1 / 18

The digestive system, thermodynamics, enzymes, and transport across membranes

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

haruko
Télécharger la présentation

The digestive system, thermodynamics, enzymes, and transport across membranes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 • X-ray crystallography • Nuclear magnetic resonance • 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. X Y Z 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 Content of 2HHB record in PDB

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

  6. Summary of PDB Structure

  7. Heme

  8. 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

  9. 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?

  10. 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.

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

  12. ?

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

  14. Oxidation Glucose + O2 + NAD+6CO2 + H2O + NADH Used for electron transport chain

  15. 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

More Related