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6.4 Genomics & Sequencing β Test 1
Q1. The sugar pucker of B-form DNA is:β C2'-endo
Q2. Bacterial genomes avoid self-cleavage by their own restriction enzymes through:β Methylation at the restriction sites (modification)
Q3. Sanger (dideoxy) sequencing depends critically on:β Chain termination by dideoxynucleotides (lacking 3'-OH)
Q4. GFP for fluorescence microscopy is derived from:β Jellyfish (Aequorea victoria)
Q5. Homopolymer tailing (adding complementary homopolymer tails) is commonly used for:β Constructing cDNA libraries (and joining blunt fragments)
Q6. Genome-wide global gene-expression profiling is done by:β DNA microarray and NGS whole-transcriptome (RNA-seq)
Q7. In a 100 kb fragment, a 6-bp cutter is expected to have about:β ~24 sites (100000/4096)
Q8. In Sanger sequencing, which statement is correct?β ddNTPs (chain terminators) are included at low levels with normal dNTPs
Q9. The Maxam-Gilbert sequencing method is based on:β Base-specific chemical modification and cleavage of end-labelled DNA
Q10. Orientation of a cloned insert in a plasmid is best checked by:β PCR with one gene-specific and one vector-specific primer
Q11. The 'Cot' value (renaturation kinetics) is:β Concentration Γ time of renaturation (DNA conc Γ time)
Q12. EcoRI (GAATTC) digesting the ~4.6 Mb E. coli genome gives about:β ~1123 fragments (4.6Γ10βΆ/4096)
Q13. Enzymes recognising 4, 6, 8 bp (P, Q, R): site frequency order is:β P > Q > R (shorter = more frequent)
Q14. TILLING (a reverse-genetics functional-genomics method) uses:β Chemical mutagenesis (e.g. EMS) followed by mutation screening
Q15. The NGS read-alignment tool used to map reads to a reference genome is:β BWA
6.4 Genomics & Sequencing β Test 2
Q16. Which NGS technology uses 'sequencing by ligation'?β SOLiD
Q17. Introns in a gene are revealed by:β Comparing genomic DNA and cDNA sequences (or DNA-mRNA hybridization R-loops)
Q18. Which enzyme has a 4-bp recognition sequence?β Sau3A (GATC)
Q19. A correct statement about TA cloning vectors:β Double-stranded circular vectors with 3'-T overhangs to clone PCR products bearing 3'-A
Q20. Which is NOT true of type-II restriction enzymes?β The recognition sequence is asymmetric (it is usually palindromic)
Q21. A method to quantitatively define a transcriptome including rare transcripts is:β Serial Analysis of Gene Expression (SAGE) / RNA-seq
Q22. Differentially expressed genes between normal and cancer cells are best found by:β RNA-seq
Q23. DNA methylation levels are mapped by:β Bisulfite sequencing
Q24. Which statement about a point mutation is INCORRECT?β It is easily detected by Southern blotting
Q25. The Z-conformation of DNA is favoured by:β Alternating purine-pyrimidine (e.g. GC repeats) with syn-guanine and high salt
Q26. Which information CANNOT be obtained from a Northern blot?β The location of restriction sites in a gene
Q27. The rate of transcription of genes is measured by:β GRO-seq (global run-on)
Q28. Which sequence is most likely a restriction site (palindrome)?β GTCGAC (palindrome β SalI)
Q29. Which technique is NOT suitable to detect specific DNA/RNA sequences?β IHC (immunohistochemistry β detects proteins)
Q30. For PstI (CTGCAG) in an 80%-GC genome, the restriction-site frequency is:β Higher (the GC-rich site is favoured in a GC-rich genome)
6.4 Genomics & Sequencing β Test 3
Q31. Maxam-Gilbert DNA sequencing essentially involves:β End-labelling followed by base-specific chemical cleavage and electrophoresis
Q32. Differential gene expression is quantified by colour/signal intensity in:β DNA microarray
Q33. Topoisomerase-I (TOPO) cloning of PCR products works because:β Topoisomerase I is pre-attached to the linearized vector ends and ligates the PCR product
Q34. Which statement set is correct? (EcoRI = GAATTC; dideoxy sequencing uses one primer; microarray probes are fluorescently labelled)β I, II and IV (EcoRI=GAATTC; one primer; fluorescent microarray probe)
Q35. Reverse genetics is the approach where one:β Starts from a known gene and disrupts it to find the phenotype/function
Q36. Physical association of a miRNA with its target mRNA is established by:β HITS-CLIP (crosslinking + immunoprecipitation + sequencing)
Q37. Polynucleotide kinase (PNK) β which statement is NOT true?β It transfers the Ξ±-phosphate from ATP
Q38. High-efficiency library screening by colony/plaque hybridization requires generating:β Replica copies (replicas) of the plated clones on membranes
Q39. Which sugar pucker/geometry is associated with A-form DNA?β C3'-endo
Q40. Massive parallel signature sequencing (MPSS) and SAGE are used to:β Quantify transcriptomes by counting short sequence tags
Q41. Which experiment directly detects introns by visualizing looped-out single-stranded regions?β R-loop / DNA-mRNA heteroduplex mapping (EM)
Q42. 'Sequencing by synthesis' is the principle of which platform?β Illumina
Q43. The Human Genome Project's draft was completed using primarily:β Automated Sanger sequencing (hierarchical and whole-genome shotgun)
Q44. Which best describes shotgun genome sequencing?β Randomly fragmenting DNA, sequencing fragments, then assembling overlaps computationally
Q45. FISH (fluorescence in situ hybridization) is used to:β Localize specific DNA/RNA sequences on chromosomes or in cells