2.docx, with your actual name in place of "Lastname" and "Firstname".

 

3) Protein Assignment 3 Due 27 March, 2019

For this assignment, you need to upload your work in Microsoft Word format to the subfolder entitled "Protein Assignment 3" in the "Protein Assignment" course Dropbox folder.

For this assignment, you need to create a detailed outline of your final paper including:

1) The topic and structure of your paper, including specific figures, topics and references for each paragraph

2) References for each topic

The goal of this assignment is to make your life easier as you sit down to write you final paper. Writing an outline is a good way to get organized and stay on point as you prepare your final paper.

You must name your file: Lastname_Firstname_ProtAssignment_3.docx, with your actual name in place of "Lastname" and "Firstname".

 

4) Protein Project Assignment 4 Due 1 April 2019

For this assignment, you need to upload your work in Microsoft Word format to the subfolder entitled "Protein Assignment 4" in the "Protein Assignment" course Dropbox folder.

Prepare Powerpoint slides depicting:

a) The reaction catalyzed by and the reaction mechanism of your chosen enzyme. You need to design this using ChemDraw, Marvinsketch or any computer based softare product.

b) A figure created in Chimera that clearly shows the binding/active site AND the residues used inthe reaction mechanism.

In short, you will be creating a textbook figure describing the function of your enzyme and your grade will be determined based upon the clarity and professionalism of your work.

This assignment will take A LOT of time, so do not wait until the last minute to initiate it.

You must name your file: Lastname_Firstname_ProtAssignment_4.docx, with your actual name in place of "Lastname" and "Firstname".

 

5) Protein Project Assignment 5 Due 10 April, 2019

For this assignment, you need to upload your work in Microsoft Word format to the subfolder entitled "Protein Assignment 5" in the "Protein Assignment" course Dropbox folder.

Perform a multiple sequence alignment of your protein with at least 5 other homolgous proteins. You should carefully choose the organisms whose homologues you use for comparison so that you have a story to tell in your presentation and paper. Just performing a BLAST search and taking the top 5 hits will not be adequate. The goal of this assignment is to get you to identify one or more of the following (more is always better):

i) Conserved domains

ii) Conserved residues

iii) Evolutionary relationships between similar organisms (eg: homologous proteins are only found in other plants or other Gram negative bacteria)

iv) Insertions or deletions in your sequence relative to other homologous sequences (but you should be able to explain what they mean)

Construct a Word document containing your alignment and provide a brief description of what information you have pulled form the alignment.

You must name your file: Lastname_Firstname_ProtAssignment_5.docx, with your actual name in place of "Lastname" and "Firstname".

 

Final Paper Grading Rubric