# Leture 5 - Lecture 5 Monday September 4 2006 Announcements...

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Lecture 5 Monday, September 4, 2006 Announcements: 1. Quiz Wed 9/6. More info at the end of today's lecture 2. Reading for this week: 136-137 & 116-135 Problems: Ch4 # 1 & 4, and LG 3-9 RasMol exercise this week: #2, Secondary Structure. BUT instructions (PDF file) are not opening. Go to Blackboard Rasmol to get instructions. 3. re Rasmol Tutorial: For PC users, the Help commands are not working! See the Blackboard Announcements for instructions on getting a working Help file. Friday’s class : What to do with an AA sequence without the 3-d structure? a. Compare the new AA sequence to a data bank of all previously-determined AA sequences, and look for matches with proteins of known function. b. Evolutionary relationships: Look at the big picture, how lifeforms are connected, by studying protein sequences. c. Special sequences: Find short stretches of AA sequence that match "special sequences" that have known function: e.g. target of a kinase; import into nucleus d. Predict protein folding (not!) Basics of x-ray diffraction, and results found for Mb. Today's lecture: What are the “construction rules” for proteins? First, consider some key interactions found in proteins: 1. Hydrogen Bonds : p. 44 a linear geometry 2.8 - 3.2 Angstroms between the electronegative atoms energy of bond10-40 kJ/mole every -OH, -NH, -SH must be in an H-bond, either to another part of the protein or to water. In whatever way the polypeptide chain actually folds, the FINAL STRUCTURE MUST ALLOW FOR (ALMOST) EVERY POSSIBLE H-BOND TO FORM . 2. Electrostatics:

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positive and negative charge attracting, or else two like charges repelling h wherever there is a + charge there must be a - charge within a few Angstroms, and vice versa energy of the attraction 10-40 kJ/mole very different from H-bond in geometry: not constrained in any direction É sometimes called a “salt bridge” or "ion pair" 3. Disulfide Bonds : have a specific geometry . This geometry is best visualized in 3-d. h it is a covalent bond with an energy about 200 kJ/mole. This is only about half the strength of a typical carbon-carbon covalent bond, but much more than the H-bonding or electrostatic interactions. 4. Weak and Weakly Directional Interactions : p. 45 Three types, each worth approx 5-10 kJ/mol: a. DIPOLE-DIPOLE: such as between two carbonyl groups. The partially negative oxygen is attracted to the partially positive carbon of another carbonyl group. It is weakly directional (see lecture demo). b. ION-DIPOLE: such as between a carbonyl group and a NH 3 + group. It is also weakly directional. c. The third such interaction goes by three different names: -- transient dipoles -- van der Waals forces -- London dispersion force This interaction arises from the transient fluctuation of the charge distribution of the electron cloud. Fluctuation occurs rapidly, and since neighboring electron clouds deform "in concert", there is a net attraction.
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• Summer '07
• FEIGENSON,GW
• atoms, LG, peptide bond, steric hindrance

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