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6.5 Expression & Proteomics — Test 1
Q1. Proteomics is the study of:✓ The entire set of expressed proteins in a cell/organism
Q2. Eastern blotting detects:✓ Protein post-translational modifications (e.g. carbohydrate/lipid epitopes)
Q3. Western blotting separates and detects:✓ Proteins (separated by SDS-PAGE, transferred, probed with antibody)
Q4. Protein-RNA binding is determined by:✓ Northwestern blotting
Q5. Protein-protein interactions are identified by:✓ The yeast two-hybrid system (and co-IP/FRET)
Q6. Pulse-chase labelling is used to determine:✓ The fate/processing/turnover of newly synthesized proteins
Q7. Southwestern blotting is used for:✓ Identifying DNA-binding proteins / their genes
Q8. Splicing (intron removal) of a gene's transcript is monitored by:✓ Northern hybridization (size shift of spliced vs unspliced)
Q9. In Western blotting transfer, the gel-membrane sandwich order (toward the membrane) is:✓ Filter paper – gel – membrane – filter paper (protein moves from gel toward membrane)
Q10. Which is NOT a DNA-sequencing method?✓ MALDI-TOF (a mass-spectrometry method)
Q11. Which technique gives genome-wide (global) gene-expression profiling?✓ DNA microarray (and RNA-seq)
Q12. Quantification of a specific mRNA is best done by:✓ Real-time (quantitative) PCR
Q13. Probing gel-separated proteins with a radiolabelled BAIT protein to find interactors is:✓ Far-Western blotting
Q14. Which detects IN VIVO DNA-protein interactions across the genome?✓ Chromatin immunoprecipitation (ChIP/ChIP-seq)
Q15. To identify the DNA sequence bound by a protein, use:✓ DNA footprinting
Q16. Translating mRNAs (those actively on ribosomes) are identified by:✓ Ribosome profiling (Ribo-seq)
6.5 Expression & Proteomics — Test 2
Q17. Genome-wide DNA-protein interactions are assessed by:✓ ChIP-on-chip (and ChIP-seq), plus EMSA/Southwestern at smaller scale
Q18. The best way to obtain a full-length, properly folded mammalian secretory protein is:✓ Cloning the gene with an affinity tag, expressing in a suitable (eukaryotic) host, and affinity-purifying
Q19. Sub-cellular localization, gene copy number, and protein-protein interaction are matched respectively to:✓ Immunofluorescence; real-time PCR; yeast two-hybrid
Q20. Protein-protein interactions can be detected by:✓ All of these
Q21. To detect the ABSENCE of a particular gene in an individual, use:✓ Southern blotting and PCR
Q22. The length of DNA protected by a bound protein is determined by:✓ DNA footprinting
Q23. Mass spectrometry in proteomics is mainly used to:✓ Identify and characterise proteins/peptides by mass (and PTMs)
Q24. 2D gel electrophoresis separates proteins by:✓ Isoelectric point (1st dimension) then size (2nd dimension)
Q25. Gene expression CANNOT be determined by:✓ Southern blot hybridization (detects DNA, not expression)
Q26. Molecules separated by electrophoresis are transferred to membranes in:✓ Southern, Northern and Western blotting (all transfer to membrane)
Q27. The protein-binding site on DNA is identified by:✓ DNA footprinting / mobility shift (EMSA)
Q28. miRNA targets in a cell are identified by:✓ HITS-CLIP (and RNA immunoprecipitation)
Q29. FRET (Förster resonance energy transfer) is used to study:✓ Close proximity/interaction between two labelled molecules (e.g. proteins) in vivo
Q30. Affinity tags (His, GST, FLAG) on a recombinant protein are used for:✓ One-step purification (and detection) of the expressed protein
Q31. A key advantage of RNA-seq over microarray for expression profiling is:✓ It can detect novel transcripts and has a wider dynamic range without prior probes