CRISPR-Cas9 and Genome Editing Indian Medical PG Practice Questions and MCQs
Practice Indian Medical PG questions for CRISPR-Cas9 and Genome Editing. These multiple choice questions (MCQs) cover important concepts and help you prepare for your exams.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 1: Which of the following techniques can be used to detect single base pair substitutions?
- A. FISH
- B. Southern blot
- C. PCR (Correct Answer)
- D. Restriction Fragment Length Polymorphism (RFLP)
CRISPR-Cas9 and Genome Editing Explanation: ***PCR (with sequencing or allele-specific methods)***
- **PCR-based techniques** are the most versatile methods for detecting single base pair substitutions (point mutations)
- **Allele-specific PCR** can directly detect known point mutations by using primers specific to mutant or wild-type alleles
- **PCR followed by Sanger sequencing** is the gold standard for identifying any single base pair substitution
- **High-resolution melting (HRM) analysis** after PCR can detect mutations based on melting curve differences
- PCR amplification is the foundation that enables these detection methods
*FISH (Fluorescence in situ hybridization)*
- FISH detects **large chromosomal abnormalities** such as aneuploidy, translocations, large deletions, and duplications
- It visualizes chromosomal-level changes using fluorescent probes
- **Not sensitive enough** to detect single base pair changes, as these are too small to visualize cytogenetically
*Southern blot*
- Southern blot detects **large DNA rearrangements**, insertions, deletions, or copy number variations
- Analyzes restriction enzyme fragments separated by gel electrophoresis
- **Generally cannot detect** single base pair substitutions unless they create or abolish a restriction enzyme recognition site
- Even when applicable, PCR-based methods are more efficient and sensitive
*Restriction Fragment Length Polymorphism (RFLP)*
- RFLP can detect single base pair substitutions **only if** they create or abolish a **restriction enzyme recognition site**
- Classic example: **Sickle cell mutation** (GAG→GTG in β-globin gene) abolishes an MstII restriction site
- **Limited applicability** - can only detect the subset of point mutations that affect restriction sites
- PCR-based methods are preferred as they can detect **any** single base pair substitution, not just those affecting restriction sites
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 2: Which of the following doesn't occur in 5' to 3' direction?
- A. DNA repair
- B. Transcription
- C. DNA replication
- D. RNA editing (Correct Answer)
CRISPR-Cas9 and Genome Editing Explanation: ***RNA editing***
- **RNA editing** involves modifications to **RNA molecules** after transcription, such as base insertions, deletions, or substitutions.
- This process does not follow a 5' to 3' synthesis direction, unlike DNA or RNA synthesis.
*DNA repair*
- **DNA repair mechanisms**, such as **excision repair**, involve synthesizing new DNA to replace damaged sections.
- This synthesis occurs in the **5' to 3' direction** by **DNA polymerases**.
*Transcription*
- **Transcription** is the process where **RNA polymerase** synthesizes an **RNA molecule** from a **DNA template**.
- This synthesis always occurs in the **5' to 3' direction**, adding nucleotides to the 3' end of the growing RNA strand.
*DNA replication*
- **DNA replication** involves the synthesis of new **DNA strands** from a **template strand**.
- **DNA polymerase** adds nucleotides exclusively in the **5' to 3' direction**, requiring a primer for initiation.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 3: What is the repair mechanism associated with CRISPR-cas9?
- A. Mismatch repair
- B. Non-homologous end joining (Correct Answer)
- C. Nucleotide excision repair
- D. Base excision repair
CRISPR-Cas9 and Genome Editing Explanation: ***Non-homologous end joining***
- **CRISPR-Cas9** creates a **double-strand break (DSB)** in DNA, which is primarily repaired by **non-homologous end joining (NHEJ)**.
- **NHEJ** is the **predominant repair pathway** in most cells, accounting for 60-90% of DSB repairs.
- **NHEJ** is an error-prone repair mechanism that ligates the broken ends directly, often leading to small **insertions or deletions (indels)** causing gene knockout.
- Note: **Homology-directed repair (HDR)** is another CRISPR-associated mechanism used for precise editing when a donor template is provided, but **NHEJ is the primary endogenous repair pathway**.
*Mismatch repair*
- This mechanism corrects errors that arise during **DNA replication**, such as incorrect base pairing.
- It does not repair **double-strand breaks** induced by CRISPR-Cas9.
*Nucleotide excision repair*
- This pathway removes **bulky DNA adducts** and lesions, such as those caused by UV radiation.
- It is not involved in repairing **CRISPR-Cas9 induced double-strand breaks**.
*Base excision repair*
- This mechanism corrects **damaged or modified bases**, typically single base changes, without affecting the sugar-phosphate backbone significantly.
- It handles different types of DNA damage than the **double-strand breaks** generated by CRISPR-Cas9.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 4: Prader-Willi syndrome and Angelman syndrome are examples of what genetic phenomenon?
- A. Gene Knockout
- B. Impaired DNA repair
- C. Genomic Imprinting (Correct Answer)
- D. RNA interference
CRISPR-Cas9 and Genome Editing Explanation: ***Genomic Imprinting***
- **Genomic imprinting** is an epigenetic phenomenon where certain genes are expressed in a **parent-of-origin-specific manner**.
- In Prader-Willi syndrome, the disease results from the loss of function of specific genes on chromosome 15 (15q11-q13) inherited from the father, while Angelman syndrome results from the loss of function of a different gene (UBE3A) in the same region, but inherited from the mother.
*RNA interference*
- **RNA interference** is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules.
- This process is not directly responsible for the parent-of-origin-specific expression patterns observed in these syndromes.
*Gene Knockout*
- A **gene knockout** is a genetic technique in which an organism's genes are made inoperative.
- While it involves modifying gene function, it does not explain the differential expression based on parental origin.
*Impaired DNA repair*
- **Impaired DNA repair** refers to defects in the mechanisms that correct DNA damage.
- This can lead to increased mutations and conditions like cancer, but it is not the underlying mechanism for Prader-Willi or Angelman syndromes.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 5: Mutations are due to changes in:
- A. DNA nucleotide sequence (Correct Answer)
- B. RNA nucleotide sequence
- C. Amino acid sequence of ribonuclease
- D. Cell membrane
CRISPR-Cas9 and Genome Editing Explanation: ***DNA nucleotide sequence***
- **Mutations** are defined as changes in the **genetic material**, which is primarily composed of **DNA**.
- These changes in the **nucleotide sequence** of DNA can alter the genetic code, leading to changes in **protein structure and function**.
*RNA nucleotide sequence*
- While RNA can have its nucleotide sequence altered, these changes are generally not considered true **mutations** in the heritable sense for most organisms.
- RNA is typically a temporary molecule, and changes to its sequence are usually not passed down to subsequent generations.
*Amino acid sequence of ribonuclease*
- An altered **amino acid sequence** in a protein like ribonuclease is a consequence of a **mutation in the DNA**, not the mutation itself.
- **Ribonucleases** are enzymes that catalyze the degradation of RNA, and their structure is determined by the **DNA sequence**.
*Cell membrane*
- The cell membrane is a **lipid bilayer** with embedded proteins that regulates cellular transport and communication.
- While its components can be affected by genetic mutations, alterations in the cell membrane itself do not constitute the primary definition of a **mutation**.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 6: Which type of RNA is primarily involved in gene silencing?
- A. rRNA
- B. tRNA
- C. miRNA (Correct Answer)
- D. mRNA
CRISPR-Cas9 and Genome Editing Explanation: ***miRNA***
- **miRNA** (microRNA) is a small non-coding RNA molecule that plays a crucial role in **post-transcriptional regulation of gene expression**.
- It functions by binding to complementary messenger RNA (mRNA) molecules, leading to **mRNA degradation** or **inhibition of translation**, thereby silencing genes.
- miRNA is the primary RNA type involved in **gene silencing** through the RNA interference (RNAi) pathway.
*rRNA*
- **rRNA** (ribosomal RNA) is a primary component of **ribosomes**, the cellular machinery responsible for protein synthesis.
- Its main function is to **catalyze peptide bond formation** and provide structural integrity to the ribosome, not gene silencing.
*tRNA*
- **tRNA** (transfer RNA) is responsible for carrying specific **amino acids** to the ribosome during protein synthesis.
- It acts as an adapter molecule, translating the **genetic code** in mRNA into an amino acid sequence.
*mRNA*
- **mRNA** (messenger RNA) carries genetic information from **DNA to ribosomes** for protein synthesis.
- While mRNA can be targeted by gene silencing mechanisms (like miRNA), it is not the RNA type that performs the silencing function itself.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 7: Which of the following statements about sickle cell disease is true?
- A. Sickling is completely reversible with oxygenation, making it clinically insignificant.
- B. Sickling leads to a significant increase in overall MCHC levels in the blood.
- C. Fetal hemoglobin inhibits sickling. (Correct Answer)
- D. Sickling occurs exclusively in the homozygous state and never in the heterozygous state.
CRISPR-Cas9 and Genome Editing Explanation: ***Sickling is reversible with oxygenation***
- When oxygen tension is restored, hemoglobin S can re-hydrate and revert to its normal shape, reducing sickling.
- This reversible process is essential for managing episodes of vaso-occlusive crisis in sickle cell disease.
*Fetal hemoglobin facilitates Sickling*
- Fetal hemoglobin (HbF) actually inhibits sickling by stabilizing the erythrocyte shape and reducing the proportion of hemoglobin S [1].
- Individuals with higher levels of HbF experience fewer sickling-related complications [1].
*Sickling occurs both in heterozygous and homozygous state*
- Sickling primarily occurs in the homozygous state (HbSS); heterozygotes (HbAS) usually do not experience significant sickling effects [1].
- Heterozygous individuals may have a selective advantage against malaria, but they are not prone to sickle cell crises.
*Sickling Leads to decreased MCHC*
- Sickling does not directly lead to decreased mean corpuscular hemoglobin concentration (MCHC); MCHC is typically normal in sickle cell patients.
- In fact, sickle cell disease often results in hemolysis and can lead to increased MCHC in some cases.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 8: Which malformation is associated with mutations in the HOX gene?
- A. Polysyndactyly (Correct Answer)
- B. Holoprosencephaly
- C. Mayer Rokitansky syndrome
- D. Gorlin syndrome
CRISPR-Cas9 and Genome Editing Explanation: ***Polysyndactyly***
- The **HOX gene** plays a critical role in limb development and is associated with the malformation of **polysyndactyly**, which is characterized by extra fingers or toes [1].
- This condition is due to the disruption of the normal **patterning** during limb formation, directly involving the action of HOX genes [1].
*Gorlin syndrome*
- Gorlin syndrome is primarily caused by mutations in the **PTCH1 gene**, linked to **basal cell carcinoma** and other abnormalities.
- It does not involve HOX gene mutations, hence is **not** related to limb malformations.
*Holoprosencephaly*
- Holoprosencephaly is a developmental condition often linked to **chromosomal anomalies** and abnormal embryonic development, **not specifically** HOX gene mutations.
- It refers to the incomplete separation of the forebrain, distinct from the **limb malformations** associated with HOX genes.
*Mayer Rokitansky syndrome*
- Mayer-Rokitansky syndrome involves **agenesis** or **hypoplasia** of the uterus and upper two-thirds of the vagina, which is due to other genetic factors.
- This condition is not related to the functions of the **HOX genes** in limb or skeletal development.
**References:**
[1] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. Bones, Joints, and Soft Tissue Tumors, p. 1186.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 9: In CRISPR-Cas9 system, which repair mechanism is predominantly used for genome editing?
- A. Nucleotide excision repair
- B. Mismatch repair
- C. Homology-Directed Repair (HDR)
- D. Non-Homologous End Joining (NHEJ) (Correct Answer)
CRISPR-Cas9 and Genome Editing Explanation: ***Non-Homologous End Joining (NHEJ)***
- **NHEJ** is the most common and error-prone repair pathway in mammalian cells, directly ligating the broken DNA ends created by **Cas9**.
- This pathway often results in **insertions** or **deletions (indels)** at the cut site, leading to gene knockout by causing frameshifts.
*Nucleotide excision repair*
- **Nucleotide excision repair (NER)** is primarily involved in removing bulky DNA adducts and pyrimidine dimers caused by UV radiation.
- It involves excising a segment of DNA around the damage, not repairing double-strand breaks induced by CRISPR-Cas9.
*Homology-Directed Repair (HDR)*
- **HDR** is a precise repair mechanism that uses a homologous DNA template to repair double-strand breaks, allowing for precise gene editing (e.g., specific base changes, gene insertion).
- While it can be leveraged in **CRISPR-Cas9**, it is less efficient and less common than **NHEJ** in most mammalian cells, especially when no exogenous template is provided.
*Mismatch repair*
- **Mismatch repair (MMR)** systems correct base-pair mismatches and small insertion/deletion loops that arise during DNA replication.
- This mechanism is not involved in repairing the double-strand breaks generated by the **CRISPR-Cas9** system.
CRISPR-Cas9 and Genome Editing Indian Medical PG Question 10: When a gene is expressed exclusively from the allele inherited from one parent while the allele from the other parent is silenced, what is this phenomenon known as?
- A. Genomic imprinting (Correct Answer)
- B. Mosaicism
- C. Alleles
- D. Chimerism
CRISPR-Cas9 and Genome Editing Explanation: ***Genomic imprinting***
- **Genomic imprinting** is an epigenetic phenomenon where certain genes are expressed in a **parent-of-origin-specific manner**.
- This means that depending on whether the gene was inherited from the **mother or the father**, only one copy (maternal or paternal) is expressed, while the other is silenced.
*Mosaicism*
- **Mosaicism** describes the presence of **two or more cell lines** with different genotypes within a single individual, originating from a single zygote.
- This typically arises from a **post-zygotic mutation** or chromosomal abnormality during early embryonic development.
*Alleles*
- **Alleles** are different forms of a **single gene** located at the same locus on homologous chromosomes.
- An individual inherits **two alleles** for each gene, one from each parent, but both are usually expressed unless one is recessive.
*Chimerism*
- **Chimerism** refers to an individual composed of cells from **two or more different zygotes**, meaning the cells originate from different genetic lineages.
- This can occur through processes like **fusion of two embryos** or organ transplantation.
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