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

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

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:
Image of page 1

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

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.
Image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.
  • Summer '07
  • FEIGENSON,GW
  • atoms, LG, peptide bond, steric hindrance

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern