niamh Flashcards
- What is the definition of proteomics?
A) The study of DNA modifications in different cell types
B) The analysis of the entire protein complement in a given cell, tissue, or organism
C) The sequencing of all RNA transcripts in a cell
D) The study of lipid metabolism in biological systems
Answer: B) The analysis of the entire protein complement in a given cell, tissue, or organism
- How does the proteome differ from the genome?
A) The proteome remains constant, while the genome changes over time
B) The genome provides static information, whereas the proteome is dynamic
C) Proteins have no relation to genomic sequences
D) The proteome is less complex than the genome
Answer: B) The genome provides static information, whereas the proteome is dynamic
. What contributes to the increased complexity of the proteome compared to the genome?
A) Alternative splicing
B) Post-translational modifications (PTMs)
C) Alternative start and stop codons
D) All of the above
Answer: D) All of the above
- What is the primary difference between top-down and bottom-up proteomics?
A) Top-down proteomics analyzes intact proteins, while bottom-up proteomics digests proteins into peptides before analysis
B) Bottom-up proteomics provides higher resolution than top-down approaches
C) Top-down proteomics is only used for bacterial proteins
D) Bottom-up proteomics does not require mass spectrometry
Answer: A) Top-down proteomics analyzes intact proteins, while bottom-up proteomics digests proteins into peptides before analysis
- Which proteomics method separates proteins based on their charge in the first dimension and by mass in the second dimension?
A) ELISA
B) Western blotting
C) Two-dimensional gel electrophoresis (2D-PAGE)
D) Chromatography
Answer: C) Two-dimensional gel electrophoresis (2D-PAGE)
- What is the purpose of using affinity chromatography in proteomics?
A) To separate proteins based on molecular weight
B) To purify proteins using specific ligand-protein interactions
C) To analyze post-translational modifications
D) To visualize protein-protein interactions
Answer: B) To purify proteins using specific ligand-protein interactions
. Which of the following statements about mass spectrometry-based proteomics is correct?
A) It is a low-throughput technique used mainly for single proteins
B) It requires gel electrophoresis before protein identification
C) It can be used for quantitative and comparative proteomics
D) It does not require any computational analysi
Answer: C) It can be used for quantitative and comparative proteomics
- What does structural proteomics focus on?
A) Identifying all proteins expressed in a cell
B) Investigating the 3D structure of proteins and their interactions
C) Measuring mRNA expression levels
D) Identifying mutations in protein-coding genes
Answer: B) Investigating the 3D structure of proteins and their interactions
- Why are post-translational modifications (PTMs) important in proteomics?
A) PTMs regulate protein activity, stability, and interactions
B) PTMs prevent proteins from interacting with each other
C) PTMs are only relevant in prokaryotic cells
D) PTMs do not impact protein function
Answer: A) PTMs regulate protein activity, stability, and interactions
- Which of the following is NOT an example of a post-translational modification?
A) Phosphorylation
B) Glycosylation
C) Splicing
D) Ubiquitination
Answer: C) Splicing
- What is a key challenge in proteomics data analysis?
A) The vast dynamic range of protein concentrations in biological samples
B) The ability to directly sequence proteins like DNA
C) The stability of proteins in all sample conditions
D) The lack of statistical methods for analyzing protein expression
Answer: A) The vast dynamic range of protein concentrations in biological samples
- In a mass spectrometry dataset, what does a peak in the spectrum represent?
A) The amount of RNA in the sample
B) The mass-to-charge ratio (m/z) of an ionized peptide
C) The number of mRNA transcripts in a cell
D) The number of post-translational modifications present
Answer: B) The mass-to-charge ratio (m/z) of an ionized peptide
- What does a heatmap represent in proteomics data visualization?
A) The clustering of proteins based on their expression levels
B) The spatial distribution of proteins in a cell
C) The number of genes in a genome
D) The exact sequence of a protein
Answer: A) The clustering of proteins based on their expression levels
- How can proteomics contribute to precision medicine?
A) By identifying protein biomarkers for disease diagnosis and treatment
B) By replacing the need for DNA sequencing
C) By measuring only small molecules in the body
D) By analyzing only extracellular proteins
Answer: A) By identifying protein biomarkers for disease diagnosis and treatment
- Which of the following is an example of a proteomics application in agriculture?
A) Investigating plant-pathogen interactions
B) Analyzing lipid metabolism
C) Studying gene sequences in plants
D) Measuring mRNA expression
Answer: A) Investigating plant-pathogen interactions
- In biomarker discovery, why is quantitative proteomics essential?
A) It allows measurement of protein abundance differences between healthy and diseased states
B) It eliminates the need for statistical validation
C) It measures DNA expression levels
D) It only identifies single proteins
Answer: A) It allows measurement of protein abundance differences between healthy and diseased states
- In a protein interaction network graph, what do the nodes represent?
A) Individual proteins
B) DNA sequences
C) Cell membranes
D) mRNA molecules
Answer: A) Individual proteins
- In a volcano plot from a proteomics study, which proteins are considered significantly differentially expressed?
A) Proteins with low p-values and high fold change
B) Proteins that remain unchanged between conditions
C) Proteins with high p-values and low fold change
D) Proteins with no detected expression
Answer: A) Proteins with low p-values and high fold change
- What does an enrichment pathway analysis in proteomics reveal?
A) Which biological pathways are significantly affected based on protein expression changes
B) The complete genome sequence of an organism
C) The mutations present in a protein coding gene
D) The charge-to-mass ratio of all proteins
Answer: A) Which biological pathways are significantly affected based on protein expression changes
- How is proteomics applied in drug discovery?
A) By identifying potential drug targets based on protein interactions
B) By sequencing DNA to find mutations
C) By replacing mass spectrometry with PCR
D) By analyzing RNA expression only
Answer: A) By identifying potential drug targets based on protein interactions
- What is the main advantage of Western blotting in proteomics?
A) It provides high-throughput protein identification
B) It allows for the detection of low-abundance proteins
C) It does not require antibodies for protein detection
D) It separates proteins based on isoelectric point
Answer: B) It allows for the detection of low-abundance proteins
- In ion-exchange chromatography, proteins are separated based on:
A) Size and shape
B) Charge differences
C) Hydrophobicity
D) Post-translational modifications (PTMs)
Answer: B) Charge differences
- What is the key principle behind affinity chromatography?
A) Separation based on molecular weight
B) Reversible interactions between a specific ligand and a protein
C) Separation of proteins by charge
D) Direct measurement of protein concentration
Answer: B) Reversible interactions between a specific ligand and a protein
- What is the role of SDS in SDS-PAGE?
A) To break disulfide bonds in proteins
B) To neutralize protein charge and allow separation based on molecular weight
C) To digest proteins into peptides
D) To detect specific proteins in a gel
Answer: B) To neutralize protein charge and allow separation based on molecular weight
- What is the primary advantage of 2D-PAGE over 1D electrophoresis?
A) 2D-PAGE can separate thousands of proteins based on isoelectric point and molecular weight
B) 1D electrophoresis has higher resolution
C) 2D-PAGE does not require staining or visualization
D) 1D electrophoresis can analyze post-translational modifications more effectively
Answer: A) 2D-PAGE can separate thousands of proteins based on isoelectric point and molecular weight
- What is a key advantage of 2D-DIGE (Two-Dimensional Differential Gel Electrophoresis)?
A) It eliminates the need for mass spectrometry
B) It uses fluorescent dyes to simultaneously compare multiple protein samples
C) It separates proteins based on size exclusion
D) It can only detect proteins with high molecular weight
Answer: B) It uses fluorescent dyes to simultaneously compare multiple protein samples
- What is the main application of functional protein microarrays?
A) Identifying DNA mutations
B) Studying protein–protein and protein–RNA interactions
C) Measuring gene expression
D) Detecting mRNA degradation
Answer: B) Studying protein–protein and protein–RNA interactions
- In reverse-phase protein microarrays, what is being analyzed?
A) Purified proteins from a cell extract
B) Cell lysates from different conditions (e.g., disease vs. normal)
C) Only post-translationally modified proteins
D) Genomic DNA sequences
Answer: B) Cell lysates from different conditions (e.g., disease vs. normal)
- What is the primary function of mass spectrometry in proteomics?
A) To determine the mass-to-charge ratio (m/z) of ionized protein fragments
B) To amplify specific proteins from a sample
C) To separate proteins based on molecular weight
D) To sequence genomic DNA
Answer: A) To determine the mass-to-charge ratio (m/z) of ionized protein fragments
- Which of the following is a major challenge in mass spectrometry-based proteomics?
A) Difficulty in detecting low-abundance proteins
B) Inability to detect post-translational modifications
C) Lack of available software tools
D) The requirement for gel electrophoresis
Answer: A) Difficulty in detecting low-abundance proteins
- What is the role of MALDI in mass spectrometry?
A) It ionizes proteins using a laser and matrix-assisted desorption
B) It separates proteins based on hydrophobicity
C) It amplifies protein signals using PCR
D) It is only used for nucleic acid sequencing
Answer: A) It ionizes proteins using a laser and matrix-assisted desorption
**12. What is the purpose of SILAC (Stable Isotope Labeling with Amino Acids in Cell Culture)?
A) To analyze protein phosphorylation
B) To compare protein expression using metabolic labeling with light and heavy amino acids
C) To separate proteins based on mass-to-charge ratio
D) To degrade proteins for further analysis
Answer: B) To compare protein expression using metabolic labeling with light and heavy amino acids
- Which technique uses isobaric tags for relative and absolute quantitation in proteomics?
A) iTRAQ
B) SDS-PAGE
C) ELISA
D) Western blot
Answer: A) iTRAQ
*14. What is the key feature of ICAT (Isotope-Coded Affinity Tagging)?
A) It uses chemical labeling to quantify proteins in complex mixtures
B) It measures protein-DNA interactions
C) It amplifies protein signals via PCR
D) It only detects proteins larger than 100 kDa
Answer: A) It uses chemical labeling to quantify proteins in complex mixtures
- What is the primary function of bioinformatics in proteomics?
A) To manage large-scale proteomics data and identify differentially expressed proteins
B) To replace mass spectrometry
C) To analyze only single proteins
D) To sequence RNA transcripts
Answer: A) To manage large-scale proteomics data and identify differentially expressed proteins
- In a heatmap of proteomics data, what do the colors represent?
A) Levels of protein abundance
B) The pH of the sample
C) The molecular weight of proteins
D) The charge-to-mass ratio
Answer: A) Levels of protein abundance
- What does a volcano plot in proteomics data analysis show?
A) Significantly upregulated and downregulated proteins based on fold change and p-values
B) The size of different proteins
C) A chromatogram of protein separation
D) The mass spectrum of a peptide
Answer: A) Significantly upregulated and downregulated proteins based on fold change and p-values
- In a protein interaction network graph, what do the edges represent?
A) The interactions between proteins
B) The fold change of protein expression
C) The pH range of protein solutions
D) The mass-to-charge ratio
Answer: A) The interactions between proteins
- What is the purpose of machine learning in proteomics data analysis?
A) To classify proteins based on expression patterns
B) To sequence nucleic acids
C) To detect protein charge variations
D) To replace mass spectrometry
Answer: A) To classify proteins based on expression patterns
- What is a major limitation of MS-based proteomics?
A) Difficulty in detecting low-abundance proteins
B) Inability to separate proteins by charge
C) Requires RNA sequencing
D) Cannot be used in clinical applications
Answer: A) Difficulty in detecting low-abundance proteins
