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Created page with "<p>What is proteome? the entire set of proteins expressed by a genome, cell tissue, or organism at a certain time.</p> <p>Type</p> <ul> <li>cellular proteome : the collection ..."
<p>What is proteome? the entire set of proteins expressed by a genome, cell tissue, or organism at a certain time.</p>
<p>Type</p>
<ul>
<li>cellular proteome : the collection of proteins found in a particular cell type </li>
<li>complete proteome : whole set of proteins </li>
</ul>
<p> </p>
<p>proteomics : study of proteome</p>
<p> </p>
<p> </p>
<p>How to study the proteome</p>
<p> </p>
<ul>
<li>separation >> gel electrophoresis</li>
<li>
<ul>
<li>isoelectric focusing (charge) + SDS-PAGE (molecular weight) --> gel dyed with comassie blue to visualization</li>
</ul>
</li>
<li>How to know their identity (their component, amino acids sequence ) >> mass spectroscopy</li>
<li>
<ul>
<li>Peptide mass fingerprinting : cleave the protein into short peptides --> deduce the protein's identity based on sequence database</li>
<li>Tandem mass spectrometry : isolate individual peptides --> collide them with non-reactive gas --> cataloguing the [fragment ion] produced (by detecting ion, they can deduce the identity of peptides)</li>
<li>
<ul>
<li>
<ul>
<li><img src="file:///C:/Users/john/AppData/Local/Temp/enhtmlclip/Tandem_mass_spectrometry.jpg" /></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
<p><img alt="" src="/ckfinder/userfiles/images/Tandem_mass_spectrometry.jpg" style="height:219px; width:421px" /></p>
<p> </p>
<p>methods</p>
<ul>
<li>cryo-electron microscopy </li>
<li>
<ul>
<li>what ? TEM studied at cryogenic temperature</li>
<li>advantage : do not require crystallization / relatively easy</li>
<li>disadvantage : low resolution</li>
</ul>
</li>
<li>microscopy</li>
<li>
<ul>
<li>source: reflection , diffraction of electromagnetic radiation beams interacting with the specimen</li>
<li>Types : TEM / SEM</li>
<li>disadvantage : limitation of resolution / show specimen by only dark or light color</li>
</ul>
</li>
<li>NMR
<ul>
<li>source : nuclear magnetic resonance. It means that electromagnetic radiation that nuclei absorb and re-emit. this radiaction is in the state of specific resonance frequency </li>
<li>frequency is directly proportional to the strength of the magnetic field</li>
<li>type
<ul>
<li>Solid-state NMR spectroscopy</li>
<li>Multi-dimensional NMR spectroscopy</li>
<li>Fourier-transform spectroscopy</li>
<li>CW spectroscopy</li>
</ul>
</li>
</ul>
</li>
</ul>
<p> </p>
<p> </p>
<p>protein structure</p>
<ul>
<li>a-helix</li>
<li>b-strand</li>
<li>coil (irregular, antibody for binding)</li>
</ul>
<p> </p>
<p> </p>
<p>Post translational modifications</p>
<ul>
<li>Glocosylation</li>
<li>Phosphorylation</li>
<li>SUMOylation</li>
</ul>
<p> </p>
<p>experimental methods >> identifying proteins</p>
<p> </p>
<ul>
<li>way
<ul>
<li>One-dimensional SDS-PAGE</li>
<li>two-dimensional SDS-PAGE</li>
</ul>
</li>
</ul>
<p> </p>
<p>Interaction proteomics</p>
<ul>
<li>application
<ul>
<li>signal transduction / trafficking / cell cycle/ gene regulation</li>
</ul>
</li>
<li>detection
<ul>
<li>Chips / Microarray</li>
</ul>
</li>
</ul>
<p>Type</p>
<ul>
<li>cellular proteome : the collection of proteins found in a particular cell type </li>
<li>complete proteome : whole set of proteins </li>
</ul>
<p> </p>
<p>proteomics : study of proteome</p>
<p> </p>
<p> </p>
<p>How to study the proteome</p>
<p> </p>
<ul>
<li>separation >> gel electrophoresis</li>
<li>
<ul>
<li>isoelectric focusing (charge) + SDS-PAGE (molecular weight) --> gel dyed with comassie blue to visualization</li>
</ul>
</li>
<li>How to know their identity (their component, amino acids sequence ) >> mass spectroscopy</li>
<li>
<ul>
<li>Peptide mass fingerprinting : cleave the protein into short peptides --> deduce the protein's identity based on sequence database</li>
<li>Tandem mass spectrometry : isolate individual peptides --> collide them with non-reactive gas --> cataloguing the [fragment ion] produced (by detecting ion, they can deduce the identity of peptides)</li>
<li>
<ul>
<li>
<ul>
<li><img src="file:///C:/Users/john/AppData/Local/Temp/enhtmlclip/Tandem_mass_spectrometry.jpg" /></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
<p><img alt="" src="/ckfinder/userfiles/images/Tandem_mass_spectrometry.jpg" style="height:219px; width:421px" /></p>
<p> </p>
<p>methods</p>
<ul>
<li>cryo-electron microscopy </li>
<li>
<ul>
<li>what ? TEM studied at cryogenic temperature</li>
<li>advantage : do not require crystallization / relatively easy</li>
<li>disadvantage : low resolution</li>
</ul>
</li>
<li>microscopy</li>
<li>
<ul>
<li>source: reflection , diffraction of electromagnetic radiation beams interacting with the specimen</li>
<li>Types : TEM / SEM</li>
<li>disadvantage : limitation of resolution / show specimen by only dark or light color</li>
</ul>
</li>
<li>NMR
<ul>
<li>source : nuclear magnetic resonance. It means that electromagnetic radiation that nuclei absorb and re-emit. this radiaction is in the state of specific resonance frequency </li>
<li>frequency is directly proportional to the strength of the magnetic field</li>
<li>type
<ul>
<li>Solid-state NMR spectroscopy</li>
<li>Multi-dimensional NMR spectroscopy</li>
<li>Fourier-transform spectroscopy</li>
<li>CW spectroscopy</li>
</ul>
</li>
</ul>
</li>
</ul>
<p> </p>
<p> </p>
<p>protein structure</p>
<ul>
<li>a-helix</li>
<li>b-strand</li>
<li>coil (irregular, antibody for binding)</li>
</ul>
<p> </p>
<p> </p>
<p>Post translational modifications</p>
<ul>
<li>Glocosylation</li>
<li>Phosphorylation</li>
<li>SUMOylation</li>
</ul>
<p> </p>
<p>experimental methods >> identifying proteins</p>
<p> </p>
<ul>
<li>way
<ul>
<li>One-dimensional SDS-PAGE</li>
<li>two-dimensional SDS-PAGE</li>
</ul>
</li>
</ul>
<p> </p>
<p>Interaction proteomics</p>
<ul>
<li>application
<ul>
<li>signal transduction / trafficking / cell cycle/ gene regulation</li>
</ul>
</li>
<li>detection
<ul>
<li>Chips / Microarray</li>
</ul>
</li>
</ul>
