Proteomics

Question 1

What is a proteome?

Answer 1

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

Question 2

What is proteomics?

Answer 2

It is the study of structure, activity, function, modification, localization, and interaction of proteins

Question 3

What is the most significant impact of alternate splicing of pre-mRNA on the proteome?

Answer 3

From one sequence, multiple proteins can form

Question 4

What are the four levels of protein structure?

Answer 4

1. Primary
2. Secondary
3. Tertiary
4. Quaternary

Question 5

What are the characteristics of primary structure of proteins?

Answer 5

This is the amino acid sequence in a polypeptide chain
ex. MTSCYFGHNALTDFL

Question 6

What are the characteristics of secondary structure of proteins?

Answer 6

This level involves the specific structures due to proper folding of the polypeptide chain
ex. a-helix, b-sheet, turns, and loops

Question 7

What are the characteristics of tertiary structure of proteins?

Answer 7

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

Question 8

What are the quaternary structure of proteins?

Answer 8

This level shows the interaction between different polypeptide subunits

Question 9

Why study proteomics?

Answer 9

• 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

Question 10

What are the three types of proteomics?

Answer 10

• Expression proteomics
• Structural proteomics
• Functional proteomics

Question 11

What are some characteristics of expression proteomics?

Answer 11

It is the quantitive study of protein expression among different samples (they differ by some variables)

Question 12

What are some characteristics of structural proteomics?

Answer 12

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

Question 13

What are some characteristics of functional proteomics?

Answer 13

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

Question 14

What equipment is used when conducting proteomics studies?

Answer 14

• Electrophoresis (1D and 2D)
• Liquid chromotography (FPLC and HPLC)
• Mass spectrometry
• Immunoassays
• X-ray crystallography and NMR spectroscopy

Question 15

What are the steps of proteomics analysis?

Answer 15

1. Sample collection (need to be in cryoprotection if being stored)
2. Separation of proteins by 2D electrophoresis
3. Protein characterization
4. Identification of proteins by MS and other techniques
5. Data storage and comparison against database for matches
6. Data analysis using bioinformatics

Question 16

What is the point of separating proteins in proteomics?

Answer 16

Helps determine what protein functions are different and network of interactions

Question 17

How does 2D electrophoresis separate proteins?

Answer 17

2D electrophoresis separates proteins based on size and charge

Review slide 17

Question 18

What are the advantages of X-ray crystallography for sequencing proteins?

Answer 18

• High resolution atomic structures for proteins
• Valuable information on protein functions and interactions
• Essential for structure-based drug design

Question 19

What are some disadvantages associated with X-ray crystallography?

Answer 19

• Time consuming
• Expensive
• Special training and equipment (ex. Synchotron)

Question 20

What is the protein microarray?

Answer 20

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

Question 21

What are some free protein databases?

Answer 21

• NCBI (provides protein sequencing information)
• RCSB (shows positions of sites of interest)