BIO 413 GENETICS AND GENOMICS
FINAL EXAM
Genome Sequencing Functional Genomics Bioinformatics
Epigenomics Gene Editing Systems Biology Questions and Answers
Verified Solutions 2026 2027
1. Which DNA sequencing strategy breaks genomic DNA into overlapping random
fragments, sequences them, and uses computer algorithms to reassemble the entire
sequence?
A. Hierarchical clone-by-clone sequencing
B. Whole-Genome Shotgun Sequencing
C. Sanger chain-termination sequencing
D. Maxam-Gilbert chemical sequencing
Rationale: Whole-genome shotgun sequencing bypasses physical mapping by shredding genomic DNA
into small fragments, sequencing them in parallel, and assembling contigs computationally using
overlapping sequences.
2. What high-throughput technique measures the expression levels of thousands of RNA
transcripts simultaneously across different cell types or experimental conditions?
A. RNA Sequencing (RNA-seq)
B. Chromatin Immunoprecipitation (ChIP)
C. Western Blotting
D. Sanger Sequencing
Rationale: RNA-seq uses next-generation sequencing to quantify cDNA synthesized from cellular RNA,
offering a comprehensive view of transcriptomes, alternative splicing, and expression levels.
3. Which enzyme provides target site specificity during genome editing with the bacterial
CRISPR-Cas9 system?
A. DNA Ligase IV
B. Cas9 nuclease alone
C. Single Guide RNA (sgRNA)
, D. Reverse Transcriptase
Rationale: The sgRNA contains a 20-nucleotide target-matching sequence that base-pairs with genomic
DNA, guiding the Cas9 endonuclease to introduce a precise double-strand break adjacent to a PAM
sequence.
4. What required short DNA motif located immediately downstream of the target genomic
sequence is recognized by Cas9 before DNA cleavage?
A. Protospacer Adjacent Motif (PAM)
B. TATA box
C. Polyadenylation signal
D. E-box motif
Rationale: Cas9 requires direct recognition of a specific PAM sequence (e.g., 5'-NGG-3' for SpCas9)
adjacent to the target site to unwind DNA and initiate cleavage.
5. What repair pathway dominates after a CRISPR-Cas9 double-strand break when no
homologous donor template is present, often yielding gene-disrupting indels?
A. Non-Homologous End Joining (NHEJ)
B. Homology-Directed Repair (HDR)
C. Base Excision Repair (BER)
D. Nucleotide Excision Repair (NER)
Rationale: NHEJ directly ligates broken DNA ends without a template, frequently introducing frameshift
insertion or deletion (indel) mutations that knock out gene function.
6. Which high-throughput method maps protein-DNA interactions across the genome by
combining antibody immunoprecipitation with next-generation sequencing?
A. RNA-seq
B. ChIP-seq (Chromatin Immunoprecipitation Sequencing)
C. ATAC-seq
D. Bisulfite sequencing
Rationale: ChIP-seq crosslinks DNA-protein complexes, uses antibodies to pull down target proteins (like
transcription factors or modified histones), and sequences the associated DNA fragments.
7. What sequencing technique identifies genome-wide regions of open, accessible
FINAL EXAM
Genome Sequencing Functional Genomics Bioinformatics
Epigenomics Gene Editing Systems Biology Questions and Answers
Verified Solutions 2026 2027
1. Which DNA sequencing strategy breaks genomic DNA into overlapping random
fragments, sequences them, and uses computer algorithms to reassemble the entire
sequence?
A. Hierarchical clone-by-clone sequencing
B. Whole-Genome Shotgun Sequencing
C. Sanger chain-termination sequencing
D. Maxam-Gilbert chemical sequencing
Rationale: Whole-genome shotgun sequencing bypasses physical mapping by shredding genomic DNA
into small fragments, sequencing them in parallel, and assembling contigs computationally using
overlapping sequences.
2. What high-throughput technique measures the expression levels of thousands of RNA
transcripts simultaneously across different cell types or experimental conditions?
A. RNA Sequencing (RNA-seq)
B. Chromatin Immunoprecipitation (ChIP)
C. Western Blotting
D. Sanger Sequencing
Rationale: RNA-seq uses next-generation sequencing to quantify cDNA synthesized from cellular RNA,
offering a comprehensive view of transcriptomes, alternative splicing, and expression levels.
3. Which enzyme provides target site specificity during genome editing with the bacterial
CRISPR-Cas9 system?
A. DNA Ligase IV
B. Cas9 nuclease alone
C. Single Guide RNA (sgRNA)
, D. Reverse Transcriptase
Rationale: The sgRNA contains a 20-nucleotide target-matching sequence that base-pairs with genomic
DNA, guiding the Cas9 endonuclease to introduce a precise double-strand break adjacent to a PAM
sequence.
4. What required short DNA motif located immediately downstream of the target genomic
sequence is recognized by Cas9 before DNA cleavage?
A. Protospacer Adjacent Motif (PAM)
B. TATA box
C. Polyadenylation signal
D. E-box motif
Rationale: Cas9 requires direct recognition of a specific PAM sequence (e.g., 5'-NGG-3' for SpCas9)
adjacent to the target site to unwind DNA and initiate cleavage.
5. What repair pathway dominates after a CRISPR-Cas9 double-strand break when no
homologous donor template is present, often yielding gene-disrupting indels?
A. Non-Homologous End Joining (NHEJ)
B. Homology-Directed Repair (HDR)
C. Base Excision Repair (BER)
D. Nucleotide Excision Repair (NER)
Rationale: NHEJ directly ligates broken DNA ends without a template, frequently introducing frameshift
insertion or deletion (indel) mutations that knock out gene function.
6. Which high-throughput method maps protein-DNA interactions across the genome by
combining antibody immunoprecipitation with next-generation sequencing?
A. RNA-seq
B. ChIP-seq (Chromatin Immunoprecipitation Sequencing)
C. ATAC-seq
D. Bisulfite sequencing
Rationale: ChIP-seq crosslinks DNA-protein complexes, uses antibodies to pull down target proteins (like
transcription factors or modified histones), and sequences the associated DNA fragments.
7. What sequencing technique identifies genome-wide regions of open, accessible
