Q.1 Which of the following best describes a feedback loop in a gene regulatory network?
A linear chain of genes where each gene activates the next one
A circuit where the output of a gene influences its own expression
A random interaction among unrelated proteins
A permanent repression of all genes in the network
Explanation - A feedback loop occurs when the product of a gene (or its downstream effect) feeds back to regulate its own transcription, either positively or negatively.
Correct answer is: A circuit where the output of a gene influences its own expression
Q.2 In signal processing terms, what does the ‘transfer function’ of a genetic circuit represent?
The number of genes in the circuit
The relationship between input stimulus and output expression level
The speed at which DNA replicates
The amount of ATP consumed by the cell
Explanation - A transfer function maps an input signal (e.g., a transcription factor concentration) to an output (e.g., protein level), analogous to electrical systems.
Correct answer is: The relationship between input stimulus and output expression level
Q.3 Which mathematical tool is commonly used to analyse oscillatory behavior in synthetic gene networks?
Fourier Transform
Laplace Transform
Z-Transform
Wavelet Transform
Explanation - Fourier analysis decomposes periodic gene expression patterns into frequency components, revealing dominant oscillation periods.
Correct answer is: Fourier Transform
Q.4 A repressilator consists of three genes that inhibit each other in a cycle. What type of system does it exemplify?
Linear time‑invariant system
Positive feedback system
Negative feedback ring oscillator
Feed‑forward network
Explanation - Each gene represses the next, creating a closed loop of negative feedback that can generate sustained oscillations.
Correct answer is: Negative feedback ring oscillator
Q.5 In a digital implementation of a gene circuit, which component plays the role of a ‘clock’?
Promoter strength
RNA polymerase concentration
Inducer addition schedule
Plasmid copy number
Explanation - A regular inducer pulse provides a timing reference akin to a clock signal in digital circuits.
Correct answer is: Inducer addition schedule
Q.6 Which of the following is a key difference between analog and digital gene‑circuit designs?
Analog circuits use DNA, digital circuits use RNA.
Analog circuits respond proportionally to input; digital circuits produce discrete ON/OFF states.
Digital circuits require higher temperatures.
Analog circuits cannot be modeled mathematically.
Explanation - Analog gene circuits generate graded responses, whereas digital circuits aim for bistable switches.
Correct answer is: Analog circuits respond proportionally to input; digital circuits produce discrete ON/OFF states.
Q.7 When modeling a gene regulatory network as a set of differential equations, what does the term ‘stiffness’ refer to?
The rigidity of the DNA double helix
Large differences in time scales between variables
The number of genes in the network
The high GC content of promoters
Explanation - Stiff systems have fast and slow dynamics together, requiring specialized numerical solvers.
Correct answer is: Large differences in time scales between variables
Q.8 Which signal processing filter would you use to remove high‑frequency noise from a time‑series of gene expression data?
Low‑pass filter
Band‑stop filter
High‑pass filter
All‑pass filter
Explanation - A low‑pass filter attenuates high‑frequency components, smoothing noisy measurements.
Correct answer is: Low‑pass filter
Q.9 In the context of systems biology, what does the term ‘bifurcation’ describe?
The splitting of DNA strands during replication
A qualitative change in system behavior as a parameter varies
The formation of a protein complex
A type of mutation in the genome
Explanation - Bifurcation points mark transitions such as from steady state to oscillations when a parameter crosses a threshold.
Correct answer is: A qualitative change in system behavior as a parameter varies
Q.10 Which of the following is an example of a feed‑forward loop (FFL) in gene regulation?
Gene A activates Gene B, which then represses Gene A.
Gene X activates Gene Y, and both together activate Gene Z.
Gene M represses Gene N, which in turn activates Gene M.
Gene P produces a protein that degrades its own mRNA.
Explanation - In an FFL, an upstream regulator controls a downstream target both directly and indirectly via an intermediate.
Correct answer is: Gene X activates Gene Y, and both together activate Gene Z.
Q.11 What does the ‘gain’ of a synthetic promoter refer to in a signal‑processing analogy?
The length of the promoter sequence
The amplification factor of transcriptional output per unit of transcription factor input
The number of ribosome binding sites
The stability of the mRNA transcript
Explanation - Gain describes how strongly a promoter responds to its activator, similar to voltage gain in amplifiers.
Correct answer is: The amplification factor of transcriptional output per unit of transcription factor input
Q.12 Which algorithm is commonly used to infer gene regulatory networks from time‑course expression data?
Dijkstra’s shortest‑path algorithm
Kalman filter
K‑means clustering
Breadth‑first search
Explanation - Kalman filters can estimate hidden states and infer dynamic interactions from noisy time‑series data.
Correct answer is: Kalman filter
Q.13 In a Boolean network model of a regulatory system, what does a node value of ‘1’ represent?
Gene is deleted
Gene is expressed (ON)
Gene is mutated
Gene is silent (OFF)
Explanation - Boolean models use binary states: 1 for active/on, 0 for inactive/off.
Correct answer is: Gene is expressed (ON)
Q.14 Which of the following is a characteristic of a ‘robust’ synthetic gene circuit?
It functions only under a narrow temperature range.
Its output is highly sensitive to small parameter variations.
It maintains functionality despite environmental and parametric fluctuations.
It requires a unique inducer that is not available commercially.
Explanation - Robustness means the circuit’s behavior is stable against disturbances.
Correct answer is: It maintains functionality despite environmental and parametric fluctuations.
Q.15 When converting a continuous‑time gene‑regulatory model to a discrete‑time version for simulation, which parameter is essential?
Sampling period (Δt)
Promoter length
GC content
Number of chromosomes
Explanation - The sampling period determines how the continuous dynamics are discretized for numerical integration.
Correct answer is: Sampling period (Δt)
Q.16 What does the term ‘signal‑to‑noise ratio (SNR)’ describe in the analysis of gene‑expression data?
The ratio of coding to non‑coding DNA
The proportion of mRNA to protein
The strength of the biological signal relative to measurement noise
The number of transcription factors per gene
Explanation - A higher SNR means the true expression pattern stands out more clearly from experimental variability.
Correct answer is: The strength of the biological signal relative to measurement noise
Q.17 In a stochastic model of gene expression, which distribution often describes the number of protein molecules produced in a fixed time interval?
Normal distribution
Poisson distribution
Uniform distribution
Exponential distribution
Explanation - Protein synthesis events are discrete and occur independently, leading to a Poisson count distribution under constant rates.
Correct answer is: Poisson distribution
Q.18 Which control strategy is analogous to using a ‘proportional‑integral‑derivative (PID)’ controller in a synthetic gene circuit?
Combining transcriptional activation, repression, and degradation rates to achieve precise set‑point tracking
Adding a fluorescent reporter to monitor expression
Using a constitutive promoter for constant expression
Inserting a ribosome binding site with fixed strength
Explanation - PID control adjusts system output based on present error (proportional), accumulated error (integral), and rate of change (derivative), which can be mimicked by layered genetic components.
Correct answer is: Combining transcriptional activation, repression, and degradation rates to achieve precise set‑point tracking
Q.19 Which of the following best captures the concept of ‘frequency modulation (FM)’ in a synthetic oscillator?
Changing the amplitude of protein expression while keeping period constant
Altering the period of oscillation in response to an external signal
Keeping the period fixed but varying the peak concentration
Switching the circuit off completely
Explanation - In FM, the frequency (inverse of period) of the oscillation encodes information from the input stimulus.
Correct answer is: Altering the period of oscillation in response to an external signal
Q.20 In the context of gene‑regulatory networks, what does the term ‘motif’ refer to?
A DNA sequence that encodes a protein
A recurring small sub‑network pattern with specific functional properties
A type of ribosome
A mutation hotspot
Explanation - Network motifs are statistically over‑represented connection patterns (e.g., feed‑forward loops) that perform distinct regulatory functions.
Correct answer is: A recurring small sub‑network pattern with specific functional properties
Q.21 Which measurement technique provides time‑resolved data suitable for signal‑processing analysis of gene circuits?
Western blot
Fluorescence time‑lapse microscopy
Chromatin immunoprecipitation (ChIP)
DNA sequencing
Explanation - Time‑lapse imaging captures dynamic changes in fluorescence reporters, yielding quantitative time series.
Correct answer is: Fluorescence time‑lapse microscopy
Q.22 When a synthetic gene circuit displays bistability, which mathematical representation typically explains this behavior?
A single linear differential equation
A hysteresis curve derived from a nonlinear transfer function with positive feedback
A Poisson distribution of mRNA counts
A purely stochastic Gillespie simulation without deterministic terms
Explanation - Positive feedback can create two stable steady states, shown as a hysteresis loop in the input‑output plot.
Correct answer is: A hysteresis curve derived from a nonlinear transfer function with positive feedback
Q.23 What is the primary purpose of adding a degradation tag (e.g., ssrA) to a protein in a synthetic circuit?
Increase protein folding efficiency
Accelerate protein turnover to fine‑tune dynamic response
Make the protein fluorescent
Prevent transcription of the gene
Explanation - Degradation tags shorten protein half‑life, allowing faster resetting of circuit states.
Correct answer is: Accelerate protein turnover to fine‑tune dynamic response
Q.24 Which of the following describes a ‘phase‑locked loop’ (PLL) concept applied to a biological oscillator?
A circuit that locks the amplitude of oscillations to a constant value
A system that synchronizes the phase of a genetic oscillator to an external periodic signal
A device that measures the pH of the growth medium
A method for sequencing DNA
Explanation - PLL in biology would adjust the oscillator’s phase to match an imposed rhythm, similar to electronic PLLs.
Correct answer is: A system that synchronizes the phase of a genetic oscillator to an external periodic signal
Q.25 In a gene‑regulatory network modeled as a weighted directed graph, what do the edge weights typically represent?
Physical distance between genes on the chromosome
Strength and type (activation/repression) of regulatory influence
Number of introns in a gene
GC content of the promoter
Explanation - Weighted edges quantify how strongly one gene influences another, often with sign indicating activation (+) or repression (−).
Correct answer is: Strength and type (activation/repression) of regulatory influence
Q.26 Which signal‑processing concept helps in detecting sudden changes (e.g., transcriptional bursts) in noisy gene‑expression data?
Low‑pass filtering
Edge detection using derivative operators
Amplitude modulation
Phase shifting
Explanation - Taking the derivative highlights rapid transitions, allowing burst detection amidst noise.
Correct answer is: Edge detection using derivative operators
Q.27 What does the term ‘orthogonal’ mean when describing two synthetic promoters used in the same cell?
They share the same transcription factor.
They respond to completely independent transcription factors without cross‑talk.
They are located on different chromosomes.
They have identical strength.
Explanation - Orthogonal promoters enable independent control of separate pathways.
Correct answer is: They respond to completely independent transcription factors without cross‑talk.
Q.28 Which of the following is a typical method to reduce cross‑talk between signaling pathways in engineered cells?
Using ribosome binding sites with high GC content
Employing synthetic insulator sequences between transcriptional units
Increasing the copy number of all plasmids
Adding extra magnesium to the growth medium
Explanation - Insulators prevent unintended interactions by blocking transcriptional read‑through and enhancer effects.
Correct answer is: Employing synthetic insulator sequences between transcriptional units
Q.29 In a system‑identification experiment, which approach estimates the parameters of a gene‑regulatory model from input‑output data?
Monte Carlo simulation
Least‑squares regression
Southern blotting
Gel electrophoresis
Explanation - Least‑squares minimizes the error between observed and predicted outputs, fitting model parameters.
Correct answer is: Least‑squares regression
Q.30 Which of the following best illustrates the concept of ‘frequency response’ in a synthetic gene circuit?
Measuring how the circuit’s output amplitude changes when the input inducer is applied at different periodicities
Counting the number of genes in the circuit
Sequencing the DNA of the circuit
Measuring the temperature dependence of the promoter
Explanation - Frequency response characterizes the circuit’s ability to follow inputs of varying frequencies.
Correct answer is: Measuring how the circuit’s output amplitude changes when the input inducer is applied at different periodicities
Q.31 In the context of regulatory networks, what does ‘crosstalk’ refer to?
Interaction between unrelated pathways leading to unintended regulation
The process of transcription initiation
The formation of ribosomes
DNA replication errors
Explanation - Crosstalk is when components of one signaling route affect another, compromising specificity.
Correct answer is: Interaction between unrelated pathways leading to unintended regulation
Q.32 A synthetic toggle switch consists of two mutually repressing genes. Which property is essential for its operation?
Both promoters must be constitutive.
Each gene must have a strong degradation tag.
The repression must be sufficiently strong to create two stable states.
The circuit must be placed on a high‑copy plasmid.
Explanation - Strong mutual repression yields bistability, allowing the system to reside in either of two states.
Correct answer is: The repression must be sufficiently strong to create two stable states.
Q.33 Which computational method is widely used to simulate stochastic gene expression at the single‑molecule level?
Euler method
Gillespie algorithm
Fast Fourier Transform
Newton‑Raphson method
Explanation - The Gillespie stochastic simulation algorithm exactly captures random reaction events in small populations.
Correct answer is: Gillespie algorithm
Q.34 When analyzing a time‑series of protein concentration, which metric quantifies the regularity of oscillations?
Mean absolute error
Coefficient of variation of inter‑peak intervals
GC content
Melting temperature
Explanation - A low CV indicates consistent period lengths, reflecting regular oscillations.
Correct answer is: Coefficient of variation of inter‑peak intervals
Q.35 In an electronic analogy, what does the ‘capacitance’ of a promoter correspond to?
The promoter’s ability to store transcription factor molecules temporarily
The number of introns in the gene
The length of the coding sequence
The speed of ribosome movement
Explanation - Capacitance reflects how a promoter can buffer TF binding, analogous to charge storage in a capacitor.
Correct answer is: The promoter’s ability to store transcription factor molecules temporarily
Q.36 Which of the following design strategies helps achieve a ‘sharp’ switch‑like response in a gene circuit?
Using a weak ribosome binding site
Incorporating cooperative binding (Hill coefficient > 1)
Increasing the mRNA degradation rate
Reducing the plasmid copy number
Explanation - Cooperativity creates a sigmoidal response, making the transition between OFF and ON abrupt.
Correct answer is: Incorporating cooperative binding (Hill coefficient > 1)
Q.37 Which of the following is a common method to quantify the information capacity (bits) of a transcriptional channel?
Shannon entropy calculation from input‑output probability distributions
Measuring the length of the gene
Counting the number of exons
Determining the molecular weight of the protein
Explanation - Information theory quantifies how many distinct input states can be reliably distinguished at the output.
Correct answer is: Shannon entropy calculation from input‑output probability distributions
Q.38 In a synthetic gene network, what is the effect of introducing a delay element (e.g., a long untranslated region) between transcription and translation?
It speeds up the response time.
It creates a time delay that can promote oscillations or improve stability.
It eliminates noise completely.
It doubles the protein production rate.
Explanation - Delays add phase lag, which can be harnessed to generate sustained oscillations or buffer fluctuations.
Correct answer is: It creates a time delay that can promote oscillations or improve stability.
Q.39 Which type of synthetic promoter architecture would you use to implement an AND logic gate at the transcriptional level?
A promoter with two binding sites that both must be occupied for activation
A promoter with a single strong binding site
A promoter that is always constitutively active
A promoter that responds to temperature only
Explanation - Both inputs must be present to recruit RNA polymerase, fulfilling AND logic.
Correct answer is: A promoter with two binding sites that both must be occupied for activation
Q.40 When a gene circuit is subjected to a sinusoidal inducer input, what does the term ‘phase lag’ describe?
The delay between the peak of the input signal and the peak of the output response
The amplitude of the output signal
The total number of genes in the circuit
The temperature at which the circuit operates
Explanation - Phase lag measures how far the output is shifted in time relative to the input waveform.
Correct answer is: The delay between the peak of the input signal and the peak of the output response
Q.41 Which of the following best explains why a high‑pass filter might be useful when analyzing single‑cell expression spikes?
It removes the low‑frequency baseline drift, highlighting rapid transient spikes.
It amplifies the overall signal amplitude.
It converts the signal to a binary format.
It reduces the number of cells needed for the experiment.
Explanation - High‑pass filtering suppresses slow trends, making quick events more visible.
Correct answer is: It removes the low‑frequency baseline drift, highlighting rapid transient spikes.
Q.42 In a synthetic network, which parameter most directly influences the system’s ‘bandwidth’—the range of input frequencies it can follow?
Promoter strength
Protein degradation rate
Plasmid copy number
GC content of the gene
Explanation - Faster degradation allows quicker turnover, enabling the circuit to track higher‑frequency inputs.
Correct answer is: Protein degradation rate
Q.43 What is the purpose of a ‘reporter gene’ (e.g., GFP) in signal‑processing experiments with synthetic circuits?
To provide a measurable output that reflects circuit activity
To increase the speed of transcription
To act as a transcription factor
To degrade unwanted proteins
Explanation - Reporters translate internal states into detectable fluorescence or luminescence signals.
Correct answer is: To provide a measurable output that reflects circuit activity
Q.44 Which concept from control theory describes the ability of a gene circuit to return to its steady state after a disturbance?
Gain margin
Stability
Bandwidth
Noise floor
Explanation - Stability ensures that perturbations decay and the system settles back to its equilibrium.
Correct answer is: Stability
Q.45 In a Boolean model, the update rule for gene A is A(t+1) = NOT B(t) AND C(t). If B=1 and C=1 at time t, what is A at time t+1?
0
1
Undefined
Depends on initial conditions
Explanation - NOT B(t) = 0; 0 AND 1 = 0, so A(t+1)=0.
Correct answer is: 0
Q.46 Which of the following describes ‘noise attenuation’ in a gene network?
Increasing transcriptional burst size
Implementing negative feedback loops
Using a weaker ribosome binding site
Adding extra copies of the gene
Explanation - Negative feedback reduces variability by counteracting fluctuations.
Correct answer is: Implementing negative feedback loops
Q.47 What is the typical unit for measuring the rate constant of transcription (k_tx) in deterministic models?
Molecules per minute
Moles per liter per second (M·s⁻¹)
Seconds (s)
Milligrams per milliliter
Explanation - Transcription rates are often expressed as the number of mRNA molecules produced per unit time.
Correct answer is: Molecules per minute
Q.48 Which of the following best captures the idea of ‘modularity’ in synthetic biology?
Designing parts that can be combined and reused without affecting each other’s function
Using only one promoter per circuit
Placing all genes on a single operon
Ensuring the circuit works only in one host strain
Explanation - Modular parts facilitate predictable assembly and scaling of complex designs.
Correct answer is: Designing parts that can be combined and reused without affecting each other’s function
Q.49 When performing a sensitivity analysis on a gene‑regulatory model, what is being evaluated?
How changes in parameter values affect model output
The sequence similarity between genes
The number of cells in the culture
The temperature dependence of enzyme activity
Explanation - Sensitivity analysis identifies which parameters most influence system behavior.
Correct answer is: How changes in parameter values affect model output
Q.50 In a synthetic gene circuit, what role does an ‘insulator’ sequence typically play?
It enhances transcriptional activation.
It blocks unintended regulatory interactions between adjacent genetic parts.
It speeds up translation.
It adds fluorescence to the protein.
Explanation - Insulators prevent promoter or enhancer spill‑over, preserving part independence.
Correct answer is: It blocks unintended regulatory interactions between adjacent genetic parts.
Q.51 Which mathematical model is most appropriate for describing the average behavior of a large population of cells with a synthetic circuit?
Stochastic Gillespie simulation
Deterministic ordinary differential equations (ODEs)
Monte Carlo integration
Binary decision trees
Explanation - ODEs capture mean dynamics when fluctuations average out across many cells.
Correct answer is: Deterministic ordinary differential equations (ODEs)
Q.52 In the context of signal processing, what does ‘aliasing’ refer to when sampling gene‑expression data at insufficient frequency?
The loss of high‑frequency information that appears as low‑frequency artifacts
The duplication of DNA sequences
The increase in protein stability
The formation of protein aggregates
Explanation - Aliasing occurs when sampling below the Nyquist rate, causing distortion of the true signal.
Correct answer is: The loss of high‑frequency information that appears as low‑frequency artifacts
Q.53 A synthetic network uses a ‘quorum‑sensing’ module to coordinate behavior across cells. Which signal processing concept does this resemble?
Centralized control
Distributed consensus filtering
Low‑pass filtering
Phase modulation
Explanation - Quorum sensing aggregates information from many cells to reach a shared decision, similar to consensus algorithms.
Correct answer is: Distributed consensus filtering
Q.54 Which of the following is a common metric for evaluating the performance of a synthetic biosensor?
Dynamic range (fold‑change between OFF and ON states)
Number of introns
Plasmid size in kilobases
GC content of the coding sequence
Explanation - Dynamic range quantifies how distinctly a sensor can discriminate between low and high inputs.
Correct answer is: Dynamic range (fold‑change between OFF and ON states)
Q.55 Which of these strategies helps to linearize a highly nonlinear gene‑expression response?
Introduce cooperative binding
Add a negative feedback loop with a proportional controller
Increase the promoter copy number
Use a stronger ribosome binding site
Explanation - Feedback can flatten the input‑output curve, making the response more linear.
Correct answer is: Add a negative feedback loop with a proportional controller
Q.56 What does the term ‘time‑delay differential equation’ (DDE) indicate in modeling gene circuits?
The system has no delays.
The rate of change depends on past states of the system.
The system is purely stochastic.
The model uses only algebraic equations.
Explanation - DDEs incorporate explicit delays, reflecting processes like transcription‑translation lag.
Correct answer is: The rate of change depends on past states of the system.
Q.57 In a synthetic gene circuit, which element functions analogously to a ‘capacitor’ that stores charge?
A transcription factor that binds and unbinds DNA
A degradation tag
A constitutive promoter
An origin of replication
Explanation - Binding stores the TF in a bound state, releasing it later, akin to charge storage.
Correct answer is: A transcription factor that binds and unbinds DNA
Q.58 When fitting a Hill function to experimental data, a Hill coefficient (n) of 4 indicates:
No cooperativity
Positive cooperativity with a steep response
Negative cooperativity
Linear response
Explanation - Higher n values create sharper, sigmoidal input‑output relationships.
Correct answer is: Positive cooperativity with a steep response
Q.59 Which of the following best describes a ‘push‑pull’ architecture in synthetic biology?
A circuit where one gene activates while another represses the same target, providing rapid response and noise reduction
Two genes that are always co‑expressed
A system that only works in anaerobic conditions
A design that uses only constitutive promoters
Explanation - Push‑pull combines opposing actions to enhance dynamic range and stability.
Correct answer is: A circuit where one gene activates while another represses the same target, providing rapid response and noise reduction
Q.60 What is the main advantage of using a microfluidic device for testing synthetic gene networks?
It allows precise temporal control of inducer concentrations, enabling dynamic signal‑processing experiments.
It increases the temperature of the culture.
It reduces the need for DNA sequencing.
It eliminates the need for promoters.
Explanation - Microfluidics can generate programmable waveforms of chemicals to probe circuit dynamics.
Correct answer is: It allows precise temporal control of inducer concentrations, enabling dynamic signal‑processing experiments.
Q.61 Which term describes the phenomenon where a synthetic circuit’s output becomes less variable as the number of cells increases?
Stochastic resonance
Law of large numbers
Cooperativity
Hysteresis
Explanation - Averaging over many independent stochastic events reduces relative fluctuations.
Correct answer is: Law of large numbers
Q.62 In an electronic filter analogy, what does a ‘band‑pass filter’ achieve when applied to gene‑expression time series?
It isolates oscillations within a specific frequency band, removing both low‑frequency drift and high‑frequency noise.
It amplifies all frequencies equally.
It blocks all signals.
It converts the signal to a binary output.
Explanation - Band‑pass filtering retains only the desired frequency range, useful for studying specific rhythmic behaviors.
Correct answer is: It isolates oscillations within a specific frequency band, removing both low‑frequency drift and high‑frequency noise.
Q.63 Which of the following is a typical signature of a Hopf bifurcation in a gene‑regulatory model?
Transition from a stable steady state to sustained oscillations as a parameter crosses a critical value
Sudden disappearance of all proteins
Increase in DNA replication speed
Formation of a double helix
Explanation - A Hopf bifurcation creates a limit cycle, leading to periodic behavior.
Correct answer is: Transition from a stable steady state to sustained oscillations as a parameter crosses a critical value
Q.64 When designing a synthetic network for information processing, why is it important to minimize ‘retroactivity’?
Retroactivity causes unwanted loading effects that alter the behavior of upstream modules.
Retroactivity increases plasmid copy number.
Retroactivity speeds up transcription.
Retroactivity makes proteins fluorescent.
Explanation - Retroactivity is the feedback effect of downstream loads on upstream dynamics, compromising modularity.
Correct answer is: Retroactivity causes unwanted loading effects that alter the behavior of upstream modules.
Q.65 What does the term ‘dead‑time’ refer to in the context of a delayed negative feedback loop?
The period during which the system cannot respond to new inputs because it is processing a previous signal
The time required for DNA replication
The duration of the cell cycle
The time needed for protein folding
Explanation - Dead‑time introduces a latency that can affect stability and oscillation characteristics.
Correct answer is: The period during which the system cannot respond to new inputs because it is processing a previous signal
Q.66 In a synthetic circuit, which type of regulator would you use to implement a NOT gate?
A repressor that blocks transcription when present
An activator that enhances transcription
A ribosome that translates mRNA
A polymerase that synthesizes DNA
Explanation - A repressor inverts the input signal, delivering a logical NOT operation.
Correct answer is: A repressor that blocks transcription when present
Q.67 Which statistical test would be appropriate for comparing the mean fluorescence intensity of two engineered strains?
Student’s t‑test
Chi‑square test
Kolmogorov‑Smirnov test for distributions
ANOVA with more than two groups
Explanation - The t‑test assesses whether two independent sample means differ significantly.
Correct answer is: Student’s t‑test
Q.68 When a synthetic network includes an incoherent feed‑forward loop (type‑1), what dynamic behavior is typically observed?
Pulse‑like transient response followed by adaptation to baseline
Sustained high expression
Complete shutdown of the circuit
Linear increase over time
Explanation - Incoherent FFLs generate a fast activation and a delayed repression, producing a pulse.
Correct answer is: Pulse‑like transient response followed by adaptation to baseline
Q.69 Which of the following best describes the role of ‘noise shaping’ in synthetic biology?
Altering the spectrum of stochastic fluctuations to move noise out of the frequency band of interest
Increasing the temperature of the culture
Adding extra ribosome binding sites
Sequencing the genome
Explanation - Noise shaping redistributes variance, making critical frequencies quieter.
Correct answer is: Altering the spectrum of stochastic fluctuations to move noise out of the frequency band of interest
Q.70 In the design of a synthetic gene circuit, what is the purpose of a ‘spacer’ sequence between regulatory elements?
To provide physical distance that reduces unintended interactions
To increase transcription speed
To encode a fluorescent protein
To act as a replication origin
Explanation - Spacers separate elements, limiting steric hindrance and cross‑talk.
Correct answer is: To provide physical distance that reduces unintended interactions
Q.71 Which of the following is a hallmark of a chaotic regime in a gene‑regulatory network?
Sensitive dependence on initial conditions leading to unpredictable long‑term behavior
Strict periodic oscillations with a fixed period
A single stable steady state
Linear increase of protein concentration over time
Explanation - Chaos is characterized by aperiodic, deterministic dynamics that are highly sensitive to tiny perturbations.
Correct answer is: Sensitive dependence on initial conditions leading to unpredictable long‑term behavior
Q.72 When modeling gene expression with a transfer function H(s) = K/(τs+1), what does the parameter τ represent?
The time constant governing the speed of response
The maximum protein concentration
The number of promoter binding sites
The GC content of the promoter
Explanation - τ sets how quickly the system reacts to changes in input, analogous to an RC time constant.
Correct answer is: The time constant governing the speed of response
Q.73 Which of the following is a common way to implement a ‘digital’ output in a synthetic gene circuit?
Designing a bistable switch that yields high or low expression states
Using a constitutive weak promoter
Increasing plasmid copy number
Adding a long untranslated region
Explanation - Bistable circuits produce discrete ON/OFF outputs, analogous to digital logic.
Correct answer is: Designing a bistable switch that yields high or low expression states
Q.74 In the context of signal processing, what does ‘filter order’ refer to?
The number of poles or zeros in the filter’s transfer function, affecting steepness of roll‑off
The number of genes in the circuit
The length of the DNA sequence
The temperature at which the filter operates
Explanation - Higher order filters have sharper cutoffs, providing better separation of frequency components.
Correct answer is: The number of poles or zeros in the filter’s transfer function, affecting steepness of roll‑off
Q.75 Which technique would you use to directly measure the concentration of a transcription factor in a living cell over time?
Fluorescence resonance energy transfer (FRET) sensor
Southern blot
PCR amplification
Mass spectrometry of cell lysate
Explanation - FRET‑based biosensors can report real‑time TF levels in vivo via fluorescence changes.
Correct answer is: Fluorescence resonance energy transfer (FRET) sensor
Q.76 What is the main benefit of using a ‘feed‑forward compensation’ strategy in a synthetic circuit?
It reduces the delay between input and output, improving response speed without sacrificing stability.
It increases the size of the plasmid.
It eliminates the need for a promoter.
It makes the circuit temperature‑independent.
Explanation - Feed‑forward paths anticipate changes, allowing quicker correction of disturbances.
Correct answer is: It reduces the delay between input and output, improving response speed without sacrificing stability.
Q.77 In a synthetic gene network, which component would you modify to change the circuit’s ‘cut‑off frequency’?
Protein degradation rate
Number of introns
GC content of the coding sequence
Plasmid origin of replication
Explanation - Faster degradation reduces the system’s memory, raising the frequency at which it can follow inputs.
Correct answer is: Protein degradation rate
Q.78 Which of the following best describes the effect of ‘coherent feed‑forward loops’ on signal dynamics?
They act as sign‑preserving filters that can delay activation or create pulse‑shaping behavior.
They always produce negative feedback.
They completely block signal transmission.
They cause immediate degradation of the signal.
Explanation - Coherent FFLs preserve the sign of the signal and can introduce a time delay or acceleration.
Correct answer is: They act as sign‑preserving filters that can delay activation or create pulse‑shaping behavior.
Q.79 When a synthetic oscillator is subjected to external periodic forcing, the phenomenon where the oscillator locks to the forcing frequency is called:
Entrainment
Resonance
Damping
Saturation
Explanation - Entrainment aligns the internal rhythm with an external periodic signal.
Correct answer is: Entrainment
Q.80 Which of the following is a typical characteristic of a ‘digital‑to‑analog converter’ (DAC) implemented with a gene circuit?
A series of promoters with graded strengths that sum to produce a continuous output level
A single constitutive promoter
A plasmid that replicates at a constant rate
A ribosome that translates at a fixed speed
Explanation - Combining multiple binary inputs via weighted promoters yields an analog output.
Correct answer is: A series of promoters with graded strengths that sum to produce a continuous output level
Q.81 In a gene regulatory network, the Jacobian matrix evaluated at a steady state is used to:
Determine the local stability of that steady state
Calculate the GC content of promoters
Measure protein half‑life
Sequence the genome
Explanation - Eigenvalues of the Jacobian reveal whether perturbations grow or decay near the equilibrium.
Correct answer is: Determine the local stability of that steady state
Q.82 Which of the following best explains why a synthetic circuit may exhibit ‘bursting’ transcriptional dynamics?
Stochastic switching of promoter states between active and inactive configurations
Constant high temperature
Uniform plasmid copy number
Absence of ribosome binding sites
Explanation - Promoter toggling creates periods of high activity (bursts) interspersed with silence.
Correct answer is: Stochastic switching of promoter states between active and inactive configurations
Q.83 When constructing a synthetic network to perform logical NAND operation, which minimal set of genetic parts is sufficient?
Two repressors that each inhibit a common downstream promoter; output is ON only when at least one repressor is absent.
Two activators that both must be present.
A single constitutive promoter.
A single repressor and a single activator acting on unrelated genes.
Explanation - NAND is true unless both inputs are true; two repressors provide that logic by suppressing output only when both are present.
Correct answer is: Two repressors that each inhibit a common downstream promoter; output is ON only when at least one repressor is absent.
Q.84 Which method allows the estimation of time‑varying parameters in a gene‑regulatory model from experimental data?
Recursive least squares (RLS) algorithm
Southern blotting
Sanger sequencing
Western blot
Explanation - RLS updates parameter estimates online as new data arrive, suitable for time‑varying systems.
Correct answer is: Recursive least squares (RLS) algorithm
Q.85 In a synthetic biology context, what does the term ‘load’ refer to?
The consumption of cellular resources (e.g., ribosomes, ATP) by an introduced circuit
The physical weight of a petri dish
The number of genes on a chromosome
The temperature of the incubator
Explanation - Load represents the burden placed on the host cell, which can affect growth and circuit performance.
Correct answer is: The consumption of cellular resources (e.g., ribosomes, ATP) by an introduced circuit
Q.86 Which of the following best characterizes a ‘low‑pass’ synthetic filter in a gene network?
It allows slowly varying signals to pass while attenuating rapid fluctuations
It blocks all signals.
It amplifies high‑frequency noise.
It inverts the input signal.
Explanation - Low‑pass behavior smooths out fast noise, preserving the underlying trend.
Correct answer is: It allows slowly varying signals to pass while attenuating rapid fluctuations
Q.87 When a synthetic circuit is designed to operate as a ‘band‑stop’ filter, what is the intended effect on the input signal?
Suppress a specific range of frequencies while passing both lower and higher frequencies
Amplify all frequencies equally
Convert the signal to a binary code
Delay the signal indefinitely
Explanation - Band‑stop (notch) filters reject a narrow frequency band, useful for removing periodic disturbances.
Correct answer is: Suppress a specific range of frequencies while passing both lower and higher frequencies
Q.88 Which of the following is a typical use of a ‘timer’ module in synthetic biology?
To generate a defined delay between the activation of two genes
To increase the transcription rate indefinitely
To reduce the cell’s growth rate
To change the DNA sequence spontaneously
Explanation - Timer modules (e.g., using degradation tags or RNA cascades) introduce programmable temporal gaps.
Correct answer is: To generate a defined delay between the activation of two genes
Q.89 In a stochastic simulation of gene expression, which factor most directly influences the variance of protein numbers?
Burst size and frequency
The length of the DNA double helix
The number of nucleotides in the promoter
The pH of the growth medium
Explanation - Larger or more frequent transcriptional bursts increase variability in protein counts.
Correct answer is: Burst size and frequency
Q.90 Which of the following statements about ‘coherence resonance’ in gene circuits is true?
Intermediate levels of noise can enhance the regularity of oscillations.
Increasing noise always destroys oscillations.
Coherence resonance only occurs in deterministic models.
It requires external periodic forcing.
Explanation - Coherence resonance describes noise‑induced ordering where optimal noise amplitude maximizes periodicity.
Correct answer is: Intermediate levels of noise can enhance the regularity of oscillations.
Q.91 When modeling a synthetic circuit with a set of linear time‑invariant (LTI) equations, which property guarantees that superposition holds?
Linearity and time invariance
Stochasticity
Non‑linearity
Presence of delays
Explanation - LTI systems obey the principle of superposition, allowing independent analysis of input components.
Correct answer is: Linearity and time invariance
Q.92 What does the term ‘gain‑bandwidth product’ refer to in the design of a synthetic analog filter?
A constant that quantifies the trade‑off between amplification (gain) and the range of frequencies (bandwidth) the filter can handle
The number of genes in the circuit
The length of the promoter sequence
The temperature at which the circuit operates
Explanation - Higher gain typically reduces bandwidth; the product often remains approximately constant for a given filter topology.
Correct answer is: A constant that quantifies the trade‑off between amplification (gain) and the range of frequencies (bandwidth) the filter can handle
Q.93 In a synthetic gene network, which component can be used to implement a ‘memory’ element that stores past input states?
A bistable toggle switch
A constitutive promoter
A ribosome binding site
A plasmid origin of replication
Explanation - Toggle switches retain their state after the input is removed, acting as binary memory.
Correct answer is: A bistable toggle switch
Q.94 Which of the following best describes the effect of increasing the Hill coefficient from 1 to 3 in a gene‑activation function?
The response becomes more ultrasensitive, with a steeper transition from low to high expression.
The promoter becomes weaker.
The gene is expressed constitutively.
The mRNA half‑life is extended.
Explanation - Higher Hill coefficients increase cooperativity, sharpening the input‑output curve.
Correct answer is: The response becomes more ultrasensitive, with a steeper transition from low to high expression.
Q.95 When analyzing a synthetic circuit’s response to a step input, the ‘rise time’ is defined as:
The time required for the output to go from 10% to 90% of its final steady‑state value
The duration of the experiment
The time needed to synthesize DNA
The half‑life of the protein
Explanation - Rise time quantifies how quickly a system reacts to a sudden change.
Correct answer is: The time required for the output to go from 10% to 90% of its final steady‑state value
Q.96 Which of the following design principles helps to reduce ‘retroactivity’ when connecting two genetic modules?
Insertion of an insulating buffer (e.g., a phosphorylation‑based signal transducer) between modules
Using a stronger promoter for the upstream module
Increasing the copy number of the downstream module
Removing ribosome binding sites
Explanation - Buffers decouple the dynamics of linked modules, limiting load‑induced feedback.
Correct answer is: Insertion of an insulating buffer (e.g., a phosphorylation‑based signal transducer) between modules
Q.97 In a synthetic circuit, a ‘pulse‑generator’ can be realized by:
An incoherent feed‑forward loop where activation is fast and repression is delayed
A constitutive promoter driving constant expression
A single repressor without any activator
A plasmid with high copy number only
Explanation - The fast activation creates a spike, while delayed repression shuts it off, forming a pulse.
Correct answer is: An incoherent feed‑forward loop where activation is fast and repression is delayed
Q.98 Which of the following best defines the ‘cut‑off frequency’ of a low‑pass filter implemented in a gene network?
The frequency at which the output amplitude falls to 70.7% (−3 dB) of the input amplitude
The number of genes in the circuit
The temperature at which the filter operates
The GC content of the promoter
Explanation - The cut‑off frequency marks the transition between pass‑band and stop‑band for a filter.
Correct answer is: The frequency at which the output amplitude falls to 70.7% (−3 dB) of the input amplitude
Q.99 When performing a Monte‑Carlo analysis of a synthetic gene network, what is the primary purpose?
To assess how parameter uncertainties propagate to output variability
To sequence the genome
To measure cell density
To count the number of plasmids
Explanation - Monte‑Carlo simulations sample parameter space repeatedly to evaluate robustness.
Correct answer is: To assess how parameter uncertainties propagate to output variability
Q.100 Which of the following is an example of a ‘negative‑feedback with integral control’ in a synthetic circuit?
A repressor that senses the accumulated protein level and reduces its own production proportionally to the integral of the error
A constitutive promoter that always drives expression
An activator that enhances its own transcription without delay
A gene that produces a fluorescent protein only once
Explanation - Integral control integrates error over time, eliminating steady‑state offset, and combined with negative feedback yields robust regulation.
Correct answer is: A repressor that senses the accumulated protein level and reduces its own production proportionally to the integral of the error
Q.101 Which of the following best describes the role of ‘diauxic shift’ in the context of synthetic biology experiments?
A change in metabolic state that can affect the performance of engineered circuits, requiring careful timing of inducer addition
A method for measuring fluorescence
A type of DNA sequencing technology
A way to increase plasmid copy number
Explanation - Diauxic shifts alter resource allocation, influencing circuit behavior and load.
Correct answer is: A change in metabolic state that can affect the performance of engineered circuits, requiring careful timing of inducer addition
Q.102 In a synthetic gene network, what does the term ‘orthogonal ribosome’ refer to?
A ribosome engineered to recognize a distinct ribosome binding site, minimizing competition with native translation machinery
A ribosome that only works at high temperature
A ribosome that degrades mRNA
A ribosome that replicates DNA
Explanation - Orthogonal ribosomes reduce translational crosstalk, improving modularity.
Correct answer is: A ribosome engineered to recognize a distinct ribosome binding site, minimizing competition with native translation machinery
Q.103 Which metric is most appropriate for quantifying the speed‑accuracy trade‑off in a synthetic decision‑making circuit?
Mean decision time versus error rate (ROC‑type analysis)
Plasmid copy number
GC content
Cellular ATP concentration
Explanation - Plotting speed versus accuracy reveals how quickly a circuit can reach a correct decision.
Correct answer is: Mean decision time versus error rate (ROC‑type analysis)
Q.104 When a synthetic network is engineered to implement a ‘band‑pass’ filter, which configuration is typically used?
Cascading a high‑pass filter followed by a low‑pass filter
Using a single constitutive promoter
Adding only a negative feedback loop
Removing all regulatory interactions
Explanation - A band‑pass passes frequencies within a specific range by combining high‑ and low‑pass characteristics.
Correct answer is: Cascading a high‑pass filter followed by a low‑pass filter
Q.105 Which of the following best explains why ‘parameter identifiability’ is crucial when fitting models to experimental data?
It ensures that each parameter can be uniquely determined from the available data, preventing ambiguous fits.
It speeds up DNA replication.
It increases the fluorescence intensity.
It changes the cell wall composition.
Explanation - Identifiable parameters give confidence that model predictions reflect true system behavior.
Correct answer is: It ensures that each parameter can be uniquely determined from the available data, preventing ambiguous fits.