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1、ProteomicsProteomicsandandmass sPectroscoPymass sPectroscoPyProteomicsProteomics The dream of having genomes completely sequenced is now a reality.The complete sequence of many genomes including the human one is known.However,the understanding of probably half a million human proteins encoded by les
2、s than 30,000 genes is still a long way away and the hard work to unravel the complexity of biological systems is yet to come.A new fundamental concept called proteome(PROTEin complement to a genOME)has recently emerged.ProteomicsProteomics should drastically help to unravel biochemical and physiolo
3、gical mechanisms of complex multivariate diseases at the functional molecular level.The discipline of proteomics has been initiated to complement physical genomic research.The term“proteome”was coined in 1994 by an Australian graduate student(Mark Wilkins),it has come to be used and defined in a var
4、iety of different waysProteomicsProteomics Definition-The identification,characterization and quantification of all proteins involved in a particular pathway,organelle,cell,tissue,organ or organism that can be studied in concert to provide accurate and comprehensive data about that system.Or-A compl
5、ete description of proteins expressed in any given cell at any given time ProteomicsProteomics A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation It can also be useful to conside
6、r an organisms complete proteome,which can be conceptualized as the complete set of proteins from all of the various cellular proteomes.This is very roughly the protein equivalent of the genome.The term proteome has also been used to refer to the collection of proteins in certain sub-cellular biolog
7、ical systems.For example,all of the proteins in a virus can be called a viral proteome.ProteomicsProteomics So where are we in our understanding of the cell?31-60 K total genes in the human genome with little difference between the fruit fly and us!Where does the diversity come from?Answer:Its the p
8、roteins!ProteomicsProteomics The proteome is larger than the genome,especially in eukaryotes,in the sense that there are more proteins than genes.This is due to:alternative splicing of genes post-translational modifications like glycosylation or Phosphorylation.alternative sPlicing of alternative sP
9、licing of genesgenes A given piece of pre-mRNA which has been transcribed from one gene can be chopped and reconnected in different ways to yield various new mRNAs which then exit the nucleus to be translated in the cytoplasm.When the pre-mRNA has been transcribed from the DNA,it includes several in
10、trons and exons.The regulation and selection of splice sites is done by Serine/Arginine-residue proteins alternative sPlicing of genesalternative sPlicing of genes Four known modes A-Alternative selection of promoters:this is the only method of splicing which can produce an alternative N-terminus do
11、main in proteins.In this case,different sets of promoters can be spliced with certain sets of other exons.B-Alternative selection of cleavage/polyadenylation sites:this is the only method of splicing which can produce an alternative C-terminus domain in proteins.In this case,different sets of polyad
12、enylation sites can be spliced with the other exons.alternative sPlicing of genesalternative sPlicing of genes Four known modes C-Intron retaining mode:Instead of splicing out an intron,the intron is retained in the mRNA transcript.However,the intron must be properly encoding for amino acids.The int
13、rons code must be properly expressible,otherwise a stop codon or a shift in the reading frame will cause the protein to be non-functional.D-Exon cassette mode:Certain exons are spliced out to alter the sequence of amino acids in the expressed protein.Post-translational Post-translational modificatio
14、nsmodifications PTMs involving addition include:Acetylation-the addition of an acetyl group,usually at the N-terminus of the protein Alkylation-the addition of an alkyl group(e.g.methyl,ethyl)Methylation-the addition of a methyl group,usually at lysine or arginine residues.(This is a type of alkylat
15、ion.)Biotinylation-acylation of conserved lysine residues with a biotin appendage Glutamylation-covalent linkage of glutamic acid residues to tubulin and some other proteins.Post-translational Post-translational modificationsmodifications PTMs involving addition include:Glycylation-covalent linkage
16、of one to more than 40 glycine residues to the tubulin C-terminal tail Glycosylation-the addition of a glycosyl group to either asparagine,hydroxylysine,serine,or threonine,resulting in a glycoprotein Isoprenylation-the addition of an isoprenoid group(e.g.farnesol and geranylgeraniol)Lipoylation-attachment of a lipoate functionality Post-translational Post-translational modificationsmodifications PTMs involving addition include:Phosphopantetheinylation-the addition of a 4-phosphopantetheinyl moi
