Q.1 What does the abbreviation "NGS" stand for in genomics?
Non-Growth Sequence
Next-Generation Sequencing
Nucleotide Genetic System
Nano-Genome Sequencer
Explanation - NGS refers to high-throughput sequencing technologies that generate large volumes of DNA sequence data quickly and cheaply.
Correct answer is: Next-Generation Sequencing
Q.2 Which of the following is NOT a primary function of bioinformatics?
Sequence alignment
Genome assembly
Protein folding prediction
Building household furniture
Explanation - Bioinformatics deals with computational analysis of biological data; it does not involve physical tasks like building furniture.
Correct answer is: Building household furniture
Q.3 During PCR, what is the purpose of the ‘denaturation’ step?
To separate the DNA strands
To copy the DNA strands
To add new nucleotides
To cool the reaction mix
Explanation - Denaturation heats the DNA to break hydrogen bonds between strands, yielding single-stranded templates for amplification.
Correct answer is: To separate the DNA strands
Q.4 Which protein is commonly used as a marker for bacterial contamination in DNA samples?
Hemoglobin
β-actin
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
16S ribosomal RNA
Explanation - 16S rRNA is a component of the small bacterial ribosomal subunit and is widely used to detect bacterial DNA.
Correct answer is: 16S ribosomal RNA
Q.5 Which bioinformatics tool is best suited for aligning short DNA reads to a reference genome?
BLAST
Clustal Omega
BWA-MEM
MUSCLE
Explanation - BWA-MEM is a fast, accurate algorithm designed for mapping high-throughput sequencing reads.
Correct answer is: BWA-MEM
Q.6 The CRISPR-Cas9 system is primarily used for:
Sequencing DNA
Editing genes
Amplifying RNA
Measuring protein mass
Explanation - CRISPR-Cas9 allows precise cutting and modification of specific DNA sequences, enabling gene editing.
Correct answer is: Editing genes
Q.7 Which mass spectrometry technique is most commonly used for protein identification in proteomics?
NMR spectroscopy
Electron spin resonance
Matrix-assisted laser desorption/ionization (MALDI)
X-ray crystallography
Explanation - MALDI coupled with time-of-flight (TOF) mass analyzers is widely used for rapid peptide mass fingerprinting.
Correct answer is: Matrix-assisted laser desorption/ionization (MALDI)
Q.8 What is the main difference between shotgun proteomics and targeted proteomics?
Shotgun uses antibodies, targeted uses mass spectrometry
Shotgun analyzes all proteins, targeted focuses on selected proteins
Shotgun is for DNA, targeted is for RNA
Shotgun requires large samples, targeted does not
Explanation - Shotgun proteomics performs unbiased, global protein identification, whereas targeted methods (e.g., SRM) quantify predefined proteins.
Correct answer is: Shotgun analyzes all proteins, targeted focuses on selected proteins
Q.9 Which of the following is a post-translational modification that often regulates protein activity?
DNA methylation
Phosphorylation
RNA splicing
Chromatin remodeling
Explanation - Adding a phosphate group to a protein can activate or inhibit its function.
Correct answer is: Phosphorylation
Q.10 In genomics, the term ‘variant call’ refers to:
The process of sequencing a genome
Identifying differences between an individual’s DNA and a reference genome
Naming a new species
Predicting protein structures
Explanation - Variant calling analyzes sequencing data to detect SNPs, indels, and other genomic variations.
Correct answer is: Identifying differences between an individual’s DNA and a reference genome
Q.11 Which algorithm is commonly used in phylogenetic tree construction based on genetic distance?
K-means clustering
UCSC Genome Browser
Neighbor-Joining
Huffman coding
Explanation - Neighbor-Joining builds trees by iteratively joining taxa with minimal distance, widely used in evolutionary studies.
Correct answer is: Neighbor-Joining
Q.12 What is the main advantage of using RNA-Seq over microarrays?
Lower cost
Higher dynamic range
Requires less sample preparation
Produces DNA data
Explanation - RNA-Seq can detect both low- and high-abundance transcripts, whereas microarrays have a more limited range.
Correct answer is: Higher dynamic range
Q.13 Which of the following is NOT a common data format for genome assemblies?
FASTA
BAM
GFF
VCF
Explanation - BAM stores aligned sequencing reads; FASTA, GFF, and VCF are used for sequences, annotations, and variants respectively.
Correct answer is: BAM
Q.14 A 'gene ontology' term describes:
The physical structure of a DNA helix
The biological role, cellular component, or molecular function of a gene product
The speed of a PCR reaction
The type of mass spectrometer used
Explanation - Gene Ontology provides standardized terms for functions, processes, and locations of gene products.
Correct answer is: The biological role, cellular component, or molecular function of a gene product
Q.15 In a two-dimensional gel electrophoresis, proteins are first separated by:
Size
pI (isoelectric point)
Charge
Hydrophobicity
Explanation - First dimension separates proteins by pI; second dimension separates them by molecular weight.
Correct answer is: pI (isoelectric point)
Q.16 Which of the following best describes a 'transcriptome'?
All proteins expressed in a cell
All DNA sequences in a genome
All RNA molecules transcribed from the genome
All metabolic pathways in a cell
Explanation - The transcriptome represents the complete set of RNA transcripts produced in a cell at a given time.
Correct answer is: All RNA molecules transcribed from the genome
Q.17 What does the term 'coverage' refer to in next-generation sequencing?
Number of samples sequenced
Depth of sequencing per base
Length of the sequencing reads
Number of base pairs per chromosome
Explanation - Coverage indicates how many times, on average, each base in the genome is read during sequencing.
Correct answer is: Depth of sequencing per base
Q.18 Which protein family is commonly used as a molecular marker for phylogenetic studies in eukaryotes?
Actin
Myosin
Histone H3
Cytochrome c oxidase subunit I (COI)
Explanation - COI is widely used for species identification (DNA barcoding) due to its high variability and mitochondrial origin.
Correct answer is: Cytochrome c oxidase subunit I (COI)
Q.19 Which of the following is a commonly used algorithm for de novo genome assembly?
BLAST
A* search
De Bruijn graph assembly
QuickSort
Explanation - De Bruijn graphs efficiently reconstruct genomes from short reads by representing k-mers and their overlaps.
Correct answer is: De Bruijn graph assembly
Q.20 In proteomics, the term 'shotgun proteomics' is analogous to:
Targeted sequencing
Random sampling of peptides
Single-molecule imaging
Chromatographic separation of DNA
Explanation - Shotgun proteomics digests proteins into peptides and analyzes them in a non-targeted, global fashion.
Correct answer is: Random sampling of peptides
Q.21 What is the primary advantage of using CRISPR interference (CRISPRi) over CRISPR knockout?
CRISPRi permanently removes genes
CRISPRi is used for gene overexpression
CRISPRi allows reversible gene silencing without cutting DNA
CRISPRi only works in prokaryotes
Explanation - CRISPRi uses a dead Cas9 fused to a repressor to block transcription without creating double-strand breaks.
Correct answer is: CRISPRi allows reversible gene silencing without cutting DNA
Q.22 Which of the following best describes a 'single nucleotide polymorphism' (SNP)?
A change of a single nucleotide in the genome
A deletion of a whole gene
An insertion of a whole chromosome
A type of protein modification
Explanation - SNPs are the most common genetic variation, involving a single base change.
Correct answer is: A change of a single nucleotide in the genome
Q.23 What role does the 'BLAST' algorithm primarily play in bioinformatics?
Aligning long genomic sequences
Predicting protein folding
Finding local sequence similarities
Designing PCR primers
Explanation - BLAST quickly identifies regions of local similarity between a query and database sequences.
Correct answer is: Finding local sequence similarities
Q.24 In the context of proteomics, what does 'label-free quantification' mean?
Using fluorescent tags to measure protein abundance
Measuring protein abundance without chemical tags
Counting DNA molecules instead of proteins
Using mass tags to label proteins
Explanation - Label-free methods estimate protein levels based on ion intensities or spectral counts, avoiding labeling steps.
Correct answer is: Measuring protein abundance without chemical tags
Q.25 Which database stores human gene annotations and functional information?
NCBI Taxonomy
Ensembl
KEGG
UniProt
Explanation - Ensembl provides genome assemblies, gene annotations, and functional data for humans and many other species.
Correct answer is: Ensembl
Q.26 The term 'coverage depth' in sequencing is best described as:
The number of times each base is sequenced on average
The total number of bases in a genome
The number of samples processed
The length of sequencing reads
Explanation - Coverage depth indicates how many sequencing reads overlap each position, influencing accuracy.
Correct answer is: The number of times each base is sequenced on average
Q.27 Which of the following is NOT typically used in a protein mass spectrometry workflow?
Protein extraction
Protein digestion
DNA sequencing
Chromatographic separation
Explanation - Mass spectrometry targets proteins, not DNA; DNA sequencing is a separate technique.
Correct answer is: DNA sequencing
Q.28 What is the purpose of a 'reference genome'?
To sequence all organisms
To provide a baseline for variant comparison
To replace all individual genomes
To sequence RNA only
Explanation - Reference genomes act as a standard to identify mutations or structural variations in sample genomes.
Correct answer is: To provide a baseline for variant comparison
Q.29 Which technique is most suitable for detecting post-translational modifications such as phosphorylation?
Western blotting with phospho-specific antibodies
PCR amplification
DNA sequencing
Mass spectrometry with enrichment steps
Explanation - MS can detect modifications after enrichment (e.g., IMAC) and identify modification sites by fragmentation patterns.
Correct answer is: Mass spectrometry with enrichment steps
Q.30 In a phylogenetic tree, a node that represents a common ancestor of all taxa in the tree is called:
Terminal node
Root node
Branch node
Leaf node
Explanation - The root node represents the most recent common ancestor of all taxa displayed.
Correct answer is: Root node
Q.31 Which of the following is a major advantage of using next-generation sequencing (NGS) for transcriptome analysis?
It only detects highly expressed genes
It provides sequence data for non-coding RNAs
It requires less computational power than microarrays
It does not need RNA extraction
Explanation - NGS captures all transcripts, including low-abundance and novel non-coding RNAs.
Correct answer is: It provides sequence data for non-coding RNAs
Q.32 The 'FASTQ' format primarily stores:
Protein structures
Sequencing reads with quality scores
Genome assembly metrics
Metabolic pathways
Explanation - FASTQ files contain nucleotide sequences and per-base quality values from sequencing instruments.
Correct answer is: Sequencing reads with quality scores
Q.33 Which type of sequencing technology generates longer reads, typically several thousand bases?
Illumina short-read sequencing
PacBio Single-Molecule Real-Time (SMRT) sequencing
Sanger sequencing of short fragments
Nanopore sequencing of short fragments
Explanation - PacBio SMRT produces long reads, enabling better assembly of repetitive regions.
Correct answer is: PacBio Single-Molecule Real-Time (SMRT) sequencing
Q.34 What is the purpose of a 'contig' in genome assembly?
A short DNA fragment used for sequencing
A contiguous sequence assembled from overlapping reads
A type of PCR primer
A computational model for protein folding
Explanation - Contigs represent continuous stretches of DNA constructed during assembly.
Correct answer is: A contiguous sequence assembled from overlapping reads
Q.35 Which bioinformatics tool is widely used for protein secondary structure prediction?
Clustal Omega
PSIPRED
Bowtie
MAFFT
Explanation - PSIPRED predicts α‑helices and β‑strands using neural networks and sequence profiles.
Correct answer is: PSIPRED
Q.36 A 'single-cell RNA-Seq' experiment primarily allows researchers to:
Sequence DNA from a single organism
Measure gene expression in individual cells
Analyze whole proteins from a single cell
Determine chromosome number
Explanation - Single-cell RNA‑Seq captures transcriptomes at single‑cell resolution, revealing cellular heterogeneity.
Correct answer is: Measure gene expression in individual cells
Q.37 Which of the following best describes 'orthologs'?
Genes that arose from a duplication event within one species
Genes in different species that evolved from a common ancestral gene
Genes that have identical sequences
Genes that are always expressed at the same time
Explanation - Orthologs maintain similar functions across species, useful for evolutionary studies.
Correct answer is: Genes in different species that evolved from a common ancestral gene
Q.38 In proteomics, what is a 'peptide mass fingerprint'?
A pattern of DNA mutations
The set of masses measured after proteolytic digestion of a protein
The sequence of a protein
A type of gel electrophoresis
Explanation - Mass fingerprints enable identification of proteins by matching observed masses to predicted peptide masses.
Correct answer is: The set of masses measured after proteolytic digestion of a protein
Q.39 What does the 'ENCODE' project aim to do?
Sequence all bacterial genomes
Identify all functional elements in the human genome
Develop new proteomics methods
Map the electrical circuits in a neuron
Explanation - ENCODE maps promoters, enhancers, and other regulatory features across the genome.
Correct answer is: Identify all functional elements in the human genome
Q.40 Which of these is a key advantage of using real-time PCR (qPCR) over traditional PCR?
It requires no thermal cycler
It provides quantitative data during amplification
It uses lower volumes of reagents
It can amplify RNA without reverse transcription
Explanation - qPCR measures fluorescence in real-time to quantify initial template amounts.
Correct answer is: It provides quantitative data during amplification
Q.41 A 'contaminant peptide' identified in a proteomics experiment most likely indicates:
A new protein discovery
A misannotation in the database
Presence of foreign proteins from the environment or reagents
A sequencing error
Explanation - Contaminants often arise from lab reagents or sample handling.
Correct answer is: Presence of foreign proteins from the environment or reagents
Q.42 Which of the following is an example of a 'short-read' sequencing technology?
Nanopore long reads
Sanger sequencing
Illumina MiSeq
PacBio HiFi
Explanation - Illumina platforms generate short reads (~150–300 bp) suitable for high-throughput sequencing.
Correct answer is: Illumina MiSeq
Q.43 In a 'gene expression microarray', what does each spot on the array represent?
A single nucleotide mutation
A specific probe that hybridizes to a particular mRNA sequence
A protein fragment
A whole chromosome
Explanation - Probes on the array capture complementary mRNA, allowing quantification of expression levels.
Correct answer is: A specific probe that hybridizes to a particular mRNA sequence
Q.44 Which of the following best describes the 'Open Reading Frame' (ORF) in genomics?
A sequence that encodes a functional protein
A sequence that codes for RNA only
A region that is always silenced
A region that contains only introns
Explanation - ORFs are contiguous stretches of codons that start with ATG and end with a stop codon.
Correct answer is: A sequence that encodes a functional protein
Q.45 Which of the following is a common type of genetic variant discovered in cancer genomics?
Single nucleotide polymorphism (SNP)
Somatic mutation
Inherited allele
Chromosome duplication in normal tissue
Explanation - Somatic mutations arise in tumor cells and are not inherited; they drive cancer progression.
Correct answer is: Somatic mutation
Q.46 Which analytical technique is typically used to separate peptides before mass spectrometry?
Gel electrophoresis
Liquid chromatography
X-ray crystallography
Fluorescence microscopy
Explanation - LC separates peptides based on hydrophobicity and other properties, improving MS detection.
Correct answer is: Liquid chromatography
Q.47 The term 'gene fusion' refers to:
The joining of two adjacent genes into a single transcriptional unit
The duplication of a gene within the genome
The deletion of a gene
The addition of a tag to a protein
Explanation - Gene fusions often result from chromosomal rearrangements and can lead to oncogenic proteins.
Correct answer is: The joining of two adjacent genes into a single transcriptional unit
Q.48 Which bioinformatics pipeline step involves aligning sequencing reads to a reference genome?
Preprocessing
Mapping
Variant calling
Annotation
Explanation - Mapping places reads onto the reference, forming the basis for downstream analysis.
Correct answer is: Mapping
Q.49 Which of these is a key difference between DNA microarrays and RNA-Seq?
Microarrays can detect novel transcripts; RNA-Seq cannot
RNA-Seq provides sequence data; microarrays only provide hybridization intensities
Microarrays require sequencing equipment; RNA-Seq does not
RNA-Seq is slower than microarrays
Explanation - RNA-Seq reads the transcript sequence itself, enabling novel transcript discovery.
Correct answer is: RNA-Seq provides sequence data; microarrays only provide hybridization intensities
Q.50 In a mass spectrometer, what does the term 'm/z' refer to?
Mass-to-charge ratio
Molarity over time
Mean zero value
Magnetic field strength
Explanation - m/z is the ratio of an ion's mass to its charge, used to identify fragments.
Correct answer is: Mass-to-charge ratio
Q.51 Which of the following best describes a 'protein isoform'?
A completely different protein unrelated to the gene
A protein that has undergone post-translational modifications
Different variants of a protein produced from the same gene
A protein that has been degraded
Explanation - Isoforms arise from alternative splicing or post-translational processing.
Correct answer is: Different variants of a protein produced from the same gene
Q.52 The 'BLASTP' algorithm is used to compare:
Protein sequences to protein databases
DNA sequences to DNA databases
RNA sequences to RNA databases
Protein sequences to DNA databases
Explanation - BLASTP searches a protein query against a protein database for homologs.
Correct answer is: Protein sequences to protein databases
Q.53 In proteomics, 'spectral library searching' differs from 'de novo sequencing' in that:
It does not require any mass spectrometer
It uses known peptide fragmentation patterns for identification
It generates new protein sequences from scratch
It only works for DNA, not proteins
Explanation - Spectral libraries contain experimentally determined spectra, enabling rapid matching.
Correct answer is: It uses known peptide fragmentation patterns for identification
Q.54 The 'Human Microbiome Project' primarily focuses on:
Sequencing the human genome
Characterizing microbial communities in human habitats
Engineering synthetic microbes
Developing new antibiotics
Explanation - The project catalogues bacteria, archaea, viruses, and fungi present in various human body sites.
Correct answer is: Characterizing microbial communities in human habitats
Q.55 What is a 'transcript isoform'?
A variant of a protein due to post-translational modification
A variant of mRNA produced from the same gene due to alternative splicing
A type of DNA mutation
An alternative promoter region
Explanation - Alternative splicing creates multiple mRNA variants from a single gene.
Correct answer is: A variant of mRNA produced from the same gene due to alternative splicing
Q.56 Which of the following best describes a 'phage display library'?
A library of DNA fragments from bacteriophages
A collection of peptides displayed on bacteriophage surfaces for binding studies
A database of viral genomes
An array of phage-based antibodies
Explanation - Phage display allows selection of peptides/proteins that bind target molecules.
Correct answer is: A collection of peptides displayed on bacteriophage surfaces for binding studies
Q.57 Which of these best defines 'epigenetics'?
Changes in DNA sequence that affect phenotype
Heritable changes in gene expression without altering DNA sequence
The process of gene duplication
The study of electrical signals in neurons
Explanation - Epigenetic mechanisms (methylation, histone modification) regulate gene activity.
Correct answer is: Heritable changes in gene expression without altering DNA sequence
Q.58 The 'SNP' stands for:
Single Nucleotide Polymorphism
Single Nucleotide Polypeptide
Serine-Glutamine Peptide
Standard Nuclear Position
Explanation - SNPs are single base changes common in populations.
Correct answer is: Single Nucleotide Polymorphism
Q.59 What is the purpose of 'RNA-Seq alignment' to the genome?
To map reads to exons, introns, and splice junctions
To assemble de novo genomes
To identify DNA mutations
To sequence proteins
Explanation - RNA‑Seq alignment places reads on the genome, allowing expression quantification and splice detection.
Correct answer is: To map reads to exons, introns, and splice junctions
Q.60 Which of the following best describes a 'DNA methyltransferase'?
An enzyme that adds methyl groups to DNA
An enzyme that removes methyl groups from DNA
A protein that reads DNA methylation marks
A DNA polymerase
Explanation - DNA methyltransferases transfer a methyl group from SAM to cytosine residues.
Correct answer is: An enzyme that adds methyl groups to DNA
Q.61 In proteomics, the term 'differential expression' refers to:
Changes in gene copy number
Differences in protein abundance between conditions
Variations in DNA methylation
Alterations in RNA splicing patterns
Explanation - Differential expression analysis compares protein levels across experimental states.
Correct answer is: Differences in protein abundance between conditions
Q.62 Which of the following is a key component of a 'genome assembly graph'?
Nodes representing k-mers, edges representing overlaps
Nodes representing proteins, edges representing interactions
Nodes representing chromosomes, edges representing centromeres
Nodes representing metabolites, edges representing reactions
Explanation - Genome assembly graphs connect overlapping k‑mers to reconstruct sequences.
Correct answer is: Nodes representing k-mers, edges representing overlaps
Q.63 What does the term 'fold change' represent in gene expression analysis?
The number of times a gene is duplicated
The ratio of expression levels between two conditions
The absolute difference in expression levels
The time it takes for a gene to fold into a protein
Explanation - Fold change quantifies up- or down-regulation by comparing expression ratios.
Correct answer is: The ratio of expression levels between two conditions
Q.64 In a 'phylogenetic tree', what does a long branch length typically indicate?
Recent speciation
High evolutionary change
Low genetic diversity
Short time since divergence
Explanation - Longer branches reflect more substitutions per site, indicating greater divergence.
Correct answer is: High evolutionary change
Q.65 Which of these is a typical use of 'Principal Component Analysis' (PCA) in genomics?
To cluster proteins by function
To reduce dimensionality of gene expression data for visualization
To align DNA reads
To design PCR primers
Explanation - PCA transforms high‑dimensional data into principal components for easier interpretation.
Correct answer is: To reduce dimensionality of gene expression data for visualization
Q.66 Which of the following describes an 'epitope'?
A domain that binds DNA
A region of a protein recognized by an antibody
A segment of RNA that codes for a protein
An enzyme that modifies histones
Explanation - Epitopes are the specific parts of antigens that antibodies or T-cell receptors bind.
Correct answer is: A region of a protein recognized by an antibody
Q.67 Which of these best describes 'transcription factor binding sites' (TFBS) in genomics?
Regions in the DNA where transcription factors bind to regulate gene expression
Regions where DNA polymerase binds during replication
Sites of DNA methylation
Regions coding for transposons
Explanation - TFBS are short DNA motifs recognized by transcription factors to control transcription.
Correct answer is: Regions in the DNA where transcription factors bind to regulate gene expression
Q.68 Which type of sequencing output is typically stored in a 'BAM' file?
Raw image data from the sequencer
Base call sequences with quality scores
Aligned sequencing reads to a reference genome
Metabolic pathway diagrams
Explanation - BAM files contain binary alignment data for efficient storage and retrieval.
Correct answer is: Aligned sequencing reads to a reference genome
Q.69 A 'microbial genome' generally contains:
Multiple chromosomes and plasmids
A single circular chromosome and often plasmids
Only plasmids
A linear chromosome with introns
Explanation - Most bacteria have one circular chromosome plus plasmids; introns are rare.
Correct answer is: A single circular chromosome and often plasmids
Q.70 What does the 'FASTA' format primarily store?
Protein structures
DNA or protein sequences without quality information
Sequencing instrument raw data
Genetic variation data
Explanation - FASTAs contain sequence headers and nucleotide or amino acid strings.
Correct answer is: DNA or protein sequences without quality information
Q.71 Which of the following is NOT a common source of contamination in proteomics samples?
Reagents containing keratin
Ambient airborne dust
Instruments used for DNA extraction
Bacterial endotoxins
Explanation - DNA extraction instruments are usually clean; keratin contamination often comes from skin and hair.
Correct answer is: Instruments used for DNA extraction
Q.72 In a 'paired-end' sequencing strategy, reads are generated from:
Both ends of the same DNA fragment
Two different fragments
A single end only
The RNA transcript
Explanation - Paired-end reads improve alignment and assembly by providing two sequences per fragment.
Correct answer is: Both ends of the same DNA fragment
Q.73 Which of these best explains a 'single-cell proteomics' experiment?
Analyzing the proteome of a single organism
Quantifying proteins in a mixture of many cells
Measuring proteins from an individual cell
Sequencing the DNA of a single cell
Explanation - Single-cell proteomics aims to detect protein expression at the cellular level.
Correct answer is: Measuring proteins from an individual cell
Q.74 A 'copy number variation' (CNV) is:
A single base change in DNA
A deletion of a single gene
A change in the number of copies of a genomic region
A point mutation that changes amino acid
Explanation - CNVs involve duplications or deletions of large DNA segments.
Correct answer is: A change in the number of copies of a genomic region
Q.75 Which of the following best describes an 'open-source bioinformatics tool'?
A proprietary software that requires a license
A freely available software whose source code can be modified
An online database for protein structures
A hardware device used in sequencing
Explanation - Open-source tools allow users to inspect, modify, and distribute the code.
Correct answer is: A freely available software whose source code can be modified
Q.76 The 'cDNA library' constructed from mRNA is used for:
Sequencing genomic DNA only
Studying the proteome directly
Cloning and expression of genes
Mapping chromosomal locations
Explanation - cDNA libraries contain reverse-transcribed mRNA, representing expressed genes.
Correct answer is: Cloning and expression of genes
Q.77 Which of the following best defines the 'Kyoto Encyclopedia of Genes and Genomes (KEGG)' database?
A collection of protein 3D structures
A resource of metabolic pathways and functional annotations
A list of genomic DNA sequences
A repository of clinical trial data
Explanation - KEGG provides pathway maps and functional information for genes and proteins.
Correct answer is: A resource of metabolic pathways and functional annotations
Q.78 A 'mass spectrometry imaging (MSI)' technique is used to:
Visualize the spatial distribution of metabolites or proteins in tissue sections
Sequence DNA across the genome
Detect protein-protein interactions
Measure electrical potentials in neurons
Explanation - MSI creates maps of molecules directly from tissue slices without labeling.
Correct answer is: Visualize the spatial distribution of metabolites or proteins in tissue sections
Q.79 The 'Human Genome Project' completed in 2003 primarily produced:
The complete human genome sequence
A list of all human proteins
A comprehensive proteomics database
A map of the human microbiome
Explanation - The HGP provided the reference sequence of the human genome.
Correct answer is: The complete human genome sequence
Q.80 What is the main difference between 'in silico' and 'in vitro' experiments?
In silico uses computer simulations; in vitro uses cell culture
In silico uses living organisms; in vitro uses machines
In silico uses animals; in vitro uses plants
In silico uses chemicals; in vitro uses DNA
Explanation - In silico refers to computational analysis; in vitro refers to experiments outside living organisms.
Correct answer is: In silico uses computer simulations; in vitro uses cell culture
Q.81 The 'MHC class I' molecules primarily present peptides to:
CD4+ T helper cells
B cells
CD8+ cytotoxic T cells
Macrophages
Explanation - MHC class I presents endogenous peptides to CD8+ T cells.
Correct answer is: CD8+ cytotoxic T cells
Q.82 Which of these is a characteristic of a 'protein domain'?
It is a DNA sequence that codes for a protein
It is a distinct functional or structural unit of a protein
It is the entire protein chain
It is a post-translational modification
Explanation - Domains can fold independently and often have specific functions.
Correct answer is: It is a distinct functional or structural unit of a protein
Q.83 Which of the following best explains 'sequence alignment' in bioinformatics?
Aligning sequences on a microscope slide
Arranging sequences to identify regions of similarity
Sequencing DNA in the correct order
Aligning proteins to their functions
Explanation - Alignment aligns nucleotides or amino acids to reveal evolutionary or functional relationships.
Correct answer is: Arranging sequences to identify regions of similarity
Q.84 In the context of proteomics, what is a 'labeling strategy'?
Marking proteins with fluorescent tags for detection
Tagging DNA for sequencing
Designing primers for PCR
Color-coding data files
Explanation - Labeling (e.g., iTRAQ, TMT) allows multiplexed quantification of proteins.
Correct answer is: Marking proteins with fluorescent tags for detection
Q.85 Which of the following best describes the 'N-terminal' of a protein?
The end of the protein that contains the start codon
The end that contains the stop codon
The middle of the protein chain
The part that is secreted
Explanation - The N‑terminus is the amino‑terminus, often the first amino acid coded.
Correct answer is: The end of the protein that contains the start codon
Q.86 What does the 'ORF' (Open Reading Frame) length indicate?
The number of exons
The size of the gene in base pairs that can potentially encode a protein
The length of the promoter region
The size of the intron
Explanation - ORFs represent contiguous coding sequences that can be translated.
Correct answer is: The size of the gene in base pairs that can potentially encode a protein
Q.87 Which of the following is an advantage of using a 'paired-end' library in sequencing?
It allows sequencing of both strands of DNA simultaneously
It provides reads from both ends of a fragment, improving assembly
It requires fewer sequencing cycles
It eliminates the need for alignment
Explanation - Paired-end reads help resolve repeats and structural variants.
Correct answer is: It provides reads from both ends of a fragment, improving assembly
Q.88 What is the primary purpose of a 'de novo' genome assembler?
To align reads to a reference genome
To reconstruct a genome from sequencing reads without a reference
To annotate genes in a known genome
To identify mutations in a sample
Explanation - De novo assemblers build genomes from scratch, useful for novel organisms.
Correct answer is: To reconstruct a genome from sequencing reads without a reference
Q.89 Which of the following is a feature of the 'Tandem Mass Tag (TMT)' labeling system?
It uses isotopic labeling for multiplexed quantitative proteomics
It labels DNA fragments for sequencing
It stains proteins for gel imaging
It is used for RNA extraction
Explanation - TMT labels peptides with isobaric tags, enabling simultaneous quantification of multiple samples.
Correct answer is: It uses isotopic labeling for multiplexed quantitative proteomics
Q.90 A 'mosaic' mutation in the genome refers to:
A mutation present in only a subset of cells
A mutation that appears in all cells of the organism
A mutation that is identical across all tissues
A mutation that only occurs in the germline
Explanation - Mosaicism involves post-zygotic mutations affecting some cell lineages.
Correct answer is: A mutation present in only a subset of cells
Q.91 Which of the following best explains 'genotype'?
The observable traits of an organism
The DNA sequence of an organism
The environment in which an organism lives
The set of proteins expressed by an organism
Explanation - Genotype refers to the genetic makeup, i.e., the DNA sequence.
Correct answer is: The DNA sequence of an organism
Q.92 What is the function of 'RNA-Seq read mapping software' such as STAR?
To assemble genomes de novo
To align RNA-Seq reads to a reference genome or transcriptome
To predict protein structures
To annotate gene functions
Explanation - STAR performs fast, spliced alignment of RNA-Seq reads.
Correct answer is: To align RNA-Seq reads to a reference genome or transcriptome
Q.93 Which of the following is a 'protein interaction network' used for?
To predict DNA mutations
To map interactions between proteins in a cell
To sequence RNA transcripts
To identify gene regulatory motifs
Explanation - Interaction networks depict physical or functional associations among proteins.
Correct answer is: To map interactions between proteins in a cell
Q.94 In proteomics, the term 'labeling-free quantification' means:
Using fluorescent dyes for protein detection
Quantifying protein abundance without any chemical tags
Using mass tags for each peptide
Measuring protein expression levels using antibodies
Explanation - Label-free methods rely on ion intensities or spectral counts for quantification.
Correct answer is: Quantifying protein abundance without any chemical tags
Q.95 The 'CRISPR' system was first discovered in:
Humans
Bacteria
Plants
Fungi
Explanation - CRISPR was identified as a bacterial adaptive immune system.
Correct answer is: Bacteria
Q.96 Which of the following best defines 'mass spectrometry'?
A technique for measuring the mass-to-charge ratio of ions to identify molecules
A method to sequence DNA strands
An imaging technique for cells
A method to amplify RNA
Explanation - Mass spectrometry ionizes molecules, separates them by m/z, and detects them.
Correct answer is: A technique for measuring the mass-to-charge ratio of ions to identify molecules
Q.97 The 'T4 DNA ligase' enzyme is commonly used for:
Sequencing DNA
Joining DNA fragments during cloning
Cutting DNA at specific sites
Transcribing RNA
Explanation - DNA ligase catalyzes phosphodiester bond formation between DNA fragments.
Correct answer is: Joining DNA fragments during cloning
Q.98 In a 'transcriptome', which of the following is a type of RNA that is typically not translated into protein?
mRNA
rRNA
tRNA
snoRNA
Explanation - Small nucleolar RNAs (snoRNA) guide chemical modifications of rRNA and are non-coding.
Correct answer is: snoRNA
Q.99 Which of these is a key benefit of using long-read sequencing technologies like PacBio?
Higher accuracy per read
Lower cost per base
Ability to resolve complex repeats and structural variants
Requirement for fewer computational resources
Explanation - Long reads span repetitive elements, improving assembly and variant detection.
Correct answer is: Ability to resolve complex repeats and structural variants
Q.100 Which of the following best defines a 'gene regulatory network'?
A collection of proteins that interact physically
A map of transcription factors and their target genes
A set of metabolic pathways
An assembly of chromosomes within a nucleus
Explanation - Gene regulatory networks describe how TFs control gene expression.
Correct answer is: A map of transcription factors and their target genes
Q.101 Which of these is a typical output of a 'protein structure prediction' algorithm?
DNA sequence alignment
3D coordinates of protein atoms
Gene expression heatmap
RNA secondary structure diagram
Explanation - Structure prediction yields atomic positions forming a 3D model.
Correct answer is: 3D coordinates of protein atoms
Q.102 What is the role of 'gap-filling' in genome assembly?
To insert gaps intentionally to reduce assembly size
To fill missing sequence information between contigs using additional data
To delete repetitive regions
To annotate genes
Explanation - Gap-filling uses longer reads or additional libraries to bridge gaps.
Correct answer is: To fill missing sequence information between contigs using additional data
Q.103 Which of the following best describes 'chromatin immunoprecipitation sequencing (ChIP-Seq)'?
A method to sequence entire chromosomes
A technique to identify DNA binding sites of proteins or histone modifications
A method to amplify RNA
A process for measuring protein abundance
Explanation - ChIP-Seq captures protein-bound DNA fragments, then sequences them.
Correct answer is: A technique to identify DNA binding sites of proteins or histone modifications
Q.104 Which of these is an example of a 'non-coding RNA' (ncRNA)?
mRNA
rRNA
tRNA
MicroRNA (miRNA)
Explanation - miRNA are small RNAs that regulate gene expression without encoding proteins.
Correct answer is: MicroRNA (miRNA)
Q.105 Which of the following tools is commonly used for multiple sequence alignment of proteins?
BLASTP
Clustal Omega
Bowtie
MAFFT
Explanation - Clustal Omega aligns multiple protein sequences efficiently.
Correct answer is: Clustal Omega
Q.106 What does the 'log2 fold change' indicate in gene expression analysis?
The natural logarithm of expression difference
The ratio of expression levels in base 10
Half the ratio of expression levels (log base 2)
The difference in expression levels in raw counts
Explanation - log2 fold change is the binary logarithm of the expression ratio.
Correct answer is: Half the ratio of expression levels (log base 2)
Q.107 Which of the following best describes an 'allele frequency'?
The number of alleles in a population
The proportion of chromosomes that carry a specific allele
The distance between alleles on a chromosome
The expression level of a gene allele
Explanation - Allele frequency quantifies how common an allele is in a population.
Correct answer is: The proportion of chromosomes that carry a specific allele
Q.108 Which of these is a common technique for detecting protein-protein interactions?
PCR
Co-immunoprecipitation (Co-IP)
DNA microarray
ChIP-Seq
Explanation - Co-IP pulls down a protein complex using an antibody, revealing interactions.
Correct answer is: Co-immunoprecipitation (Co-IP)
Q.109 Which of these best explains 'RNA velocity' in single-cell RNA-Seq studies?
The speed at which RNA molecules are synthesized
The predicted future state of a cell based on spliced/unspliced transcripts
The rate of RNA degradation
The velocity of RNA moving through a cell
Explanation - RNA velocity infers cell state transitions using dynamic RNA kinetics.
Correct answer is: The predicted future state of a cell based on spliced/unspliced transcripts
Q.110 What is the primary function of a 'PCR thermal cycler'?
To sequence DNA strands
To amplify DNA by repeated heating and cooling cycles
To separate proteins by electrophoresis
To measure protein mass
Explanation - The cycler cycles between temperatures for denaturation, annealing, and extension.
Correct answer is: To amplify DNA by repeated heating and cooling cycles
Q.111 Which of the following best describes a 'copy number alteration' (CNA) in cancer?
A single nucleotide change in the DNA
An increase or decrease in the number of copies of a genomic region
A translocation of a chromosome segment
A point mutation that creates a stop codon
Explanation - CNAs involve gains or losses of large DNA segments.
Correct answer is: An increase or decrease in the number of copies of a genomic region
Q.112 Which of these is a common use of a 'phylogenetic tree' in genomics?
Predicting protein folding
Mapping evolutionary relationships between species
Sequencing genomes
Visualizing metabolic pathways
Explanation - Phylogenetic trees illustrate evolutionary descent based on genetic data.
Correct answer is: Mapping evolutionary relationships between species
Q.113 What is a 'k-mer' in the context of genome assembly?
A short DNA sequence of length k used to construct assembly graphs
A protein domain of length k amino acids
A region of the genome containing k genes
A type of sequencing read
Explanation - k-mers are substrings of length k used in overlap detection for assembly.
Correct answer is: A short DNA sequence of length k used to construct assembly graphs
Q.114 Which of the following best describes the 'FastQC' tool?
A tool for aligning RNA-Seq reads
A tool for quality control of raw sequencing data
A tool for predicting protein secondary structure
A tool for designing PCR primers
Explanation - FastQC generates QC metrics for sequencing libraries.
Correct answer is: A tool for quality control of raw sequencing data
Q.115 Which of the following best explains 'gene knockdown' using RNAi?
Complete removal of a gene from the genome
Reduction of gene expression by small interfering RNAs
Introduction of a new gene into the genome
Amplification of gene expression by plasmid insertion
Explanation - RNAi uses siRNAs to degrade mRNA, lowering protein production.
Correct answer is: Reduction of gene expression by small interfering RNAs
Q.116 Which of the following best describes a 'metagene' in RNA-Seq analysis?
The sum of all gene transcripts in a cell
A composite average profile of read coverage across gene bodies
A gene that regulates multiple other genes
A gene found only in metazoans
Explanation - Metagene plots average read densities over a set of genes.
Correct answer is: A composite average profile of read coverage across gene bodies
Q.117 What is the primary purpose of the 'MASCOT' software in proteomics?
Predicting protein 3D structures
Identifying proteins from tandem MS data
Sequencing DNA fragments
Annotating genomic features
Explanation - MASCOT matches MS/MS spectra to theoretical spectra to identify proteins.
Correct answer is: Identifying proteins from tandem MS data
Q.118 Which of the following is a typical output of a 'variant caller' like GATK?
A list of SNPs and indels with genotype information
A 3D protein structure model
An alignment of RNA-Seq reads
A metabolic pathway diagram
Explanation - Variant callers detect genomic variants and report genotype calls.
Correct answer is: A list of SNPs and indels with genotype information
Q.119 What does the 'fold enrichment' of a ChIP-Seq peak indicate?
The absolute number of reads in the peak
The ratio of peak signal compared to background
The length of the DNA fragment
The amount of protein bound
Explanation - Fold enrichment measures how much the signal exceeds the expected background.
Correct answer is: The ratio of peak signal compared to background
Q.120 Which of these is a key advantage of 'label-free' mass spectrometry in proteomics?
Higher dynamic range
No need for isotope labeling
Reduced instrument cost
Increased sample throughput
Explanation - Label-free methods avoid the costs and complexity of labeling reagents.
Correct answer is: No need for isotope labeling
Q.121 Which of the following best describes 'phasing' in genomics?
Separating homologous chromosomes into maternal and paternal sets
Determining the order of nucleotides in a sequence
Aligning reads to a reference
Sequencing the entire genome in one run
Explanation - Phasing resolves which alleles reside on the same chromosome copy.
Correct answer is: Separating homologous chromosomes into maternal and paternal sets
Q.122 Which of the following is a key step in preparing samples for a 'mass spectrometry-based proteomics' experiment?
Amplifying DNA by PCR
Digesting proteins with trypsin
Reverse transcribing RNA
Cloning into a plasmid
Explanation - Trypsin cleaves proteins at Lys/Arg residues to generate peptides for MS.
Correct answer is: Digesting proteins with trypsin
Q.123 The 'cDNA' is synthesized from:
DNA fragments only
mRNA templates via reverse transcriptase
Proteins via translation
Metabolites via reverse transcription
Explanation - cDNA is a complementary DNA copy of mRNA, produced by reverse transcriptase.
Correct answer is: mRNA templates via reverse transcriptase
Q.124 Which of these best explains 'DNA methylation' in epigenetics?
Adding methyl groups to histones
Removing nucleotides from DNA
Adding methyl groups to cytosine bases
Phosphorylating DNA strands
Explanation - DNA methyltransferases transfer a methyl group to cytosine, usually at CpG sites.
Correct answer is: Adding methyl groups to cytosine bases
Q.125 Which of these is an example of a 'DNA sequencing platform'?
Illumina NovaSeq
Tandem Mass Tag
SDS-PAGE
qRT-PCR
Explanation - Illumina NovaSeq is a high-throughput sequencing machine.
Correct answer is: Illumina NovaSeq
Q.126 What is the main goal of 'differential splicing analysis' in RNA-Seq data?
To identify genes with varying expression levels
To detect changes in splice variant usage between conditions
To determine DNA sequence mutations
To quantify protein abundance
Explanation - Differential splicing compares exon inclusion/exclusion across samples.
Correct answer is: To detect changes in splice variant usage between conditions
Q.127 Which of these tools is specifically designed to predict subcellular localization of proteins?
SignalP
TMHMM
TargetP
Clustal Omega
Explanation - TargetP predicts mitochondrial, chloroplast, or secretory pathway targeting.
Correct answer is: TargetP
Q.128 Which of the following is a characteristic of a 'transposable element'?
It is a stable gene that never moves
It can copy or cut and paste itself within the genome
It is found only in bacteria
It codes for a ribosomal protein
Explanation - Transposable elements are mobile DNA sequences.
Correct answer is: It can copy or cut and paste itself within the genome
Q.129 What is the primary role of 'ribosome profiling' (Ribo-Seq)?
Sequencing DNA genomes
Measuring RNA splicing events
Mapping ribosome occupancy on mRNA to study translation
Analyzing protein post-translational modifications
Explanation - Ribo-Seq captures ribosome-protected fragments, revealing active translation sites.
Correct answer is: Mapping ribosome occupancy on mRNA to study translation
Q.130 Which of these best describes a 'haplotype'?
The complete sequence of a chromosome
A combination of alleles at multiple loci that are inherited together
A single nucleotide polymorphism
A type of protein domain
Explanation - Haplotypes represent linked variants across a genomic region.
Correct answer is: A combination of alleles at multiple loci that are inherited together
Q.131 In bioinformatics, which of the following is a common method for correcting sequencing errors in reads?
PCR amplification
Error-correction algorithms like BFC or SPAdes' read correction
Increasing read length
Using only single-end reads
Explanation - Error-correction tools use k-mer frequencies to identify and fix errors.
Correct answer is: Error-correction algorithms like BFC or SPAdes' read correction
Q.132 Which of the following best explains a 'CRISPR off-target effect'?
The intended gene is successfully edited
Unintended edits occur at genomic sites similar to the target sequence
The Cas9 enzyme is degraded
The guide RNA fails to bind
Explanation - Off-target effects arise when Cas9 cuts at sites with partial complementarity.
Correct answer is: Unintended edits occur at genomic sites similar to the target sequence
Q.133 Which of these is an application of 'protein–protein docking'?
Sequencing DNA fragments
Predicting how two proteins interact physically
Measuring DNA methylation
Amplifying RNA
Explanation - Docking models the binding interface between proteins.
Correct answer is: Predicting how two proteins interact physically
Q.134 Which of these best defines a 'transcript isoform'?
A variant of a protein due to post-translational modification
A variant of mRNA produced from the same gene by alternative splicing
A type of DNA mutation
A promoter region
Explanation - Alternative splicing generates multiple mRNA transcripts from one gene.
Correct answer is: A variant of mRNA produced from the same gene by alternative splicing
Q.135 The 'HOMER' software is commonly used for:
Protein structure prediction
Motif discovery and enrichment analysis in genomic datasets
Assembling genomes de novo
RNA sequencing alignment
Explanation - HOMER identifies DNA sequence motifs in ChIP-Seq peaks, etc.
Correct answer is: Motif discovery and enrichment analysis in genomic datasets
Q.136 Which of the following is an example of a 'gene knockout' strategy?
RNA interference (RNAi)
CRISPR/Cas9-mediated deletion of a gene
Overexpressing a gene
Using a promoter to drive gene expression
Explanation - Gene knockouts remove the functional gene sequence entirely.
Correct answer is: CRISPR/Cas9-mediated deletion of a gene
Q.137 Which of these is a key component of a 'protein interaction network'?
A gene expression heatmap
Nodes representing proteins and edges representing interactions
A DNA sequence alignment
An RNA secondary structure diagram
Explanation - The network visually displays relationships between proteins.
Correct answer is: Nodes representing proteins and edges representing interactions
Q.138 What does the term 'mRNA stability' refer to?
The duration an mRNA transcript remains intact before degradation
The ability of mRNA to be translated into protein
The rate of mRNA splicing
The number of exons in an mRNA
Explanation - Stability influences protein expression levels and gene regulation.
Correct answer is: The duration an mRNA transcript remains intact before degradation
Q.139 Which of the following best describes a 'peptide mass fingerprint' in proteomics?
A method for sequencing DNA
A list of masses of peptides generated from a protein digested by trypsin
A type of 3D protein structure model
A graph of RNA abundance
Explanation - Mass fingerprints help identify proteins by matching observed masses to predicted ones.
Correct answer is: A list of masses of peptides generated from a protein digested by trypsin