Lecture 4 - Lecture 4, Friday September 1, 2006...

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Lecture 4, Friday September 1, 2006 Announcements: 1. re quiz on 9/6: the first 3 lectures form a "unit" on AA and peptides. Today's lecture starts real discussion of proteins. So quiz 1 will cover only lectures 1, 2, and 3, and the RasMol tutorial. 2. Use the Virtual Office Hours! Send e-mail to [email protected] . 3. Any interested students: “How to Find a Research Lab at Cornell. What are they looking for?!” Comstock B106 at 1:25PM today. 4. Enrollment in this class: if not already enrolled, must get Prof.’s signature. Wednesday's lecture: The peptide bond The hydrophobic effect : water has many ways to H-bond to its neighbors, forming on average 3-4 H-bonds per water at physiological temperatures. In other words, there are many ways for “free” water to have the same energy. Note: many ways higher probability more favorable, i.e. higher entropy. But nonpolar groups in water reduce the number of ways for water to H-bond to its neighbors, i.e. fewer ways less probable less favorable, lower entropy . Thus, the nonpolar groups tend to get out of the water ("are driven out of water"), thereby reducing the number of water neighbors of nonpolar groups. Intro to Mb Isozymes Today's lecture: In past years, Prof. F. has lectured about various methods, e.g. for purifying Mb, finding its M.W., finding its AA sequence. But this year, we will not consider these many laboratory methods, but instead, focus more on protein structure. p. 37 Today, ~ 4 million protein sequences are known! But what do we do with all this information?! In other words, how do we use protein AA sequence information without having the protein 3D structure? The key is to find the relatedness of the new AA sequence to that of a protein with an already known function . Commercially available software can find a match for about 50% of new AA sequences. Matching up related sequences is more difficult than you might think, because when comparing 2 entire protein sequences, there may be pieces of one sequence that do not exist in the other sequence, but both proteins still can have related sequences. Sophisticated information processing is used. 1a. Function: enzyme activity : Here is one example of using the sequence to deduce function: About 35 years ago, researchers discovered that several
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genes, and the protein products of those genes, were found in several types of cancer. Such genes are called oncogenes, the proteins, oncoproteins. Many of these oncoproteins associated with cancer have a sequence like that of protein kinases , which catalyze reactions that phosphorylate enzymes. First just a guess from sequence analysis, later verified by experiments, oncoproteins are often protein kinases. Now we know that protein kinases are the largest superfamily (related structure and function) of eukaryotic proteins. 1b.
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This note was uploaded on 02/13/2008 for the course BIOBM 3310 taught by Professor Feigenson,gw during the Fall '07 term at Cornell.

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Lecture 4 - Lecture 4, Friday September 1, 2006...

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