proteomics Flashcards
What are the basics of proteomics?
DNA is transcribed into RNA
RNA is translated into proteins
proteins go under enzymatic reactions which leads us to metabolite
what is proteomics
the study of all proteins in a cell, organism, tissue etc
why should we look at proteomics?
we can use proteins from animal cells, samples etc for: drug resistance, diagnostics, disease progression and vaccination development
is proteomics part of functional genomics?
yes. it is part of it as it deals with how the genome functions
what samples do you need for proteomics?
infected and non-infected samples
what are the approaches of proteomics?
Examine proteins through separation and identification
PAGE - seperate proteins
LC - seperate proteins
MS/MS - identify
why do we need genomic support
allows for proteomic success
it is based on protein identification
proteomics cannot be done without a complete genome
what happens if you dont have a full genome?
use transcriptome support - helps find a range of proteins that people are able to map the data too
why should you study protein expression?
the central dogma of DNA - gets transcribed into RNA which translates into proteins.
levels of RNA produced does not tally up to the amount of proteins
why doesnt RNA tally up to the same amount of proteins
just like RNA proteins an be stored, broken down meaning RNA cannot correlate to the protein levels
what are the steps of gene expression
starts in nuclues
DNA transcribed into RNA transcripted
RNA processing control then turns to mRNA
mRNA is shuttled to the cytosol
mRNA is then translated to proteins some will be degraded, some will be shuttled to protein production
does mRNA level correlate to protein levels?
there is no real correlation showing the level of abundances are equal to RNA abundance
what does the analysis of protein abundance involve?
seperation of complex moisture
ID components
quantitavel analysis
what does current proteomics tehnologies use?
catalogues - gives a base level of knowledge of proteins expressed in the sample
differential expression - understanding of how proteins change as a result of a conditionw
what are the challenges of proteomics
depends on the sample depends on the amount of proteins.
the dynamic range of proteins - some ases need small amount of proteins but others need a bunch
what samples are best for proteomics?
stool sample
blood - look at antibodies
urine - non-invasive
saliva
what are the current proteomic technologies?
seperation - SDS-PAGE and liquid chromatography
identification - peptide mass fingerprintt and tandem mass spectromy
how does the sepeation period work in protemoics?
seperate through exploiting its size
look at molecular weight
or
exploit protein by its charge
how do you exploit proteins by its charge?
put them on an immobilsied gradient
run electrode through it
seperates protein from positive to negative charge
then seperate the proteins by size to really break down the proteins
what do you use to identify proteins
use mass projectromer to measure the weight/size of proteins
what is trypsin digestion
the process where proteins are chopped into peptides
why do we add trypsin to the protein?
it is easue to sequence a peptide than a whole protien
how does trypsin work?
take protein and add trypsin
cuts protein into equal sections
allows us to take each individual bit to identify and then sequence it at the end
what is peptide mass fingerprinting
first step of proteomics
looks at the characteristic patterns in data to assign protein identification
