Sean Flashcards
Which of the following best describes metabolomics?
a) The study of DNA sequences in an organism
b) The study of proteins expressed in a cell
c) The comprehensive study of metabolites within a biological system
d) The study of gene expression patterns
C
Why is it challenging to study 500,000 seemingly identical cells in metabolomics?
a) Metabolite levels are stable across all cells
b) Cells are always at the same metabolic stage
c) Cellular processes fluctuate, affecting metabolic consistency
d) Only genetic information determines metabolic differences
C
Which of the following methods can synchronize cells to ensure consistent pathway expression?
a) Depriving or exposing cells to excess glucose
b) Using cell checkpoint inhibitors
c) Creating resistant phenotypes through chronic exposure
d) All of the above
D
Which two technologies are most commonly used to generate metabolomics data?
a) Western blotting and ELISA
b) LC-MS and GC-MS
c) qPCR and microarrays
d) NMR and flow cytometry
B
What is the primary difference between LC and GC in chromatography?
a) LC uses a gas mobile phase, GC uses a liquid mobile phase
b) LC uses a liquid mobile phase, GC uses a gas mobile phase
c) GC has higher resolution than LC
d) LC is only used for volatile compounds
B
Which alternative metabolomics technique utilizes laser scattering to identify molecular vibrations?
a) Capillary electrophoresis
b) Raman spectroscopy
c) Diode-array detection
d) Infrared spectroscopy
B
What is the fundamental principle of mass spectrometry?
a) Separating metabolites by size
b) Ionizing molecules and measuring their mass-to-charge ratio
c) Detecting fluorescence emitted by metabolites
d) Counting the number of metabolite molecules in a sample
B
Why are different ion sources (e.g., ESI and MALDI) used in mass spectrometry?
a) They provide complementary peptide detection capabilities
b) They are interchangeable with no effect on results
c) They only work on specific types of metabolites
d) They improve DNA sequencing accuracy
A
Which of the following mass spectrometry methods has the highest resolution?
a) Quadrupole (Q)
b) Time-of-flight (TOF)
c) Fourier-transform ion cyclotron resonance (FTICR)
d) Orbitrap (OT)
C
Which factor primarily determines the separation of metabolites in chromatography?
a) Their molecular weight
b) Their retention time based on interactions with the stationary phase
c) Their fluorescence intensity
d) Their solubility in water
B
What is the role of the stationary phase in chromatography?
a) To ionize metabolites
b) To allow metabolites to separate based on their chemical interactions
c) To provide energy for metabolite movement
d) To store metabolites before analysis
B
What is a key advantage of capillary columns in gas chromatography?
a) Greater sample capacity
b) Higher resolution and sensitivity
c) Broader peaks and longer retention times
d) Lower cost and ease of use
B
Which gas is commonly used as a carrier in gas chromatography?
a) Oxygen (O₂)
b) Nitrogen (N₂)
c) Carbon dioxide (CO₂)
d) Sulfur hexafluoride (SF₆)
B
Which detector in gas chromatography is the most widely used?
a) Flame ionization detector (FID)
b) Atomic-emission detector (AED)
c) Electron-capture detector (ECD)
d) Chemiluminescence detector
A
How does a flame ionization detector (FID) work?
a) It burns organic compounds and measures resulting ionized electrons
b) It captures fluorescent signals from metabolites
c) It measures light absorption of metabolites
d) It detects metabolites through magnetic resonance
A
What is the purpose of metabolite enrichment analysis?
a) To determine the exact mass of a metabolite
b) To identify biologically meaningful groups of metabolites
c) To separate metabolites in a sample
d) To quantify all detected metabolites in a sample
B
Which statistical technique is commonly used in metabolomics to identify significant changes in metabolite levels?
a) Pairwise t-tests
b) ANOVA
c) Principal Component Analysis (PCA)
d) Hierarchical clustering
A
What does pathway analysis in metabolomics aim to accomplish?
a) To identify metabolite structures
b) To assess how metabolic pathways are altered in different conditions
c) To improve chromatography resolution
d) To sequence DNA using mass spectrometry
B
A diagram in the lecture shows a flowchart of the metabolomic analysis pipeline. What is the first step in this pipeline?
a) Statistical analysis
b) Data acquisition
c) Metabolite identification
d) Metabolic pathway visualization
B
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is used in metabolomics for what purpose?
a) Identifying protein structures
b) Predicting DNA mutations
c) Mapping metabolic pathways
d) Detecting unknown metabolites
C
What is the primary purpose of compound detection in metabolomics?
a) To modify metabolites in a sample
b) To identify and quantify metabolites in biological samples
c) To change the chemical structure of metabolites
d) To visualize metabolic pathways
B
Which technologies are primarily used for compound detection in metabolomics?
a) GC-MS and LC-MS
b) Western blot and ELISA
c) qPCR and microarrays
d) Flow cytometry and NMR
A
What is the main disadvantage of GC/LC-MS for metabolomics analysis?
a) Low resolution
b) Limited sample compatibility
c) High cost of analysis and maintenance
d) Slow data acquisition
C
What is the main goal of data preprocessing in metabolomics?
a) To remove biological metabolites from the data
b) To convert raw signals into a usable format for further analysis
c) To add artificial peaks for better detection
d) To alter the chemical properties of metabolites
B
Which software is commonly used for metabolomics data preprocessing?
a) SPSS
b) MZmine3, MAVEN, and XCMS
c) Photoshop
d) Excel
B
What is the purpose of retention time correction in data preprocessing?
a) To change the ionization state of metabolites
b) To adjust for peak drift and ensure accurate metabolite identification
c) To remove outlier metabolites
d) To artificially amplify metabolite signals
B
Why is quality control (QC) important in metabolomics data processing?
a) To determine whether data obtained is of high or low quality
b) To change metabolite concentrations for better visualization
c) To eliminate all variations in the dataset
d) To increase the number of metabolites detected
A
Which of the following is a key feature assessed in QC analysis?
a) Retention time drift
b) Sample variance
c) Metabolite fluorescence intensity
d) DNA sequence homology
B
Which method is commonly used to correct for multiple testing errors in statistical analysis?
a) Bonferroni correction
b) Fourier transform
c) Gel electrophoresis
d) Polymerase chain reaction
A
Which type of statistical analysis is used for comparing two groups of metabolomic data?
a) Principal Component Analysis (PCA)
b) Hierarchical clustering
c) T-tests and fold change analysis
d) Metabolic pathway mapping
C
What is a major limitation of univariate statistical analysis in metabolomics?
a) It cannot detect metabolite concentration changes
b) It does not account for interactions between multiple metabolites
c) It requires manual data entry
d) It is only useful for DNA sequencing
B
What is the advantage of using a volcano plot in metabolomics analysis?
a) It provides a clear visualization of significant metabolite changes
b) It removes low-concentration metabolites
c) It identifies all metabolites in a sample
d) It modifies metabolite intensities for better clarity
A
What is the primary goal of Principal Component Analysis (PCA) in metabolomics?
a) To identify significant metabolite changes between groups
b) To visualize patterns and clustering in complex data
c) To compare metabolite retention times
d) To directly sequence metabolite structures
B
Which of the following techniques is most closely related to PCA in metabolomics?
a) Mass spectrometry
b) Partial Least Squares Discriminant Analysis (PLS-DA)
c) Western blotting
d) Gel electrophoresis
B
In a PCA plot, what does clustering of quality control (QC) samples indicate?
a) Poor data quality
b) Consistent and reliable metabolomics measurements
c) High variability in metabolite detection
d) Incorrect metabolite identification
B
Which software platform is commonly used for metabolomics data integration and analysis?
a) Photoshop
b) MetaboAnalyst 6.0
c) Google Docs
d) BLAST
B
Which of the following is NOT a function of MetaboAnalyst 6.0?
a) Metabolic pathway analysis
b) Time-series analysis
c) Compound ID conversion
d) DNA sequence alignment
D
Why is it beneficial to integrate metabolomics with other omics data?
a) To provide a more comprehensive understanding of biological systems
b) To increase the number of detected metabolites artificially
c) To remove redundant metabolite signals
d) To replace mass spectrometry as the primary detection method
A
What is a major challenge in metabolomics data integration?
a) Limited availability of metabolomics instruments
b) Difficulty in visualizing multi-omics data without losing clarity
c) Metabolomics data cannot be combined with other omics
d) High cost of PCR sequencing
B
Which of the following statements best describes the “unknown unknowns” challenge in data integration?
a) There are metabolites we do not know exist yet
b) We have identified all metabolites in biological systems
c) Data integration eliminates all inconsistencies
d) Metabolomics cannot provide new biological insights
A
What does the term “Omics” refer to?
a) The study of a single biological molecule
b) The collective technologies used to analyze pools of biological molecules
c) The study of synthetic chemical compounds
d) A method of genome editing
b
Which of the following is NOT an “Omics” field?
a) Genomics
b) Proteomics
c) Meteoromics
d) Metabolomics
c
What is the primary purpose of a multi-omics approach?
a) To study biological molecules in isolation
b) To integrate different layers of biological information for a comprehensive understanding
c) To focus only on genetic mutations
d) To replace traditional diagnostics
B
Which of the following best describes metabolomics?
a) The study of metabolic pathways in bacteria
b) The systematic identification and quantification of small molecules in biological systems
c) The study of DNA methylation patterns
d) The analysis of RNA sequences in cells
B
Which type of molecules does metabolomics typically analyze?
a) DNA and RNA
b) Proteins and peptides
c) Small molecules and metabolites
d) Lipids only
C
Which statement about metabolomics is correct?
a) It provides a snapshot of an organism’s current metabolic state
b) It can predict future genetic mutations
c) It is only useful for studying bacteria
d) It cannot be integrated with other omics approaches
A
What is the Warburg Effect?
a) A process where cells generate ATP primarily through oxidative phosphorylation
b) A metabolic shift in cancer cells favoring aerobic glycolysis over oxidative phosphorylation
c) The inhibition of glycolysis in cancer cells
d) The increased use of fatty acids for energy production in normal cells
B
Which of the following is a key reason why cancer cells favor glycolysis over oxidative phosphorylation?
a) It allows for faster ATP production
b) It reduces oxygen consumption
c) It creates an acidic environment that promotes tumor progression
d) All of the above
D
The Kyoto Encyclopedia of Genes and Genomes (KEGG) is primarily used for:
a) Sequencing DNA samples
b) Mapping known metabolic pathways
c) Identifying protein structures
d) Analyzing epigenetic modifications
B
Which of the following is a key difference between targeted and non-targeted metabolomics?
a) Targeted metabolomics focuses on known metabolites, while non-targeted metabolomics explores unknown metabolites
b) Targeted metabolomics is qualitative, whereas non-targeted metabolomics is quantitative
c) Non-targeted metabolomics requires prior knowledge of metabolic pathways
d) Targeted metabolomics does not require specialized instrumentation
A
Which of the following is a limitation of non-targeted metabolomics?
a) It cannot identify novel metabolites
b) It requires specialized knowledge for data interpretation
c) It is not useful for disease biomarker discovery
d) It does not provide information about metabolite concentrations
B
Which analytical technique is commonly used for both targeted and non-targeted metabolomics?
a) Western blotting
b) Mass spectrometry (MS)
c) PCR
d) X-ray crystallography
B
What is the primary goal of metabolic pathway analysis?
a) To predict future genetic mutations
b) To understand how metabolites interact within biological systems
c) To sequence the entire human genome
d) To study protein-protein interactions
B
Which software tool is commonly used for metabolic pathway analysis?
a) BLAST
b) MetaboAnalyst
c) CRISPR-Cas9
d) PyMOL
B
What is a major challenge in metabolomics data analysis?
a) The lack of available metabolites in biological samples
b) The large volume of complex data that must be processed
c) The inability to detect any metabolites using current technology
d) The lack of interest in metabolomics research
B
Which of the following is NOT a common application of metabolomics?
a) Identifying biomarkers for disease
b) Studying the impact of nutrition on health
c) Investigating environmental influences on metabolism
d) Sequencing the human genome
D
Why is metabolomics important in clinical diagnostics?
a) It can detect metabolic imbalances associated with diseases
b) It provides immediate treatment options
c) It replaces the need for genetic testing
d) It can modify a patient’s metabolic pathways in real-time
A
Which of the following is an advantage of using metabolomics for disease diagnosis?
a) It allows for early detection of metabolic disorders
b) It eliminates the need for blood tests
c) It can predict the exact cause of every disease
d) It only works for bacterial infections
A
Which of the following is a potential future challenge in metabolomics?
a) The complete lack of interest in the field
b) The need for improved data integration with other omics fields
c) The inability to detect any metabolites
d) The lack of connection between metabolism and disease
B
Which of the following best describes the significance of metabolomics in modern biology?
a) It bridges the gap between genotype and phenotype by analyzing metabolic changes
b) It replaces the need for proteomics and genomics
c) It focuses exclusively on bacterial metabolism
d) It is only useful for agricultural research
A
