36 Questions
What is the primary goal of proteomics research?
To identify and quantify proteins expressed in a cell
Which of the following techniques is NOT used in proteomics?
Cell culture
Why is protein study important in therapeutic intervention?
Because proteins are important targets for therapeutic intervention
What is a limitation of using genomic data and bioinformatics to predict genes and their structures?
It is not possible to accurately predict genes and their structures
What is the relationship between protein expression and mRNA levels?
Protein expression is not directly reflected in mRNA levels
Why do proteins expressed by a gene vary under different conditions?
Because of post-translational modification and other factors
What is the purpose of proteomics in biological discovery?
To deliver the basis for biological discovery and aid in drug development
Why is proteomics established as a research field?
To address the limitations of genomic data and bioinformatics in predicting genes and their structures
What is a common challenge when analyzing biomolecules using conventional ionization methods?
They are fragile and tend to fragment
What is the primary difference between MALDI and SELDI?
The surface on which the sample is applied
What is the purpose of the matrix material in MALDI?
To facilitate the desorption and ionization of the sample
What is the goal of systems biology research?
To elucidate the complex interactions and networks within cells
What is the advantage of using TOFMS in biomolecule analysis?
It is less sensitive to sample fragmentation
What is the relationship between SELDI and MALDI?
SELDI is an extension of MALDI that uses a surface-bound approach
What is the primary purpose of identifying aberrantly expressed proteins in proteomics?
To develop new mono- or combination-drug therapies
Which of the following databases is primarily used for storing and analyzing proteomics data?
NextProt
What is the purpose of follow-up analysis after treatment in proteomics?
To redirect treatment to the new signaling pathways
Which of the following studies is related to the application of proteomics in cancer biomarker discovery?
Kwon, et al. (2021)
What is the relationship between protein expression and therapeutic targets in proteomics?
Protein expression is directly related to therapeutic targets
What is the purpose of comparing protein expression profiles between tumor samples and normal tissues in proteomics?
To identify aberrantly expressed proteins that serve as potential therapeutic targets
What is the primary purpose of protein fractionation in proteomic analysis?
To separate proteins into different fractions based on their properties
What is the function of trypsin in protein digestion?
To break down proteins into smaller peptides
What is the main difference between MALDI-TOF and SELDI-TOF mass spectrometry techniques?
The type of matrix used to create ions from large molecules
What is the purpose of 2-D PAGE in proteomic analysis?
To separate proteins based on their molecular weight and pH
What is the role of centrifugation in protein extraction?
To separate proteins from other cellular components
What is the primary application of mass spectrometry in proteomic analysis?
To identify proteins in a mixture
What is the purpose of LC-MS analysis in proteomic analysis?
To analyze the digested peptides produced by protein digestion
What is the main difference between structural and functional proteomics?
The focus of the analysis on protein structure or function
What is the primary goal of proteomics in cancer research?
To identify specific biomarkers for cancer growth
What is the role of PYCR2 in cancer research?
Regulating proline biosynthesis
What is the consequence of downregulating ADH1A?
Dysregulated xenobiotics metabolism
What is the significance of metastasis in cancer research?
It is a common feature of malignant cancer
What is the goal of studying the metastatic cascade in cancer research?
To develop successful therapeutics for cancer
What is the role of ADH1A in the liver?
Metabolizing xenobiotic compounds
What is the significance of PYCR2 and ADH1A in cancer research?
They are involved in proline biosynthesis and xenobiotic metabolism
What is the application of proteomics in cancer research?
To develop successful therapeutics for cancer
Study Notes
Proteomics Definition and Importance
- Proteomics is a research field that involves the large-scale identification, characterization, and quantitation of proteins expressed in a cell line, tissue, or organism under given conditions.
- Proteomics helps in deciphering disease processes, provides diagnosis and prognosis of diseases, aids in drug development, and delivers the basis for biological discovery.
Proteomics Techniques
- 2-D PAGE (two-dimensional polyacrylamide gel electrophoresis)
- Mass spectrometry
- Genomic database
- Bioinformatics
- Protein microarrays
Proteins and Genes
- Proteins are functional molecules in cells and represent important targets for therapeutic intervention.
- It is impossible to accurately predict genes and their structures by genomic data and bioinformatics.
- Protein study can confirm the existence of a particular gene and characterize the protein expressed by the gene.
Proteomics Types
- Expression proteomics
- Structural proteomics
- Functional proteomics
Steps in Proteomic Analysis
- Protein extraction
- Protein fractionation
- Protein digestion
- LC-MS analysis
- Identification of proteins by LC-MS and proteome database
2-D PAGE
- Begins with electrophoresis in the first dimension and then separates the molecules perpendicularly from the first to create an electropherogram in the second dimension.
Mass Spectrometry
- Ionizes chemical species and sorts the ions based on their mass-to-charge ratio.
- Used to identify proteins in a mixture.
MALDI-TOF
- Matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation.
- Time-of-flight mass spectrometry (TOFMS) is a method of mass spectrometry in which an ion's mass-to-charge ratio is determined by a time of flight measurement.
SELDI-TOF
- Surface-enhanced laser desorption/ionization.
- Extension of MALDI-TOF.
- In SELDI, proteins of interest in a sample become bound to a surface before MS analysis.
Applications of Proteomics
- Reverse translational research strategy.
- System biology - understand cell pathways, network, and complex interaction.
- Discovery of specific biomarkers for cancer growth.
Proteomics in Cancer Research
- Identification of aberrantly expressed proteins that serve as potential therapeutic targets.
- Follow-up analysis to identify signalling reprogramming after treatment (resistance), and redirect treatment to the new signalling.
Proteomics Data Repositories
This quiz covers the basics of proteomics, including its definition, importance, and various techniques used in the field. Topics include 2-D PAGE, protein identification, and more.
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