C581 Web Site

Reading:

Nucleic Acids: There is no single required text for this half of the course. Nonetheless, assigned readings will play a major role in this course. These readings will be taken largely from the following texts:

• Wolfram Saenger, Principles of Nucleic Acid Structure.
• Charles R. Cantor & Paul R. Schimmel, Biophysical Chemistry, Vols 1 & 3.
• J. Sambrook, E.F. Fritsch, & T. Maniatis, Molecular Cloning : a Laboratory
• Manual
• Fritz Eckstein, David M.J. Lilley (eds.), Catalytic RNA.
• David M.J. Lilley, ed., DNA-Protein: Structural Interactions.
• Kiyoshi Nagai and Iain W. Mattaj (eds.), RNA-Protein Interactions.

Grades

Exam Dates, Times and Locations:

Other Important Dates:

Molecular Graphics Workshop:

Pet Protein Assignment (20%)

Step 1: Choose a Pet Protein - Deadline: Sept. 8
Choose a small protein that is of interest to you. It should be less than 250 amino acids to make the remainder of this project more practical - smaller than ~150 aa would be even better. Note that your choice should be for a specific protein from a specific organism (e.g. human interleukin-8) and the 3D structure must be available in the PDB. It should not be a protein that you are working on in the lab. It must be different from the proteins that other class members have chosen (not the same protein from a different organism). See the C581 PDB Directory for a list of proteins that others have chosen. Register your choice on the class web page no later than Sept. 8 (just the protein name, not the organism name).

Step 2: Description of the Protein Function - Suggested completion date: Sept. 15
Include in your assignment:
(a) The name of your protein, the name of the PDB file, and the protein sequence.
(b) A one page description of the biological and biochemical function of your pet protein.

Step 3: Sequence Searching and Alignment - Suggested completion date: Sept. 29
Do a protein sequence search and identify a group of proteins with varying degrees of sequence similarity to your protein. Align the sequences. The proteins you find should include: 2-3 with very similar sequences to your protein (e.g. they may be the same protein from a different species or a very similar protein from the same species); 2-3 with moderately similar sequences (e.g. they may be members of the same protein superfamily); and 2-3 with only slight similarity (e.g. proteins that you would not have guessed would be similar but whose similarity you can rationalize). Include in your assignment:

• Your alignment.
• A list of the names and functions of the similar proteins.
• One paragraph (less than half a page) describing how you did the searching and alignment (written as you would write it for a paper).
• One page comparing the function of the query protein with those of the other proteins (and relating the comparison to the sequences if possible).

Step 4: Structure and Function - Deadline: Oct. 22
Examine your protein using InsightII and read any papers you think are important about the structure and structure-function relationships of your protein. Include in your assignment:

• A 2 page discussion of the structure of the protein and its relationship to the function of the protein. You should include descriptions of secondary and tertiary structural features, and any regions that are functionally important, e.g. active site strutcures, etc.
• Also produce a color figure showing the 3D structure and save it in an Insight folder with the name Xxx.psv, in which Xxx is the name of the pdb file. Include in your assignment the name and directory location of this folder. If I cannot find it easily, you will lose the points for this section.

Step 5: Oral Presentation - Deadline Oct. 22
Be prepared to make a 5 minute oral presentation to the class describing the structure and structure-function relationships of your protein. You should prepare 1-2 .psv folders with informative graphics representations. You may also use 1-2 overheads. I will call on people in class (in A400) on Oct 22 and 24 to make these presentations. Note that not everyone will end up doing one.

Grades for Pet Protein Project
The 20% grade will be broken down as follows:

3%:	Description of protein function
6%:	Alignment and comparison with similar proteins
5%:	Description of structure and structure-function relationships
3%:	Graphics representation
3%:	Writing style and organization

See also the Gallery of Protein Projects

Exams, Problem Sets, and Papers

Proteins Final Exam (20%): A two-hour final will be held on Wednesday, October 29 at 7-9 pm (rooms to be announced). This exam will cover the entire proteins portion of the course.

Nucleic Acids Problem Sets (5%): You will be assigned a series of short molecular modeling tutorials designed to help you to gain familiarity with various nucleic acid structures and complexes. These exercises will be accessible through the web and should be submitted to the AI by the dates listed in the course schedule. The problem sets will be scored on a pass/fail basis. The associate instructor will not be required to grade late assignments.

Nucleic Acids Midterm Exam (10%): One two-hour exam will be given on Wednesday, November 19 from 7 to 9 PM in Room C122. Let me know as soon as possible if you anticipate a scheduling conflict.

Nucleic Acids Term Paper (15%): A 1500-word term paper is due at the beginning of the last week of classes, Monday, December 8 at 9 AM. You will be given a list of topics related to those that will be covered in class. Your paper should take the form of a short review article and should also discuss potential future directions within the field. You should present a current view of the topic; papers that fail to include references from 1996 or 1997 will be marked down.
Remember that this is an assignment for C581; papers should therefore emphasize the structure-function aspects of the topics listed. For example, an organic chemist might be more interested in a natural product than in RNA-binding proteins, but the paper should focus on the interactions of the natural product with DNA, not on the synthesis of the molecule. Similarly, a biologist writing on a transcription factor should emphasize protein-nucleic acid recognition, not transcriptional regulation.
Papers based on your lab research project, or on any work underway in your research group or rotation labs, are NOT acceptable. You may choose a topic that is not on the list, provided you clear your idea with the instructor no later than Monday, November 24. No exceptions will be made to this rule, and the instructor will not grade papers written on inappropriate topics.
Finally, please note that work that has previously been used or will be used concurrently for another class may not be submitted for C581. Any offense will be treated as an academic violation.

Nucleic Acids Final Exam (20%): A two-hour final will be given during the regularly scheduled final examination period. This exam will cover the entire nucleic acids portion of the course and will also revisit important biophysical concepts from the proteins half of the course.