Proteomics

Question 1

What is proteomics?

Answer 1

large scale analysis of a proteome

Question 2

What is a proteome?

Answer 2

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

Question 3

True or false: proteomics is more complex and complicated than genomics and transcriptomics

Answer 3

true

Question 4

What is proteomics used for?

Answer 4

to study structure, activity, function, modification, localization and interaction of proteins

Question 5

Briefly describe the steps in protein synthesis.

Answer 5

DNA–>RNA–>mRNA–>protein
protein can then undergo: proteolysis, modification, compartmentalization

Question 6

What is primary structure?

Answer 6

amino acid sequence in a polypeptide chain

Question 7

What is secondary structure?

Answer 7

specific structures due to proper folding of the polypeptide chain
-alpha helix, B sheets, turns, loops

Question 8

What is tertiary structure?

Answer 8

3D folding of a polypeptide due to interactions of the secondary structures

Question 9

What is a quaternary structure?

Answer 9

interaction between different polypeptide units

Question 10

Why do we study proteomics?

Answer 10

1. fold change of a gene or mRNA transcript does not always proportionally translate into fold change of the protein
2. due to pre-mRNA alternative splicing, a multi-exon gene may encode different proteins
3. proteins may have to undergo post translation modifications to be fully functional
4. some proteins may carry out biological functions only at specific sites inside the cells
5. one protein may carry out multiple functions, and multiple proteins may carry out the same function

Question 11

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?

Answer 11

mRNA degradation
insufficiency of protein translation

Question 12

What are the types of proteomics?

Answer 12

expression proteomics
structural proteomics
functional proteomics

Question 13

What is expression proteomics?

Answer 13

quantitative study of protein expression among different samples
-the samples differ by some variables

Question 14

What is structural proteomics?

Answer 14

determination of 3D protein structures on a genome-wide scale and application of structural information for prediction of functions

Question 15

What is functional proteomics?

Answer 15

characterization of the molecular protein network in a cell, tissue or organism

Question 16

Differentiate top-down and bottom-up.

Answer 16

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

Question 17

What are the key technologies used in proteomics?

Answer 17

electrophoresis (1D and 2D)
liquid chromatography (FPLC and HPLC)
mass spectrometry
immunoassays
X-ray crystallography and NMR spectroscopy

Question 18

What are the steps in proteomics analysis?

Answer 18

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

Question 19

What are the advantages and disadvantages of X-ray crystallography?

Answer 19

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

Question 20

Describe protein microarray.

Answer 20

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