Leture 5 - Lecture 5 Monday, September 4, 2006...

Info iconThis preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
Lecture 5 Monday, September 4, 2006 Announcements: 1. Quiz Wed 9/6. More info at the end of today's lecture 2. Problems: Ch4 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:
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
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
Background image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

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 University (Engineering School).

Page1 / 6

Leture 5 - Lecture 5 Monday, September 4, 2006...

This preview shows document pages 1 - 3. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online