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veterinary infectious diseases > proteomics > Flashcards

proteomics Flashcards

1
Q

What are the basics of proteomics?

A

DNA is transcribed into RNA
RNA is translated into proteins
proteins go under enzymatic reactions which leads us to metabolite

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2
Q

what is proteomics

A

the study of all proteins in a cell, organism, tissue etc

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3
Q

why should we look at proteomics?

A

we can use proteins from animal cells, samples etc for: drug resistance, diagnostics, disease progression and vaccination development

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4
Q

is proteomics part of functional genomics?

A

yes. it is part of it as it deals with how the genome functions

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5
Q

what samples do you need for proteomics?

A

infected and non-infected samples

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6
Q

what are the approaches of proteomics?

A

Examine proteins through separation and identification
PAGE - seperate proteins
LC - seperate proteins
MS/MS - identify

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7
Q

why do we need genomic support

A

allows for proteomic success
it is based on protein identification
proteomics cannot be done without a complete genome

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8
Q

what happens if you dont have a full genome?

A

use transcriptome support - helps find a range of proteins that people are able to map the data too

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9
Q

why should you study protein expression?

A

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

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10
Q

why doesnt RNA tally up to the same amount of proteins

A

just like RNA proteins an be stored, broken down meaning RNA cannot correlate to the protein levels

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11
Q

what are the steps of gene expression

A

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

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12
Q

does mRNA level correlate to protein levels?

A

there is no real correlation showing the level of abundances are equal to RNA abundance

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13
Q

what does the analysis of protein abundance involve?

A

seperation of complex moisture
ID components
quantitavel analysis

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14
Q

what does current proteomics tehnologies use?

A

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

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15
Q

what are the challenges of proteomics

A

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

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16
Q

what samples are best for proteomics?

A

stool sample
blood - look at antibodies
urine - non-invasive
saliva

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17
Q

what are the current proteomic technologies?

A

seperation - SDS-PAGE and liquid chromatography
identification - peptide mass fingerprintt and tandem mass spectromy

18
Q

how does the sepeation period work in protemoics?

A

seperate through exploiting its size
look at molecular weight
or
exploit protein by its charge

19
Q

how do you exploit proteins by its charge?

A

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

20
Q

what do you use to identify proteins

A

use mass projectromer to measure the weight/size of proteins

21
Q

what is trypsin digestion

A

the process where proteins are chopped into peptides

22
Q

why do we add trypsin to the protein?

A

it is easue to sequence a peptide than a whole protien

23
Q

how does trypsin work?

A

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

24
Q

what is peptide mass fingerprinting

A

first step of proteomics
looks at the characteristic patterns in data to assign protein identification

25
Q

how does peptide mass fingerpring identification work

A

match measured peptide masses to data
calculates peptide masses
protein/nucleotide sequence data bases
needs a good predicted data base for it to work

26
Q

what is mass spectotometry?

A

comparison of peptides on a data base of all known proteins and then match back the proteins to see which one matches

27
Q

in peptide mass freqeucning what happens after electrophoresis?

A

look at protein - see which one matches the marker protein
cut out the well with the protein still in it using a scalpel
add trypsin to protein
use solution/peptide and put it in mass spectrometry to measure weight of peptide

28
Q

what is tandem mass spectrometry?

A

get protein of intrest
use trypsin to turn protein into peptides
measure weight
peptides then go into another section of the mass spectrometer where it collides with things to make small fragments

29
Q

why is tandem spectromy good?

A

break the proteins on the back bone - so protein breaks are predictable

30
Q

how does protein sequencing work? Tandem

A

two mass analyser in series
collision of cells with protein breaks them up
fragmentation then occurs - peptide bonds split between amino acids, it creates daughter ions
daughter ion masses are measured and matched to databases

31
Q

what is liquid chromatography

A

seperates proteins in a special way

32
Q

what are the phases of liquid chromatography

A

protein liquid - mobile phase
pass the protein over soemthing to seperate them out which is the stationary phase

33
Q

what ways can we use liquid chromatography to seperate the proteins?

A

size
charge
hydrophobicity

34
Q

why do we use liquid chromatography

A

get rid of gel approaches
limitations of 2DE overcome
use large sample volumes - see smaller changes
can use challenging protein samples such as membrane based proteins

35
Q

what is good about liquid chromatography?

A

analyse proteins and peptides
often ion exhange and reverse phase - used to seperate proteins
resolution comparible to 2DE

36
Q

Tandem thingy

A

take complex protein
feed mixture into chromatography separation
it will seperate these proteins between size, charge etc
you identify the peptides
sequence the amino acids
search it against the database

37
Q

what is the probelm with proteomics

A

not all proteins can get looked in a sample as some proteins can get lost in the mixture

38
Q

what is GelC approaches?

A

combination os SDS-PAGE, 2DLC
it offers:
gel base
gel free
gel and chromatography

39
Q

how does GelC work?

A

seperate proteins - height charge etc peptide mass fingerpring
cut gel into chucnks
digest them in trypsin
take small fragments of complete sample to get more proteins sequenced - allows you to see them in detail

40
Q

What sample should you use for lice proteomics

A

Skin samples - skin biopsy
Lice samples
To understand the host lice interaction to disrupt this
Compare the proteomic profiles of both lie and host to identify drug induced changes

veterinary infectious diseases (6 decks)

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