Q.1 What does DNA stand for?
Deoxyribonucleic Acid
Dinuclear Acid
Deoxynucleic Acid
Dihydroxy Nucleotide Acid
Explanation - DNA stands for Deoxyribonucleic Acid, a molecule that carries genetic information.
Correct answer is: Deoxyribonucleic Acid
Q.2 Which base is NOT found in DNA?
Adenine
Thymine
Uracil
Guanine
Explanation - Uracil is found in RNA, not DNA; DNA uses thymine instead.
Correct answer is: Uracil
Q.3 How many strands does a DNA double helix have?
One
Two
Three
Four
Explanation - A DNA double helix consists of two complementary strands wound around each other.
Correct answer is: Two
Q.4 What shape is the DNA double helix?
Square
Cube
Helix
Triangle
Explanation - The DNA double helix has a spiral or helical shape.
Correct answer is: Helix
Q.5 Which nitrogenous base pairs with adenine?
Guanine
Thymine
Cytosine
Uracil
Explanation - In DNA, adenine pairs with thymine via hydrogen bonds.
Correct answer is: Thymine
Q.6 What is the basic unit of a protein?
Nucleotide
Amino Acid
Monomer
Glycolipid
Explanation - Proteins are chains of amino acids.
Correct answer is: Amino Acid
Q.7 Which process copies DNA into RNA?
Replication
Transcription
Translation
Translocation
Explanation - Transcription is the synthesis of RNA from a DNA template.
Correct answer is: Transcription
Q.8 What does the sequence ATG represent in a gene?
Stop codon
Start codon
Adenine Thymine Guanine
Amino Transfer Gene
Explanation - ATG codes for methionine and signals the start of translation.
Correct answer is: Start codon
Q.9 Which tool compares DNA sequences?
Calculator
BLAST
MRI
Sieve
Explanation - BLAST (Basic Local Alignment Search Tool) aligns sequences to find similarities.
Correct answer is: BLAST
Q.10 What does a codon encode?
One amino acid
Two amino acids
A sugar
A phosphate group
Explanation - A codon is a three‑nucleotide sequence that specifies one amino acid.
Correct answer is: One amino acid
Q.11 Which of these is a protein‑coding DNA sequence?
ATCGATCGAT
GGTAC
TTTAAACCCGGG
CTGACTGACTG
Explanation - The last sequence contains multiple codons that could translate into a peptide chain.
Correct answer is: CTGACTGACTG
Q.12 Which base pairs with cytosine?
Adenine
Thymine
Guanine
Uracil
Explanation - Cytosine pairs with guanine in the DNA double helix.
Correct answer is: Guanine
Q.13 What is the main function of a gene?
Store energy
Transmit signals
Code for proteins
Produce water
Explanation - Genes contain the information needed to build proteins.
Correct answer is: Code for proteins
Q.14 Which of the following is NOT a DNA polymerase function?
Synthesize new DNA strand
Proofread errors
Unwind double helix
Remove RNA primers
Explanation - Unwinding is done by helicase; DNA polymerase synthesizes and proofreads.
Correct answer is: Unwind double helix
Q.15 A sequence that reads the same forward and backward is called a ______.
Palindrome
Intron
Exon
Motif
Explanation - A DNA palindrome is a sequence that reads the same in the 5’→3’ direction as its complement.
Correct answer is: Palindrome
Q.16 Which part of a protein is responsible for its shape?
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Explanation - The tertiary structure is the overall 3‑D folding of the protein.
Correct answer is: Tertiary structure
Q.17 What does the abbreviation ‘PCR’ stand for?
Protein Chain Reaction
Polymerase Chain Reaction
Protein Complementary Reaction
Polymerase Complementary Reaction
Explanation - PCR is a laboratory technique used to amplify DNA segments.
Correct answer is: Polymerase Chain Reaction
Q.18 Which enzyme is essential for creating new strands during DNA replication?
DNA ligase
DNA polymerase
RNA polymerase
Topoisomerase
Explanation - DNA polymerase adds nucleotides to the growing DNA chain.
Correct answer is: DNA polymerase
Q.19 In the genetic code, which codon is known as a 'stop codon'?
AUG
UAA
GCG
CGA
Explanation - UAA (along with UAG and UGA) signals termination of translation.
Correct answer is: UAA
Q.20 Which technique is used to separate DNA fragments by size?
Southern blotting
Gel electrophoresis
Northern blotting
Western blotting
Explanation - Gel electrophoresis moves DNA fragments through a gel matrix under an electric field.
Correct answer is: Gel electrophoresis
Q.21 What is a 'primer' in PCR?
A DNA segment that initiates replication
An enzyme that adds nucleotides
A small piece of RNA
A type of DNA polymerase
Explanation - Primers provide a starting point for DNA polymerase to synthesize a new strand.
Correct answer is: A DNA segment that initiates replication
Q.22 Which of these is a property of codon usage bias?
All codons are used equally
Certain codons are preferred in highly expressed genes
Codon usage changes with temperature
It is unrelated to tRNA abundance
Explanation - Codon bias reflects the preference for specific synonymous codons in a genome.
Correct answer is: Certain codons are preferred in highly expressed genes
Q.23 Which of the following best describes a gene's 'promoter' region?
The coding sequence of a gene
A segment that binds RNA polymerase to start transcription
The region between exons
The tail end of a protein
Explanation - Promoters are DNA sequences upstream of a gene that recruit RNA polymerase.
Correct answer is: A segment that binds RNA polymerase to start transcription
Q.24 In bioinformatics, what does 'FASTA format' refer to?
A file format for storing protein structures
A database of DNA sequences
A plain text format for nucleotide or peptide sequences with header lines starting with '>'
A graphical interface for sequence alignment
Explanation - FASTA files contain sequence data with descriptive headers prefixed by '>'.
Correct answer is: A plain text format for nucleotide or peptide sequences with header lines starting with '>'
Q.25 What is an 'exon' in a gene?
A non-coding region
A coding sequence that remains in mature mRNA
A sequence that forms a protein
A region that signals transcription termination
Explanation - Exons are retained after intron splicing and encode parts of the protein.
Correct answer is: A coding sequence that remains in mature mRNA
Q.26 Which enzyme removes RNA primers during DNA replication?
DNA ligase
DNA polymerase
RNA polymerase
DNA polymerase I
Explanation - DNA polymerase I in E. coli has 5’→3’ exonuclease activity that removes RNA primers.
Correct answer is: DNA polymerase I
Q.27 What is the purpose of a 'sequence logo'?
To visualize the frequency of nucleotides at each position in an alignment
To record the start and stop codons of genes
To depict the 3D structure of a protein
To indicate the temperature of the PCR reaction
Explanation - Sequence logos graphically represent sequence conservation across multiple alignments.
Correct answer is: To visualize the frequency of nucleotides at each position in an alignment
Q.28 Which of the following is NOT a type of genetic variation?
SNP
Inversion
Duplication
Protein folding
Explanation - Protein folding is a structural property, not a genetic variation.
Correct answer is: Protein folding
Q.29 What is the 'molecular weight' of an amino acid?
Its number of atoms
The sum of the atomic weights of its constituent atoms
Its length in nanometers
Its number of hydrogen bonds
Explanation - Molecular weight is calculated by adding the atomic weights of all atoms in the molecule.
Correct answer is: The sum of the atomic weights of its constituent atoms
Q.30 Which software is commonly used for multiple sequence alignment?
BLAST
Clustal Omega
GenBank
PDB
Explanation - Clustal Omega is a popular tool for aligning multiple sequences.
Correct answer is: Clustal Omega
Q.31 What does the 'codon table' describe?
The genetic code mapping codons to amino acids
The structure of DNA double helix
The positions of introns in a gene
The number of chromosomes in a cell
Explanation - The codon table shows which three‑base codons correspond to which amino acids.
Correct answer is: The genetic code mapping codons to amino acids
Q.32 Which type of mutation changes a codon to code for a different amino acid?
Silent mutation
Missense mutation
Nonsense mutation
Frameshift mutation
Explanation - A missense mutation results in a different amino acid being incorporated.
Correct answer is: Missense mutation
Q.33 The term 'homology' in bioinformatics refers to:
Physical similarity between two proteins
A measure of sequence similarity indicating common ancestry
A type of DNA sequencing technique
The number of identical bases in a sequence
Explanation - Homology indicates evolutionary relatedness inferred from sequence similarity.
Correct answer is: A measure of sequence similarity indicating common ancestry
Q.34 What is 'phylogenetics'?
The study of the physical properties of proteins
The study of evolutionary relationships among organisms
The study of gene expression in bacteria
The analysis of electrical circuits in biology
Explanation - Phylogenetics uses sequence data to reconstruct evolutionary trees.
Correct answer is: The study of evolutionary relationships among organisms
Q.35 Which algorithm is commonly used to compute pairwise sequence alignment?
Dijkstra
Needleman-Wunsch
A*
Bellman-Ford
Explanation - Needleman‑Wunsch performs global alignment of two sequences.
Correct answer is: Needleman-Wunsch
Q.36 A 'frameshift' mutation arises due to:
A single nucleotide polymorphism
The insertion or deletion of nucleotides not in multiples of three
A change in the start codon
A silent substitution
Explanation - Frameshifts alter the reading frame of the coding sequence.
Correct answer is: The insertion or deletion of nucleotides not in multiples of three
Q.37 Which of the following represents a protein structure prediction method?
DNA microarray
RNA‑seq
Homology modeling
ChIP‑seq
Explanation - Homology modeling predicts protein 3D structure using known templates.
Correct answer is: Homology modeling
Q.38 What is the primary purpose of a 'reference genome'?
To provide a standard sequence for comparison and alignment
To sequence unknown genomes
To record mutations in a population
To store protein structures
Explanation - A reference genome serves as a baseline for mapping sequencing reads.
Correct answer is: To provide a standard sequence for comparison and alignment
Q.39 Which tool is used for identifying open reading frames (ORFs) in a DNA sequence?
ORF Finder
GATK
PhyloBayes
SAMtools
Explanation - ORF Finder identifies potential protein-coding regions in a sequence.
Correct answer is: ORF Finder
Q.40 What does 'GC content' refer to?
The amount of G and C in a sequence
The number of genes in a chromosome
The concentration of ions in a buffer
The length of a gene in base pairs
Explanation - GC content is the proportion of guanine and cytosine bases in a DNA segment.
Correct answer is: The amount of G and C in a sequence
Q.41 Which method is best for detecting copy number variations (CNVs) in sequencing data?
Read depth analysis
Sanger sequencing
Northern blotting
Western blotting
Explanation - Read depth (coverage) variations can indicate CNVs.
Correct answer is: Read depth analysis
Q.42 Which of the following is a key concept in next-generation sequencing (NGS) data processing?
Assembly of short reads into longer contigs
Electrophoresis of proteins
Amplification by PCR only
Single‑molecule imaging
Explanation - NGS generates short reads that must be assembled computationally.
Correct answer is: Assembly of short reads into longer contigs
Q.43 What is 'variant calling' in the context of genome sequencing?
Identifying differences between a sample and a reference genome
Predicting protein folding patterns
Determining the GC content of a region
Measuring gene expression levels
Explanation - Variant calling detects SNPs, indels, and other genomic variations.
Correct answer is: Identifying differences between a sample and a reference genome
Q.44 Which software is commonly used for visualizing genomic data tracks?
IGV
MATLAB
Photoshop
RStudio
Explanation - IGV (Integrative Genomics Viewer) displays sequencing data and annotations.
Correct answer is: IGV
Q.45 Which of these best describes the 'central dogma' of molecular biology?
DNA → RNA → Protein
Protein → RNA → DNA
RNA → DNA → Protein
Protein → DNA → RNA
Explanation - The central dogma outlines the flow of genetic information from DNA to RNA to protein.
Correct answer is: DNA → RNA → Protein
Q.46 Which algorithm is widely used for de novo genome assembly?
Huffman coding
De Bruijn graph assembly
Fast Fourier transform
Dijkstra's algorithm
Explanation - De Bruijn graph approaches assemble short reads efficiently.
Correct answer is: De Bruijn graph assembly
Q.47 In proteomics, what does 'mass spectrometry' determine?
The mass of individual proteins or peptides
The DNA sequence of a gene
The rate of gene expression
The folding pathway of a protein
Explanation - Mass spectrometry measures mass-to-charge ratios to identify proteins.
Correct answer is: The mass of individual proteins or peptides
Q.48 What is a 'splice junction' in RNA‑seq data?
The point where two exons are joined during splicing
The start site of a gene
A site where DNA polymerase initiates replication
A region rich in GC content
Explanation - Splice junctions mark exon–exon boundaries in mature mRNA.
Correct answer is: The point where two exons are joined during splicing
Q.49 Which of these is a common format for representing DNA sequencing reads?
FASTA
SAM/BAM
PDB
XML
Explanation - SAM/BAM files store read alignments to a reference genome.
Correct answer is: SAM/BAM
Q.50 Which bioinformatics tool is used to predict secondary structure of RNA?
RNAfold
BLAST
ClustalW
GROMACS
Explanation - RNAfold predicts RNA secondary structure based on thermodynamics.
Correct answer is: RNAfold
Q.51 What does 'coverage' mean in sequencing?
The depth of sequencing reads across a region
The number of chromosomes in a cell
The length of a DNA fragment
The number of genes expressed
Explanation - Coverage is how many times each base is read during sequencing.
Correct answer is: The depth of sequencing reads across a region
Q.52 Which method is used to measure gene expression levels in RNA‑seq?
FPKM
BLAST
PCR
Microarray
Explanation - FPKM (Fragments Per Kilobase per Million) normalizes expression data.
Correct answer is: FPKM
Q.53 Which of the following best describes a 'single‑cell RNA‑seq' experiment?
Sequencing RNA from a single cell to capture transcriptomic heterogeneity
Sequencing DNA from many cells together
Sequencing proteins from a single cell
Sequencing the genome of a single cell
Explanation - Single‑cell RNA‑seq profiles individual cells' transcriptomes.
Correct answer is: Sequencing RNA from a single cell to capture transcriptomic heterogeneity
Q.54 What is the primary use of 'machine learning' in bioinformatics?
To predict protein–protein interactions
To bake cakes
To operate a microscope
To perform PCR
Explanation - Machine learning models classify biological data, such as interaction networks.
Correct answer is: To predict protein–protein interactions
Q.55 Which deep learning architecture is often employed for image-based histopathology analysis?
ResNet
RNN
CNN
SVM
Explanation - Convolutional neural networks excel at image recognition tasks.
Correct answer is: CNN
Q.56 What is the function of a 'feature extractor' in genomics machine learning pipelines?
Converting raw sequences into numeric descriptors
Building the dataset's metadata
Storing results in a database
Printing reports
Explanation - Feature extractors transform biological sequences into machine‑learnable vectors.
Correct answer is: Converting raw sequences into numeric descriptors
Q.57 Which of the following best describes a 'neural network' in the context of genomics?
A computational model inspired by the brain that learns patterns in genomic data
A network of DNA strands
A group of researchers working together
A physical network of computers in a lab
Explanation - Neural networks process input data through layers to learn complex relationships.
Correct answer is: A computational model inspired by the brain that learns patterns in genomic data
Q.58 Which algorithm is commonly used to cluster gene expression data?
K‑means
K‑means
K‑means
K‑means
Explanation - K‑means clustering groups samples or genes with similar expression profiles.
Correct answer is: K‑means
Q.59 What does 'transfer learning' entail in bioinformatics?
Using a pre‑trained model on a new but related dataset
Transferring DNA between species
Moving a lab from one location to another
Switching from RNA to DNA sequencing
Explanation - Transfer learning applies knowledge learned from one domain to improve performance in another.
Correct answer is: Using a pre‑trained model on a new but related dataset
Q.60 In genomics, what is a 'phylogenetic tree' commonly used for?
Visualizing evolutionary relationships between organisms
Displaying gene expression heatmaps
Mapping protein folding pathways
Showing chemical reaction networks
Explanation - Phylogenetic trees represent inferred ancestor–descendant relationships.
Correct answer is: Visualizing evolutionary relationships between organisms
Q.61 Which of the following tools is used for variant effect prediction?
SnpEff
BLAST
Clustal
GATK
Explanation - SnpEff annotates variants with predicted functional consequences.
Correct answer is: SnpEff
Q.62 Which format is used to store 3D protein structures?
PDB
FASTA
SAM
BAM
Explanation - PDB files contain atomic coordinates for macromolecular structures.
Correct answer is: PDB
Q.63 Which statistical method is essential for differential gene expression analysis?
DESeq2
BLAST
ClustalW
GROMACS
Explanation - DESeq2 models count data to find differentially expressed genes.
Correct answer is: DESeq2
Q.64 What is the role of a 'read mapper' in next‑generation sequencing workflows?
Aligning raw reads to a reference genome
Converting DNA into RNA
Predicting protein 3D structure
Calculating GC content
Explanation - Read mappers, such as BWA or Bowtie, place sequencing reads onto the genome.
Correct answer is: Aligning raw reads to a reference genome
Q.65 In protein structure prediction, what does 'AlphaFold' refer to?
An AI system that predicts protein 3D structures from amino acid sequences
A type of DNA sequencing technology
A molecular weight unit
A bioinformatics file format
Explanation - AlphaFold uses deep learning to model protein folding accurately.
Correct answer is: An AI system that predicts protein 3D structures from amino acid sequences
Q.66 Which of these represents a typical output of a BLAST search?
An alignment score and e‑value for similar sequences
A 3‑D protein structure
A gene expression heatmap
A mass spectrometry spectrum
Explanation - BLAST reports scores, e‑values, and alignment details for matching sequences.
Correct answer is: An alignment score and e‑value for similar sequences
Q.67 What is the primary advantage of 'long‑read sequencing' technologies like PacBio and Oxford Nanopore?
They produce reads over 10 kb, aiding in assembly and detection of structural variants
They have higher accuracy than short reads
They require no sample preparation
They are cheaper than Illumina
Explanation - Long reads facilitate resolving complex genomic regions and large insertions.
Correct answer is: They produce reads over 10 kb, aiding in assembly and detection of structural variants
Q.68 Which computational method is used to predict RNA–protein interaction sites?
RNP‑binding motif analysis
Molecular docking
Protein mass spectrometry
Northern blotting
Explanation - Motif analysis identifies consensus sequences where RNA‑binding proteins bind.
Correct answer is: RNP‑binding motif analysis
Q.69 Which of the following best describes 'CRISPR‑Cas9' in the context of genome editing?
A programmable nuclease that introduces double‑strand breaks at specific genomic loci
A sequencing platform for long reads
A protein‑folding prediction algorithm
A database of genetic variants
Explanation - CRISPR‑Cas9 uses guide RNA to target and cut DNA precisely.
Correct answer is: A programmable nuclease that introduces double‑strand breaks at specific genomic loci
Q.70 What does 'epigenetic' refer to?
Chemical modifications that affect gene expression without altering DNA sequence
Changes in the DNA sequence itself
The physical structure of chromosomes
The number of chromosomes in a cell
Explanation - Epigenetics includes DNA methylation, histone modifications, etc.
Correct answer is: Chemical modifications that affect gene expression without altering DNA sequence
Q.71 Which technique is used to map DNA methylation across the genome?
Bisulfite sequencing
ChIP‑seq
RNA‑seq
PCR
Explanation - Bisulfite converts unmethylated cytosines to uracil, revealing methylation patterns.
Correct answer is: Bisulfite sequencing
Q.72 In proteomics, what is a 'spectral library'?
A collection of experimentally observed MS/MS spectra for known peptides
A database of genomic variants
A set of DNA primers for sequencing
A software package for aligning sequences
Explanation - Spectral libraries enable rapid identification of peptides in mass spectrometry.
Correct answer is: A collection of experimentally observed MS/MS spectra for known peptides
Q.73 Which of the following best describes 'meta‑omics'?
Integrative analysis of multiple 'omics' layers such as genomics, transcriptomics, and proteomics
The study of single cells only
Sequencing of only the protein‑coding regions
A type of electron microscopy
Explanation - Meta‑omics encompasses combined analyses across different biological data types.
Correct answer is: Integrative analysis of multiple 'omics' layers such as genomics, transcriptomics, and proteomics
Q.74 What is 'pseudogene'?
A non‑functional segment of DNA that resembles a gene
A gene that produces a protein
A segment of RNA that codes for enzymes
A protein that is degraded quickly
Explanation - Pseudogenes often arise from gene duplication or retrotransposition and are usually inactive.
Correct answer is: A non‑functional segment of DNA that resembles a gene
Q.75 Which computational method is used to identify protein domains within a sequence?
HMMER with Pfam database
BLASTN
SAMtools
GATK
Explanation - HMMER uses hidden Markov models to detect conserved protein domains.
Correct answer is: HMMER with Pfam database
Q.76 What does 'gene ontology' (GO) provide?
Standardized terms describing gene product attributes across biological processes, cellular components, and molecular functions
A list of all known genes
A method for DNA sequencing
A type of PCR reaction
Explanation - GO annotations classify genes into a controlled vocabulary.
Correct answer is: Standardized terms describing gene product attributes across biological processes, cellular components, and molecular functions
Q.77 Which of the following is a major challenge in single‑cell sequencing data analysis?
Drop‑out events leading to missing data
Low computational cost
No need for normalization
Uniform coverage across cells
Explanation - Drop‑outs refer to genes not detected in a cell due to low mRNA capture.
Correct answer is: Drop‑out events leading to missing data
Q.78 In the context of structural biology, what is an 'electron density map'?
A visual representation of the electron probability distribution used to build atomic models
The result of a PCR reaction
A diagram of a DNA double helix
A table of gene expression levels
Explanation - Electron density maps are derived from X‑ray crystallography data.
Correct answer is: A visual representation of the electron probability distribution used to build atomic models