Proteomics: Definition and Techniques
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Questions and Answers

What is the primary goal of proteomics research?

  • To understand the function of mRNA molecules
  • To identify and quantify proteins expressed in a cell (correct)
  • To develop new bioinformatics tools
  • To study the structure of genes

    • Which of the following techniques is NOT used in proteomics?

  • 2-D PAGE
  • Cell culture (correct)
  • Mass spectrometry
  • Genomic database

    • Why is protein study important in therapeutic intervention?

  • Because proteins are not functional molecules in cells
  • Because proteins are easily predicted by genomic data
  • Because proteins are not subject to post-translational modification
  • Because proteins are important targets for therapeutic intervention (correct)

    • What is a limitation of using genomic data and bioinformatics to predict genes and their structures?

    <p>It is not possible to accurately predict genes and their structures</p> Signup and view all the answers

    What is the relationship between protein expression and mRNA levels?

    <p>Protein expression is not directly reflected in mRNA levels</p> Signup and view all the answers

    Why do proteins expressed by a gene vary under different conditions?

    <p>Because of post-translational modification and other factors</p> Signup and view all the answers

    What is the purpose of proteomics in biological discovery?

    <p>To deliver the basis for biological discovery and aid in drug development</p> Signup and view all the answers

    Why is proteomics established as a research field?

    <p>To address the limitations of genomic data and bioinformatics in predicting genes and their structures</p> Signup and view all the answers

    What is a common challenge when analyzing biomolecules using conventional ionization methods?

    <p>They are fragile and tend to fragment</p> Signup and view all the answers

    What is the primary difference between MALDI and SELDI?

    <p>The surface on which the sample is applied</p> Signup and view all the answers

    What is the purpose of the matrix material in MALDI?

    <p>To facilitate the desorption and ionization of the sample</p> Signup and view all the answers

    What is the goal of systems biology research?

    <p>To elucidate the complex interactions and networks within cells</p> Signup and view all the answers

    What is the advantage of using TOFMS in biomolecule analysis?

    <p>It is less sensitive to sample fragmentation</p> Signup and view all the answers

    What is the relationship between SELDI and MALDI?

    <p>SELDI is an extension of MALDI that uses a surface-bound approach</p> Signup and view all the answers

    What is the primary purpose of identifying aberrantly expressed proteins in proteomics?

    <p>To develop new mono- or combination-drug therapies</p> Signup and view all the answers

    Which of the following databases is primarily used for storing and analyzing proteomics data?

    <p>NextProt</p> Signup and view all the answers

    What is the purpose of follow-up analysis after treatment in proteomics?

    <p>To redirect treatment to the new signaling pathways</p> Signup and view all the answers

    Which of the following studies is related to the application of proteomics in cancer biomarker discovery?

    <p>Kwon, et al. (2021)</p> Signup and view all the answers

    What is the relationship between protein expression and therapeutic targets in proteomics?

    <p>Protein expression is directly related to therapeutic targets</p> Signup and view all the answers

    What is the purpose of comparing protein expression profiles between tumor samples and normal tissues in proteomics?

    <p>To identify aberrantly expressed proteins that serve as potential therapeutic targets</p> Signup and view all the answers

    What is the primary purpose of protein fractionation in proteomic analysis?

    <p>To separate proteins into different fractions based on their properties</p> Signup and view all the answers

    What is the function of trypsin in protein digestion?

    <p>To break down proteins into smaller peptides</p> Signup and view all the answers

    What is the main difference between MALDI-TOF and SELDI-TOF mass spectrometry techniques?

    <p>The type of matrix used to create ions from large molecules</p> Signup and view all the answers

    What is the purpose of 2-D PAGE in proteomic analysis?

    <p>To separate proteins based on their molecular weight and pH</p> Signup and view all the answers

    What is the role of centrifugation in protein extraction?

    <p>To separate proteins from other cellular components</p> Signup and view all the answers

    What is the primary application of mass spectrometry in proteomic analysis?

    <p>To identify proteins in a mixture</p> Signup and view all the answers

    What is the purpose of LC-MS analysis in proteomic analysis?

    <p>To analyze the digested peptides produced by protein digestion</p> Signup and view all the answers

    What is the main difference between structural and functional proteomics?

    <p>The focus of the analysis on protein structure or function</p> Signup and view all the answers

    What is the primary goal of proteomics in cancer research?

    <p>To identify specific biomarkers for cancer growth</p> Signup and view all the answers

    What is the role of PYCR2 in cancer research?

    <p>Regulating proline biosynthesis</p> Signup and view all the answers

    What is the consequence of downregulating ADH1A?

    <p>Dysregulated xenobiotics metabolism</p> Signup and view all the answers

    What is the significance of metastasis in cancer research?

    <p>It is a common feature of malignant cancer</p> Signup and view all the answers

    What is the goal of studying the metastatic cascade in cancer research?

    <p>To develop successful therapeutics for cancer</p> Signup and view all the answers

    What is the role of ADH1A in the liver?

    <p>Metabolizing xenobiotic compounds</p> Signup and view all the answers

    What is the significance of PYCR2 and ADH1A in cancer research?

    <p>They are involved in proline biosynthesis and xenobiotic metabolism</p> Signup and view all the answers

    What is the application of proteomics in cancer research?

    <p>To develop successful therapeutics for cancer</p> Signup and view all the answers

    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

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    Description

    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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