Genome organization and gene expression regulation MCQs With Answer

Introduction: This quiz collection on Genome Organization and Gene Expression Regulation is tailored for M.Pharm students studying Cellular and Molecular Pharmacology. It focuses on molecular mechanisms that control chromatin structure, transcriptional and post-transcriptional regulation, epigenetic marks, and higher-order genome architecture relevant to drug action and therapeutic modulation. Questions emphasize concepts such as nucleosome dynamics, histone modifications, DNA methylation, enhancers, promoters, chromatin remodeling complexes, non-coding RNAs, and pharmacological targets like HDACs and DNMTs. These MCQs are designed to deepen understanding, strengthen critical thinking, and prepare students for exams and research applications in pharmacology and molecular therapeutics.

Q1. Which structural unit of chromatin is composed of DNA wrapped around an octamer of histone proteins?

• Nucleosome
• Chromatosome
• Chromonema
• Selenoprotein complex

Correct Answer: Nucleosome

Q2. Which histone modification is most commonly associated with active transcription start sites in eukaryotes?

• H3K9me3
• H3K27me3
• H3K4me3
• H4K20me0

Correct Answer: H3K4me3

Q3. CpG islands located in promoter regions are typically associated with which regulatory feature?

• Stable heterochromatin formation
• Transcriptional repression when unmethylated
• Transcriptional activation when unmethylated
• Recruitment of ribosomal subunits

Correct Answer: Transcriptional activation when unmethylated

Q4. Which protein complex uses ATP hydrolysis to reposition or evict nucleosomes and thereby regulates DNA accessibility?

• Polycomb Repressive Complex 2 (PRC2)
• SWI/SNF (BAF) chromatin remodeling complex
• RNA-induced silencing complex (RISC)
• Histone acetyltransferase (HAT) complex

Correct Answer: SWI/SNF (BAF) chromatin remodeling complex

Q5. The TATA box in many eukaryotic promoters primarily serves to:

• Recruit DNA methyltransferases
• Bind general transcription factors and position RNA polymerase II
• Terminate transcription by RNA polymerase I
• Promote alternative splicing

Correct Answer: Bind general transcription factors and position RNA polymerase II

Q6. Which epigenetic drug class is designed to inhibit histone deacetylases and can reactivate silenced genes?

• DNMT inhibitors (e.g., 5-azacytidine)
• HDAC inhibitors (e.g., vorinostat)
• Proteasome inhibitors (e.g., bortezomib)
• Topoisomerase inhibitors (e.g., doxorubicin)

Correct Answer: HDAC inhibitors (e.g., vorinostat)

Q7. Topologically associating domains (TADs) in the genome primarily function to:

• Facilitate long-range enhancer-promoter interactions within the domain
• Serve as replication origins exclusively
• Encode microRNAs and small RNAs
• Directly catalyze histone acetylation

Correct Answer: Facilitate long-range enhancer-promoter interactions within the domain

Q8. Which non-coding RNA class commonly represses gene expression post-transcriptionally by base-pairing with target mRNAs?

• Long non-coding RNAs (>200 nt)
• microRNAs (miRNAs)
• rRNA
• snRNA involved in splicing

Correct Answer: microRNAs (miRNAs)

Q9. DNA methylation of cytosines in CpG dinucleotides is primarily catalyzed by which enzyme family?

• Histone methyltransferases (HMTs)
• DNA methyltransferases (DNMTs)
• TET family dioxygenases
• Uracil-DNA glycosylases

Correct Answer: DNA methyltransferases (DNMTs)

Q10. Which chromatin state is typically enriched for H3K27me3 and associated with developmental gene silencing?

• Constitutive heterochromatin
• Polycomb-repressed facultative heterochromatin
• Active euchromatin
• Promoter-proximal paused chromatin

Correct Answer: Polycomb-repressed facultative heterochromatin

Q11. Alternative splicing increases proteomic diversity by:

• Changing genomic DNA sequence in different tissues
• Generating multiple mRNA isoforms from a single pre-mRNA
• Altering ribosomal RNA structure
• Inducing DNA methylation at exons

Correct Answer: Generating multiple mRNA isoforms from a single pre-mRNA

Q12. In prokaryotic operons, the lac repressor controls the lac operon by which mechanism?

• Recruiting RNA polymerase to the promoter
• Blocking promoter escape by RNA polymerase in presence of lactose
• Binding operator sequence to prevent transcription when lactose is absent
• Modifying histones to silence the operon

Correct Answer: Binding operator sequence to prevent transcription when lactose is absent

Q13. Which of the following best describes enhancer elements?

• Short sequences that must be immediately adjacent to the promoter
• DNA elements that can increase transcription independent of orientation and distance
• RNA sequences that block splicing
• Protein complexes that degrade mRNA

Correct Answer: DNA elements that can increase transcription independent of orientation and distance

Q14. Promoter-proximal pausing of RNA polymerase II is relieved primarily by which factor/activity?

• TATA-binding protein (TBP) alone
• P-TEFb kinase activity that phosphorylates the polymerase and negative elongation factors
• DNA ligase activity
• DNMT-mediated methylation

Correct Answer: P-TEFb kinase activity that phosphorylates the polymerase and negative elongation factors

Q15. Which histone modification is most directly associated with transcriptional activation by increasing chromatin accessibility?

• Histone acetylation (e.g., H3K27ac)
• Histone ubiquitination at H2B solely linked to repression
• H3K9me3
• DNA crosslinking

Correct Answer: Histone acetylation (e.g., H3K27ac)

Q16. TET enzymes contribute to epigenetic regulation by:

• Methylating cytosines to form 5-methylcytosine
• Oxidizing 5-methylcytosine to promote DNA demethylation
• Directly acetylating histone tails
• Degrading microRNAs

Correct Answer: Oxidizing 5-methylcytosine to promote DNA demethylation

Q17. Insulator elements in the genome are primarily important because they:

• Catalyze histone methylation
• Block inappropriate interactions between enhancers and promoters and can stop the spread of heterochromatin
• Serve as replication forks
• Encode small peptides that regulate transcription

Correct Answer: Block inappropriate interactions between enhancers and promoters and can stop the spread of heterochromatin

Q18. MicroRNA-mediated repression of target mRNAs commonly involves:

• Direct genomic DNA cleavage
• Translational repression and/or mRNA degradation via RISC
• Histone deacetylation at the gene promoter
• Enhancement of ribosomal biogenesis

Correct Answer: Translational repression and/or mRNA degradation via RISC

Q19. The centromere is essential for chromosome segregation because it:

• Is the primary site of DNA replication initiation
• Serves as the assembly site for the kinetochore and microtubule attachment
• Promotes gene transcription across the chromosome
• Contains CpG islands that regulate all genes

Correct Answer: Serves as the assembly site for the kinetochore and microtubule attachment

Q20. Which therapeutic approach directly targets DNA methylation to reactivate tumor suppressor genes in cancer?

• HDAC inhibitors only
• DNMT inhibitors such as 5-azacytidine and decitabine
• Protease inhibitors
• RNA polymerase I inhibitors

Correct Answer: DNMT inhibitors such as 5-azacytidine and decitabine

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