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<p><span style="font-size:16px"><strong>Lecture5. Proteomics</strong></span></p> <p>* Protein<br /> - Protein is polymer and has diverse of shape<br /> - Protein switching > state change<br /> - How many protein species? ▶ we don't know.<br /> ** Prediction **<br /> 20,000 genes ▶ 7-8 alternative splicing per gene ▶ a few 100,000 ~ 200,000 proteins<br /> - How many structure in 100,000 proteins ▶ more than 100,000 : I think there is alternative form in one sequence.<br /> - How many structure type (protein family ▶ have well conserved structure)<br /> ** Prediction **<br /> <100,000 ▶ 4,000 (by Professor) </p> <p> </p> <p>* The level of protein in the cell at any given time is controlled by<br /> 1. Rate of transcription of the gene<br /> 2. The efficiency of translation of mRNA into protein<br /> 3. The rate of degradation (half-life) of protein in the cell</p> <p> </p> <p>* Protein structure<br /> - Primary structure : sequence of specific amino acid<br /> - Secondary structure : the primary polypeptide chain gets properly folded in of alpha-helix, beta pleated sheet, random coils and turns. (The reason that there is no gamma structure - all of protein structure is consisted of similar alpha and beta structure)<br /> - Tertiary structure : secondary structure interact with each other chemically to form the 3 dimensional shape of proteins. (start : N terminal, end : C terminal)<br /> - quaternary structure : interaction between different polypeptide unit</p> <p> </p> <p>** Sequence-structure relationship - same structure from different sequences<br /><br />* Protein domain : Discrete portions of the proteins that fold independently from the rest of protein and they have their own function and serve as <u>one of the building blocks</u> of that proteins.</p> <p> </p> <p>* Determining the protein structure/polypeptide sequence by<br /> 1. X-ray crystallogrphy<br /> 2. Nuclear magnetic resonance<br /> 3. Protein predicting programmes - computer based (hard about long sequences)</p> <p> </p> <p>* Relationship between <strong>structure and function</strong><br /> - 1:1 relationship<br /> - In sepcific environment, there can be many functions in one structure<br /> - How can we predict function of protein? ▶ predict structure based on sequence ▶ predict function based on structure<br /> - ex) hydrophobicity is determined by primary and secondary structure</p> <p> </p> <p>* Post translational modifications<br /> - glycosylation<br /> - phosphorylation<br /> - sulfation</p> <hr /><p> </p> <p>* Three major areas of proteomics<br /> - Mass sepc, protein chip, protein interaction (function analysis) + protein sequencing (early stage)</p> <p> </p> <p>* Type of proteomics<br /> 1. Interation proteomics ▶ protein-protein interaction<br /> - proteins always work with interaction<br /> - ligand : anything binding to a protein (ex. cofactor)<br /> 2. Expression proteomics ▶ protein quantification</p> <p> </p> <p>* Protein database<br /> - PDB, Pfam, SCOP (classification), Swissprot, UNIPROT, Interproscan (protein domain), NCBI NR (compaction of proteins based on similarity), etc.</p> <p> </p> <p>* Protein and peptide separations done by one-dimensional / two-dimensional SDS-PAGE<br /> - 2D : run the gel vertically ▶ run the gel horizontally</p> <p> </p> <p>* We cannot sequencing protein. So, we predict by mass sepctrometer<br /> - Mass spectrometry<br /> : Identify proteins which separates charged particles or ions according to mass.<br /> : 2 types ▶ MALDI-TOF, ESI-MS-MS</p> <p> </p> <p>* Protein Microarrays<br /> - Target : something that we like to catch<br /> - a very small amount of different purified proteins are placed on a glass slide in a pattern of rows and columns. Followed addition of various types of the probe molecules, that are <strong>fluorescent dye</strong> labeled to the array ▶ count amount of dye (intensity of light) ▶ we can get information about protein type and amount</p> <p> </p> <p> </p> <p> </p> <hr /><p><span style="font-size:16px"><strong>Lecture 6. Epigenomics</strong></span></p> <p>* Epigenetic modification - something change open structure on the DNA, reversible.</p> <p>* Epigenetic modification play an important role in gene expression<br /> - DNA methylation (suppress gene expression)<br /> - DNA acetylation (activate gene expression)<br /> ▶ regulate chromatin accessibility<br /> ▶ methylation is usually occurred in CpG site<br /> ▶ DNA methyltransferase<br /> ▶ natural role : imprinting, x chromosome inactivation, heterochromatin maintenance, developmental controls, tissue specific expression controls<br /> ▶ cancer : there is different pattern of methylation (different epigenetic pathway)<br /> ▶ methylation and aging : getting order, higher methylation<br /> <br /> - Histone modification<br /> ▶ histone : open up when acetylation is occurred<br /> ▶ different residue of histone detected by different epigenetic marker<br /><br /> - RNA interference<br /> ▶ siRNA mediated heterochromatin maintenance</p> <p> </p> <p>* Studying about epigenetics<br /> - 'Bisulfite treatment of cytosine'<br /> 1. Obtain blood (control) and tissue (test) from cancer person<br /> 2. Obtain sequence and do bisulfite treatment<br /> 3. Unmethylated C is changed to U (bisulfite conversion)<br /> 4. We can find original methylated C<br /> ▶ tissue specific methylation pattern study, cancer marker finding<br /> ▶ different with genomic sequencing</p>
