Question Bank: Genomics & Proteomics
A proteome is the complete set of proteins expressed by a cell, tissue, or organism at a specific time. The genome is relatively constant, whereas the proteome is dynamic and changes with cell type, environment, and disease state.
Proteomics is more complex because proteins vary in abundance, stability, structure, and undergo post-translational modifications. In addition, protein expression changes over time and differs between tissues, unlike the relatively stable genome.
Mass spectrometry is used to identify and quantify proteins by measuring their mass-to-charge ratio. It allows detection of proteins, their abundance, and post-translational modifications even at very low concentrations.
Post-translational modifications are chemical changes made to proteins after translation that regulate their activity and stability. Examples include phosphorylation and glycosylation.
The Human Protein Atlas (HPA) is a comprehensive, open-access database that maps where and when proteins are expressed in the human body, down to the tissue, cell, and even subcellular level. Its primary use is to provide spatial and functional context to genomic and proteomic data, allowing researchers to see if a protein of interest is present in a specific organ, cell type, or disease state—information crucial for understanding protein function, validating disease biomarkers, and identifying new therapeutic targets.
(Choose the ONE best answer)
Part C: True or False (1 mark each)
[E] Answer True or False for the following statements.
Part C: Answer Key
Part D: Fill in the Blanks (1 mark each)
Fill in the appropriate term in each blank. Difficulty Easy (E)
Part D: Answer Key
E. Critical Thinking / Higher-Order Questions (5 questions) (H)
Answer in (6–10 sentences)
46. Why does proteomics provide more functional insight than genomics alone? (H)
Genomics reveals which genes are present, but it does not show whether those genes are actively producing proteins. Proteomics directly measures proteins, which carry out cellular functions. Protein levels, modifications, and interactions change in response to disease and environment, providing a real-time picture of cellular activity that genomics alone cannot offer.
47. How can abnormal protein activity occur despite normal gene expression? (H)
Normal gene expression does not guarantee normal protein function. Proteins may be improperly folded, modified incorrectly, degraded rapidly, or inhibited by other molecules. Post-translational modifications and protein–protein interactions can alter activity without changes in gene expression.
48. How can UniProt, PDB, AlphaFold, and HPA be integrated to study a cancer drug target? (H)
UniProt identifies protein function and disease relevance. PDB provides experimentally determined structures for drug binding analysis. AlphaFold predicts full protein structures when experimental data are missing. The Human Protein Atlas shows tissue and cancer-specific expression. Together, these databases enable identification, structural analysis, and clinical relevance assessment of drug targets.
49. Why are protein signatures more reliable than single biomarkers? (H)
Single biomarkers can give false-negative or false-positive results due to biological variability. Protein signatures analyze multiple proteins simultaneously, increasing sensitivity and specificity. This combined approach better reflects disease complexity and improves diagnostic accuracy.
50. How do post-translational modifications contribute to disease? (H)
Post-translational modifications regulate protein activity, localization, and stability. Abnormal modifications can activate oncogenes or inactivate tumor suppressors. For example, excessive phosphorylation of signaling proteins can lead to uncontrolled cell division and cancer.
51. Define the term "post-translational modification" (PTM) and explain why mapping PTMs is a core objective of proteomics, rather than genomics.
A post-translational modification (PTM) is a covalent, often reversible, chemical modification to a protein after translation (e.g., phosphorylation, glycosylation). Proteomics focuses on PTMs because they directly regulate protein function, activity, localization, and interactions—critical functional information not encoded in the static DNA sequence studied by genomics.