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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

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

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  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

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