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

The Protein Data Bank Contains three-D coordinates for several thousand proteins and other molecules.This is experimentally-derived data from three sourcesX-ray crystallographyNuclear magnetic resonanceAb initio calculations (very few)

The Protein Data Bank contains records that consists of twoparts: header and content.The header contains annotations and the content contains the x, y, z coordinates of each atom in the protein

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

Content of 2HHB record in PDB

PDB file summaryCATH: Structural ClassificationClass(C), Architecture(A), Topology(T) and Homologous superfamily (H). PDBSum: Summary of PDB StructureSCOP: Structural Classification

Summary of PDB Structure

Heme

Deep View-an image display programCreated by Glaxo-Smith-Kline

Download to the self-extracting file to desktopChoose 1crn PDB file from Download folder to displayDisplay the molecule and the control panel

Instructions for WorkshopSelect the first alpha helix in the control panel for displayChange view so that you are looking through the hole of the alpha helixRemove 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?

Instructions for Workshop (2)Display a tripeptide.Capture the image on the screen and import into power pointAnnotate 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.

Metabolism-the sum of all the chemical changes takingplace in an organismCell respiration-decomposition pathway that providesATP for cellular functions.

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Three stages of cellular respiration-Glycolysis,Krebs cycle, Electron transport (OxPhos)Glycolysis(cytoplasm)Krebs cycle(mitochondriamatrix)Electron transport(mitochondriainner membrane)

OxidationGlucose + O2 + NAD+ 6CO2 + H2O + NADHUsed for electrontransport chain

Homework Due May 19Read 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