Proteomics Flashcards
What is proteomics?
large scale analysis of a proteome
What is a proteome?
the total set of proteins from a cell, tissue or organism under a specific condition
-theoretically may contain from 10,000 to several billion different proteins
True or false: proteomics is more complex and complicated than genomics and transcriptomics
true
What is proteomics used for?
to study structure, activity, function, modification, localization and interaction of proteins
Briefly describe the steps in protein synthesis.
DNA–>RNA–>mRNA–>protein
protein can then undergo: proteolysis, modification, compartmentalization
What is primary structure?
amino acid sequence in a polypeptide chain
What is secondary structure?
specific structures due to proper folding of the polypeptide chain
-alpha helix, B sheets, turns, loops
What is tertiary structure?
3D folding of a polypeptide due to interactions of the secondary structures
What is a quaternary structure?
interaction between different polypeptide units
Why do we study proteomics?
- fold change of a gene or mRNA transcript does not always proportionally translate into fold change of the protein
- due to pre-mRNA alternative splicing, a multi-exon gene may encode different proteins
- proteins may have to undergo post translation modifications to be fully functional
- some proteins may carry out biological functions only at specific sites inside the cells
- one protein may carry out multiple functions, and multiple proteins may carry out the same function
What are two reasons why a fold change of a gene or mRNA transcript does not always proportionally translate into fold change of the encoded protein?
mRNA degradation
insufficiency of protein translation
What are the types of proteomics?
expression proteomics
structural proteomics
functional proteomics
What is expression proteomics?
quantitative study of protein expression among different samples
-the samples differ by some variables
What is structural proteomics?
determination of 3D protein structures on a genome-wide scale and application of structural information for prediction of functions
What is functional proteomics?
characterization of the molecular protein network in a cell, tissue or organism
Differentiate top-down and bottom-up.
top-down:
-have a mixture of proteins
-proteins are charged, sent into mass spec
-harder the more proteins you have
bottom-up:
-using enzymes/trypsins to cut large proteins into peptides
-then ionize and use mass spec
-all modifications are lost but its cheaper
What are the key technologies used in proteomics?
electrophoresis (1D and 2D)
liquid chromatography (FPLC and HPLC)
mass spectrometry
immunoassays
X-ray crystallography and NMR spectroscopy
What are the steps in proteomics analysis?
sample collection, handling and storage
separation of proteins by 2D-electrophoresis
protein characterization
identification of proteins by mass spec and other techniques
data storage and comparison with database
data analysis using bioinformatics tools to advance studies in various fields
What are the advantages and disadvantages of X-ray crystallography?
advantages:
-high resolution of atomic structures for proteins
-valuable information on protein functions and interactions
-essential for structure-based drug design
disadvantages:
-time consuming
-expensive
-special training and equipment
Describe protein microarray.
high throughput method
miniaturized multi-analyte, solid-phased immunoassay
thousands of proteins are immobilized on a protein chip
used for purification, expression profiling and interaction profiling of proteins
generate information on protein interactions and functions
