Proteomics Flashcards
What is a proteome?
It is the total set of proteins from a cell, tissue, or organism under a specific condition
Can contain from 10,000 to several billion different proteins
What is proteomics?
It is the study of structure, activity, function, modification, localization, and interaction of proteins
What is the most significant impact of alternate splicing of pre-mRNA on the proteome?
From one sequence, multiple proteins can form
What are the four levels of protein structure?
- Primary
- Secondary
- Tertiary
- Quaternary
What are the characteristics of primary structure of proteins?
This is the amino acid sequence in a polypeptide chain
ex. MTSCYFGHNALTDFL
What are the characteristics of secondary structure of proteins?
This level involves the specific structures due to proper folding of the polypeptide chain
ex. a-helix, b-sheet, turns, and loops
What are the characteristics of tertiary structure of proteins?
This is the 3D folding of a polypeptide due to interactions of the secondary structures
What are the quaternary structure of proteins?
This level shows the interaction between different polypeptide subunits
Why study proteomics?
- Changes in gene or mRNA transcript does not always proportionally translate into fold change of the encoded protein due to mRNA degradation or insufficiency of protein translation
- Due to alternative splicing, a multi-exon gene may encode different proteins
- Proteins may have to undergo postranslational modifications such as glycosylation and phosphorylation
- One protein may carry out multiple functions, and multiple proteins may carry out the same function
What are the three types of proteomics?
- Expression proteomics
- Structural proteomics
- Functional proteomics
What are some characteristics of expression proteomics?
It is the quantitive study of protein expression among different samples (they differ by some variables)
What are some characteristics of structural proteomics?
It is the determination of 3D protein structures on a genome-wide scale and application of structural information for prediction of functions
What are some characteristics of functional proteomics?
It is the characterization of the molecular protein network in a cell, tissue or organism
What equipment is used when conducting proteomics studies?
- Electrophoresis (1D and 2D)
- Liquid chromotography (FPLC and HPLC)
- Mass spectrometry
- Immunoassays
- X-ray crystallography and NMR spectroscopy
What are the steps of proteomics analysis?
- Sample collection (need to be in cryoprotection if being stored)
- Separation of proteins by 2D electrophoresis
- Protein characterization
- Identification of proteins by MS and other techniques
- Data storage and comparison against database for matches
- Data analysis using bioinformatics
What is the point of separating proteins in proteomics?
Helps determine what protein functions are different and network of interactions
How does 2D electrophoresis separate proteins?
2D electrophoresis separates proteins based on size and charge
Review slide 17
What are the advantages of X-ray crystallography for sequencing proteins?
- High resolution atomic structures for proteins
- Valuable information on protein functions and interactions
- Essential for structure-based drug design
What are some disadvantages associated with X-ray crystallography?
- Time consuming
- Expensive
- Special training and equipment (ex. Synchotron)
What is the protein microarray?
It is a high throughput, miniaturized multi-analyte, solid-phased immunoassay
Thousands of proteins are immobilized on a protein chip
Protein microarrays can generate information on protein interactions and functions
What are some free protein databases?
- NCBI (provides protein sequencing information)
- RCSB (shows positions of sites of interest)
