Biology 1108H BIOLOGY HONORS COURSE |
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Spring 2005 "How new proteins are discovered and characterized"Instructors: James Prestegard and Will YorkThis seminar/discussion section will provide a forum for more in-depth discussion of some of the material related to that covered in Biology 1107 lectures. We have chosen as theme "How new proteins are discovered and characterized." This builds on the wealth of material that has come out of recent genome sequencing efforts. Hundreds of genomes have now been sequenced and thousands of genes within each of these genomes have been identified. However, on average, only about fifty percent of the proteins coded by these genes have known functions. This is an opportunity for discovery - one that we can tap with readily available web-based tools. We will explore some of these tools and some of the questions that arise when we gain information about what proteins might do. Information / updates: http://tesla.ccrc.uga.edu/courses/1108. Time and place: 3:30 - 5:00, Thursdays, C130 Life Sciences Course Requirements:
Students are expected to attend the weekly discussion sections and participate in discussion. A moderate amount of outside reading or web-based searching will be required (1 hr/wk). Grades will be based on participation (25%) and a short final report (75%). |
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Course Schedule |
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01/13 York |
Introduction Science, Technology, and Truth Please read the following web pages. These are very short essays on philosophical ideas that have had profound effects on the way http://www.sar.bolton.ac.uk/ltl/lecture2/intro.htm |
01/20
York |
Philosophy of Science |
01/27
Prestegard |
The Cystic Fibrosis story click on Galileo Databases, then click on Academic Search Premier Type Cystic Fibrosis in Find box; type The Scientific American in Journal box; type 1995 in both Published Date boxes, then click on Search. The article by Michael Welsh and Alan Smith will appear. |
02/03 York |
Looking at Genomic Databases Assignment: Try to find a gene or protein associated with an inherited disease. Use the search option on websites such as: Expasy: Entrez: click on Entrez, then click on nucleotide, and then on map viewer |
02/10
Prestegard |
Looking for Homologous Sequences Explore the use of BLAST for comparing protein or nucleotide sequences. BLAST site: http://www.ncbi.nlm.nih.gov/education/BLAST info/information3.html Read Query Tutorial and BLAST Tutorial and More Information. Paste in a protein or nucleic acid sequence connected with a human genetic disorder (or any human protein). Find a homolog in another organism. |
02/17
York |
Protein Motifs |
02/24
York |
Looking at Proteins Please check into these two sites: Protein Architecture Additional material: |
03/03
York |
Protein Structure Visualization Tools Please click on the link below and follow the instructions that are |
03/10
Prestegard |
Looking for Structural Homologies This is a way of searching for possible structural homologs of an unknown protein (or its gene) using just its sequence. One can find GenThreader on the PSIPRED site http://bioinf.cs.ucl.ac.uk/psipred/. Go to the server. Paste in a sequence of a protein in FASTA format (one letter codes). Choose GenThreader (quick) as a prediction method. Enter your email and a short name for you project. Click predict. You will be mailed the results in a few minutes. If you get "certain" or "high" confidence hits, copy the Protein Data Bank codes to the right of the output (1fk0, for example, ignoring the A etc at the end). Go the the protein data bank (http://www.rcsb.org/pdb/) . Paste in a PDB code and examine the information on the protein. The PDB will often give you an accession number for Swiss prot. You can go the the EXPASY server for additional information about your homologs. |
03/14-18 |
SPRING BREAK |
03/24 Prestegard/York |
Visit to CCRC labs. Please meet in our usual room (C130 - Life Sciences) at 3:30. We have arranged for one of our colleagues to meet you there and provide transportation to the CCRC. We will have you back to Life Sciences before 5PM. schedule for tour URL for CCRC faculty members contact information |
03/31 Prestegard |
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04/07 Prestegard
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Student Presentations |
04/14 York |
Student Presentations |
04/21 Prestegard/York |
Student Presentations |
04/28 Prestegard/York |
Student Presentations |