Q.1 What is the primary goal of structural genomics?
To sequence the DNA of an organism
To determine the three-dimensional structures of proteins
To model electrical circuits in biology
To identify genetic mutations in cancer
Explanation - Structural genomics focuses on elucidating the 3D structures of proteins, which helps understand their function and interaction mechanisms.
Correct answer is: To determine the three-dimensional structures of proteins
Q.2 Which technique is commonly used to crystallize proteins for X‑ray diffraction?
Gel electrophoresis
Crystallization by vapor diffusion
Western blotting
PCR amplification
Explanation - Vapor diffusion is a standard method for growing protein crystals suitable for X‑ray diffraction analysis.
Correct answer is: Crystallization by vapor diffusion
Q.3 What does the Protein Data Bank (PDB) primarily store?
DNA sequences
Protein 3D structures
Metabolic pathways
Gene expression data
Explanation - The PDB is a repository that provides 3D coordinates of proteins and nucleic acids solved experimentally.
Correct answer is: Protein 3D structures
Q.4 Which software is widely used for homology modeling of protein structures?
MATLAB
MODELLER
AutoCAD
SPSS
Explanation - MODELLER automates comparative modeling by aligning target sequences with known structures to predict 3D models.
Correct answer is: MODELLER
Q.5 In structural genomics, what is the purpose of using NMR spectroscopy?
To determine protein folding pathways
To visualize proteins in living cells
To identify DNA binding sites
To measure electrical conductivity of proteins
Explanation - NMR provides detailed information on protein structure and dynamics in solution, useful for studying folding mechanisms.
Correct answer is: To determine protein folding pathways
Q.6 Which of the following is a key challenge in solving protein structures by cryo‑EM?
High radiation damage to the sample
Low resolution due to ice contamination
Requirement of large crystal size
Difficulty in aligning the electron beam
Explanation - Cryo‑EM samples can suffer from ice layering that reduces image quality, making high‑resolution reconstruction difficult.
Correct answer is: Low resolution due to ice contamination
Q.7 What role does the Rosetta suite play in structural genomics?
It predicts protein–protein interactions
It designs genetic circuits in bacteria
It performs sequence alignment of genomes
It simulates electrical properties of proteins
Explanation - Rosetta includes algorithms for protein structure prediction and docking, aiding in understanding interaction interfaces.
Correct answer is: It predicts protein–protein interactions
Q.8 Which property of a protein is most directly inferred from its 3D structure?
Its gene name
Its cellular location
Its ligand-binding sites
Its evolutionary age
Explanation - Structural analysis reveals pockets and surfaces that interact with ligands, crucial for functional annotation.
Correct answer is: Its ligand-binding sites
Q.9 What is a major advantage of using computational docking in drug discovery?
It eliminates the need for clinical trials
It predicts how a drug will bind to its target
It guarantees 100% efficacy of the drug
It measures the electrical conductivity of the drug
Explanation - Docking simulations estimate the binding mode and affinity of small molecules to proteins, guiding medicinal chemistry.
Correct answer is: It predicts how a drug will bind to its target
Q.10 Which algorithm is commonly used for protein secondary structure prediction?
BLAST
PSIPRED
K-means
FFT
Explanation - PSIPRED uses neural networks and sequence profiles to predict alpha‑helices and beta‑strands in proteins.
Correct answer is: PSIPRED
Q.11 In the context of structural genomics, what does 'ab initio' modeling refer to?
Modeling based on known homologous structures
Predicting structures from sequence alone
Using experimental diffraction data directly
Simulating folding in a cell
Explanation - 'Ab initio' approaches build models purely from the amino acid sequence without relying on templates.
Correct answer is: Predicting structures from sequence alone
Q.12 What is the main difference between X‑ray crystallography and cryo‑EM?
X‑ray uses photons while cryo‑EM uses electrons
X‑ray requires a crystal, cryo‑EM does not
Cryo‑EM gives atomic resolution, X‑ray does not
X‑ray can only study proteins in solution
Explanation - X‑ray diffraction needs crystalline samples, whereas cryo‑EM analyzes frozen-hydrated molecules directly in solution.
Correct answer is: X‑ray requires a crystal, cryo‑EM does not
Q.13 Which of the following is NOT typically considered a structural genomics project?
The Protein Structure Initiative
The Structural Genomics Consortium
The Human Genome Project
The Structural Genomics of Mycobacterium tuberculosis
Explanation - The Human Genome Project sequenced DNA, while structural genomics projects focus on determining protein structures.
Correct answer is: The Human Genome Project
Q.14 What does the Ramachandran plot illustrate in protein structure analysis?
Residue conservation across species
Allowed phi‑psi dihedral angles for amino acids
Protein folding kinetics
Three‑dimensional coordinates of a protein
Explanation - Ramachandran plots show the sterically allowed regions of backbone torsion angles, indicating structural validity.
Correct answer is: Allowed phi‑psi dihedral angles for amino acids
Q.15 Which computational technique is used to refine a protein structure against X‑ray diffraction data?
Molecular dynamics
Simulated annealing
Principal component analysis
Cluster analysis
Explanation - Simulated annealing optimizes a model to best fit diffraction data while maintaining reasonable geometry.
Correct answer is: Simulated annealing
Q.16 Why is multiple sequence alignment important before homology modeling?
It identifies conserved regions likely to share structural motifs
It determines the protein’s molecular weight
It calculates the protein’s melting temperature
It predicts the protein’s electrical conductivity
Explanation - Conserved residues often correspond to structurally or functionally critical areas, guiding accurate modeling.
Correct answer is: It identifies conserved regions likely to share structural motifs
Q.17 Which of the following best describes 'phasing' in X‑ray crystallography?
Determining the direction of diffraction spots
Calculating the electron density map from diffraction intensities
Aligning protein sequences
Simulating protein dynamics
Explanation - Phasing solves the phase problem, enabling construction of the electron density necessary for model building.
Correct answer is: Calculating the electron density map from diffraction intensities
Q.18 What is the primary output of an AlphaFold prediction?
The protein’s genetic code
The protein’s 3D structure coordinates
The protein’s ligand affinity
The protein’s evolutionary tree
Explanation - AlphaFold provides predicted atomic coordinates for the target protein’s tertiary structure.
Correct answer is: The protein’s 3D structure coordinates
Q.19 Which term refers to the study of how proteins fold into their functional shapes?
Proteomics
Pharmacology
Protein folding
Metabolomics
Explanation - Protein folding investigates the processes and mechanisms by which linear chains of amino acids adopt their native 3D structures.
Correct answer is: Protein folding
Q.20 In structural genomics, why are membrane proteins particularly challenging?
They are too small for X‑ray diffraction
They require detergent micelles for solubilization
They cannot be expressed in any system
They have no known sequence
Explanation - Membrane proteins are hydrophobic and need detergents or other systems to stay soluble for crystallization or cryo‑EM.
Correct answer is: They require detergent micelles for solubilization
Q.21 Which database provides information on protein–protein interactions?
PDB
STRING
GenBank
UniProt
Explanation - STRING compiles known and predicted protein–protein interaction networks across species.
Correct answer is: STRING
Q.22 What is a 'resolution' in the context of protein crystal structures?
The accuracy of the atomic coordinates in Ångströms
The number of atoms in the protein
The temperature at which the crystal was grown
The size of the crystal lattice
Explanation - Resolution indicates the level of detail; lower Ångström values mean higher detail in the structure.
Correct answer is: The accuracy of the atomic coordinates in Ångströms
Q.23 Which computational method predicts the dynamic behavior of proteins over time?
Molecular dynamics
Docking
Homology modeling
Sequence alignment
Explanation - Molecular dynamics simulates the motion of atoms, revealing conformational changes and stability.
Correct answer is: Molecular dynamics
Q.24 What is the role of a 'template' in comparative modeling?
It provides the amino acid sequence of the target
It offers a known structure to guide the target model
It supplies the experimental diffraction data
It defines the protein’s function
Explanation - Templates are solved structures with sequence similarity, used as frameworks for modeling unknown proteins.
Correct answer is: It offers a known structure to guide the target model
Q.25 Which of the following best describes the 'fold' of a protein?
Its overall three‑dimensional shape
Its gene regulatory sequence
Its electrophoretic mobility
Its rate of synthesis
Explanation - A protein fold refers to the common arrangement of secondary structure elements forming the tertiary structure.
Correct answer is: Its overall three‑dimensional shape
Q.26 What is the purpose of 'refinement' in a protein structure determination workflow?
To improve the resolution of the crystal
To optimize the model against experimental data
To clone the gene encoding the protein
To label the protein with fluorescent tags
Explanation - Refinement adjusts atomic positions and parameters to best fit the observed diffraction data and maintain good geometry.
Correct answer is: To optimize the model against experimental data
Q.27 Which of these is a common source of errors in NMR structure determination?
Inaccurate mass spectrometry data
Poor sample purity leading to overlapping signals
Misaligned X‑ray detectors
Incorrect cryo‑EM grid preparation
Explanation - Contaminants can generate overlapping NMR peaks, complicating resonance assignment and structure calculation.
Correct answer is: Poor sample purity leading to overlapping signals
Q.28 Which of the following describes a 'beta‑hairpin' in protein secondary structure?
A loop connecting two alpha‑helices
A turn between two beta‑strands
An extended alpha‑helix
A disordered region
Explanation - Beta‑hairpin consists of two anti‑parallel beta‑strands connected by a tight turn.
Correct answer is: A turn between two beta‑strands
Q.29 Which software package is specifically designed for cryo‑EM map processing?
RELION
BLAST
Cytoscape
Geneious
Explanation - RELION provides tools for particle picking, alignment, classification, and 3D reconstruction in cryo‑EM.
Correct answer is: RELION
Q.30 In the context of protein structure validation, what does the 'MolProbity score' assess?
The accuracy of the gene annotation
The overall quality of a 3D model
The binding affinity of a ligand
The number of disulfide bonds
Explanation - MolProbity evaluates all-atom contacts, rotamers, and geometry to provide an overall model quality metric.
Correct answer is: The overall quality of a 3D model
Q.31 Why is 'model bias' a concern in crystallographic refinement?
It leads to over‑fitting of the data
It reduces the resolution of the diffraction data
It increases the noise in NMR spectra
It causes misfolding of proteins in vivo
Explanation - Using a biased starting model can cause refinement to fit noise rather than true signal, compromising accuracy.
Correct answer is: It leads to over‑fitting of the data
Q.32 Which of the following is NOT a typical step in a structural genomics pipeline?
Gene synthesis
Protein expression and purification
Mass spectrometry for quantification
Structure determination
Explanation - While MS can be used for other studies, structural genomics focuses mainly on expression, purification, and structure solving.
Correct answer is: Mass spectrometry for quantification
Q.33 What does the 'R-factor' indicate in crystallography?
The ratio of the number of atoms to residues
The agreement between observed and calculated reflections
The resolution limit of the crystal
The percentage of solvent in the crystal
Explanation - R-factor quantifies how well the model explains the measured diffraction intensities; lower values mean better fit.
Correct answer is: The agreement between observed and calculated reflections
Q.34 In homology modeling, which sequence identity threshold generally yields reliable models?
Below 20%
Between 30–50%
Above 90%
Below 5%
Explanation - A sequence identity above 30% typically provides enough alignment to build accurate comparative models.
Correct answer is: Between 30–50%
Q.35 Which of the following best describes the 'Molecular Replacement' method?
Using a known structure as a starting model for phase determination
Directly measuring phase angles via anomalous dispersion
Collecting diffraction data at multiple wavelengths
Refining a model using gradient descent
Explanation - Molecular replacement estimates phases by positioning a homologous model within the crystal lattice.
Correct answer is: Using a known structure as a starting model for phase determination
Q.36 What is the significance of a protein's 'active site' in structural genomics?
It determines the protein's electrical charge
It is the region where catalysis occurs
It binds to DNA exclusively
It is irrelevant to protein function
Explanation - The active site contains residues essential for enzymatic activity and is often targeted for drug design.
Correct answer is: It is the region where catalysis occurs
Q.37 Which technique combines electron density maps with prior chemical knowledge to produce a model?
Molecular dynamics
Ab initio phasing
Model building
Mass spectrometry
Explanation - Model building interprets electron density maps, placing atoms guided by known bond lengths and angles.
Correct answer is: Model building
Q.38 What does 'B-factor' (or temperature factor) represent in a PDB file?
The number of atoms in a residue
The atomic displacement or flexibility
The binding energy of the protein
The pH of the crystallization buffer
Explanation - B-factors indicate how much an atom deviates from its average position, reflecting mobility or disorder.
Correct answer is: The atomic displacement or flexibility
Q.39 Which of the following is a key output of a docking simulation?
The predicted 3D structure of a protein
The binding pose and affinity of a ligand
The evolutionary relationship between proteins
The crystallization conditions
Explanation - Docking predicts how a ligand fits into a protein's binding site and estimates the strength of interaction.
Correct answer is: The binding pose and affinity of a ligand
Q.40 In structural biology, what is the 'phase problem'?
Determining the sequence of DNA
Calculating the phases of diffraction waves
Predicting the protein's function
Aligning multiple protein structures
Explanation - Diffraction gives intensities but not phases; solving the phase problem is essential for building electron density maps.
Correct answer is: Calculating the phases of diffraction waves
Q.41 Which type of mutation is most likely to disrupt protein folding?
A silent mutation
A missense mutation in the hydrophobic core
A synonymous codon change
A non‑coding region mutation
Explanation - Replacing a core residue can destabilize folding by introducing a polar or bulky side chain.
Correct answer is: A missense mutation in the hydrophobic core
Q.42 What is the purpose of 'solvent flattening' during refinement?
To remove water molecules from the model
To impose ideal geometry on solvent regions
To increase the resolution of the crystal
To predict ligand binding
Explanation - Solvent flattening reduces noise in electron density by assuming ideal electron densities for solvent sites.
Correct answer is: To impose ideal geometry on solvent regions
Q.43 Which computational tool is used for protein sequence alignment?
Clustal Omega
Phenix
Coot
NAMD
Explanation - Clustal Omega performs multiple sequence alignments, a prerequisite for homology modeling and phylogenetics.
Correct answer is: Clustal Omega
Q.44 What is a 'loop' in the context of protein secondary structure?
A disordered flexible segment connecting elements
A hydrophobic core region
An alpha‑helix
A beta‑sheet
Explanation - Loops are short, often flexible regions that bridge secondary structure elements in proteins.
Correct answer is: A disordered flexible segment connecting elements
Q.45 Which parameter is NOT used in assessing protein crystallization success?
Unit cell dimensions
Crystal size
Ligand concentration
Space group symmetry
Explanation - While ligand presence can affect structure, crystallization assessment focuses on lattice parameters and crystal quality.
Correct answer is: Ligand concentration
Q.46 In cryo‑EM, what does the term 'pixel size' refer to?
The size of each camera pixel in Å
The size of the protein in nanometers
The resolution limit of the microscope
The number of electrons per second
Explanation - Pixel size is the real‑space distance represented by each image pixel, influencing the achievable resolution.
Correct answer is: The size of each camera pixel in Å
Q.47 Which of these best describes the 'Rosetta@home' project?
A distributed computing project for protein structure prediction
A high‑throughput sequencing facility
An NMR spectroscopy consortium
A microarray data analysis platform
Explanation - Rosetta@home utilizes volunteer computing power to model protein structures using Rosetta algorithms.
Correct answer is: A distributed computing project for protein structure prediction
Q.48 What is the main advantage of using 'in silico' mutagenesis?
It avoids the need for wet‑lab experiments
It provides real‑time protein folding data
It guarantees a protein will fold correctly
It can replace all experimental methods
Explanation - In silico mutagenesis predicts the effect of mutations on structure and function, saving time and resources.
Correct answer is: It avoids the need for wet‑lab experiments
Q.49 Which of the following best explains 'backbone torsion angles'?
Angles between side chains and the backbone
Dihedral angles φ and ψ along the protein backbone
The angles between adjacent helices
The curvature of the protein chain
Explanation - φ (phi) and ψ (psi) angles determine the conformation of the protein backbone and are critical for folding.
Correct answer is: Dihedral angles φ and ψ along the protein backbone
Q.50 Which technique is commonly used to determine protein oligomeric state?
Size‑exclusion chromatography coupled with multi‑angle light scattering (SEC‑MALS)
Gel electrophoresis
Mass spectrometry
DNA sequencing
Explanation - SEC‑MALS measures the absolute molecular weight of proteins in solution, revealing oligomeric states.
Correct answer is: Size‑exclusion chromatography coupled with multi‑angle light scattering (SEC‑MALS)
Q.51 What is the purpose of 'water refinement' in protein structure modeling?
To remove all water molecules from the crystal
To add solvent molecules to improve the model fit
To replace metal ions with water
To calculate the hydrophobic core
Explanation - Water refinement introduces solvent atoms where electron density indicates, enhancing model accuracy.
Correct answer is: To add solvent molecules to improve the model fit
Q.52 Which of the following best describes 'protein flexibility' in computational simulations?
The ability of a protein to change its sequence
The conformational changes a protein undergoes over time
The protein's electrical conductivity
The rate of protein synthesis
Explanation - Protein flexibility refers to the dynamic movements and conformational alterations accessible to a protein in solution.
Correct answer is: The conformational changes a protein undergoes over time
Q.53 Which of the following is a common error in homology modeling when sequence identity is low?
Overestimation of side‑chain rotamers
Underestimation of secondary structure
Accurate modeling of the core
Precise determination of ligand binding
Explanation - Low sequence identity leads to unreliable side‑chain placements, often resulting in incorrect rotamers.
Correct answer is: Overestimation of side‑chain rotamers
Q.54 What is the main benefit of using 'multiple model averaging' in cryo‑EM?
It speeds up data collection
It reduces random noise and improves map quality
It eliminates the need for detergents
It predicts protein folding pathways
Explanation - Averaging many particle images enhances signal‑to‑noise ratio, yielding higher resolution structures.
Correct answer is: It reduces random noise and improves map quality
Q.55 Which parameter is most critical for determining the quality of a cryo‑EM reconstruction?
The number of collected images
The pixel size of the detector
The buffer composition
The DNA sequence of the gene
Explanation - More particles generally lead to better statistics and higher resolution in the final map.
Correct answer is: The number of collected images
Q.56 Which of the following best describes the 'Ramachandran plot' used in structure validation?
A plot of B-factors versus residue number
A scatter plot of allowed phi‑psi angles
A chart of protein expression levels
A table of ligand binding energies
Explanation - The plot visualizes the sterically allowed and disallowed backbone dihedral angles for amino acids in a protein.
Correct answer is: A scatter plot of allowed phi‑psi angles
Q.57 What is the main reason for using 'deuterated samples' in NMR?
To increase the speed of data acquisition
To reduce background hydrogen signals
To enhance X‑ray diffraction intensity
To improve cryo‑EM image contrast
Explanation - Deuteration replaces labile hydrogens, reducing unwanted signals and improving spectral quality.
Correct answer is: To reduce background hydrogen signals
Q.58 Which of the following is NOT a typical output of an AlphaFold prediction?
Predicted coordinates of each atom
Estimated confidence scores (pLDDT)
The DNA sequence encoding the protein
Predicted side‑chain conformations
Explanation - AlphaFold predicts protein 3D structure from sequence input; it does not output the gene sequence itself.
Correct answer is: The DNA sequence encoding the protein
Q.59 Which of the following best describes 'phasing by multiple isomorphous replacement (MIR)?
Using heavy‑atom derivatives to solve phases
Using anomalous scattering of selenium
Using the phase information from NMR
Using computer simulations
Explanation - MIR obtains phase information by comparing diffraction from crystals with added heavy atoms.
Correct answer is: Using heavy‑atom derivatives to solve phases
Q.60 In a typical X‑ray diffraction experiment, what does a diffraction spot represent?
An atom in the crystal
A specific electron density feature
An interference pattern of waves
A measurement of crystal size
Explanation - Diffraction spots arise from constructive interference of X‑rays scattered by the periodic crystal lattice.
Correct answer is: An interference pattern of waves
Q.61 What is the role of 'ligand‑bound crystals' in structural biology?
To determine the protein's active site
To sequence the protein's gene
To measure protein mass
To assess protein solubility
Explanation - Co‑crystallizing with a ligand captures the protein in a functional conformation, revealing binding interactions.
Correct answer is: To determine the protein's active site
Q.62 Which software is commonly used to analyze cryo‑EM density maps?
COOT
Chimera
PyMOL
All of the above
Explanation - Chimera, COOT, and PyMOL are popular tools for visualizing and fitting models into cryo‑EM density.
Correct answer is: All of the above
Q.63 Which of the following best describes the 'central pore' of ion channels?
A hydrophobic cavity that excludes water
An aqueous pathway that allows ion passage
A disordered flexible region
A metal binding site
Explanation - The central pore forms the conduction pathway for ions across the membrane.
Correct answer is: An aqueous pathway that allows ion passage
Q.64 Which of the following is a typical data quality metric in cryo‑EM?
R‑factor
Fourier shell correlation (FSC)
B-factor
Sequence alignment score
Explanation - FSC measures the agreement between two independently refined half‑maps, indicating resolution.
Correct answer is: Fourier shell correlation (FSC)
Q.65 What is the purpose of using 'phasing by single-wavelength anomalous dispersion (SAD)?
To solve the phase problem using anomalous scattering
To measure the protein's weight
To determine the protein's gene sequence
To estimate the solvent content
Explanation - SAD exploits the anomalous signal of heavy atoms at a single wavelength to compute phases.
Correct answer is: To solve the phase problem using anomalous scattering
Q.66 Which of the following best explains 'side‑chain rotamer libraries'?
Predefined positions for backbone atoms
Standard conformations for side chains to aid modeling
Lists of ligand binding sites
Tables of DNA codons
Explanation - Rotamer libraries provide statistically favored side‑chain angles, improving model accuracy.
Correct answer is: Standard conformations for side chains to aid modeling
Q.67 Why are 'low‑resolution' cryo‑EM maps still useful?
They can reveal overall architecture and domain arrangement
They provide detailed side‑chain positions
They are not useful at all
They replace the need for X‑ray data
Explanation - Even at lower resolutions, cryo‑EM maps help delineate large structural features and subunit organization.
Correct answer is: They can reveal overall architecture and domain arrangement
Q.68 In molecular dynamics, what is the 'force field'?
The software used for NMR analysis
A set of equations and parameters defining interactions
The experimental X‑ray beamline
The pathway for protein synthesis
Explanation - Force fields like CHARMM or AMBER specify how atoms interact in MD simulations.
Correct answer is: A set of equations and parameters defining interactions
Q.69 Which of the following describes 'protein engineering'?
Studying natural protein sequences only
Designing proteins with new or improved functions
Sequencing DNA from proteins
Measuring protein electrical activity
Explanation - Protein engineering modifies proteins to achieve desired properties, often guided by structural information.
Correct answer is: Designing proteins with new or improved functions
Q.70 Which of the following best explains the 'Fourier transform' in the context of crystallography?
Converting real‑space coordinates to momentum space
Transforming diffraction intensities into electron density
Measuring the speed of protein folding
Analyzing gene expression levels
Explanation - Fourier transform relates diffraction data to the spatial distribution of electrons in a crystal.
Correct answer is: Transforming diffraction intensities into electron density
Q.71 What is a 'cryo‑EM grid' used for?
Mounting protein crystals for X‑ray analysis
Placing protein samples for electron microscopy
Storing DNA samples
Holding electrodes in electrical experiments
Explanation - Cryo‑EM grids support thin layers of vitrified sample for imaging by electron microscopes.
Correct answer is: Placing protein samples for electron microscopy
Q.72 Which of the following best describes the 'chemical shift' in NMR?
The energy required to flip a proton's spin
A measure of an atom's electronic environment
The rate of protein folding
The temperature at which the protein denatures
Explanation - Chemical shifts provide information about the local chemical environment of nuclei in a molecule.
Correct answer is: A measure of an atom's electronic environment
Q.73 What is the purpose of 'grid search' in docking simulations?
To systematically explore ligand poses within the binding site
To identify crystal defects
To determine protein expression levels
To compute protein folding pathways
Explanation - Grid search samples orientations and positions of ligands to identify favorable binding modes.
Correct answer is: To systematically explore ligand poses within the binding site
Q.74 Which of the following is NOT an input for a homology modeling pipeline?
Target sequence
Template structure
NMR spectra
Alignment file
Explanation - Homology modeling typically requires sequence, template, and alignment; NMR data is not directly used.
Correct answer is: NMR spectra
Q.75 What does 'anisotropic B‑factors' indicate?
Uniform atomic displacement in all directions
Direction-dependent atomic displacement
The presence of disulfide bonds
The crystal's unit cell parameters
Explanation - Anisotropic B‑factors model different displacements along different axes for improved geometry.
Correct answer is: Direction-dependent atomic displacement
Q.76 In cryo‑EM data processing, why is 'particle picking' important?
To select crystals for X‑ray diffraction
To identify individual molecules in images for reconstruction
To choose DNA sequences for cloning
To isolate ligands from solutions
Explanation - Particle picking extracts 2D images of individual proteins from micrographs for alignment and reconstruction.
Correct answer is: To identify individual molecules in images for reconstruction
Q.77 What is the 'unit cell' in crystallography?
The smallest repeating unit that defines the crystal lattice
The entire crystal structure
The solvent region of a crystal
The protein's active site
Explanation - The unit cell contains the fundamental arrangement of atoms that repeats throughout the crystal.
Correct answer is: The smallest repeating unit that defines the crystal lattice
Q.78 Which of the following best describes 'secondary structure prediction' accuracy?
It is always 100% accurate
It achieves around 70–80% accuracy for most proteins
It is not possible for proteins
It depends only on protein length
Explanation - Secondary structure predictors reach ~70–80% accuracy, but improvements continue with new methods.
Correct answer is: It achieves around 70–80% accuracy for most proteins
Q.79 Which of these is a typical application of structural genomics data?
Designing better battery materials
Developing new antibiotics
Improving fiber optics
Predicting weather patterns
Explanation - Structural genomics provides protein targets for drug design, including antibiotics against pathogens.
Correct answer is: Developing new antibiotics
Q.80 What is the role of 'chemical cross‑linking' in structural studies?
To stabilize protein complexes for analysis
To sequence DNA
To measure protein mass
To determine electrical conductivity
Explanation - Cross‑linking covalently links interacting partners, aiding in capturing transient complexes for analysis.
Correct answer is: To stabilize protein complexes for analysis
Q.81 Which of the following best explains 'protein disorder'?
The protein's high melting temperature
A lack of well‑defined secondary structure under physiological conditions
The presence of disulfide bonds
The protein’s ability to conduct electricity
Explanation - Disordered proteins lack stable tertiary structure, often involved in signaling and regulation.
Correct answer is: A lack of well‑defined secondary structure under physiological conditions
Q.82 Which of these is a common step after obtaining an initial cryo‑EM reconstruction?
Refining the model to fit the density map
Sequencing the gene again
Running an X‑ray diffraction experiment
Performing a Western blot
Explanation - Model fitting adjusts atomic coordinates to best match the cryo‑EM density, improving accuracy.
Correct answer is: Refining the model to fit the density map
Q.83 What does the 'protein data bank (PDB) entry ID' indicate?
The publication where the protein was first described
A unique identifier for a specific 3D structure
The protein’s molecular weight
The number of residues in the protein
Explanation - Each PDB entry has a four‑character ID that uniquely identifies the deposited structure.
Correct answer is: A unique identifier for a specific 3D structure
Q.84 Why are 'buffer conditions' critical for successful protein crystallization?
They determine the protein's folding temperature
They influence crystal growth and stability
They affect DNA sequencing
They control the protein's charge only
Explanation - Buffer pH, ionic strength, and additives can greatly impact nucleation and crystal quality.
Correct answer is: They influence crystal growth and stability
Q.85 Which of these best describes 'protein folding energy landscape'?
A representation of possible folding pathways and their energetic barriers
The list of all possible amino acids in a protein
The speed at which a protein folds
The genetic sequence of the protein
Explanation - The energy landscape maps the stability and transition states of proteins during folding.
Correct answer is: A representation of possible folding pathways and their energetic barriers
Q.86 Which of the following is NOT a typical output of a cryo‑EM pipeline?
3D reconstruction map
Estimated resolution
Protein sequence
Classified particle images
Explanation - Cryo‑EM pipelines generate density maps and models but do not produce the amino acid sequence.
Correct answer is: Protein sequence
Q.87 What is the function of 'electrophoretic mobility shift assay (EMSA)' in structural biology?
To detect DNA–protein interactions
To sequence protein DNA
To determine protein crystallization conditions
To measure protein folding rate
Explanation - EMSA shows shifts in DNA mobility when bound to proteins, indicating interaction.
Correct answer is: To detect DNA–protein interactions
Q.88 Which of the following best describes a 'binding pocket' in a protein?
An empty space on the protein surface
A region that can accommodate a ligand or substrate
The protein's active site only
A region of disordered structure
Explanation - Binding pockets are cavities formed by amino acids that allow ligands to interact specifically.
Correct answer is: A region that can accommodate a ligand or substrate
Q.89 Which of these computational methods helps predict how a protein will behave in a lipid bilayer?
Molecular dynamics with a membrane environment
NMR spectroscopy
X‑ray crystallography
DNA sequencing
Explanation - MD simulations with lipid bilayers model protein–lipid interactions and membrane insertion.
Correct answer is: Molecular dynamics with a membrane environment
Q.90 What is the main purpose of 'mutagenesis libraries' in protein engineering?
To generate a diverse set of protein variants for screening
To sequence the protein's gene
To measure protein's electrical resistance
To determine the protein's crystal structure
Explanation - Mutagenesis libraries allow systematic exploration of sequence space to identify improved functions.
Correct answer is: To generate a diverse set of protein variants for screening
Q.91 Which of the following best explains 'protein–DNA interaction energy calculation'?
Computing the energy difference between bound and unbound states
Sequencing the DNA bound to protein
Measuring the protein's mass
Determining the protein's pH
Explanation - Interaction energy is the free‑energy difference reflecting binding affinity between protein and DNA.
Correct answer is: Computing the energy difference between bound and unbound states