Q.1 Which of the following is the correct order of protein structure levels?
Primary, secondary, tertiary, quaternary
Tertiary, secondary, primary, quaternary
Quaternary, tertiary, secondary, primary
Primary, tertiary, secondary, quaternary
Explanation - Proteins have four hierarchical levels of structure: primary (sequence), secondary (local folding like alpha‑helix and beta‑sheet), tertiary (3D folding of a single polypeptide), and quaternary (assembly of multiple polypeptides).
Correct answer is: Primary, secondary, tertiary, quaternary
Q.2 What technique uses X-rays to determine the 3D arrangement of atoms in a crystal?
Mass spectrometry
X-ray crystallography
NMR spectroscopy
Electron microscopy
Explanation - X‑ray crystallography shoots X‑rays through a protein crystal; the diffraction pattern is used to reconstruct the 3D atomic structure.
Correct answer is: X-ray crystallography
Q.3 Which element is NOT a major component of DNA?
Phosphorus
Calcium
Hydrogen
Oxygen
Explanation - DNA’s backbone contains phosphorus, oxygen, and hydrogen atoms, but calcium is not part of DNA’s structure.
Correct answer is: Calcium
Q.4 Which of these is a common type of protein secondary structure?
Alpha‑helix
Beta‑sheet
Random coil
All of the above
Explanation - Alpha‑helix, beta‑sheet, and random coil are all standard secondary structure elements found in proteins.
Correct answer is: All of the above
Q.5 What does BLAST stand for in bioinformatics?
Basic Local Alignment Search Tool
Binary Linear Algorithm for Sequence Tagging
Biological Lexical Analysis Software Toolkit
Base Length Alignment Sequence Test
Explanation - BLAST is a widely used program that quickly finds regions of similarity between biological sequences.
Correct answer is: Basic Local Alignment Search Tool
Q.6 Which of the following best describes a protein's quaternary structure?
The sequence of amino acids
The pattern of hydrogen bonds in a helix
The assembly of multiple subunits
The local folding of a single polypeptide
Explanation - Quaternary structure refers to how multiple protein chains (subunits) come together to form a functional complex.
Correct answer is: The assembly of multiple subunits
Q.7 What is the main difference between X‑ray crystallography and NMR spectroscopy?
X‑ray works on liquids, NMR on solids
X‑ray needs crystals, NMR works in solution
X‑ray uses magnetic fields, NMR uses X‑rays
They are the same technique
Explanation - X‑ray crystallography requires a crystal of the molecule, while NMR can analyze proteins in solution.
Correct answer is: X‑ray needs crystals, NMR works in solution
Q.8 Which of these is a function of a bioinformatics tool?
Cooking food
Predicting protein folding
Fixing broken computers
Tuning musical instruments
Explanation - Bioinformatics tools analyze biological data, including predicting how proteins fold from their sequences.
Correct answer is: Predicting protein folding
Q.9 What does a PDB file contain?
Protein Data Bank coordinates of atoms
A list of DNA sequences
A recipe for laboratory experiments
A schedule of conference talks
Explanation - PDB files store the 3‑D coordinates of atoms in protein structures available in the Protein Data Bank.
Correct answer is: Protein Data Bank coordinates of atoms
Q.10 Which of the following best describes the function of a molecular docking program?
It predicts which antibiotics will kill a bacterium
It simulates how two molecules might fit together
It records the temperature of a cell
It measures the size of a protein
Explanation - Molecular docking predicts how a ligand, such as a drug, might bind to a target protein’s active site.
Correct answer is: It simulates how two molecules might fit together
Q.11 Which of these is a secondary structure motif found in many proteins?
Beta‑turn
Coiled‑coil
Helix‑turn‑helix
All of the above
Explanation - Beta‑turns, coiled‑coils, and helix‑turn‑helix motifs are common elements that help stabilize protein structure.
Correct answer is: All of the above
Q.12 What is the role of a hydrophobic core in a protein?
It attracts water molecules
It stabilizes the protein’s 3D fold
It acts as a catalytic site
It helps the protein bind DNA
Explanation - Non‑polar amino acids cluster in the interior of proteins, forming a hydrophobic core that stabilizes the folded structure.
Correct answer is: It stabilizes the protein’s 3D fold
Q.13 Which software is commonly used for homology modeling of protein structures?
AutoDock
MODELLER
BLAST
Clustal Omega
Explanation - MODELLER builds 3‑D models of proteins by aligning with known homologous structures.
Correct answer is: MODELLER
Q.14 Which of the following best describes a Ramachandran plot?
A chart that shows protein folding kinetics
A graph of allowed backbone angles (phi, psi) for amino acids
A plot of protein mass versus charge
A diagram of the genetic code
Explanation - The Ramachandran plot displays the sterically allowed regions for the dihedral angles φ and ψ in protein backbones.
Correct answer is: A graph of allowed backbone angles (phi, psi) for amino acids
Q.15 Which method is used to determine the distance between atoms in an NMR experiment?
COSY
NOESY
FTIR
X‑ray diffraction
Explanation - NOESY (Nuclear Overhauser Effect Spectroscopy) provides cross‑peak intensities that are inversely related to inter‑atomic distances.
Correct answer is: NOESY
Q.16 What does the ‘RMSD’ value represent in protein structure comparison?
Average distance between corresponding atoms
Number of hydrogen bonds
Rate of molecular evolution
Residue mass difference
Explanation - Root‑Mean‑Square Deviation (RMSD) measures how closely two protein structures align by averaging atomic distances.
Correct answer is: Average distance between corresponding atoms
Q.17 Which of these is NOT a typical component of a protein’s primary structure?
Amino acid sequence
Peptide bonds
3D folding
Genetic codon specification
Explanation - Primary structure is the linear amino acid sequence; 3D folding refers to higher‑order structures.
Correct answer is: 3D folding
Q.18 What is the purpose of a 'sequence alignment' in bioinformatics?
To compare two DNA or protein sequences for similarity
To calculate the molecular weight of a protein
To predict the pH of a solution
To measure the size of a crystal
Explanation - Sequence alignment identifies homologous regions and infers evolutionary relationships.
Correct answer is: To compare two DNA or protein sequences for similarity
Q.19 Which of the following best describes an 'energy function' used in protein modeling?
A formula that predicts how many proteins are in a cell
A mathematical expression that estimates the stability of a protein conformation
A table of protein masses
A guide to cooking proteins
Explanation - Energy functions calculate the free energy of a structure; lower energy typically corresponds to a more stable conformation.
Correct answer is: A mathematical expression that estimates the stability of a protein conformation
Q.20 What does the ‘Cα atom’ refer to in a protein backbone?
The central carbon atom of the amino acid side chain
The alpha carbon connecting the side chain to the backbone
The carbonyl carbon of the peptide bond
The carbon in the terminal carboxyl group
Explanation - The Cα atom is the central carbon in the amino acid backbone to which the side chain is attached.
Correct answer is: The alpha carbon connecting the side chain to the backbone
Q.21 Which technique is most suitable for studying flexible or disordered proteins?
X‑ray crystallography
NMR spectroscopy
Cryo‑EM
Mass spectrometry
Explanation - NMR can capture solution dynamics and is effective for flexible or intrinsically disordered proteins.
Correct answer is: NMR spectroscopy
Q.22 What is a ‘binding pocket’ in the context of protein structure?
A region where a ligand can bind
A type of secondary structure
The area where DNA binds to a protein
A pocket used for protein storage
Explanation - A binding pocket is a cleft or cavity on the protein surface that accommodates small molecules or other proteins.
Correct answer is: A region where a ligand can bind
Q.23 Which of the following is NOT a commonly used force field in molecular dynamics simulations?
AMBER
CHARMM
GROMOS
BLAST
Explanation - AMBER, CHARMM, and GROMOS are force fields; BLAST is a sequence alignment tool.
Correct answer is: BLAST
Q.24 What does the term ‘secondary structure propensity’ refer to?
The probability that a protein will be in a crystalline state
The tendency of an amino acid sequence to form alpha‑helices or beta‑sheets
The likelihood of a protein to be secreted by a cell
The chance of a protein undergoing post‑translational modification
Explanation - Secondary structure propensity scores predict the likelihood of a residue adopting a particular secondary structure.
Correct answer is: The tendency of an amino acid sequence to form alpha‑helices or beta‑sheets
Q.25 In molecular docking, what is a ‘scoring function’ used for?
To determine the best fit of the ligand to the protein
To calculate the molecular weight of the protein
To sequence the DNA of an organism
To measure the temperature of the binding event
Explanation - The scoring function estimates the binding affinity or fit quality of a ligand conformation in the binding site.
Correct answer is: To determine the best fit of the ligand to the protein
Q.26 Which of the following describes a ‘co‑crystallization’ approach?
Crystallizing two proteins together to observe interactions
Crystallizing a protein in the absence of any ligand
Using cryo‑EM to capture snapshots
Applying NMR to determine structures in solution
Explanation - Co‑crystallization involves forming a crystal of a protein complex to study protein–protein interfaces.
Correct answer is: Crystallizing two proteins together to observe interactions
Q.27 What is a ‘decoy structure’ in the context of protein structure prediction?
A fake protein used as a negative control
A wrong model generated to test scoring functions
An alternate fold that is biologically active
A template used for homology modeling
Explanation - Decoy structures are intentionally incorrect conformations used to benchmark scoring functions.
Correct answer is: A wrong model generated to test scoring functions
Q.28 Which of the following is a key advantage of using AlphaFold for structure prediction?
It requires no computational resources
It can predict structures with high accuracy across many proteins
It replaces the need for experimental data entirely
It only works for small peptides
Explanation - AlphaFold has achieved remarkable accuracy in the CASP competitions, providing reliable predictions for many proteins.
Correct answer is: It can predict structures with high accuracy across many proteins
Q.29 Which type of molecular dynamics simulation is most suitable for studying large ribosomal complexes?
All‑atom MD
Coarse‑grained MD
Quantum mechanics MD
Monte Carlo MD
Explanation - Coarse‑grained simulations reduce the system’s resolution, making it computationally feasible to simulate large complexes like ribosomes.
Correct answer is: Coarse‑grained MD
Q.30 In a Ramachandran plot, which region corresponds to beta‑sheet conformations?
Near (−120°, +120°)
Near (0°, 0°)
Near (±180°, ±180°)
Near (−90°, +90°)
Explanation - Beta‑sheet regions cluster around φ≈−120° and ψ≈+120° in the Ramachandran plot.
Correct answer is: Near (−120°, +120°)
Q.31 What does the 'Cα trace' of a protein represent?
The path traced by the alpha carbon atoms in the backbone
The trajectory of the protein during an MD simulation
The sequence of amino acids
The set of all hydrogen bonds in the protein
Explanation - The Cα trace is a simplified representation of the protein backbone formed by connecting alpha carbons.
Correct answer is: The path traced by the alpha carbon atoms in the backbone
Q.32 Which of the following best describes a 'pseudoknot' in nucleic acid structure?
A type of secondary structure where base‑pairs cross each other
A loop in a protein structure
A motif found only in DNA not RNA
A type of protein tertiary fold
Explanation - Pseudoknots involve crossing base‑pair interactions, making them more complex than simple hairpins.
Correct answer is: A type of secondary structure where base‑pairs cross each other
Q.33 What is the purpose of the ‘contact map’ in structural bioinformatics?
To map protein‑protein interactions across a cell
To record pairwise distances between residues in a protein
To visualize gene expression levels
To measure the mechanical stress on a protein
Explanation - A contact map indicates which residues are close in 3D space, useful for fold recognition and validation.
Correct answer is: To record pairwise distances between residues in a protein
Q.34 Which computational method is commonly used to predict the free energy of ligand binding?
Molecular mechanics Poisson‑Boltzmann surface area (MM‑PBSA)
BLAST
X‑ray crystallography
COBRA
Explanation - MM‑PBSA estimates binding free energy by combining molecular mechanics with solvation terms.
Correct answer is: Molecular mechanics Poisson‑Boltzmann surface area (MM‑PBSA)
Q.35 Which of the following is a key assumption of the 'rigid‑body docking' approach?
Both protein and ligand are flexible during docking
Only the ligand is flexible; the protein remains rigid
Both protein and ligand are considered rigid during docking
The solvent is not considered
Explanation - Rigid‑body docking treats both partners as inflexible, simplifying the search space.
Correct answer is: Both protein and ligand are considered rigid during docking
Q.36 Which of the following best defines a ‘solvent‑accessible surface area (SASA)’?
The area of the protein that is buried inside the cell
The area of the protein exposed to the surrounding solvent
The surface area of the cell membrane
The area used for protein folding
Explanation - SASA quantifies how much of the protein surface is accessible to water molecules.
Correct answer is: The area of the protein exposed to the surrounding solvent
Q.37 Which of the following is a common challenge in de novo protein structure prediction?
Identifying the correct primary sequence
Sampling the vast conformational space
Sequencing the DNA that encodes the protein
Determining the protein’s molecular weight
Explanation - De novo methods must explore an enormous number of possible folds to find the native conformation.
Correct answer is: Sampling the vast conformational space
Q.38 What is a 'homology modeling' pipeline primarily dependent on?
The availability of a close homologous template structure
Random guessing of the protein fold
The protein’s mass spectrum
The cell’s metabolic profile
Explanation - Homology modeling uses a known template; the more similar the template, the higher the expected accuracy.
Correct answer is: The availability of a close homologous template structure
Q.39 Which of the following best describes the 'Rosetta' software suite?
A tool for aligning DNA sequences
A program for predicting protein folding and designing proteins
An instrument for measuring protein mass
A database of protein‑protein interactions
Explanation - Rosetta employs fragment assembly, Monte Carlo sampling, and energy functions for structure prediction and design.
Correct answer is: A program for predicting protein folding and designing proteins
Q.40 Which of these is NOT a typical output of a molecular dynamics simulation?
Trajectory file of atomic positions over time
Binding free energy estimate
Electronic absorption spectra
Temperature profile of the system
Explanation - MD focuses on atomic motions; absorption spectra are derived from quantum calculations, not classical MD.
Correct answer is: Electronic absorption spectra
Q.41 What does a 'flexibility index' measure in protein structures?
The number of disulfide bonds
The dynamic fluctuations of residues over a trajectory
The rate of protein synthesis
The stability of the protein’s primary sequence
Explanation - Flexibility indices quantify how much each residue moves, often derived from B‑factors or RMSF values.
Correct answer is: The dynamic fluctuations of residues over a trajectory
Q.42 Which of the following best explains the concept of 'coarse‑graining' in simulations?
Representing groups of atoms as single interaction sites to reduce computational cost
Adding more detail to each atom for higher accuracy
Simulating only the solvent and ignoring the protein
Using a finer grid for spatial discretization
Explanation - Coarse‑graining aggregates atoms into beads, simplifying the system while retaining essential physics.
Correct answer is: Representing groups of atoms as single interaction sites to reduce computational cost
Q.43 What is the main difference between a 'blind' and a 'template‑based' protein structure prediction?
Blind uses no prior structural information; template‑based uses homologous templates
Blind uses a known structure; template‑based guesses randomly
Blind relies on X‑ray data; template‑based uses NMR
They are the same approach
Explanation - Blind prediction (de novo) starts from scratch, whereas template‑based prediction leverages existing homologous structures.
Correct answer is: Blind uses no prior structural information; template‑based uses homologous templates
Q.44 Which of the following best describes a 'principal component analysis (PCA)' applied to MD trajectories?
A method to predict the secondary structure
A technique to identify dominant motions in the simulation
A way to calculate the binding free energy
A method for aligning protein sequences
Explanation - PCA reduces high‑dimensional trajectory data to a few orthogonal motions that capture most variance.
Correct answer is: A technique to identify dominant motions in the simulation
Q.45 Which of the following is a primary use of the 'FoldX' software?
Predicting protein folding from scratch
Estimating the effect of point mutations on protein stability
Calculating the protein’s molecular weight
Aligning multiple DNA sequences
Explanation - FoldX calculates changes in free energy (ΔΔG) upon mutations, aiding in protein engineering.
Correct answer is: Estimating the effect of point mutations on protein stability
Q.46 What is a key advantage of using cryo‑electron microscopy (cryo‑EM) for large macromolecular complexes?
It requires crystalline samples
It can capture multiple conformational states without crystallization
It provides atomic resolution for all proteins
It measures the mass of the complex directly
Explanation - Cryo‑EM images frozen particles, enabling reconstruction of large complexes and their dynamic states.
Correct answer is: It can capture multiple conformational states without crystallization
Q.47 Which of the following best defines a 'binding affinity' in quantitative terms?
The number of hydrogen bonds formed
The dissociation constant (K_d) of a ligand–protein complex
The mass of the ligand
The length of the binding site
Explanation - Binding affinity is commonly expressed as K_d; lower values indicate tighter binding.
Correct answer is: The dissociation constant (K_d) of a ligand–protein complex
Q.48 Which of these is NOT typically considered in a 'solvent‑accessible surface area (SASA)' calculation?
Probe radius used to simulate water molecules
Atomic van der Waals radii
The pH of the solution
The atomic coordinates
Explanation - SASA depends on atomic geometry and probe radius; pH is irrelevant to the calculation.
Correct answer is: The pH of the solution
Q.49 What does the term 'molecular replacement' refer to in X‑ray crystallography?
Replacing the protein in a crystal with a similar one
Using a known structure to solve the phase problem of a new crystal
Swapping one ligand for another
Changing the crystal lattice type
Explanation - Molecular replacement uses a homologous model’s phases to calculate the electron density of a new crystal.
Correct answer is: Using a known structure to solve the phase problem of a new crystal
Q.50 Which of the following is a common metric for assessing protein‑protein docking accuracy?
Docking score
Root‑mean‑square deviation (RMSD) of interface residues
Secondary structure content
Molecular weight ratio
Explanation - Interface RMSD measures how well the docking pose aligns with the known native complex.
Correct answer is: Root‑mean‑square deviation (RMSD) of interface residues
Q.51 In the context of protein design, what is the term 'de novo protein design'?
Designing a protein by modifying an existing sequence
Designing a protein from scratch without relying on known structures
Designing a protein based on evolutionary data
Designing a protein using only DNA data
Explanation - De novo design constructs novel protein folds that have not been observed in nature.
Correct answer is: Designing a protein from scratch without relying on known structures
Q.52 Which of the following best describes the 'flooding' algorithm in contact map prediction?
An algorithm that identifies solvent channels in proteins
A method to iteratively add contacts until a threshold density is reached
A way to determine protein mass by flooding the sample
A technique for visualizing protein surfaces
Explanation - Flooding starts with a seed contact and expands until enough contacts are added to build a plausible map.
Correct answer is: A method to iteratively add contacts until a threshold density is reached
Q.53 Which computational approach is most suitable for modeling enzyme catalysis at the atomic level?
Quantum mechanics/molecular mechanics (QM/MM)
Coarse‑grained molecular dynamics
Homology modeling
Rosetta design
Explanation - QM/MM treats the reactive site quantum‑mechanically while the rest of the protein remains classical, enabling accurate catalysis modeling.
Correct answer is: Quantum mechanics/molecular mechanics (QM/MM)