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by: Trace Mante MD


Trace Mante MD

GPA 3.61


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Class Notes
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This 55 page Class Notes was uploaded by Trace Mante MD on Monday October 26, 2015. The Class Notes belongs to CSCE 769 at University of South Carolina - Columbia taught by Staff in Fall. Since its upload, it has received 34 views. For similar materials see /class/229592/csce-769-university-of-south-carolina-columbia in Computer Science and Engineering at University of South Carolina - Columbia.

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Date Created: 10/26/15
COMPUTER SCIENCE amp ENGINEERING Introduction to Cell Biology Homayoun Valafar Depamnenl of Computer Science and Engineering USC Taxonomy of Life I Live organisms can be classi ed into various groups ANIMALIA CHORDATA MAMMALIA PRIMATA HOMINIDAE HOMO SAPIENS I Three main groups at the Domain level I Archaea I Bacteria I Eukarya I They are distinguished on the basis of their cellular structures and features I Prokaryote I Eukaryotes gm i Cell Biological I Smallest unit of life I Smallest collection of matter that can live I What is life Hard to answer Order 39 Reproduction sexualasexual Growth and development Energy utilization metabolism Response to environment Homeostasis Evolutionary adaptation Two Types of Cell I Eukaryotic Cell I Higher organisms Animals Plants Fungi Protists 39 Human 39 Mouse 39 Drosophilia melanogaster Fruit y 39 Caenorhabditis elegans C Elegans earth worm 39 Prokaryotic Cell Bacteria and Archaea l Bacteria and Cyanobacteria bluegreen algae 39 Escherichia Colz39 E Colt 39 Pyrococcus Furious P Furious Anatomy of Cells Prokaryotic Cell Structure Flagella Flgure1 Analomy of the Animal Cell M achondrla ll Mlcrofllaments Rough Endoplasmic Rellculum Rough Endoplasmlc Retlculum Endoplasmlc Reticulum RJbosomes Figum 1 Anatomy of a Eukaryotic Cell Anammy of the Animal Cell Mlmchomlrla h w Microfilamems Rough Cytoplasm Lysos L x I Emmmm Organelle Nucleus Nucleus Plasma Membrane r Nucleclus Rough Endoplasmlc Retlculum Endoplasmlc Reticulum ijosomes Figure 1 Encapsulates all functional components of the cell and the Cytoplasm Insulates and isolates cell internals from external elements Composed of lipid bilayer Water insoluble Contains embedded trans membrane proteins Surface Carbohydrates as markers Plasma Membrane Structure Glycoprotain Carbohydrate SideCh In a 7 Protein Hydrophobic Regions Hydrophilzc Regions v Cytoplasm I The entire portion ofthe Anammy of the Animal Cell V M achondrla cell 1ntenor not occup1ed by L WWW Rough ysosome 39 Eag gl aliw lc the nucleus Perox39some I Very dynamic environment 39 if 1 Nucleus 39 39 39 quot35 Plasma Membrane Envelope Chromalln Rough Endoplasmlc Retlculum ijosomes Figure 1 Endoplasmlc Reticulum Organelle Golgi Apparatus 39 Membranebound intracellular if T K A A compartments p quot quot I quot Distinct and highly organized Vesicles quot Contain speci c chemicals to perform 39 i mum speci c cellular function 39 H 39 39 quot Suspended in the cytoplasm 39 Only in Eukaryotic cells i 39 Wh Nuclear Envelope l f mm Enl me V complexes Figure 1 Nucleus I Intracellular structure that contains the genetic material I Pseudo spherical in shape I Usually near the center of the cell The Cell Nucleus Nuclealus Nuclear 4 y 39 7 a Chromosomes Chromatin Figure1 Mitochondria I Cellular organelle responsible for energy production Mitochondria Inner Structure I Contains enzymes for K l r fMembrane wk 4 7 Ouler f Memhrane oxidative phosphorylation 7 I Site of Krebs cycle conversion of sugar byproducts into units of energy Most peculiar made up of double bilayer membranes Figure 1 Evidence of evolution Ribosome I Protein synthesis machinery l Free oating in cytoplasm l Bound to rough Endoplasmic Reticulum RER in Eukaryotes I Consists of multiple subunits composed of RNA protein complexes Rihosome Structure Large Subun 39 Small Subunll Central l l V Fromberance Figure1 Endoplasmic Reticulum Organelle consisting of network of uid lled tubules and attened sacs Synthesis of proteins and lipids for formation of new cell membrane and other cellular components Manufactures products of secretion Rough or smooth types Rough Endoplasmic Reticulum Membrane k2 nu Figure1 Golgi Apparatus Golgi Complex I Organelle consisting of network of uid lled tubules and attened sacs Processes raw material transported to if from the ER into nished material Glycocylation etc quot Mgmgg Sorts the nished products 7 quot patties and directs them to their nal destination Golgi Apparatus Other Organells I Lysosome l The main function of these microbodies is digestion Lysosomes break down cellular waste products and debris from outside the cell into simple compounds which are transferred to the cytoplasm as new cellbuilding materials I Peroxisomes I Peroxisomes function to rid the cell of toxic substances in particular hydrogen peroxide Lysosume Structure Slngle Wall Membrane Enxyme Complexes Figure 1 Eukaryotic versus Prokaryotic In general Prokaryotic cells are much simpler in anatomy than the Eukaryotes Prokaryotes do not possess organelles Prokaryotes do not have nucleus membrane bound DNA Nucleoid region region of the cell with high density of DNA in Prokaryotes Eukaryotes usually consist of more complex DNA in number and coding intronsexons later COMPUTER SCIENCE amp ENGINEERING Amino Acids Polypeptides and Proteins Homayoun Valafar Depamnenl of Computer Science and Engineering USC 20 amino acids General structure of an AA Differences due to side chain R Can be categorized as quot 39 quot OI39 gatively charged Anatomy of Amino Acids Much simpler structure compared to nucleotides C06 H a Carboxyl aCIdlc Side chain R Carboxylic group acidic Amide amine group alkaline Zwitterion Ca and Ha Amine alkaline Amide proton Amide Proton n Carbonyl carbon 7 u S Carbonyl Carbon ChemicalPhysical Properties of AA Hydrophobic versus hydrophilic Isoelectric point pl Acidic versus alkaline basic Mass Amino acid full names three letter and single letter abbreviations l Alanine ALA A Etc Stereo Chemistry of Amino Acids Amino acids are three dimensional ent1t1es Carbon forms 4 bonds In SF3 hybridization these four bonds form a tetrahedron Stereoisomer two identical molecules that can not be super1mposed D and L are two different enant1omers A mixture of equal amounts of both enantlomers 1s sa1d to be a racem1c m1xture Vast majority of aa found in prote1ns are L aa I Polymerization of AA The family of molecules formed from the linking of various c n SuF w lif may u42mg Two amino acids link through an amide bond or peptide bond Two linked amino acids form a peptide plane more later Polymerization of AA I N terminus Cterminus 1 H H HO 0 3 o H I a a A e Polymerization of AA N terminus Cterminus Protein Proteins are functional units of cell Proteins are made of 20 amino acid subunits Hr H D H l L HEW 2 5 l w l L l l w Proteins fold to create a their own F 121332 characteristic fold three dimensional Hisndme H1 r H l 9 Ll H3 mquot 390in P1011113 Pm r p cock Glutaxm Acid Aspartn Arnl Glu I E rAsp e D fl Vilma vlrfilll 39AE Met v M W31 J m Protein Structure Hierarchy Primary sequence 1quot l linear order of connected amino acids Secondary Structure 2quot I Internal stable segments 06 Helix 3 Strand Tertiary Structure 3quot Protein Data Bank PDB Most prominent database of structures Contains structures for proteins DNA RNA carbohydrates and other biomolecules Data disseminated in two formats PDB and mmCIF Become familiar with this database I Learn to download files and use them I Learn search and other various tools on this site I Browse links Molecular Visualization Tools I A number of tools available or different computing environments I Rasmol l MolMol PyMol I I VMD I Etc Why Protein Structure I Proteins provide metabolic and mechanical support for biological organisms I Structure gives rise to function I Structure is necessary not sufficient for function I Proteins are of special interest due to their therapeutic potential Why not DNA AA AA 7 Ohio 1 H30 6lt w n P C y g N a N I L W o z o u SOg39k be COMPUTER SCIENCE amp ENGINEERING Experimental Techniques in Structure Determination Homayoun Valafar Deparnnenl of Computer Science and Engineering USC Two Main Experimental Methods I XRay crystallography I Nuclear Magnetic Resonance I Some proteins are more challenging I Membrane proteins I Complex carbohydrates I Posttranslationally modi ed proteins I Multi subunit protein complexes I ProteinLigand complexes I Dynamical proteins Protein Structure Drawings of the structures ofproteinsofte11 conveythe im ression of a xed rigid structure1n wh1ch the s1decha1ns of 1nd1v1dual ammo ac1 res1dues are locked mto pos1t1on Nothing could be further from the truth The changes that occur in the structure of hemo lobin when oxygen binds to the hemes are so large that crystals of deoxygenate hemoglob1n shatter when exposed to oxygen Further evidence for the exibility of proteins can be obtained by noting that there 1s no path 1n the crystal structures of myoglob1n and hemoglob1n along wh1ch an 02 molecule can travel to reach the heme group The fact that these proteins reversibl bindoxygen suggests that they must undergo s1mple chan es 1n the1r con ormat1on changes that have been called breathing motions t at open up and then close down the pathway along wh1ch an 02 molecule travels as 1t enters the protem Computer simulations of themotion within proteins suggests that the interior of a protem has a s1gn1 cant quot u1d1tyquot w1th groups movmg w1th1n the protem by as much as 20 nm XRay Crystallography Principally it is similar to medical Xray imaging Automated analysis of the diffraction patterns yields structure Most critical part is the attainment of the crystal Even good quality crystals may not diffract well enough Xray Crystallography Summary Advantages I Very routine and high potential for automation l Fast structure determination From data to structure under 6 hours I Disadvantages Crystal growth is a major unsolved problem Crystals maybe obtained at irrelevant conditions Semidesiccated environment may in uence structure Crystal packing forces may in uence structure Aqueous proteins exist in a conformational ensemble It can be argued that X ray may lter for the conformation that crystallizes Glycosylation will normally render the protein hard to crystallize Multiunit proteins are hard to crystallize Motion impedes crystallization H Crystallization perturbs motion Crystallization of Proteins 18 16 NMR only X Ray Structures 0 01 02 03 04 05 06 Residue Fraction gt 4A RMSD Prestegard 1H Valafar H Glushka I et al Nuclear magnetic resonance in the era of sttuctural genomics BIOCHEMISTRY 40 30 86778685 JUL 31 2001 Nuclear Magnetic Resonance NMR Utilizes the magnetic property of nuclei 1H 15N and 13C are magnetically active Conventional NMR methods rely on the NOE Nuclear Overhauser Enhancement data NOE signal strength is related to the distance of two interacting nuclei by lr6r is the distance Can see only out to 5A distance The limited range is usually useful for side chains Structure Determination with NOE l Collect as many NOEs as possible I Convert NOEs to distances I Use the distance restraints to fold the protein Restrained Optimization I Experimentally collected data can be used as restraints I Restraints can be Distances Dihedrals Residual Dipolar Couplings Relaxation Electron density map diffraction pattern Radius of Gyration Diffusion I Etc Dihedral Restraints in XPLORNIH I Example 2 assign resid l and name c resid 2 and name n resid 2 and name ca resid 2 and name c 10 1050 400 2 3 assign resid 2 and name c resid 3 and name n resid 3 and name ca resid 3 and name c 10 1150 300 2 I Make a table of these in a separate le I Typically named filenamedihetbl I Include directives in your main Xplor script to load the le Distance Restraints in XPLORNIH I Example 1 CaHi NHj long range 2 and name HA resid 4 and name HA resid 5 and name HA resid 6 and name HA resid 8 and name HA resid assign resid assign resid assign resid assign resid assign resid 18 and nameHN 40 2210 18 and name HN 40 22 10 52 and name HN 25 07 02 16 and name HN 40 2210 14 and name HN 40 2210 I Make a table of these in a separate le I Typically named filenamenoetbl I Include directives in your main Xplor script to load the le Consequence of Missing Data How many distances are needed to determine the 2 structures How many distance are needed to align the 2 structures get the 3 structure What are the consequences of missing data Motion or just missing data Motion 0r Lack of Data 1A57 INTESTINAL FATTY ACID BINDING PROTEIN NOE Based NMR Summary I Advantages l Protein is in its physiological environment I Disadvantages Requires full isotope labeling of the protein Requires relatively high concentration of the sample Isotope labeling is expensive time and money Very slow From data to structure in months Acquisition of data can take up to months Consequence of missing data is unclear NOE is very susceptible to motion Residual Dipolar Couplings I Uniform molecular tumbling reduces the average to zero I Uniform molecular tumbling can be perturbed using a crystalline solution I Nonuniform tumbling of the molecules at the interface of the crystalline solution will resurrect RDC I Crystalline solution can consist of Bicelle Phage cellulose fragments PEG and etc Description of Alignment I Alignment needs to quantify two types of information I Strength of alignment I Direction of alignment I What is the minimum representation of this information I How many variables I Five variables to illy describe an alignment I Three Euler angles I Two degrees of motion and uncertainty about two principal axes of alignment I Can be collected into a 3 X3 order tensor matrix I But this is 9 parameters Order Tensor Description of Molecular Alignment Order Tensor Matrix sXX sxy SXY Syy sz Syz I Order tensor matrix OTM is symmetric Order tensor matrix is traceless U XZ yZ DU I How many parameters needed to Jlly construct an order tensor matrix S can be thought of as the covariance matrix of the spatial variation of the vector of interest Decomposition of OTM I How do we extract the information content of OTM I Strength of alignment I Orientation of alignment I Both can be obtained by observing the eigenvalueeigenvectors of OTM I Diagonalization of OTM reveals both infomiation I Diagonalized form of OTM Where SIE O SIyy O Information Content of The Rotation Matrix R I Alignment refers to reference to the external magnetic eld The R matrix describes the alignment of the molecule relative to its current description in PDB All elements of the same molecule must point to the same external magnetic field Can use this information to construct a molecule from smaller components De Novo Structure Determination 39 Use peptide planes as the rigid entities 39 6 RDC data can be collected per peptide plane 39 Each peptide plane can be oriented in space individually 39 Order tensor can be obtained for each individual plane Backbone Solution Structures of Proteins Using Residual Dipolar Couplings Application to a Novel Structural Genomics Target H Valafar et al Journal of Structural and Functional Genomics in print De NOVO Structure Determination De Novo Structure Determination I Use peptide planes as the rigid entities Hot Cquot l Appropriate torsion angliare dete ned from the collected data Order Tensor Matrix Solutions 39 The order tensor matrix can be solved by 5 independent RDCs ngt5 I Use Singular Value Decomposition SVD to solve an overdetermined system of linear equations Use Monte Carlo sampling to accommodate error Use the 9 RDCs collected from two adjacent peptide planes De Novo Structure Determination Target 1016942


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