19 - Friday, October 8, 2010 Lecture 19 Announcements: 1....

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Friday, October 8, 2010 Lecture 19 Announcements : 1. Quiz 5 results: A 20.6 B 20.6 C 19.0 2. PyMOL Reviews will not take place until after Fall Break: Sun 10/17 3 – 5PM in Carpenter Hall Red Computer Lab; and Tu 10/19 4:30 - 6PM in Malott 251 3. Midterm exam Th 10/21 at 7:30PM, room TBA Make-up exam: Sat 10/23, 11AM – 1:30PM ( MUST e-mail Prof with conflict before Fall Break!! ). Room TBA 4. How to study for the midterm exam: Discussion on Friday 10/15 at 1:25PM in Comstock B108 a. Last year’s exam is on our web site (Blackboard). Don’t look yet at the key! Take the exam after you are 3/4 done with studying, and only then look at the key. b. Be able to answer every question from the first 5 quizzes. c. Understand every word from every lecture. d. Use the text as a supplement. Wednesday's lecture: Proteins require non-amino acid components (metal ions, coenzymes); One way to regulate enzymes is to control their concentration: synthesis is controlled Today's lecture: p. 142 B. Control of Protein Degradation: (continued from the Wed lecture) . during the cell cycle, some proteins appear briefly, perform their function, then are degraded. 4. Locations: degradation of proteins occurs in both the cytosol, and in the specialized organelle, the lysosome. p. 142 There are several different kinds of cytosolic protein degradation. One case is especially interesting: Ubiquitin is a highly conserved, 76-amino acid protein that binds to and thereby marks proteins for hydrolysis. Ubiquitin is found in all cells, hence its name. Once ubiquitin binds to a protein, that protein is marked for destruction. Specific enzymes (these are the key control points!) catalyze the ATP-dependent addition of multiple copies of ubiquitin to a protein. A proteasome (barrel shaped, 4 rings of 7 subunits each, total MW 2000kD; see bottom of p. 142) binds to the ubiquitin marker, and swallows the protein. The ubiquitin escapes, but the protein is hydrolyzed, leaving just peptide fragments. 6 years ago, the discovery of the ubiquitin system for protein degradation was recognized by the award of a Nobel prize to Ciechanover, Hershko, and Rose. The work was done in the 1980s. The Nobel committee cited the relevance of this type of
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protein degradation for cell division, DNA repair, "quality control" of newly synthesized proteins, and aspects of immune function. II. Control of enzyme activity page 143 We can divide into two general ways the types of regulation of enzyme activity (not every enzyme can be regulated!). One way is via covalent modification-- either a cleavage of a covalent bond, or else the formation of a new covalent bond in the enzyme. A second way is via allosteric changes in the enzyme structure-- binding at a site that affects substrate binding and/or the catalytic steps. Note that a modification can be covalent, e.g. a phosphorylation, but also have an
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19 - Friday, October 8, 2010 Lecture 19 Announcements: 1....

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