1. The digestive system, thermodynamics, enzymes, and transport across membranes May 12, 2003 Learning objectives- Be capable of manipulating protein structures using the freeware, Deep View Understand the structure of the alpha helix in proteins Know the difference between anaerobic energy production and aerobic energy production Understand the major reactions in glycolysis, Krebs cycle and oxidative phosphorylation Workshop-Display tripeptide of a protein. Capture the image, export to Power Point, label amino terminus, etc. Homework and reading assignment-see last slide

2. The Protein Data Bank Contains three-D coordinates for several thousand proteins and other molecules. This is experimentally-derived data from three sources 1) X-ray crystallography 2) Nuclear magnetic resonance 3) Ab initio calculations (very few) The Protein Data Bank contains records that consists of two parts: header and content. The header contains annotations and the content contains the x, y, z coordinates of each atom in the protein

3. Content of 2HHB record in PDB HEADER OXYGEN TRANSPORT 07-MAR-84 2HHB 2HHB 3 COMPND HEMOGLOBIN (DEOXY) 2HHB 4 SOURCE HUMAN (HOMO SAPIENS) 2HHB 5 AUTHOR G.FERMI,M.F.PERUTZ 2HHB 6 REVDAT 2 15-OCT-89 2HHBA 3 MTRIX 2HHBA 1 REVDAT 1 18-JUL-84 2HHB 0 2HHB 7 SPRSDE 18-JUL-84 2HHB 1HHB 2HHB 8 JRNL AUTH G.FERMI,M.F.PERUTZ,B.SHAANAN,R.FOURME 2HHB 9 JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN..10 JRNL TITL 2 1.74 ANGSTROMS RESOLUTION 2HHB 11 JRNL REF J.MOL.BIOL. V. 175 159 1984 2HHB 12 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070 2HHB 13 REMARK 1 2HHB 14 REMARK 1 REFERENCE 1 2HHB 15 REMARK 1 AUTH M.F.PERUTZ,S.S.HASNAIN,P.J.DUKE,J.L.SESSLER, 2HHB 16

4. Content of 2HHB record in PDB ATOM 1 N VAL A 1 6.130 16.559 4.905 7.00 41.29 2HHB 206 ATOM 2 CA VAL A 1 6.870 17.784 4.702 6.00 41.33 2HHB 207 ATOM 3 C VAL A 1 8.377 17.548 4.913 6.00 31.64 2HHB 208 ATOM 4 O VAL A 1 8.820 16.980 5.922 8.00 38.31 2HHB 209 ATOM 5 CB VAL A 1 6.345 18.763 5.731 6.00 52.26 2HHB 210 ATOM 6 CG1 VAL A 1 6.745 20.188 5.356 6.00 52.75 2HHB 211 ATOM 7 CG2 VAL A 1 4.826 18.612 5.847 6.00 58.75 2HHB 212 X YZ

5. PDB file summary CATH: Structural ClassificationCATH:Structural Classification Class(C), Architecture(A), Topology(T) and Homologous superfamily (H). Class(C)Architecture(A)Topology(T) Homologous superfamily (H) PDBSum: Summary of PDB Structure PDBSum:Summary of PDB Structure SCOP: Structural Classification SCOP:Structural Classification

7. Summary of PDB Structure

9. Heme

10. Deep View-an image display program Created by Glaxo-Smith-Kline Download to the self-extracting file to desktop Choose 1crn PDB file from Download folder to display Display the molecule and the control panel

11. Instructions for Workshop Select the first alpha helix in the control panel for display Change view so that you are looking through the “hole” of the alpha helix Remove residues one at a time and add back residues. Convince yourself that side chains are on the outside of the helix. Without the side chains display the H-bonds. How many residues are interspersed within the alpha chain between a pair of amino acids bound by H-bonds?

12. Instructions for Workshop (2) Display a tripeptide. Capture the image on the screen and import into power point Annotate the power point slide to point out the amino terminus, carboxyl terminus and side chain. Is your side chain hydrophobic or hydrophilic? Show your instructor when you are finished.

13. Metabolism-the sum of all the chemical changes taking place in an organism Cell respiration-decomposition pathway that provides ATP for cellular functions.

14. ?

16. Three stages of cellular respiration-Glycolysis, Krebs cycle, Electron transport (OxPhos) Glycolysis (cytoplasm) Krebs cycle (mitochondria matrix) Electron transport (mitochondria inner membrane)

17. Oxidation Glucose + O 2 + NAD +  6CO 2 + H 2 O + NADH Used for electron transport chain

18. Homework Due May 19 Read pp 129-150. Answer Reviewing Ideas on p. 50, problems 1, 2, 4-6; Using Concepts on p. 151, problems 1, 2, 4, 6, 8, 9. Extensions on p. 151, problem 1