Q.1 What does the term “systems biology” primarily refer to?
Studying isolated genes in a test tube
Analyzing whole biological systems using computational models
Measuring the voltage of a neuron
Designing electronic circuits for medical devices
Explanation - Systems biology focuses on the integration of experimental data with computational models to understand interactions within entire biological systems.
Correct answer is: Analyzing whole biological systems using computational models
Q.2 Which of the following is a common mathematical representation of a gene regulatory network?
Ohm’s law
Differential equations
Fourier transform
Kirchhoff’s current law
Explanation - Gene regulatory networks are often modeled using ordinary differential equations to describe changes in gene expression over time.
Correct answer is: Differential equations
Q.3 In a metabolic pathway model, what does the term ‘steady‑state’ imply?
All concentrations are zero
All reaction rates are equal and unchanging over time
The system is oscillating
The temperature is constant
Explanation - Steady‑state means that metabolite concentrations remain constant because the rates of production and consumption balance each other.
Correct answer is: All reaction rates are equal and unchanging over time
Q.4 Which of the following best describes a ‘feedback loop’ in a biological system?
A circuit that amplifies a signal without limits
A process where the output of a system influences its own input
A linear pathway with no regulation
A random fluctuation in gene expression
Explanation - Feedback loops can be positive (amplifying) or negative (dampening) and are crucial for regulation in biological networks.
Correct answer is: A process where the output of a system influences its own input
Q.5 Which software tool is frequently used for simulating biochemical networks?
MATLAB Simulink
SPICE
COPASI
LabVIEW
Explanation - COPASI (COmplex PAthway SImulator) is a widely used application for modeling and simulation of biochemical networks.
Correct answer is: COPASI
Q.6 In the context of systems biology, what does ‘omics’ refer to?
The study of single cells only
High‑throughput analyses of large sets of biological molecules
A type of electrical circuit
The measurement of electromagnetic fields in cells
Explanation - ‘Omics’ (genomics, proteomics, metabolomics, etc.) involve comprehensive profiling of molecules to understand system‑wide behavior.
Correct answer is: High‑throughput analyses of large sets of biological molecules
Q.7 Which of the following is NOT a typical component of a systems biology model?
Kinetic parameters
Circuit board layout
Stoichiometric matrix
Regulatory rules
Explanation - Circuit board layout is unrelated to biological modeling; kinetic parameters, stoichiometry, and regulatory rules are essential components.
Correct answer is: Circuit board layout
Q.8 A Boolean network model of a gene circuit uses which type of variable to represent gene states?
Continuous concentration values
Binary (0 or 1) states
Voltage levels
Frequency of oscillation
Explanation - Boolean models simplify gene expression to ON (1) or OFF (0) states to study network dynamics.
Correct answer is: Binary (0 or 1) states
Q.9 What does the term ‘flux balance analysis’ (FBA) compute in a metabolic network?
Electrical resistance of cell membranes
Steady‑state flow of metabolites that maximizes a given objective
The pH of the cytoplasm
The temperature of the organism
Explanation - FBA uses linear programming to predict the distribution of metabolic fluxes that optimize a cellular objective, such as growth.
Correct answer is: Steady‑state flow of metabolites that maximizes a given objective
Q.10 Which of the following is a key advantage of using a systems biology approach over traditional reductionist methods?
It requires fewer experiments
It can capture emergent properties arising from interactions
It eliminates the need for mathematics
It only studies DNA
Explanation - Systems biology integrates multiple components, allowing the discovery of behaviors that are not evident when studying parts in isolation.
Correct answer is: It can capture emergent properties arising from interactions
Q.11 In an electrical analogy of a cell membrane, the capacitance corresponds to:
Ion channel conductance
Membrane lipid bilayer storing charge
ATP concentration
RNA polymerase activity
Explanation - The lipid bilayer acts like a capacitor, separating charge across the membrane.
Correct answer is: Membrane lipid bilayer storing charge
Q.12 Which type of data is essential for constructing a kinetic model of an enzymatic reaction?
Voltage measurements
Enzyme concentration, substrate concentration, and reaction rate
Magnetic field strength
Audio frequency spectrum
Explanation - Kinetic models need quantitative data on enzyme, substrate, and observed rates to estimate parameters like Km and Vmax.
Correct answer is: Enzyme concentration, substrate concentration, and reaction rate
Q.13 What does the term ‘parameter sensitivity analysis’ assess in a biological model?
How changes in model parameters affect output behavior
The electrical power consumption of a lab instrument
The color of cells under a microscope
The speed of data transmission in a network
Explanation - Sensitivity analysis identifies which parameters most influence model predictions, guiding experiments and model refinement.
Correct answer is: How changes in model parameters affect output behavior
Q.14 Which of the following is a common method for validating a systems biology model?
Comparing model predictions with independent experimental data
Measuring the weight of the computer running the simulation
Counting the number of lines of code
Testing the model on a different planet
Explanation - Validation involves checking whether the model can accurately reproduce results not used during its construction.
Correct answer is: Comparing model predictions with independent experimental data
Q.15 In the context of gene regulatory networks, what is a ‘motif’?
A repeated DNA sequence that codes for proteins
A small, recurring circuit pattern that performs a specific function
The physical shape of a cell
An electrical waveform
Explanation - Network motifs are over‑represented sub‑graphs (e.g., feed‑forward loops) that carry out characteristic regulatory tasks.
Correct answer is: A small, recurring circuit pattern that performs a specific function
Q.16 Which of the following best describes a ‘negative feedback’ loop?
The output amplifies the input, leading to runaway behavior
The output reduces the input, stabilizing the system
The system oscillates without damping
The input is ignored completely
Explanation - Negative feedback counteracts deviations, helping maintain homeostasis in biological systems.
Correct answer is: The output reduces the input, stabilizing the system
Q.17 What is the primary purpose of a ‘stoichiometric matrix’ in metabolic modeling?
To record the voltage across each reaction
To represent the quantitative relationships between metabolites and reactions
To list all the genes in a genome
To display the temperature profile of a cell
Explanation - The stoichiometric matrix encodes how each reaction consumes and produces metabolites, forming the basis for constraint‑based analyses.
Correct answer is: To represent the quantitative relationships between metabolites and reactions
Q.18 Which of the following experimental techniques provides time‑resolved data suitable for dynamic modeling?
RNA‑seq (snapshot)
Chromatin immunoprecipitation (ChIP‑seq)
Live‑cell fluorescence microscopy
Western blot
Explanation - Live‑cell imaging captures dynamic changes in protein concentrations or localization over time, essential for kinetic models.
Correct answer is: Live‑cell fluorescence microscopy
Q.19 In an electrical circuit analogy, a resistor is often used to model which biological feature?
Membrane capacitance
Ion channel conductance
Gene transcription rate
Enzyme turnover number
Explanation - Resistors impede current flow, analogous to the limited conductance of ion channels across the membrane.
Correct answer is: Ion channel conductance
Q.20 Which statistical method is commonly used to infer network connections from high‑throughput data?
Principal Component Analysis (PCA)
Gaussian elimination
Maximum likelihood estimation
Monte Carlo integration
Explanation - Maximum likelihood methods can estimate parameters of probabilistic models that describe network interactions from data.
Correct answer is: Maximum likelihood estimation
Q.21 A ‘bifurcation’ in the context of dynamical systems refers to:
A point where the system splits into two independent circuits
A change in system behavior when a parameter passes a critical value
The division of a cell into two daughter cells
A type of electrical connector
Explanation - Bifurcations indicate qualitative shifts, such as from stable to oscillatory dynamics, as model parameters vary.
Correct answer is: A change in system behavior when a parameter passes a critical value
Q.22 Which of the following best describes a ‘robust’ biological network?
It fails under the slightest perturbation
It maintains functionality despite variations in parameters or environmental conditions
It only works at a single temperature
It is extremely sensitive to noise
Explanation - Robustness is the ability of a system to preserve its output in the face of internal or external disturbances.
Correct answer is: It maintains functionality despite variations in parameters or environmental conditions
Q.23 In the context of synthetic biology, a ‘genetic toggle switch’ is an example of:
A linear pathway
A bistable circuit that can exist in two stable states
An oscillatory clock
A voltage regulator
Explanation - A toggle switch consists of two mutually repressing genes, giving rise to two alternative stable expression states.
Correct answer is: A bistable circuit that can exist in two stable states
Q.24 Which of the following is NOT a typical output of a systems biology simulation?
Time‑course of metabolite concentrations
Predicted gene expression levels
Voltage drop across a power line
Flux distribution in a metabolic network
Explanation - Systems biology simulations focus on biological variables, not electrical power‑grid metrics.
Correct answer is: Voltage drop across a power line
Q.25 What does the Hill coefficient in a gene regulation model describe?
The speed of an electrical signal
The degree of cooperativity in ligand binding
The resistance of a membrane
The temperature dependence of a reaction
Explanation - The Hill coefficient quantifies how the binding of one ligand molecule affects the binding of others, influencing the steepness of response curves.
Correct answer is: The degree of cooperativity in ligand binding
Q.26 In a deterministic model of a biochemical system, the system’s state is described by:
A probability distribution
A single set of ordinary differential equations
Random noise
A set of binary bits
Explanation - Deterministic models use ODEs to predict a unique trajectory for given initial conditions.
Correct answer is: A single set of ordinary differential equations
Q.27 Which method would you use to reduce a high‑dimensional gene expression dataset to its most informative components?
Laplace transform
Principal Component Analysis (PCA)
Kirchhoff’s voltage law
Fourier series expansion
Explanation - PCA projects data onto orthogonal axes that capture maximum variance, simplifying downstream modeling.
Correct answer is: Principal Component Analysis (PCA)
Q.28 What is the main purpose of using a ‘Monte Carlo’ approach in systems biology?
To solve deterministic equations analytically
To sample parameter space and assess uncertainty
To design printed circuit boards
To measure electric current
Explanation - Monte Carlo simulations randomly explore parameter values, providing insight into variability and confidence intervals of model predictions.
Correct answer is: To sample parameter space and assess uncertainty
Q.29 In a model of a signaling cascade, the term ‘kinase cascade’ refers to:
A series of electrical amplifiers
A chain of enzymes that phosphorylate each other sequentially
A set of genes that are turned off simultaneously
A network of ion channels
Explanation - Kinase cascades amplify signals through successive phosphorylation steps, a common motif in cell signaling.
Correct answer is: A chain of enzymes that phosphorylate each other sequentially
Q.30 Which of the following best describes ‘parameter identifiability’?
The ability to uniquely estimate model parameters from data
The capacity of a system to resist electrical noise
The speed at which a reaction occurs
The visual appearance of a cell
Explanation - Identifiability determines whether parameters can be determined unambiguously given the experimental measurements.
Correct answer is: The ability to uniquely estimate model parameters from data
Q.31 What is the role of ‘mass balance’ in constructing metabolic network models?
Ensuring that total electrical charge is conserved
Ensuring that the sum of inputs and outputs for each metabolite is zero at steady‑state
Balancing the number of genes in a genome
Adjusting the temperature of the system
Explanation - Mass balance enforces that production and consumption of each metabolite are balanced, a core principle in constraint‑based modeling.
Correct answer is: Ensuring that the sum of inputs and outputs for each metabolite is zero at steady‑state
Q.32 In the context of synthetic gene circuits, an ‘inducer’ is:
A voltage source
A molecule that activates gene expression
A resistor
A type of computer processor
Explanation - Inducers bind to regulatory proteins or promoters to initiate transcription in engineered circuits.
Correct answer is: A molecule that activates gene expression
Q.33 Which of the following is a typical assumption of the Michaelis‑Menten kinetic model?
Enzyme concentration changes rapidly during the reaction
Substrate concentration is much greater than enzyme concentration
The reaction follows a sinusoidal pattern
Temperature is variable throughout the experiment
Explanation - The Michaelis‑Menten model assumes a quasi‑steady‑state where substrate is in excess, allowing simplification of the rate equation.
Correct answer is: Substrate concentration is much greater than enzyme concentration
Q.34 What does a ‘phase portrait’ represent in the analysis of a biological system?
A diagram showing electrical wiring
A graphical depiction of trajectories of system variables in state space
A table of gene sequences
A map of neuronal connections
Explanation - Phase portraits visualize how system variables evolve over time, revealing attractors, limit cycles, and other dynamic features.
Correct answer is: A graphical depiction of trajectories of system variables in state space
Q.35 Which of the following is a limitation of using ODE‑based models for cellular processes?
They cannot represent stochastic fluctuations inherent in low‑copy‑number molecules
They are always computationally slow
They require a power supply
They only work for electrical circuits
Explanation - ODE models assume continuous concentrations and ignore random noise, which can be significant in small molecular populations.
Correct answer is: They cannot represent stochastic fluctuations inherent in low‑copy‑number molecules
Q.36 When constructing a model of a bacterial quorum‑sensing system, the key signaling molecule is typically:
A neurotransmitter
An autoinducer peptide or acyl‑homoserine lactone
A voltage‑gated ion channel
A metal ion
Explanation - Quorum sensing relies on small diffusible molecules (autoinducers) that accumulate as population density increases.
Correct answer is: An autoinducer peptide or acyl‑homoserine lactone
Q.37 In systems biology, the term ‘omics integration’ refers to:
Connecting electrical components on a PCB
Combining data from genomics, proteomics, metabolomics, etc., into a unified model
Merging two electrical circuits
Integrating audio and video signals
Explanation - Integration of multi‑omics data enables a comprehensive view of biological systems across different molecular layers.
Correct answer is: Combining data from genomics, proteomics, metabolomics, etc., into a unified model
Q.38 A ‘limit cycle’ in a dynamical system is:
A trajectory that never repeats
A closed trajectory representing sustained oscillations
A linear increase in concentration
A point where the system crashes
Explanation - Limit cycles correspond to stable periodic behavior, such as circadian rhythms or synthetic oscillators.
Correct answer is: A closed trajectory representing sustained oscillations
Q.39 Which of the following is a common way to represent a gene regulatory network graphically?
Schematic of a PCB
Directed graph with nodes (genes) and edges (regulatory interactions)
Bar chart of protein concentrations
Pie chart of nucleotide composition
Explanation - Directed graphs capture the directionality of regulation (activation or repression) between genes.
Correct answer is: Directed graph with nodes (genes) and edges (regulatory interactions)
Q.40 The ‘Gillespie algorithm’ is used for:
Deterministic simulation of ODEs
Stochastic simulation of chemical reactions at the molecular level
Designing digital filters
Calculating electrical resistance
Explanation - Gillespie’s method generates statistically exact trajectories for systems where randomness is important.
Correct answer is: Stochastic simulation of chemical reactions at the molecular level
Q.41 Which of the following best illustrates the concept of ‘modularity’ in biological networks?
All genes are equally connected to each other
The network can be divided into relatively independent sub‑networks performing distinct functions
The network has a single linear pathway
The network changes shape with temperature
Explanation - Modular organization allows parts of the system to function semi‑independently, facilitating evolution and robustness.
Correct answer is: The network can be divided into relatively independent sub‑networks performing distinct functions
Q.42 What does a ‘receiver operating characteristic (ROC) curve’ evaluate in model performance?
The electrical power consumption of the computer
The trade‑off between true positive rate and false positive rate
The speed of a reaction
The temperature of a cell culture
Explanation - ROC curves assess classification performance, useful when models predict binary outcomes such as active/inactive pathways.
Correct answer is: The trade‑off between true positive rate and false positive rate
Q.43 Which term describes the phenomenon where a small change in an input leads to a large change in system output?
Linear scaling
Signal amplification
Noise reduction
Voltage drop
Explanation - Amplification is common in signaling cascades where enzymatic steps multiply the original stimulus.
Correct answer is: Signal amplification
Q.44 In a synthetic biology context, a ‘ribosome binding site (RBS)’ controls:
The rate of transcription
The rate of translation initiation
The membrane potential
The electrical conductivity of the cell
Explanation - The RBS sequence determines how efficiently ribosomes bind to mRNA, influencing protein synthesis levels.
Correct answer is: The rate of translation initiation
Q.45 Which of the following is a hallmark of a ‘scale‑free’ network?
All nodes have the same number of connections
A few nodes (hubs) have many connections while most have few
The network size stays constant over time
The network is arranged in a perfect grid
Explanation - Scale‑free networks follow a power‑law degree distribution, making them robust to random failures but vulnerable to targeted attacks.
Correct answer is: A few nodes (hubs) have many connections while most have few
Q.46 What is the primary purpose of performing a ‘knock‑out’ experiment in a model organism?
To increase the organism’s electrical conductivity
To remove or disable a specific gene and observe phenotypic effects
To measure voltage across the cell membrane
To enhance the organism’s speed
Explanation - Gene knock‑outs help determine the functional role of a gene by observing changes when it is absent.
Correct answer is: To remove or disable a specific gene and observe phenotypic effects
Q.47 In a kinetic model, the term ‘Vmax’ represents:
The maximum voltage achievable
The maximum reaction rate when the enzyme is saturated with substrate
The maximum temperature of the system
The maximum number of genes expressed
Explanation - Vmax is a parameter of the Michaelis‑Menten equation indicating the asymptotic rate at high substrate concentrations.
Correct answer is: The maximum reaction rate when the enzyme is saturated with substrate
Q.48 Which type of data is essential for constructing a ‘gene regulatory network’ using a Bayesian approach?
Time‑series gene expression measurements
Electrical impedance spectroscopy
Magnetic resonance images
Acoustic recordings
Explanation - Bayesian network inference often relies on temporal expression data to infer probabilistic causal relationships.
Correct answer is: Time‑series gene expression measurements
Q.49 A ‘feed‑forward loop’ in a transcriptional network typically:
Creates a delay or pulse in the output response
Amplifies noise indefinitely
Eliminates all feedback
Prevents any transcription
Explanation - Feed‑forward loops can generate fast responses, temporal filters, or pulse‑like dynamics depending on their architecture.
Correct answer is: Creates a delay or pulse in the output response
Q.50 Which of the following best describes ‘homeostasis’ in biological systems?
A system that constantly changes without regulation
The maintenance of internal stability through regulatory mechanisms
An electrical circuit with no resistors
A random distribution of molecules
Explanation - Homeostasis is achieved via feedback loops that keep variables such as temperature, pH, or metabolite levels within narrow limits.
Correct answer is: The maintenance of internal stability through regulatory mechanisms
Q.51 In the context of model reduction, the term ‘lumped parameter’ refers to:
A single resistor that replaces a complex sub‑network
A type of gene promoter
A high‑frequency oscillation
A data storage unit
Explanation - Lumped‑parameter models simplify a detailed system by aggregating many components into a few effective parameters.
Correct answer is: A single resistor that replaces a complex sub‑network
Q.52 What is the primary use of a ‘sensitivity matrix’ in a biochemical model?
To compute the electrical resistance of the system
To quantify how small changes in parameters affect model outputs
To measure the speed of light
To record audio signals
Explanation - The sensitivity matrix contains partial derivatives of outputs with respect to each parameter, informing robustness and experimental design.
Correct answer is: To quantify how small changes in parameters affect model outputs
Q.53 When a biological system exhibits ‘bistability’, it means:
It has two distinct stable steady states under the same conditions
It oscillates with two frequencies
It has exactly two genes
It can conduct electricity in two directions
Explanation - Bistable systems can switch between two stable states, often used for memory storage in synthetic circuits.
Correct answer is: It has two distinct stable steady states under the same conditions
Q.54 Which of the following experimental techniques provides quantitative information about protein‑protein interactions?
Yeast two‑hybrid assay
PCR
Northern blot
Electrophysiology
Explanation - The yeast two‑hybrid system detects and quantifies interactions between two proteins in vivo.
Correct answer is: Yeast two‑hybrid assay
Q.55 In a deterministic ODE model, the Jacobian matrix evaluated at an equilibrium point is used to:
Calculate the total energy of the system
Determine the stability of that equilibrium
Measure the temperature of the cell
Encode DNA sequences
Explanation - Eigenvalues of the Jacobian indicate whether perturbations decay (stable) or grow (unstable) near the equilibrium.
Correct answer is: Determine the stability of that equilibrium
Q.56 Which of the following is a typical output of a ‘flux variability analysis’ (FVA) in metabolic modeling?
A range of possible fluxes for each reaction while still achieving the optimal objective
The voltage across each reaction
The DNA sequence of each enzyme
The color of the culture medium
Explanation - FVA determines the minimum and maximum allowable fluxes for each reaction compatible with the optimal solution, revealing alternative pathways.
Correct answer is: A range of possible fluxes for each reaction while still achieving the optimal objective
Q.57 What does the term ‘epistasis’ refer to in genetic networks?
When one gene’s effect masks or modifies the effect of another gene
The electrical resistance of a gene
The speed at which a gene is transcribed
The temperature dependence of DNA replication
Explanation - Epistatic interactions indicate non‑additive effects between genes, crucial for understanding network behavior.
Correct answer is: When one gene’s effect masks or modifies the effect of another gene
Q.58 Which of the following statements about ‘stochastic differential equations’ (SDEs) is true?
They ignore randomness in the system
They incorporate random noise terms to model intrinsic fluctuations
They are only used for electrical circuits
They replace all deterministic terms
Explanation - SDEs extend ODEs by adding stochastic components, capturing variability inherent in molecular systems.
Correct answer is: They incorporate random noise terms to model intrinsic fluctuations
Q.59 In the context of a synthetic oscillator (e.g., the repressilator), the key design principle is:
A linear cascade of activators
A negative feedback loop with sufficient delay
An electrical transformer
A high‑gain amplifier
Explanation - Oscillations arise when negative feedback is combined with a time delay, allowing the system to overshoot and cycle.
Correct answer is: A negative feedback loop with sufficient delay
Q.60 Which of the following best describes a ‘digital twin’ in systems biology?
A physical replica of a cell
A computational model that mirrors the behavior of a real biological system in real time
A pair of identical DNA strands
A dual‑core processor
Explanation - Digital twins integrate live data streams with simulations to predict and control biological processes dynamically.
Correct answer is: A computational model that mirrors the behavior of a real biological system in real time
Q.61 Which of the following is NOT a typical feature of a well‑curated biological database used for modeling?
Standardized identifiers (e.g., UniProt IDs)
Validated kinetic parameters
Randomly generated gene sequences
Cross‑references to other resources
Explanation - High‑quality databases contain curated, experimentally validated data, not random sequences.
Correct answer is: Randomly generated gene sequences
Q.62 In a cell‑signaling network, the term ‘crosstalk’ refers to:
Electrical interference between wires
Interactions where one pathway influences another
Noise in the data acquisition system
The binding of two identical ligands
Explanation - Crosstalk creates integration of signals, adding complexity to cellular decision‑making.
Correct answer is: Interactions where one pathway influences another
Q.63 What is the purpose of ‘parameter fitting’ in systems biology modeling?
To increase the voltage of a circuit
To adjust model parameters so that simulated outputs match experimental data
To measure the mass of a cell
To design a new chip
Explanation - Parameter fitting (e.g., using least squares) tunes model constants for best agreement with observed data.
Correct answer is: To adjust model parameters so that simulated outputs match experimental data
Q.64 Which of the following is a characteristic of a ‘high‑throughput’ experiment?
It analyzes a single sample at a time
It generates large amounts of data rapidly across many samples or conditions
It requires manual counting of cells
It cannot be used for omics studies
Explanation - High‑throughput platforms (e.g., RNA‑seq) enable systematic collection of data needed for systems‑level analysis.
Correct answer is: It generates large amounts of data rapidly across many samples or conditions
Q.65 Which mathematical concept is used to describe the probability of transitioning between states in a stochastic model?
Markov chain
Ohm’s law
Fourier transform
Laplace’s equation
Explanation - Markov chains model memoryless transitions between discrete states, often applied to gene expression bursts.
Correct answer is: Markov chain
Q.66 In a metabolic model, the term ‘dead‑end metabolite’ refers to:
A metabolite that is both produced and consumed
A metabolite that can be produced but not consumed (or vice versa) under the given network constraints
A metabolite that has no charge
A metabolite that fluoresces
Explanation - Dead‑ends indicate gaps or missing reactions and need to be addressed for realistic simulations.
Correct answer is: A metabolite that can be produced but not consumed (or vice versa) under the given network constraints
Q.67 Which of the following best describes a ‘synthetic biology chassis’?
A type of electrical connector
A host organism or platform engineered to carry and express synthetic gene circuits
A carbon skeleton of a molecule
A software IDE
Explanation - Chassis organisms (e.g., E. coli, yeast) provide a standardized background for implementing synthetic designs.
Correct answer is: A host organism or platform engineered to carry and express synthetic gene circuits
Q.68 What is a ‘null model’ used for in network analysis?
A model that predicts electrical currents
A random network preserving certain properties, used as a baseline for statistical comparison
A model that has no genes
A model that only includes water molecules
Explanation - Null models help assess whether observed network features (e.g., clustering) are statistically significant.
Correct answer is: A random network preserving certain properties, used as a baseline for statistical comparison
Q.69 Which of the following best captures the idea of ‘emergent behavior’ in a biological system?
A property that can be predicted by looking at a single component alone
A new behavior that arises from interactions among components and is not evident from the parts in isolation
A constant, unchanging output
A linear increase in concentration over time
Explanation - Emergent properties, such as oscillations or bistability, stem from network interactions rather than single elements.
Correct answer is: A new behavior that arises from interactions among components and is not evident from the parts in isolation
Q.70 In the context of model validation, the term ‘cross‑validation’ refers to:
Testing the model on the same data used for training
Dividing data into subsets, training on some and testing on others to assess predictive power
Running the model on a different computer
Measuring electrical resistance of the model components
Explanation - Cross‑validation prevents over‑fitting and evaluates how well a model generalizes to unseen data.
Correct answer is: Dividing data into subsets, training on some and testing on others to assess predictive power
Q.71 Which of the following best describes the role of an ‘allosteric regulator’ in enzymatic reactions?
It directly supplies electrons
It binds to a site other than the active site, altering enzyme activity
It changes the temperature of the reaction
It provides the substrate
Explanation - Allosteric effectors modulate enzyme kinetics by inducing conformational changes.
Correct answer is: It binds to a site other than the active site, altering enzyme activity
Q.72 When a biological system is modeled using a ‘Petri net’, the places represent:
Electrical nodes
Molecular species or states
Temperature values
Signal frequencies
Explanation - In Petri nets, places hold tokens (e.g., molecule counts) and transitions represent reactions.
Correct answer is: Molecular species or states
Q.73 Which of the following is a typical feature of a ‘negative autoregulation’ motif?
The gene product enhances its own expression
The gene product represses its own expression, leading to faster response times and reduced noise
The gene product has no effect on its own expression
The gene product destroys the DNA
Explanation - Negative autoregulation provides rapid adaptation and stabilizes expression levels.
Correct answer is: The gene product represses its own expression, leading to faster response times and reduced noise
Q.74 In the context of metabolic engineering, ‘overexpression’ of a gene typically aims to:
Decrease the cell’s electrical conductivity
Increase the amount of enzyme to boost pathway flux
Make the cell glow in the dark
Reduce the cell’s size
Explanation - Overexpressing a gene elevates enzyme concentration, potentially increasing the throughput of a metabolic route.
Correct answer is: Increase the amount of enzyme to boost pathway flux
Q.75 Which of the following is an example of a ‘global sensitivity analysis’ method?
One‑at‑a‑time (OAT) perturbation
Sobol’ variance‑based method
Measuring voltage across a resistor
Counting cells under a microscope
Explanation - Sobol’ analysis quantifies the contribution of each parameter (and interactions) to output variance over the whole parameter space.
Correct answer is: Sobol’ variance‑based method
Q.76 What does a ‘Hill function’ typically model in systems biology?
Electrical current flow
Cooperative binding of ligands to a macromolecule
Temperature changes
Acoustic vibrations
Explanation - Hill functions describe sigmoidal response curves characteristic of cooperative interactions.
Correct answer is: Cooperative binding of ligands to a macromolecule
Q.77 In a Boolean model, the update scheme where all nodes are updated simultaneously at each time step is called:
Asynchronous update
Synchronous update
Random update
Continuous update
Explanation - Synchronous update applies the logical rules to all nodes at once, simplifying analysis of state transitions.
Correct answer is: Synchronous update
Q.78 Which of the following best explains why ‘parameter identifiability’ is often a problem in large-scale models?
There are too many parameters relative to the amount of data available
The models are too simple
Electrical interference corrupts the data
The temperature is too high
Explanation - Overparameterization leads to multiple parameter sets fitting the data equally well, making unique estimation difficult.
Correct answer is: There are too many parameters relative to the amount of data available
Q.79 A ‘receiver operating characteristic (ROC) curve’ is plotted with:
True positive rate vs. false positive rate
Voltage vs. current
Concentration vs. time
Temperature vs. pressure
Explanation - ROC curves assess classification performance across varying decision thresholds.
Correct answer is: True positive rate vs. false positive rate
Q.80 Which of the following statements about ‘stochastic resonance’ in cellular signaling is true?
Noise always degrades signal quality
A certain level of noise can actually enhance the detection of weak signals
It only occurs in electrical circuits
It requires high temperature
Explanation - Stochastic resonance describes how optimal noise levels can improve signal transduction in nonlinear systems.
Correct answer is: A certain level of noise can actually enhance the detection of weak signals
Q.81 In the context of a ‘gene circuit’, a ‘reporter gene’ is used to:
Control the cell’s voltage
Produce an easily measurable output (e.g., fluorescence) indicating circuit activity
Destroy the host genome
Increase the temperature of the cell
Explanation - Reporter genes such as GFP allow researchers to monitor the expression state of a synthetic circuit.
Correct answer is: Produce an easily measurable output (e.g., fluorescence) indicating circuit activity
Q.82 Which of the following best characterizes a ‘linear pathway’ in a metabolic network?
A series of reactions where each product is the substrate for the next, without branches
A network with many feedback loops
A pathway that includes cycles
A system that never reaches steady‑state
Explanation - Linear pathways have a single chain of reactions; they are simpler to model than branched networks.
Correct answer is: A series of reactions where each product is the substrate for the next, without branches
Q.83 What is the purpose of a ‘parameter sweep’ in computational modeling?
To vary model parameters systematically and observe effects on output
To measure the voltage across a resistor
To change the color of the simulation
To increase the speed of the computer
Explanation - Parameter sweeps help explore model behavior across a range of values, identifying regions of interest or robustness.
Correct answer is: To vary model parameters systematically and observe effects on output
Q.84 In a synthetic biology project, the term ‘BioBrick’ refers to:
A type of electrical resistor
A standardized DNA part that can be assembled with others in a predictable way
A metal alloy used in labs
A computational algorithm
Explanation - BioBricks are modular genetic components designed for easy assembly and reuse in synthetic circuits.
Correct answer is: A standardized DNA part that can be assembled with others in a predictable way
Q.85 Which of the following best describes a ‘steady‑state approximation’ used in enzyme kinetics?
Assuming the substrate concentration is zero
Assuming the concentration of the enzyme‑substrate complex changes very slowly over time
Assuming the temperature is constant
Assuming the reaction is instantaneous
Explanation - The steady‑state approximation simplifies the derivation of the Michaelis‑Menten equation.
Correct answer is: Assuming the concentration of the enzyme‑substrate complex changes very slowly over time
Q.86 Which of the following is a common measure of model fit when comparing simulated and experimental time‑course data?
Root‑mean‑square error (RMSE)
Ohm’s law
Fourier coefficient
Coulomb’s law
Explanation - RMSE quantifies the average magnitude of the differences between predicted and observed values.
Correct answer is: Root‑mean‑square error (RMSE)
Q.87 In a kinetic model of gene expression, the term ‘burst size’ refers to:
The voltage amplitude of an action potential
The number of mRNA molecules produced during a transcriptional burst
The size of the cell nucleus
The length of the DNA helix
Explanation - Burst size quantifies the stochastic production of transcripts in bursty gene expression regimes.
Correct answer is: The number of mRNA molecules produced during a transcriptional burst
Q.88 Which of the following is an example of a ‘negative feedback’ motif that can generate adaptation?
A feed‑forward loop with activation only
A negative feedback loop with an integral controller
A positive feedback loop
A linear cascade with no regulation
Explanation - Integral feedback can drive the system back to a set‑point after a perturbation, achieving perfect adaptation.
Correct answer is: A negative feedback loop with an integral controller
Q.89 What is the main advantage of using a ‘hybrid model’ that combines ODEs and stochastic elements?
It runs faster than pure ODE models
It captures both deterministic trends and stochastic fluctuations where they matter most
It eliminates the need for parameter estimation
It works without any data
Explanation - Hybrid models apply ODEs to abundant species and stochastic simulations to low‑copy‑number components, balancing accuracy and efficiency.
Correct answer is: It captures both deterministic trends and stochastic fluctuations where they matter most
Q.90 Which of the following best describes the purpose of a ‘knock‑down’ experiment (e.g., using RNAi)?
To permanently delete a gene
To transiently reduce the expression level of a target gene
To increase the voltage across a membrane
To heat the cells
Explanation - RNA interference (RNAi) degrades specific mRNA molecules, lowering protein production without altering the genome.
Correct answer is: To transiently reduce the expression level of a target gene
Q.91 In systems biology, the term ‘dose‑response curve’ typically plots:
Voltage vs. current
Output (e.g., expression level) vs. stimulus intensity (e.g., ligand concentration)
Temperature vs. pressure
Time vs. distance
Explanation - Dose‑response curves characterize how a system’s output changes with varying input levels, often revealing cooperativity.
Correct answer is: Output (e.g., expression level) vs. stimulus intensity (e.g., ligand concentration)
Q.92 Which of the following is NOT a typical step in the workflow of building a systems biology model?
Data acquisition and preprocessing
Model formulation and parameter estimation
Electrical wiring of the laboratory
Model validation and analysis
Explanation - Modeling workflow involves data, formulation, fitting, and validation; wiring is unrelated to computational modeling.
Correct answer is: Electrical wiring of the laboratory
Q.93 What is the primary reason to use a ‘log‑scale’ when plotting concentration data that spans several orders of magnitude?
To hide data variability
To compress large ranges and make trends more visible
To convert concentrations to voltages
To make the plot look more modern
Explanation - Logarithmic scaling reduces skewness, allowing easier visual comparison of low and high values.
Correct answer is: To compress large ranges and make trends more visible
Q.94 In the context of a ‘cell‑free expression system’, the main advantage is:
It eliminates the need for a living host, allowing rapid prototyping of genetic circuits
It provides a high‑voltage power source
It heats the reaction to extreme temperatures
It produces electricity directly
Explanation - Cell‑free systems contain the transcription‑translation machinery in vitro, enabling fast testing of synthetic constructs.
Correct answer is: It eliminates the need for a living host, allowing rapid prototyping of genetic circuits
Q.95 Which of the following best describes an ‘integral controller’ in a synthetic biological circuit?
A component that adds up (integrates) the error over time to adjust the system output
A resistor that limits current
A device that measures temperature
A gene that never changes its expression
Explanation - Integral control accumulates deviation from a set point, enabling perfect adaptation in engineered circuits.
Correct answer is: A component that adds up (integrates) the error over time to adjust the system output
Q.96 Which of the following is a typical outcome when a model exhibits ‘parameter sloppiness’?
All parameters are precisely determined
Many parameter combinations produce similar model outputs, making precise estimation difficult
The model runs faster
The system becomes electrically unstable
Explanation - Sloppy models have directions in parameter space that weakly affect predictions, leading to large uncertainties.
Correct answer is: Many parameter combinations produce similar model outputs, making precise estimation difficult
Q.97 What is the main purpose of a ‘co‑expression network’ analysis?
To identify genes whose expression levels vary together across conditions, suggesting functional relationships
To measure the electrical current in a cell
To compute the mass of a protein
To generate random DNA sequences
Explanation - Co‑expression networks cluster genes with correlated expression patterns, aiding functional inference.
Correct answer is: To identify genes whose expression levels vary together across conditions, suggesting functional relationships
Q.98 Which of the following best explains why ‘temperature’ is often a critical parameter in kinetic models?
Temperature directly changes voltage
Reaction rates typically follow the Arrhenius equation, making them highly temperature‑dependent
Temperature determines the color of the solution
Temperature has no effect on biochemical reactions
Explanation - The Arrhenius relationship shows that small temperature changes can cause large variations in reaction kinetics.
Correct answer is: Reaction rates typically follow the Arrhenius equation, making them highly temperature‑dependent
Q.99 In a gene regulatory network, a ‘master regulator’ is:
A gene that controls many downstream genes and determines cell fate
A resistor with the highest resistance
A protein that never binds DNA
A molecule that only functions at high temperature
Explanation - Master regulators sit at the top of hierarchical networks, orchestrating large transcriptional programs.
Correct answer is: A gene that controls many downstream genes and determines cell fate
Q.100 Which of the following best describes the role of a ‘promoter’ in a synthetic gene circuit?
It acts as a resistor in an electrical circuit
It provides a binding site for RNA polymerase to initiate transcription
It stores electrical charge
It measures the pH of the medium
Explanation - Promoters are DNA elements that dictate where and how strongly transcription starts.
Correct answer is: It provides a binding site for RNA polymerase to initiate transcription
Q.101 What does the term ‘dynamic range’ refer to in the context of a biosensor?
The voltage difference between its terminals
The ratio between the maximum and minimum detectable signal
The physical size of the sensor
The temperature range it can operate in
Explanation - Dynamic range quantifies how well a sensor can differentiate low from high input signals.
Correct answer is: The ratio between the maximum and minimum detectable signal
Q.102 Which of the following best describes a ‘synthetic riboswitch’?
A DNA sequence that changes its conformation in response to a small molecule, regulating translation
A type of electrical connector
A temperature sensor
A protein that degrades RNA
Explanation - Synthetic riboswitches are engineered RNA elements that modulate gene expression upon ligand binding.
Correct answer is: A DNA sequence that changes its conformation in response to a small molecule, regulating translation
Q.103 In a deterministic model of a signaling cascade, the term ‘time constant’ typically refers to:
The time it takes for the output to reach ~63% of its final value after a step input
The resistance of the cell membrane
The voltage of the power supply
The temperature of the incubator
Explanation - The time constant τ characterizes the speed of response in first‑order systems.
Correct answer is: The time it takes for the output to reach ~63% of its final value after a step input
Q.104 Which of the following is a common way to represent a metabolic network graphically?
A directed bipartite graph with metabolite nodes and reaction nodes
A circuit diagram with resistors and capacitors
A heat map of temperature
A waveform plot
Explanation - Bipartite graphs separate metabolites and reactions, clarifying substrate‑product relationships.
Correct answer is: A directed bipartite graph with metabolite nodes and reaction nodes
Q.105 When performing a ‘global sensitivity analysis’, why is it important to sample parameter values from realistic ranges?
To ensure the model runs faster
To avoid exploring biologically implausible regimes that could mislead conclusions
To change the color of the output plots
To increase the voltage of the computer
Explanation - Realistic parameter bounds keep the analysis relevant to actual biological behavior.
Correct answer is: To avoid exploring biologically implausible regimes that could mislead conclusions
Q.106 In the context of a ‘cellular automaton’ model for tissue growth, each cell’s state is updated based on:
The voltage across the cell membrane
The states of its neighboring cells according to simple rules
The magnetic field of the lab
The speed of light
Explanation - Cellular automata use local interaction rules to generate complex global patterns, useful for modeling tissue dynamics.
Correct answer is: The states of its neighboring cells according to simple rules
Q.107 Which of the following best defines the term ‘noise’ in gene expression?
Electrical interference from laboratory equipment
Random fluctuations in mRNA or protein levels among identical cells
Background music in the lab
The temperature of the incubator
Explanation - Noise captures intrinsic and extrinsic variability in molecular processes, influencing phenotypic diversity.
Correct answer is: Random fluctuations in mRNA or protein levels among identical cells
Q.108 What does the term ‘circuit abstraction’ imply when modeling a biochemical network?
Representing biochemical reactions as electrical components (e.g., resistors, capacitors) to simplify analysis
Drawing a picture of the lab bench
Measuring the weight of the sample
Calculating the speed of sound
Explanation - Circuit abstraction maps kinetic and regulatory interactions onto analog electrical elements, facilitating intuition and analysis.
Correct answer is: Representing biochemical reactions as electrical components (e.g., resistors, capacitors) to simplify analysis
Q.109 Which of the following is an advantage of using ‘cloud‑based’ platforms for systems biology simulations?
They automatically generate DNA sequences
They provide scalable computational resources, enabling large‑scale simulations without local hardware constraints
They cool the laboratory
They increase the voltage of the computer
Explanation - Cloud platforms allow on‑demand CPU/GPU resources, essential for intensive simulations and collaborative work.
Correct answer is: They provide scalable computational resources, enabling large‑scale simulations without local hardware constraints
Q.110 In a synthetic biology context, a ‘kill switch’ is designed to:
Increase the voltage of a circuit
Induce cell death under specific conditions to prevent uncontrolled proliferation
Enhance fluorescence
Accelerate DNA replication
Explanation - Kill switches provide biosafety by triggering self‑destruction when certain environmental cues are detected.
Correct answer is: Induce cell death under specific conditions to prevent uncontrolled proliferation
Q.111 Which of the following best describes the concept of ‘modular cloning’ (MoClo) in synthetic biology?
Assembling genetic parts using standardized overhangs and restriction enzymes for rapid construction of complex circuits
Wiring electronic components on a board
Measuring the mass of a protein
Sequencing DNA by hand
Explanation - MoClo enables hierarchical, scarless assembly of multiple DNA modules, streamlining the design‑build cycle.
Correct answer is: Assembling genetic parts using standardized overhangs and restriction enzymes for rapid construction of complex circuits
Q.112 In a deterministic model, what does the term ‘stiffness’ refer to?
The rigidity of the cell wall
The presence of widely differing time scales that make numerical integration challenging
The resistance of a resistor
The temperature of the incubator
Explanation - Stiff systems require specialized solvers (e.g., implicit methods) to maintain stability and accuracy.
Correct answer is: The presence of widely differing time scales that make numerical integration challenging
Q.113 Which of the following is a primary use of ‘machine learning’ in systems biology?
Designing power supplies
Predicting phenotypic outcomes from high‑dimensional omics data
Measuring electrical resistance
Generating random numbers
Explanation - Machine learning algorithms can uncover complex patterns linking genotype to phenotype across large datasets.
Correct answer is: Predicting phenotypic outcomes from high‑dimensional omics data
Q.114 In a synthetic gene circuit, the term ‘leakiness’ refers to:
Unintended background expression of a gene even when it is supposed to be OFF
Loss of voltage in a wire
The temperature increase of the system
The speed of DNA polymerase
Explanation - Leakiness reduces the contrast between ON and OFF states, affecting circuit performance.
Correct answer is: Unintended background expression of a gene even when it is supposed to be OFF
Q.115 Which of the following best describes the principle of ‘orthogonality’ in synthetic biology parts?
Components that operate independently without cross‑talk, allowing modular combination
A resistor that does not conduct electricity
A gene that cannot be transcribed
A molecule that cannot bind any protein
Explanation - Orthogonal parts minimize interference, facilitating predictable assembly of larger systems.
Correct answer is: Components that operate independently without cross‑talk, allowing modular combination
Q.116 When applying ‘principal component analysis’ (PCA) to gene expression data, the first principal component typically:
Represents the direction of greatest variance in the dataset
Measures the voltage across a membrane
Controls the temperature of the incubator
Is always zero
Explanation - PCA transforms correlated variables into orthogonal components, with the first capturing the most variability.
Correct answer is: Represents the direction of greatest variance in the dataset
Q.117 In a kinetic model, what does the symbol ‘k_cat’ represent?
The rate constant for the forward reaction in a reversible reaction
The catalytic turnover number – the maximum number of substrate molecules converted per enzyme per unit time
The temperature coefficient
The voltage across a membrane
Explanation - k_cat quantifies the speed at which an enzyme processes substrate when fully saturated.
Correct answer is: The catalytic turnover number – the maximum number of substrate molecules converted per enzyme per unit time
Q.118 Which of the following best explains why ‘compartmentalization’ is important in eukaryotic cell models?
It reduces computational load by ignoring organelles
Different cellular compartments have distinct biochemical environments that affect reaction rates and pathways
It creates electrical circuits inside the cell
It changes the color of the cell
Explanation - Compartmentalization introduces spatial heterogeneity, influencing diffusion, concentration, and reaction dynamics.
Correct answer is: Different cellular compartments have distinct biochemical environments that affect reaction rates and pathways
Q.119 What is the primary purpose of a ‘receiver operating characteristic (ROC) curve’ in evaluating a classifier that predicts gene essentiality?
To plot the relationship between voltage and current
To visualize the trade‑off between sensitivity (true positive rate) and 1‑specificity (false positive rate)
To measure the temperature of the culture
To display the size distribution of proteins
Explanation - ROC curves help assess classifier performance across different decision thresholds.
Correct answer is: To visualize the trade‑off between sensitivity (true positive rate) and 1‑specificity (false positive rate)
Q.120 In a Boolean model, what does the term ‘attractor’ refer to?
A set of states toward which the system eventually evolves and remains
A type of resistor
The maximum voltage of a circuit
A random fluctuation
Explanation - Attractors (fixed points or cycles) represent stable long‑term behaviors of the network.
Correct answer is: A set of states toward which the system eventually evolves and remains
Q.121 Which of the following best describes ‘elastic net’ regularization used in parameter fitting?
A method that combines L1 (lasso) and L2 (ridge) penalties to prevent over‑fitting and select relevant parameters
A technique to increase the voltage of a circuit
A way to cool the reaction mixture
A method for measuring temperature
Explanation - Elastic net balances sparsity and shrinkage, improving predictive performance in high‑dimensional models.
Correct answer is: A method that combines L1 (lasso) and L2 (ridge) penalties to prevent over‑fitting and select relevant parameters
Q.122 In the context of ‘synthetic quorum sensing’, why is the diffusion coefficient of the autoinducer important?
It determines how quickly the signal spreads through the population, affecting coordination
It sets the voltage across the cell membrane
It changes the color of the culture
It measures the temperature of the incubator
Explanation - Diffusion influences the spatial range and timing of quorum‑sensing communication.
Correct answer is: It determines how quickly the signal spreads through the population, affecting coordination
Q.123 Which of the following best defines the term ‘synthetic lethality’ in a systems biology context?
When two non‑essential genes, when simultaneously knocked out, cause cell death
When a circuit burns out
When temperature rises beyond a threshold
When a protein folds incorrectly
Explanation - Synthetic lethality reveals functional interactions and can be exploited for targeted therapies.
Correct answer is: When two non‑essential genes, when simultaneously knocked out, cause cell death
Q.124 What is the purpose of a ‘delay element’ (e.g., a genetic timer) in a synthetic oscillator?
To provide a time lag that is essential for generating sustained oscillations
To increase the voltage of the circuit
To cool down the reaction
To change the pH of the medium
Explanation - Delays introduce phase shifts that prevent the system from settling at a steady state, enabling rhythmic behavior.
Correct answer is: To provide a time lag that is essential for generating sustained oscillations