Question 1

Which of the following best describes the process of gene targeting in embryonic stem (ES) cells as shown in the first image?

Accepted Answer

Homologous recombination between a targeting vector and the endogenous gene, followed by positive-negative selection to isolate targeted ES cells.

Question 2

In the process of generating transgenic mice using ES cells, why are the progeny of the foster mother often mosaic for the genetic modification?

Accepted Answer

Because not all cells in the developing embryo are derived from the injected ES cells, resulting in a mixture of modified and unmodified cells.

Question 3

Which of the following is a key difference between gene insertion and gene replacement strategies in homologous recombination-based gene targeting?

Accepted Answer

Gene insertion disrupts the target gene by inserting foreign DNA, while gene replacement substitutes the endogenous gene sequence with a modified sequence.

Question 4

In the natural CRISPR pathway in bacteria, what is the role of the guide RNA (gRNA)?

Accepted Answer

It directs the Cas9 protein to a specific DNA sequence complementary to the gRNA for cleavage.

Question 5

A researcher uses CRISPR-Cas9 to introduce a double-strand break (DSB) in a gene but does not provide a repair template. Which DNA repair pathway is most likely to occur, and what is the typical outcome?

Accepted Answer

Non-homologous end joining (NHEJ); introduction of insertions or deletions (indels) causing gene disruption.

Question 6

Which feature of the CRISPR-Cas9 system allows it to target almost any gene in the genome?

Accepted Answer

The requirement for a PAM (NGG) sequence near the target site.

Question 7

Golden rice was engineered to address vitamin A deficiency. Which of the following best describes how this was achieved?

Accepted Answer

By introducing four genes (two from daffodil and two from bacteria) involved in the beta-carotene biosynthesis pathway into rice.

Question 8

A patient with sickle cell disease receives a CRISPR-based therapy that targets the BCL11A gene in their hematopoietic stem cells. What is the intended therapeutic effect?

Accepted Answer

To reactivate fetal hemoglobin expression, compensating for defective adult hemoglobin.

Question 9

Which of the following is a major ethical concern regarding germline gene editing in humans?

Accepted Answer

The potential for heritable changes that affect future generations.

Question 10

Which sequencing method uses dideoxynucleotides (ddNTPs) to terminate DNA synthesis at specific bases, allowing the determination of DNA sequence?

Accepted Answer

Sanger sequencing.

Question 11

In a DNA microarray experiment comparing gene expression between two tissues, a spot appears yellow. What does this indicate about the gene represented by that spot?

Accepted Answer

The gene is equally expressed in both tissues.

Question 12

Which of the following best describes the main advantage of next-generation sequencing (NGS) over Sanger sequencing?

Accepted Answer

NGS allows massively parallel sequencing of millions of short DNA fragments, greatly increasing throughput and reducing cost.

Question 13

Which of the following is a direct application of functional genomics?

Accepted Answer

Analyzing genome-wide patterns of gene expression under different conditions.

Question 14

A scientist uses chromatin immunoprecipitation sequencing (ChIP-seq) to study a transcription factor. What information does this technique provide?

Accepted Answer

The locations across the genome where the transcription factor binds DNA.

Question 15

Which of the following is a limitation of traditional homologous recombination-based gene targeting in mice compared to CRISPR-based editing?

Accepted Answer

It is time-consuming and labor-intensive, requiring selection and breeding of ES cells.

Question 16

Which of the following best explains why a PAM sequence is required for CRISPR-Cas9 genome editing?

Accepted Answer

The PAM sequence is necessary for Cas9 to bind and cleave the target DNA.

Question 17

Which of the following is a real-world example of gene therapy approved for clinical use?

Accepted Answer

Delivering a normal copy of the RPE65 gene to treat inherited vision loss.

Question 18

Which of the following best describes the process of genome annotation after sequencing?

Accepted Answer

Assigning explanatory notes to the sequence, including identification of exons, introns, regulatory elements, and non-coding RNAs.

Question 19

A researcher wants to compare the transcriptomes of cancerous and normal tissue. Which technique would provide the most comprehensive and quantitative data?

Accepted Answer

RNA sequencing (RNA-seq).

Genetic Engineering, Genome Editing, and Functional Genomics: Study Notes for Genetics Students

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