Prokaryotic gene families MCQs With Answer

Introduction:

This quiz collection on Prokaryotic Gene Families is designed for M.Pharm students studying Bioinformatics and Computational Biotechnology. It focuses on gene family concepts essential for understanding bacterial genetics, horizontal gene transfer, functional annotation, and antibiotic resistance evolution. Questions cover orthologs and paralogs, pangenome and core/accessory genome notions, common gene family databases (COG, Pfam), mobile genetic elements, and computational methods used to identify and analyze prokaryotic gene families. The format emphasizes applied knowledge relevant to pharmacology research—such as resistance gene tracking and target discovery—while reinforcing bioinformatic approaches used in modern microbial genomics.

Q1. Which definition best describes a prokaryotic orthologous gene?

• A gene duplicated within the same genome that acquires a new function
• A gene in different species that diverged after a speciation event and typically retains the same function
• A gene acquired via horizontal transfer from a distant lineage
• A non-coding regulatory RNA found across multiple strains

Correct Answer: A gene in different species that diverged after a speciation event and typically retains the same function

Q2. What is the primary difference between paralogs and orthologs in bacteria?

• Paralogs arise by horizontal gene transfer; orthologs arise by gene loss
• Paralogs result from gene duplication within a genome; orthologs result from speciation
• Paralogs are always nonfunctional remnants; orthologs are always functional
• Paralogs are only found on plasmids; orthologs are chromosomal

Correct Answer: Paralogs result from gene duplication within a genome; orthologs result from speciation

Q3. Which database is commonly used to group prokaryotic proteins into clusters of orthologous groups (COGs)?

• KEGG
• PFAM
• COG database (eggNOG/COG)
• UniProtKB/Swiss-Prot only

Correct Answer: COG database (eggNOG/COG)

Q4. In pangenome analysis, what does the ‘core genome’ represent?

• All genes present in at least one strain of the species
• Genes unique to plasmids across strains
• Genes conserved and present in all strains analyzed
• Genes present only in pathogenic strains

Correct Answer: Genes conserved and present in all strains analyzed

Q5. Which computational approach is most appropriate for finding distant homologous gene families across prokaryotes?

• Pairwise BLASTN with strict e-value cutoff only
• Hidden Markov Model (HMM) profile searches using tools like HMMER
• Simple motif scanning for short sequences
• Counting GC content only

Correct Answer: Hidden Markov Model (HMM) profile searches using tools like HMMER

Q6. Which gene family is commonly associated with antimicrobial resistance in bacteria?

• Sigma factor family
• Beta-lactamase family
• Ribosomal protein S10 family
• tRNA synthetase family

Correct Answer: Beta-lactamase family

Q7. What is an accessory genome in prokaryotic genomics?

• The set of genes present in all species across a genus
• Genes found in some but not all strains of a species, often linked to niche adaptation
• Genes encoding only metabolic enzymes
• Only ribosomal RNA genes

Correct Answer: Genes found in some but not all strains of a species, often linked to niche adaptation

Q8. Which mechanism most directly contributes to creating new gene families in prokaryotes?

• Point mutations in housekeeping genes without duplication
• Gene duplication and divergence, and horizontal gene transfer
• Splicing of introns to form new exons
• Only post-translational modifications

Correct Answer: Gene duplication and divergence, and horizontal gene transfer

Q9. Which class of mobile genetic elements frequently carries antibiotic resistance gene families between bacteria?

• rRNA operons
• Integrons and transposons (mobile elements)
• Housekeeping gene cassettes
• Tandemly duplicated ribosomal protein clusters

Correct Answer: Integrons and transposons (mobile elements)

Q10. In gene family annotation, what advantage does Pfam provide?

• Pfam provides whole-genome assembly algorithms
• Pfam provides curated protein family HMMs allowing domain-level annotation
• Pfam sequences are exclusively non-coding RNAs
• Pfam predicts metabolic flux through pathways

Correct Answer: Pfam provides curated protein family HMMs allowing domain-level annotation

Q11. Which of the following is a common bioinformatic method to identify orthologous gene families across multiple bacterial genomes?

• Using southern blot patterns
• Reciprocal best BLAST hits (RBH) and clustering algorithms
• Measuring colony morphology differences
• Counting protein isoelectric points only

Correct Answer: Reciprocal best BLAST hits (RBH) and clustering algorithms

Q12. Which gene family is central to prokaryotic transcription initiation specificity?

• Two-component sensor kinases
• Sigma factor family
• Chaperonin GroEL family
• DNA polymerase III sliding-clamp family

Correct Answer: Sigma factor family

Q13. What role do toxin–antitoxin (TA) gene families play in bacteria?

• Primary function is in DNA replication accuracy
• They help in plasmid maintenance, stress response, and persistence
• They encode dominant metabolic enzymes
• They only serve as transcription factors

Correct Answer: They help in plasmid maintenance, stress response, and persistence

Q14. Which statement about pangenome openness is correct?

• An ‘open’ pangenome means adding more genomes stops revealing new genes
• An ‘open’ pangenome indicates new genes are continually discovered as more genomes are sampled
• Open pangenomes exist only for eukaryotes
• ‘Open’ pangenome refers to the set of plasmid-only genes

Correct Answer: An ‘open’ pangenome indicates new genes are continually discovered as more genomes are sampled

Q15. Which gene family type would you expect to be most highly conserved across diverse bacteria?

• Antibiotic resistance enzymes
• Ribosomal protein families
• Restriction-modification specificity subunits
• Phage tail fiber proteins

Correct Answer: Ribosomal protein families

Q16. CRISPR-Cas systems in prokaryotes are considered what kind of gene family from an evolutionary perspective?

• Highly conserved single-copy housekeeping genes
• Adaptive immune-related gene families with diverse subtypes and frequent horizontal transfer
• Only plasmid replication genes
• Non-functional pseudogenes in most bacteria

Correct Answer: Adaptive immune-related gene families with diverse subtypes and frequent horizontal transfer

Q17. Which feature is commonly used to cluster proteins into gene families computationally?

• Similar subcellular localization only
• Sequence similarity and conserved domains
• Shared GC skew pattern exclusively
• Presence in the same growth medium

Correct Answer: Sequence similarity and conserved domains

Q18. Which analytic result would suggest that a set of genes belongs to the same prokaryotic gene family?

• They have unrelated sequences but similar expression levels
• They share significant sequence homology, conserved motifs, and similar domain architecture
• They are located on different replicons with different GC contents only
• They are always adjacent to rRNA operons

Correct Answer: They share significant sequence homology, conserved motifs, and similar domain architecture

Q19. Which prokaryotic gene family is often used as a phylogenetic marker because of its conservation?

• Beta-lactamase
• 16S rRNA gene and ribosomal protein families
• Integrase gene family
• Transposase family

Correct Answer: 16S rRNA gene and ribosomal protein families

Q20. When annotating gene families, why is it important to distinguish between paralogs and recently horizontally transferred homologs?

• It is not important; both are functionally identical
• Because evolutionary origin affects functional inference, transferability, and epidemiology of traits like drug resistance
• Only paralogs can be drug targets
• Horizontally transferred genes never encode enzymes

Correct Answer: Because evolutionary origin affects functional inference, transferability, and epidemiology of traits like drug resistance

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