MCQ Quiz- Special Recombination

MCQ Quiz: A Guide to Special Recombination

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Special recombination encompasses a set of highly specific and regulated DNA rearrangement reactions that are crucial for processes ranging from viral life cycles to the generation of immune system diversity. Unlike general recombination, these mechanisms rely on unique enzymes that recognize specific DNA sequences. This quiz for PharmD students will test your knowledge of the major types of special recombination—site-specific, transpositional, and V(D)J—and the key enzymes and principles that drive them.

1. “Special Recombination” events differ from “General/Homologous Recombination” in that they:

  • Occur randomly anywhere in the genome.
  • Require extensive regions of sequence homology.
  • Are catalyzed by specific enzymes that recognize short, defined DNA sequences.
  • Are primarily involved in repairing DNA double-strand breaks during meiosis.

Answer: Are catalyzed by specific enzymes that recognize short, defined DNA sequences.

2. Which of the following is a major category of special recombination?

  • Site-specific recombination
  • Transpositional recombination
  • V(D)J recombination
  • All of the above

Answer: All of the above

3. “Site-specific recombination” is best defined as:

  • The exchange of DNA between two completely random sites.
  • The movement of a “jumping gene” to a new location.
  • A recombination event that is mediated by a recombinase enzyme acting at specific target DNA sequences.
  • The process that generates antibody diversity.

Answer: A recombination event that is mediated by a recombinase enzyme acting at specific target DNA sequences.

4. The integration of the bacteriophage lambda genome into the E. coli chromosome is a classic example of:

  • Transposition
  • V(D)J recombination
  • Site-specific recombination
  • DNA repair

Answer: Site-specific recombination

5. The enzyme that catalyzes the integration and excision of the lambda phage genome is a(n):

  • Transposase
  • RAG recombinase
  • Integrase
  • DNA polymerase

Answer: Integrase

6. The Cre-Lox system is a powerful tool in molecular biology used for:

  • Amplifying DNA in a test tube.
  • Inducing site-specific recombination to delete, invert, or translocate a specific segment of DNA.
  • Sequencing an entire genome.
  • Separating proteins by size.

Answer: Inducing site-specific recombination to delete, invert, or translocate a specific segment of DNA.

7. In the Cre-Lox system, “Cre recombinase” is the ________, and the “LoxP” site is the ________.

  • DNA sequence; enzyme
  • Enzyme; DNA sequence
  • Product; substrate
  • Vector; host

Answer: Enzyme; DNA sequence

8. Site-specific recombinases are broadly classified into two families based on the amino acid residue at their active site. These are the:

  • Leucine and Glycine families.
  • Serine and Tyrosine families.
  • Cysteine and Histidine families.
  • Aspartate and Glutamate families.

Answer: Serine and Tyrosine families.

9. The Hin invertase in Salmonella controls the expression of flagellin genes. This is an example of a site-specific recombination event that results in a(n):

  • Insertion
  • Deletion
  • Inversion
  • Translocation

Answer: Inversion

10. “Transpositional recombination” or “transposition” is the movement of a:

  • Chromosome from one cell to another.
  • Specific DNA segment, a transposon, from one location to another in the genome.
  • Gene from a plasmid to a chromosome.
  • Ribosome along an mRNA molecule.

Answer: Specific DNA segment, a transposon, from one location to another in the genome.

11. The enzyme that catalyzes the movement of a DNA transposon is called:

  • Integrase
  • DNA ligase
  • Transposase
  • Reverse transcriptase

Answer: Transposase

12. The “cut-and-paste” mechanism of transposition involves:

  • The transposon being replicated, with one copy remaining at the original site.
  • The transposon being excised from its original location and inserted into a new location.
  • The conversion of the transposon to RNA and back to DNA.
  • A site-specific inversion of the transposon.

Answer: The transposon being excised from its original location and inserted into a new location.

13. “Retrotransposons” are a class of transposable elements that move via a “copy-and-paste” mechanism that requires:

  • A DNA intermediate.
  • The enzyme transposase only.
  • An RNA intermediate and the enzyme reverse transcriptase.
  • A protein intermediate.

Answer: An RNA intermediate and the enzyme reverse transcriptase.

14. Which of the following are examples of retrotransposons that are abundant in the human genome?

  • Insertion sequences (IS elements)
  • P elements
  • LINEs and SINEs
  • Tn3 transposons

Answer: LINEs and SINEs

15. A major consequence of transposition is that it can:

  • Cause mutations by inserting into a gene.
  • Lead to genome rearrangements.
  • Introduce new genetic information.
  • All of the above.

Answer: All of the above.

16. The vast diversity of antibodies and T-cell receptors in the vertebrate immune system is generated by which form of special recombination?

  • Transposition
  • Site-specific recombination
  • V(D)J recombination
  • General homologous recombination

Answer: V(D)J recombination

17. V(D)J recombination occurs in which type of developing cells?

  • All somatic cells.
  • Germline cells only.
  • B-lymphocytes and T-lymphocytes.
  • Neurons and glial cells.

Answer: B-lymphocytes and T-lymphocytes.

18. The enzymes that are unique to V(D)J recombination and are responsible for initiating the process are:

  • DNA polymerase and ligase.
  • Cre and LoxP.
  • RAG1 and RAG2.
  • Transposase and reverse transcriptase.

Answer: RAG1 and RAG2.

19. The RAG1/RAG2 recombinase complex recognizes and binds to specific DNA sequences that flank the V, D, and J gene segments. These sequences are known as:

  • Promoters
  • Enhancers
  • Recombination Signal Sequences (RSS).
  • Telomeres

Answer: Recombination Signal Sequences (RSS).

20. After the RAG proteins make a double-strand break in the DNA during V(D)J recombination, the DNA ends are processed and joined by which cellular pathway?

  • Homologous recombination.
  • Non-homologous end joining (NHEJ).
  • Mismatch repair.
  • Nucleotide excision repair.

Answer: Non-homologous end joining (NHEJ).

21. A “Holliday junction” is a key four-stranded DNA intermediate formed during which process?

  • Site-specific recombination by tyrosine recombinases.
  • General homologous recombination.
  • V(D)J recombination.
  • Both A and B are correct.

Answer: Both A and B are correct.

22. A “resolvase” is a type of site-specific recombinase that:

  • Integrates a viral genome into a host chromosome.
  • Inverts a DNA segment.
  • Catalyzes the resolution of a cointegrate intermediate in replicative transposition.
  • Is the primary enzyme in V(D)J recombination.

Answer: Catalyzes the resolution of a cointegrate intermediate in replicative transposition.

23. Unlike site-specific recombination, transposition is often characterized by:

  • The use of a highly specific target site.
  • A lack of specificity for the insertion target site.
  • The requirement for a specific protein cofactor.
  • The formation of a stable cointegrate.

Answer: A lack of specificity for the insertion target site.

24. The generation of “junctional diversity” during V(D)J recombination, which further increases antibody variability, is a result of:

  • The precise, error-free joining of the gene segments.
  • The imprecise joining process, which can involve the addition or deletion of nucleotides at the junctions.
  • The action of telomerase.
  • The process of transcription.

Answer: The imprecise joining process, which can involve the addition or deletion of nucleotides at the junctions.

25. A “knockout mouse” is often created using a molecular biology technique that harnesses:

  • Transposition.
  • Site-specific recombination (e.g., Cre-Lox) to conditionally delete a gene.
  • V(D)J recombination.
  • The natural process of aging.

Answer: Site-specific recombination (e.g., Cre-Lox) to conditionally delete a gene.

26. The “cloning” of a gene into a plasmid vector relies on which enzymes that are also used in DNA metabolism and repair?

  • Restriction enzymes and DNA ligase.
  • RAG1 and RAG2.
  • Transposase.
  • Reverse transcriptase.

Answer: Restriction enzymes and DNA ligase.

27. The ability of certain antibiotics to spread between different bacterial species is often mediated by:

  • V(D)J recombination.
  • Transposons carrying antibiotic resistance genes.
  • The Cre-Lox system.
  • The process of mitosis.

Answer: Transposons carrying antibiotic resistance genes.

28. From a “leadership” perspective, a scientist guiding a research project on gene therapy using the Cre-Lox system must have a deep understanding of:

  • Site-specific recombination.
  • The financial budget of the lab.
  • The personalities of their team members.
  • All of the above.

Answer: All of the above.

29. The “regulation” of gene therapy technologies, which often use principles of special recombination, is the responsibility of the:

  • DEA.
  • FDA.
  • CMS.
  • EPA.

Answer: The FDA.

30. A “business plan” for a new company developing a CAR-T cell therapy would be based on a form of:

  • Special recombination to engineer the T-cell receptor.
  • Genetic engineering that uses principles learned from molecular biology.
  • A novel drug delivery system.
  • A new small molecule drug.

Answer: Genetic engineering that uses principles learned from molecular biology.

31. The enzyme “reverse transcriptase” is a key tool in molecular biology and is also the primary enzyme for which type of special recombination?

  • Replicative transposition.
  • Site-specific inversion.
  • Retransposition (movement of retrotransposons).
  • V(D)J recombination.

Answer: Retransposition (movement of retrotransposons).

32. Serine recombinases differ from tyrosine recombinases in that they:

  • Form a Holliday junction intermediate.
  • Generate single-strand breaks.
  • Generate double-strand breaks and rotate the DNA segments before rejoining.
  • Do not require a specific recognition site.

Answer: Generate double-strand breaks and rotate the DNA segments before rejoining.

33. The generation of a monoclonal antibody for a “chemotherapeutic” like rituximab relies on the natural process of:

  • Transposition in the tumor cells.
  • Site-specific recombination in the manufacturing cells.
  • V(D)J recombination to create the initial antibody diversity.
  • DNA repair mechanisms only.

Answer: V(D)J recombination to create the initial antibody diversity.

34. The “forging ahead” mindset in pharmacy means embracing new personalized medicines, some of which are made possible by:

  • A deep understanding of special recombination to engineer therapies.
  • Traditional compounding techniques only.
  • A focus on small molecule drugs exclusively.
  • Resisting all new technologies.

Answer: A deep understanding of special recombination to engineer therapies.

35. A “policy” debate surrounding the use of gene editing (CRISPR), a technique related to DNA repair and recombination, centers on its:

  • Use in basic laboratory research.
  • Ethical implications for editing the human germline.
  • High cost.
  • All of the above.

Answer: All of the above.

36. A key part of the “Introduction to Pharmacy Informatics” is understanding that a patient’s EHR might one day contain data on:

  • Their unique antibody repertoire, generated by V(D)J recombination.
  • Their entire genomic sequence.
  • Their risk for certain genetic diseases.
  • All of the above.

Answer: All of the above.

37. The “enzymes of DNA metabolism” like DNA ligase and various nucleases are also essential players in the final steps of:

  • V(D)J recombination.
  • DNA repair.
  • Molecular cloning.
  • All of the above.

Answer: All of the above.

38. A “health disparity” could arise if a new, highly effective gene therapy based on recombination principles is:

  • So expensive that it is only accessible to the wealthiest patients.
  • Made available to all patients regardless of cost.
  • Covered by all government insurance plans.
  • Easy to manufacture and distribute.

Answer: So expensive that it is only accessible to the wealthiest patients.

39. A “negotiation” for the rights to a new biotechnology based on site-specific recombination would heavily depend on the strength of the:

  • Patent protecting the technology.
  • Marketing plan.
  • Sales team.
  • Company’s location.

Answer: Patent protecting the technology.

40. The “human resources” department of a gene therapy company would need to recruit scientists with expertise in:

  • Molecular biology and special recombination.
  • Regulatory affairs.
  • Clinical trial management.
  • All of the above.

Answer: All of the above.

41. The role of “Artemis” in V(D)J recombination is to:

  • Recognize the RSS sites.
  • Make the initial double-strand break.
  • Open the hairpin loops created by the RAG proteins, acting as a nuclease.
  • Ligate the final DNA ends together.

Answer: Open the hairpin loops created by the RAG proteins, acting as a nuclease.

42. Unlike V(D)J recombination, which only occurs in lymphocytes, transposition can occur in:

  • Only germline cells.
  • Both germline and somatic cells.
  • Only bacterial cells.
  • Only yeast cells.

Answer: Both germline and somatic cells.

43. A key difference between DNA transposons and retrotransposons is that:

  • DNA transposons increase in number during the “cut-and-paste” mechanism.
  • Retrotransposons always increase the number of copies of the element in the genome.
  • DNA transposons use an RNA intermediate.
  • Retrotransposons are only found in bacteria.

Answer: Retrotransposons always increase the number of copies of the element in the genome.

44. The “services” a highly specialized clinical pharmacist provides for a patient receiving a gene therapy would include:

  • Counseling on the complex procedure and monitoring for unique side effects.
  • Compounding the gene therapy vector in a community pharmacy.
  • Administering the therapy.
  • Diagnosing the genetic condition.

Answer: Counseling on the complex procedure and monitoring for unique side effects.

45. A “Clinical Decision Support” system of the future might use a patient’s V(D)J repertoire data to:

  • Predict their response to an immunotherapy or vaccine.
  • Dispense an antibiotic.
  • Bill for a hospital stay.
  • It cannot use this type of data.

Answer: Predict their response to an immunotherapy or vaccine.

46. The “12/23 rule” in V(D)J recombination ensures that:

  • A gene segment flanked by a 12-bp spacer RSS only recombines with one flanked by a 23-bp spacer RSS.
  • Recombination occurs in the correct order.
  • The RAG proteins bind correctly.
  • All of the above.

Answer: All of the above.

47. A “drug-gene” interaction can be thought of as a principle of pharmacogenomics. A disease caused by a faulty recombination enzyme would be an example of a principle from:

  • Molecular genetics.
  • Clinical pharmacology.
  • Toxicology.
  • Health economics.

Answer: Molecular genetics.

48. An “analytics and reporting system” is crucial in modern immunology research to:

  • Analyze the massive datasets generated from sequencing the antibody and T-cell receptor repertoires of many individuals.
  • Manage a single patient’s lab results.
  • Track pharmacy inventory.
  • Schedule appointments.

Answer: Analyze the massive datasets generated from sequencing the antibody and T-cell receptor repertoires of many individuals.

49. “Antibody class switching” is another DNA recombination event that occurs in B-cells and allows them to:

  • Change the antigen-binding site of their antibody.
  • Keep the same antigen-binding site but change the constant region (e.g., from IgM to IgG).
  • Stop producing antibodies.
  • Become a T-cell.

Answer: Keep the same antigen-binding site but change the constant region (e.g., from IgM to IgG).

50. The ultimate principle of why pharmacists study special recombination is that these processes are:

  • Clinically irrelevant.
  • Fundamental to immunology, genetic engineering, and the development of many modern biopharmaceuticals.
  • Easy to understand and require no special study.
  • Only important for basic scientists.

Answer: Fundamental to immunology, genetic engineering, and the development of many modern biopharmaceuticals.

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