Q.1 What does the acronym FBA stand for in constraint-based modeling?
Flux Balance Analysis
Functional Binary Approximation
Fast Bifurcation Algorithm
Finite Basis Algebra
Explanation - FBA is the most common constraint‑based method used to predict steady‑state flux distributions in metabolic networks.
Correct answer is: Flux Balance Analysis
Q.2 In a stoichiometric matrix S, what do the rows represent?
Metabolites
Reactions
Genes
Enzymes
Explanation - Each row corresponds to a metabolite, while columns correspond to reactions.
Correct answer is: Metabolites
Q.3 Which of the following is a typical objective function used in FBA for a growing cell?
Maximizing ATP production
Minimizing oxygen uptake
Maximizing biomass synthesis
Minimizing glucose uptake
Explanation - Biomass synthesis is a proxy for cell growth and is commonly maximized in FBA models of microbes.
Correct answer is: Maximizing biomass synthesis
Q.4 What constraint ensures mass balance in a constraint‑based model?
S·v = 0
v ≥ 0
v ≤ ub
v ≥ lb
Explanation - The equation S·v = 0 enforces that the production and consumption rates of each metabolite balance out at steady state.
Correct answer is: S·v = 0
Q.5 In a metabolic model, a reversible reaction is represented by:
A single column with bounds [-1000, 1000]
Two separate forward and reverse reactions
A column with bounds [0, 1000]
A column with bounds [0, 0]
Explanation - Reversible reactions have both positive and negative flux limits, allowing flux in either direction.
Correct answer is: A single column with bounds [-1000, 1000]
Q.6 Which software package is widely used for performing constraint‑based modeling?
COBRA Toolbox
MATLAB Simulink
LTspice
ANSYS Fluent
Explanation - The COBRA (COnstraints-Based Reconstruction and Analysis) Toolbox provides functions for building and analyzing metabolic models.
Correct answer is: COBRA Toolbox
Q.7 What does the term 'shadow price' refer to in FBA sensitivity analysis?
The cost of a metabolite in the objective function
The dual value associated with a constraint
The price of buying simulation software
The price of electricity in a power grid
Explanation - Shadow prices indicate how much the objective would improve per unit increase in a constraint’s bound.
Correct answer is: The dual value associated with a constraint
Q.8 When performing Flux Variability Analysis (FVA), what is being calculated?
The range of possible fluxes for each reaction while keeping the objective optimal
The variance of metabolite concentrations over time
The standard deviation of gene expression levels
The electrical resistance of a circuit
Explanation - FVA determines the minimum and maximum allowable flux through each reaction without decreasing the optimal objective value.
Correct answer is: The range of possible fluxes for each reaction while keeping the objective optimal
Q.9 In a constraint‑based model, which parameter is typically set to a very large positive number to simulate an effectively unbounded reaction?
Upper bound (ub)
Lower bound (lb)
Stoichiometric coefficient
Objective coefficient
Explanation - A large ub (e.g., 1000) allows the reaction to carry as much flux as needed, limited only by other constraints.
Correct answer is: Upper bound (ub)
Q.10 Which of the following best describes the 'gap-filling' step in model reconstruction?
Adding reactions to enable growth under defined conditions
Removing dead‑end metabolites
Optimizing the objective function
Measuring intracellular metabolite concentrations
Explanation - Gap-filling introduces missing reactions that allow the model to produce essential biomass components.
Correct answer is: Adding reactions to enable growth under defined conditions
Q.11 A dead‑end metabolite in a metabolic network is:
A metabolite that is only produced or only consumed
A metabolite with zero molecular weight
A metabolite that cannot cross the membrane
A metabolite with a negative Gibbs free energy
Explanation - Dead‑ends have no balancing reactions, causing infeasibility unless resolved.
Correct answer is: A metabolite that is only produced or only consumed
Q.12 Which linear programming method is commonly used to solve FBA problems?
Simplex algorithm
Newton‑Raphson method
Fast Fourier Transform
Monte Carlo simulation
Explanation - FBA is a linear programming problem; the simplex method efficiently finds the optimal solution.
Correct answer is: Simplex algorithm
Q.13 In a constraint‑based model, the term 'exchange reaction' refers to:
A reaction that imports or exports metabolites between the system and the environment
A reaction that swaps two metabolites inside the cell
A reversible enzymatic step
A reaction that consumes ATP
Explanation - Exchange reactions model transport of metabolites across the system boundary, allowing nutrient uptake and product secretion.
Correct answer is: A reaction that imports or exports metabolites between the system and the environment
Q.14 What is the typical purpose of setting a lower bound of zero for a reaction in FBA?
To make the reaction irreversible in the forward direction
To allow negative flux values
To disable the reaction
To enforce a maximal flux
Explanation - A lower bound of 0 prevents the reaction from carrying flux in the reverse direction.
Correct answer is: To make the reaction irreversible in the forward direction
Q.15 Which of the following is NOT a typical assumption of constraint‑based modeling?
Steady‑state metabolism
Linear relationship between fluxes
Known kinetic parameters for all enzymes
Mass balance at each metabolite
Explanation - Constraint‑based models avoid kinetic parameters; they rely on stoichiometry and bounds.
Correct answer is: Known kinetic parameters for all enzymes
Q.16 When performing gene‑protein‑reaction (GPR) mapping, which logical operator is used to represent that multiple genes are required for a single enzyme complex?
AND
OR
NOT
XOR
Explanation - All genes connected by AND must be present for the enzyme complex to be functional.
Correct answer is: AND
Q.17 In a model with a biomass reaction, which metabolite is typically NOT included as a component?
Water
DNA
ATP
Carbon dioxide
Explanation - Biomass formulations include macromolecular precursors; CO₂ is a waste product, not a cellular component.
Correct answer is: Carbon dioxide
Q.18 What does the term 'parsimonious FBA (pFBA)' aim to achieve?
Find a flux distribution with the minimal total flux while achieving the optimal objective
Maximize ATP production above the biomass objective
Introduce stochasticity into the solution
Eliminate all reversible reactions
Explanation - pFBA adds a secondary objective to minimize the sum of absolute fluxes, yielding a more biologically realistic solution.
Correct answer is: Find a flux distribution with the minimal total flux while achieving the optimal objective
Q.19 Which data type is most commonly integrated with constraint‑based models to improve prediction accuracy?
Transcriptomics
Spectroscopy
Seismic data
Astronomical observations
Explanation - Gene expression data can be used to adjust reaction bounds (e.g., via GIMME, iMAT) and tailor models to specific conditions.
Correct answer is: Transcriptomics
Q.20 The term 'thermodynamic feasibility' in constraint‑based modeling refers to:
Ensuring reaction directions comply with Gibbs free energy changes
Balancing the electrical power consumption of the model
Guaranteeing that all metabolites have integer coefficients
Limiting the number of reactions in the network
Explanation - Thermodynamic constraints prevent infeasible cycles by imposing directionality based on ΔG⁰' values.
Correct answer is: Ensuring reaction directions comply with Gibbs free energy changes
Q.21 Which method can be used to detect and eliminate thermodynamically infeasible loops in a metabolic model?
Loopless FBA
Monte Carlo sampling
Principal component analysis
Fourier transform spectroscopy
Explanation - Loopless FBA adds additional constraints that forbid internal cycles carrying flux without net conversion.
Correct answer is: Loopless FBA
Q.22 In a stoichiometric matrix, what does a negative entry indicate?
Consumption of a metabolite in a reaction
Production of a metabolite in a reaction
Presence of an inhibitor
Reaction reversibility
Explanation - Negative coefficients correspond to substrates (consumed), while positive coefficients correspond to products (produced).
Correct answer is: Consumption of a metabolite in a reaction
Q.23 Which of the following best describes a 'minimal media' simulation in FBA?
Finding the smallest set of nutrients that still supports growth
Maximizing ATP yield from glucose
Determining the fastest growth rate possible
Simulating anaerobic respiration only
Explanation - Minimal media analysis searches for the minimal nutrient composition that yields a non‑zero biomass flux.
Correct answer is: Finding the smallest set of nutrients that still supports growth
Q.24 When performing a knockout simulation in a constraint‑based model, the reaction is typically:
Set to have both lower and upper bounds equal to zero
Removed from the stoichiometric matrix
Reversed in direction
Given an infinite upper bound
Explanation - Constraining both bounds to zero disables flux through the reaction, mimicking a gene knockout.
Correct answer is: Set to have both lower and upper bounds equal to zero
Q.25 What is the purpose of performing a 'gene essentiality' analysis using a constraint‑based model?
To predict which genes are required for growth under specific conditions
To calculate the exact concentration of each metabolite
To determine the electrical resistance of cellular membranes
To estimate the half‑life of proteins
Explanation - Essentiality analysis tests the impact of deleting each gene on the ability of the model to achieve a non‑zero biomass flux.
Correct answer is: To predict which genes are required for growth under specific conditions
Q.26 Which of the following is a common limitation of standard FBA?
Inability to predict dynamic changes over time
Requirement for detailed kinetic parameters
Need for high‑resolution microscopy data
Dependence on quantum mechanical calculations
Explanation - FBA assumes a steady‑state; it does not capture transient dynamics without extensions such as dynamic FBA.
Correct answer is: Inability to predict dynamic changes over time
Q.27 Dynamic FBA (dFBA) extends traditional FBA by:
Coupling flux balance with ordinary differential equations for extracellular metabolites
Adding stochastic noise to fluxes
Using integer programming instead of linear programming
Removing the biomass objective
Explanation - dFBA iteratively updates extracellular concentrations based on fluxes, allowing simulation of batch growth.
Correct answer is: Coupling flux balance with ordinary differential equations for extracellular metabolites
Q.28 In the context of constraint‑based modeling, 'parsimonious' refers to:
Minimizing the total flux while achieving the same objective value
Maximizing the number of active reactions
Ensuring all reactions have the same flux magnitude
Eliminating all reversible reactions
Explanation - A parsimonious solution prefers the simplest flux distribution that still meets the objective.
Correct answer is: Minimizing the total flux while achieving the same objective value
Q.29 When integrating proteomics data into a constraint‑based model, the typical approach is to:
Adjust reaction upper bounds based on measured protein abundance
Replace the stoichiometric matrix with protein interaction data
Set all reaction lower bounds to zero
Add new metabolites representing proteins
Explanation - Higher protein levels can increase the permissible flux through associated reactions; low levels may limit them.
Correct answer is: Adjust reaction upper bounds based on measured protein abundance
Q.30 Which of the following best defines a 'flux cone' in linear programming terms?
The set of all feasible flux vectors that satisfy S·v = 0 and bound constraints
A geometric shape representing metabolite concentrations
A probability distribution of gene expression levels
An electrical circuit diagram
Explanation - The flux cone is a convex polyhedral set defined by the linear constraints of the model.
Correct answer is: The set of all feasible flux vectors that satisfy S·v = 0 and bound constraints
Q.31 Which linear programming dual variable corresponds to the shadow price of a metabolite?
π (pi) associated with the mass‑balance equation of that metabolite
λ (lambda) associated with the objective function
σ (sigma) associated with reaction reversibility
θ (theta) associated with the exchange reaction
Explanation - In the dual problem, each metabolite balance equation has an associated dual variable (π) representing its shadow price.
Correct answer is: π (pi) associated with the mass‑balance equation of that metabolite
Q.32 What does the term 'Metabolic Flux Analysis (MFA)' differ from FBA?
MFA uses measured labeling data to quantify fluxes, while FBA predicts them based on optimization
MFA requires a stoichiometric matrix, FBA does not
MFA is only applicable to electrical circuits
MFA ignores mass balance constraints
Explanation - MFA incorporates experimental ^13C labeling data to solve for actual flux values, whereas FBA relies on an objective function.
Correct answer is: MFA uses measured labeling data to quantify fluxes, while FBA predicts them based on optimization
Q.33 A common way to simulate aerobic vs. anaerobic conditions in a model is to:
Toggle the oxygen exchange reaction bounds
Change the biomass composition
Remove all reversible reactions
Alter the stoichiometric coefficients of glucose
Explanation - Setting the oxygen uptake bound to zero forces anaerobic metabolism; allowing uptake enables aerobic pathways.
Correct answer is: Toggle the oxygen exchange reaction bounds
Q.34 In a model, a reaction that converts ADP + Pi → ATP is typically assigned:
A positive flux direction consistent with ATP synthesis
A negative lower bound only
Zero flux under all conditions
An infinite upper bound without any lower bound
Explanation - The reaction direction is set so that a positive flux corresponds to ATP generation, matching cellular energetics.
Correct answer is: A positive flux direction consistent with ATP synthesis
Q.35 Which of the following is a valid reason to perform 'reaction knockout' rather than 'gene knockout' in a model?
When the GPR rule is unknown or ambiguous
When the gene is essential for cell viability
When the reaction is not mass‑balanced
When the model contains no genes
Explanation - Directly disabling a reaction bypasses uncertainties in gene‑protein mapping.
Correct answer is: When the GPR rule is unknown or ambiguous
Q.36 Which method can be used to sample the feasible solution space of a metabolic model?
Monte Carlo (Hit‑and‑Run) sampling
Gaussian elimination
Fast Fourier Transform
K‑means clustering
Explanation - Random sampling algorithms explore the high‑dimensional flux cone to generate diverse feasible flux vectors.
Correct answer is: Monte Carlo (Hit‑and‑Run) sampling
Q.37 A 'thermodynamically infeasible cycle' in a metabolic model:
Produces net energy without consuming substrates
Violates mass balance
Requires a gene that does not exist
Is always reversible
Explanation - Such cycles create artificial ATP generation, contradicting thermodynamic laws.
Correct answer is: Produces net energy without consuming substrates
Q.38 The concept of 'reaction coupling' in constraint‑based modeling means:
Two reactions must carry flux in a fixed ratio
Two reactions share the same substrate
Two reactions are catalyzed by the same enzyme
Two reactions occur in different cellular compartments
Explanation - Coupling constraints enforce a proportional relationship, often used for transport and intracellular steps.
Correct answer is: Two reactions must carry flux in a fixed ratio
Q.39 Which of the following statements about 'objective function weighting' is true?
Changing weights can prioritize production of a target metabolite over biomass
Weights have no effect on the solution
All weights must be equal to one
Weights are only used in integer programming
Explanation - Assigning a higher coefficient to a reaction in the objective biases the solution toward that flux.
Correct answer is: Changing weights can prioritize production of a target metabolite over biomass
Q.40 When converting a genome annotation to a metabolic model, the main step is:
Mapping genes to reactions via GPR rules
Measuring metabolite concentrations experimentally
Building an electrical circuit analog
Running a finite element analysis
Explanation - Annotation provides gene functions that are translated into enzymatic reactions for the model.
Correct answer is: Mapping genes to reactions via GPR rules
Q.41 Which of these is a typical output file format for a reconstructed metabolic model?
SBML (Systems Biology Markup Language)
MATLAB .mdl file for Simulink
.circuit file for SPICE
.json file for web servers only
Explanation - SBML is a standard XML‑based format for exchanging biochemical network models.
Correct answer is: SBML (Systems Biology Markup Language)
Q.42 In the context of constraint‑based modeling, 'Flux Coupling Analysis (FCA)' is used to:
Identify relationships where the activity of one reaction forces activity of another
Calculate the electrical current through metabolic pathways
Determine the 3‑D structure of enzymes
Measure the temperature dependence of reactions
Explanation - FCA classifies reactions as fully, directionally, or partially coupled based on feasible flux space.
Correct answer is: Identify relationships where the activity of one reaction forces activity of another
Q.43 Which of the following constraints would you add to prevent a model from producing metabolites that are not observed experimentally?
Set upper bounds of the corresponding exchange reactions to zero
Increase the lower bounds of all reactions
Remove all reversible reactions
Set the objective to minimize ATP consumption
Explanation - Limiting export or uptake prevents synthesis or secretion of unwanted metabolites.
Correct answer is: Set upper bounds of the corresponding exchange reactions to zero
Q.44 A common approach to incorporate enzyme capacity constraints into a model is:
Add inequality constraints linking reaction flux to enzyme abundance via kcat values
Replace the stoichiometric matrix with kinetic rate laws
Set all lower bounds to -1000
Remove the biomass reaction
Explanation - Enzyme-constrained models (ecFBA) limit fluxes by the amount of enzyme and its catalytic turnover number.
Correct answer is: Add inequality constraints linking reaction flux to enzyme abundance via kcat values
Q.45 Which method is specifically designed to predict essential nutrients for an organism’s growth?
Essential nutrient analysis (ENA)
Flux balance analysis (FBA)
Monte Carlo sampling
Principal component analysis
Explanation - ENA evaluates the impact of removing each nutrient from the medium on the biomass flux.
Correct answer is: Essential nutrient analysis (ENA)
Q.46 What does the term 'biomass precursor' refer to in a metabolic model?
A metabolite required for the synthesis of cellular macromolecules
A gene that encodes a transcription factor
An electrical component in a circuit diagram
A unit of energy stored in ATP
Explanation - Precursors such as amino acids, nucleotides, and lipids are consumed by the biomass reaction to represent cell growth.
Correct answer is: A metabolite required for the synthesis of cellular macromolecules
Q.47 Which of the following is NOT a typical step in the reconstruction of a genome‑scale metabolic model?
Curating the stoichiometric matrix manually
Running a finite element analysis
Defining a biomass equation
Assigning reaction directionality
Explanation - Finite element methods are used for physical simulations, not metabolic network reconstruction.
Correct answer is: Running a finite element analysis
Q.48 In a multi‑objective optimization of a metabolic model, the Pareto front represents:
The set of non‑dominated solutions balancing multiple objectives
The fastest growth rate achievable
The minimum ATP consumption
The unique optimal solution
Explanation - Pareto optimality captures trade‑offs, such as between growth and product formation.
Correct answer is: The set of non‑dominated solutions balancing multiple objectives
Q.49 When integrating ^13C labeling data into a model, the method commonly used is:
13C‑Metabolic Flux Analysis (13C‑MFA)
Flux Balance Analysis (FBA)
Linear Discriminant Analysis (LDA)
Fast Fourier Transform (FFT)
Explanation - 13C‑MFA fits the measured labeling patterns to a set of fluxes, providing quantitative estimates.
Correct answer is: 13C‑Metabolic Flux Analysis (13C‑MFA)
Q.50 A model that includes compartmentalization (e.g., cytosol, mitochondria) must also specify:
Transport reactions between compartments
The color of each metabolite
The magnetic field strength of the cell
The voltage across the membrane
Explanation - Compartmental models need explicit transport steps to move metabolites across membranes.
Correct answer is: Transport reactions between compartments
Q.51 The term 'flux distribution' refers to:
A vector of flux values for all reactions in a feasible solution
A histogram of gene expression levels
A map of electrical currents in a circuit
A probability distribution of metabolite concentrations
Explanation - Flux distribution is the set of numerical fluxes assigned to each reaction after solving the LP.
Correct answer is: A vector of flux values for all reactions in a feasible solution
Q.52 Which of the following is a typical reason to perform 'reaction splitting' in a model?
To separate forward and reverse directions for better control of bounds
To increase the number of metabolites
To reduce computational time by halving the matrix size
To eliminate all reversible reactions
Explanation - Splitting enables independent constraints on each direction, improving model flexibility.
Correct answer is: To separate forward and reverse directions for better control of bounds
Q.53 When a model predicts a growth rate higher than experimentally observed, a common remedy is to:
Add additional constraints, such as enzyme capacity or maintenance ATP requirements
Increase the upper bound of all reactions
Remove the biomass reaction
Set all lower bounds to zero
Explanation - Additional physiological constraints tighten the feasible space, yielding more realistic predictions.
Correct answer is: Add additional constraints, such as enzyme capacity or maintenance ATP requirements
Q.54 The 'maintenance ATP' term in a biomass equation accounts for:
Non‑growth‑associated energy consumption
The ATP used for DNA replication only
The ATP generated during photosynthesis
The ATP needed for electrical signaling
Explanation - Maintenance ATP represents basal energy needs unrelated to biomass synthesis, such as ion pumping.
Correct answer is: Non‑growth‑associated energy consumption
Q.55 A 'thermodynamic constraint' can be expressed mathematically as:
ΔG' ≤ 0 for forward direction and ΔG' ≥ 0 for reverse direction
v ≤ 0 for all reactions
S·v = 1
All bounds set to ±∞
Explanation - A negative Gibbs free energy indicates a spontaneous forward reaction; the reverse direction is limited accordingly.
Correct answer is: ΔG' ≤ 0 for forward direction and ΔG' ≥ 0 for reverse direction
Q.56 Which of the following best describes a 'core' metabolic model?
A reduced network containing only essential pathways for growth
A model that includes every possible reaction in a cell
A model used solely for electrical circuit analysis
A model that only contains transport reactions
Explanation - Core models simplify analysis by focusing on central metabolism while retaining predictive power.
Correct answer is: A reduced network containing only essential pathways for growth
Q.57 In constraint‑based modeling, the term 'feasibility' means:
Existence of at least one flux vector satisfying all constraints
Maximum possible biomass production
Highest possible ATP yield
Minimum number of reactions used
Explanation - A feasible solution respects mass balance, bounds, and any additional constraints.
Correct answer is: Existence of at least one flux vector satisfying all constraints
Q.58 Which of the following is an advantage of using mixed‑integer linear programming (MILP) in metabolic modeling?
It can enforce binary on/off decisions for reactions (e.g., gene knockouts)
It solves models instantly without any computation time
It eliminates the need for a stoichiometric matrix
It provides exact kinetic parameters
Explanation - MILP allows integer variables to model presence/absence of reactions or pathways.
Correct answer is: It can enforce binary on/off decisions for reactions (e.g., gene knockouts)
Q.59 When constructing a community metabolic model (multiple species), a common approach is to:
Create a combined stoichiometric matrix with shared exchange metabolites
Merge all genomes into a single genome
Ignore all transport reactions
Use only a single biomass reaction for the whole community
Explanation - Community models link individual species via shared extracellular metabolites, enabling interaction simulation.
Correct answer is: Create a combined stoichiometric matrix with shared exchange metabolites
Q.60 Which of the following is NOT a typical output of a Flux Variability Analysis (FVA)?
Exact time‑course concentration profiles
Minimum and maximum possible flux for each reaction
Identification of reactions with zero variability
Ranges that indicate alternative optimal solutions
Explanation - FVA provides static flux ranges; it does not generate dynamic concentration data.
Correct answer is: Exact time‑course concentration profiles
Q.61 The term 'Stoichiometric consistency' refers to:
The property that all internal metabolites have balanced production and consumption
The equality of all reaction fluxes
The use of integer coefficients only
The similarity between two different models
Explanation - A consistent model has no net creation or destruction of mass at steady state.
Correct answer is: The property that all internal metabolites have balanced production and consumption
Q.62 Which of the following tools can perform both FBA and thermodynamic feasibility analysis?
ThermoFBA (part of the COBRA Toolbox)
MATLAB Simulink
SPICE
Microsoft Excel
Explanation - ThermoFBA integrates thermodynamic data to constrain reaction directionality within COBRA.
Correct answer is: ThermoFBA (part of the COBRA Toolbox)
Q.63 A 'minimal cut set' (MCS) in a metabolic network is:
A smallest set of reactions whose removal disables a particular function (e.g., growth)
A set of reactions that maximizes ATP production
A group of metabolites with zero concentration
A collection of genes with identical expression levels
Explanation - MCS analysis identifies vulnerabilities and potential drug targets by finding minimal intervention sets.
Correct answer is: A smallest set of reactions whose removal disables a particular function (e.g., growth)
Q.64 In constraint‑based modeling, the 'dual problem' provides information about:
Sensitivity of the objective to each constraint (shadow prices)
Exact concentrations of metabolites
Electrical resistance of cellular components
The three‑dimensional structure of enzymes
Explanation - The dual variables (shadow prices) quantify how changes in constraints affect the optimal objective.
Correct answer is: Sensitivity of the objective to each constraint (shadow prices)
Q.65 When a model includes 'alternative optima', it means:
Multiple distinct flux distributions achieve the same optimal objective value
The model has no feasible solution
All fluxes are zero
The objective function is not defined
Explanation - Alternative optima reflect redundancy in the network, often explored using FVA or sampling.
Correct answer is: Multiple distinct flux distributions achieve the same optimal objective value
Q.66 Which of the following is a common method for reducing the size of a genome‑scale model while preserving its predictive capability?
Model reduction via reaction lumping
Increasing all upper bounds to infinity
Removing the biomass reaction
Setting all lower bounds to -1000
Explanation - Lumping combines sequences of reactions into a single step, decreasing model complexity.
Correct answer is: Model reduction via reaction lumping
Q.67 The term 'exchange reaction' in a compartmentalized model typically has which stoichiometry?
Metabolite (outside) ↔ Metabolite (inside)
Metabolite + ATP → ADP
Metabolite → Metabolite + Energy
Metabolite + Enzyme → Complex
Explanation - Exchange reactions shuttle metabolites between the extracellular environment and the intracellular compartment.
Correct answer is: Metabolite (outside) ↔ Metabolite (inside)
Q.68 Which of the following statements about 'reaction reversibility' is true?
Reversible reactions can carry flux in both positive and negative directions within their bounds
Reversible reactions always have a zero net flux
Irreversible reactions are defined by a negative lower bound
Reversible reactions are ignored in FBA
Explanation - Bounds like [-1000, 1000] allow a reversible reaction to operate forward or backward.
Correct answer is: Reversible reactions can carry flux in both positive and negative directions within their bounds
Q.69 A 'flux split' method is often used to:
Separate forward and reverse fluxes for improved numerical stability
Combine multiple reactions into one
Eliminate the need for a biomass reaction
Transform the stoichiometric matrix into a diagonal matrix
Explanation - Splitting avoids negative fluxes in linear programming solvers that handle only non‑negative variables.
Correct answer is: Separate forward and reverse fluxes for improved numerical stability
Q.70 Which of the following is an example of a 'hard' constraint in constraint‑based modeling?
Mass balance (S·v = 0)
Preference for higher ATP yield
Goal to maximize biomass
Desire to reduce carbon waste
Explanation - Hard constraints must be satisfied exactly, unlike soft objectives that guide optimization.
Correct answer is: Mass balance (S·v = 0)
Q.71 In the context of metabolic engineering, the term 'over‑expression' of a gene is simulated by:
Increasing the upper bound of the associated reaction(s)
Setting the lower bound to zero
Removing the reaction from the model
Changing the stoichiometric coefficients
Explanation - Higher enzyme levels allow greater possible flux through the catalyzed reaction.
Correct answer is: Increasing the upper bound of the associated reaction(s)
Q.72 Which of the following is a typical reason to use 'COBRApy' instead of the MATLAB COBRA Toolbox?
Preference for an open‑source Python environment
Need for Simulink integration
Requirement for Windows‑only operation
Desire to run SPICE simulations
Explanation - COBRApy provides similar functionality in Python, facilitating integration with other scientific libraries.
Correct answer is: Preference for an open‑source Python environment
Q.73 What does the 'exchange reaction' for glucose typically look like in a model?
glc[e] ↔ glc[c]
glc[c] + ATP → glc[e] + ADP
glc[e] → glc[e] + ATP
glc[c] → glc[c] + CO₂
Explanation - The exchange reaction transports glucose between extracellular (e) and cytosolic (c) compartments.
Correct answer is: glc[e] ↔ glc[c]
Q.74 In constraint‑based models, the term 'dead‑end reaction' refers to:
A reaction that cannot carry flux because its substrates or products are not connected to the rest of the network
A reaction that has the highest flux
A reversible reaction with infinite bounds
A reaction that is part of the biomass equation
Explanation - Dead‑end reactions create infeasibility unless removed or supplemented with artificial transport.
Correct answer is: A reaction that cannot carry flux because its substrates or products are not connected to the rest of the network
Q.75 Which of the following techniques can be used to identify metabolic pathways that are essential for pathogen survival but absent in the host?
Comparative essentiality analysis using constraint‑based models of both organisms
Measuring electrical potentials across bacterial membranes
Running a finite element analysis of cell walls
Sequencing the host genome only
Explanation - By comparing knockout impacts, unique essential pathways in the pathogen can be highlighted as drug targets.
Correct answer is: Comparative essentiality analysis using constraint‑based models of both organisms
Q.76 When a model includes a 'maintenance ATP' reaction, its typical stoichiometry is:
ATP → ADP + Pi
ADP + Pi → ATP
ATP + H₂O → ADP + Pi + H⁺
Glucose → 2 ATP
Explanation - Maintenance ATP consumes ATP without producing biomass, representing basal energy demand.
Correct answer is: ATP → ADP + Pi
Q.77 What is the primary purpose of 'GapFind' in metabolic model reconstruction?
To locate metabolites that cannot be produced or consumed in the current network
To maximize biomass production
To calculate the electrical power of the cell
To simulate time‑dependent dynamics
Explanation - GapFind identifies dead‑ends that need to be resolved via gap‑filling.
Correct answer is: To locate metabolites that cannot be produced or consumed in the current network
Q.78 Which of the following best describes the difference between 'hard' and 'soft' constraints?
Hard constraints must be strictly satisfied; soft constraints are part of the objective function and can be violated at a cost
Hard constraints are optional, soft constraints are mandatory
Hard constraints are always linear, soft constraints are non‑linear
Hard constraints are used only in integer programming
Explanation - Hard constraints define the feasible region; soft constraints guide optimization within that region.
Correct answer is: Hard constraints must be strictly satisfied; soft constraints are part of the objective function and can be violated at a cost
Q.79 In a multi‑objective FBA problem aiming to maximize both biomass and product formation, a common technique is:
Weighted sum of the two objectives
Subtracting product flux from biomass
Setting product flux to zero
Increasing the upper bound of the biomass reaction only
Explanation - Assigning weights converts multiple objectives into a single scalar objective for linear programming.
Correct answer is: Weighted sum of the two objectives
Q.80 When performing 'Monte Carlo sampling' of a metabolic model, the main goal is to:
Explore the diversity of feasible flux distributions
Find the single optimal flux distribution
Determine the exact kinetic parameters of enzymes
Calculate the electrical resistance of pathways
Explanation - Sampling generates many random points within the feasible region, revealing possible metabolic states.
Correct answer is: Explore the diversity of feasible flux distributions
Q.81 In constraint‑based modeling, 'reaction reversibility' is often inferred from:
Thermodynamic data (ΔG') and known enzyme directionality
The color of the metabolite
The length of the gene sequence
The position of the reaction in the genome
Explanation - A negative ΔG' indicates a spontaneous forward direction; if near zero, the reaction may be reversible.
Correct answer is: Thermodynamic data (ΔG') and known enzyme directionality
Q.82 Which of the following best explains why constraint‑based models are scalable to genome‑scale networks?
They rely on linear programming, which can handle thousands of variables efficiently
They require detailed kinetic parameters for each reaction
They need 3‑D structural data for every enzyme
They simulate each metabolite concentration over time
Explanation - LP solvers are optimized for large, sparse systems, enabling genome‑scale analyses.
Correct answer is: They rely on linear programming, which can handle thousands of variables efficiently
Q.83 When a model includes an 'artificial' sink reaction for a metabolite, its purpose is to:
Allow accumulation or removal of that metabolite without specifying a physiological transport mechanism
Increase the biomass yield
Force the metabolite to be a dead‑end
Represent a gene knockout
Explanation - Sinks provide flexibility for metabolites whose true fate is unknown or not modeled explicitly.
Correct answer is: Allow accumulation or removal of that metabolite without specifying a physiological transport mechanism
Q.84 Which of the following is a typical outcome of performing a 'single‑reaction deletion' study?
Identification of reactions whose removal abolishes growth (essential reactions)
Increase in the total number of metabolites
Conversion of all reversible reactions to irreversible
Elimination of the biomass reaction
Explanation - Systematically knocking out each reaction reveals which are critical for achieving a non‑zero biomass flux.
Correct answer is: Identification of reactions whose removal abolishes growth (essential reactions)
Q.85 In a model that includes gene‑protein‑reaction (GPR) associations, a reaction is considered 'inactive' if:
All associated genes are expressed below a threshold
Its flux is greater than zero
It is marked as reversible
It participates in the biomass reaction
Explanation - GPR logic combined with expression data can turn off reactions when the required genes are not expressed.
Correct answer is: All associated genes are expressed below a threshold
Q.86 Which of the following constraints would you add to model the effect of limited enzyme capacity for reaction i?
v_i ≤ kcat_i × [E_i]
v_i = 0
S·v = 1
v_i ≥ -1000
Explanation - The flux cannot exceed the product of enzyme amount and its catalytic rate constant.
Correct answer is: v_i ≤ kcat_i × [E_i]
Q.87 When integrating a 'thermodynamic feasibility' check, the reaction directionality is constrained by:
The sign of ΔG' under physiological conditions
The number of carbon atoms in the substrate
The gene expression level only
The reaction's position in the genome
Explanation - A negative ΔG' supports forward direction; a positive ΔG' would prohibit it unless conditions change.
Correct answer is: The sign of ΔG' under physiological conditions
Q.88 A model predicts that knocking out reaction A eliminates growth, but experimentally the organism still grows. Which of the following is the most plausible explanation?
Alternative pathways not captured in the model compensate for the loss
The model uses the wrong objective function
Reaction A is actually irreversible
The biomass reaction is incorrectly defined
Explanation - Missing redundancy or unknown isoenzymes can cause discrepancies between model predictions and reality.
Correct answer is: Alternative pathways not captured in the model compensate for the loss
Q.89 In a constraint‑based model of a photosynthetic organism, the light reaction is typically represented as:
An exchange reaction that provides photons as an energy source
A reversible reaction converting CO₂ to glucose
A sink reaction for oxygen
An irreversible reaction producing ATP from light
Explanation - Light availability is modeled as an external input that drives downstream photochemical reactions.
Correct answer is: An exchange reaction that provides photons as an energy source
Q.90 Which of the following is a correct statement about the 'stoichiometric matrix' S in constraint‑based modeling?
Rows correspond to metabolites, columns to reactions, and entries are integer stoichiometric coefficients
Rows correspond to reactions, columns to metabolites, and entries are decimal concentrations
It is a square matrix of size equal to the number of genes
All entries are either 0 or 1
Explanation - S captures how each metabolite participates in each reaction, using signed integer coefficients.
Correct answer is: Rows correspond to metabolites, columns to reactions, and entries are integer stoichiometric coefficients
Q.91 When performing 'Flux Balance Analysis' on a model with multiple possible optimal solutions, one way to obtain a unique solution is to:
Apply parsimonious FBA (pFBA) as a secondary objective
Randomly select fluxes
Increase the upper bound of all reactions
Remove the biomass reaction
Explanation - pFBA minimizes total flux after achieving the primary objective, often yielding a unique solution.
Correct answer is: Apply parsimonious FBA (pFBA) as a secondary objective
Q.92 The term 'exchange reaction' for oxygen in an aerobic simulation typically has which bound settings?
Lower bound negative (allow uptake), upper bound zero (no secretion)
Both bounds zero
Lower bound zero, upper bound positive (only secretion)
Both bounds infinite
Explanation - A negative lower bound permits oxygen import; setting the upper bound to zero blocks oxygen export.
Correct answer is: Lower bound negative (allow uptake), upper bound zero (no secretion)
Q.93 Which of the following is a common way to validate a constraint‑based model?
Comparing predicted growth rates and essential genes with experimental data
Measuring the model's runtime on a computer
Counting the number of reactions in the model
Checking the color scheme used in the model diagram
Explanation - Validation involves testing model predictions against laboratory measurements such as growth, knockout effects, and metabolite production.
Correct answer is: Comparing predicted growth rates and essential genes with experimental data
Q.94 In constraint‑based modeling, a 'soft constraint' can be implemented by:
Adding a penalty term to the objective function for violating a bound
Setting a strict equality constraint
Removing all bounds from the model
Fixing all fluxes to zero
Explanation - Soft constraints are often modeled as cost penalties, allowing limited violations if beneficial.
Correct answer is: Adding a penalty term to the objective function for violating a bound
Q.95 Which of the following describes the purpose of 'Reaction Subsystem' annotation in a metabolic model?
To group reactions into functional pathways for easier interpretation
To assign electrical voltage values
To define the order of reactions in a time series
To set the temperature for each reaction
Explanation - Subsystems help organize reactions (e.g., glycolysis, TCA cycle) within the model.
Correct answer is: To group reactions into functional pathways for easier interpretation
Q.96 When a model includes a 'thermodynamic loop' that can generate ATP from nothing, the appropriate corrective action is to:
Apply loopless constraints or add thermodynamic directionality
Increase the upper bound of the ATP synthase reaction
Remove all reversible reactions
Set all exchange reactions to zero
Explanation - Loopless FBA or thermodynamic constraints prevent non‑physical cycles that create energy from nothing.
Correct answer is: Apply loopless constraints or add thermodynamic directionality
Q.97 Which of the following best describes 'metabolic network reconstruction'?
The process of compiling genome annotation, reaction stoichiometry, and compartmentalization into a coherent model
Measuring the electrical conductivity of cell membranes
Sequencing the entire genome of an organism
Running a Monte Carlo simulation of metabolite concentrations
Explanation - Reconstruction assembles biological knowledge into a computational representation.
Correct answer is: The process of compiling genome annotation, reaction stoichiometry, and compartmentalization into a coherent model
Q.98 In the context of constraint‑based modeling, 'dual variables' are associated with:
The constraints of the primal problem (e.g., mass balances)
The metabolites themselves
The objective function coefficients
The reaction names
Explanation - Dual variables correspond to each constraint and provide shadow prices indicating sensitivity.
Correct answer is: The constraints of the primal problem (e.g., mass balances)
Q.99 A model predicts a flux of zero through a reaction under a given condition. Which of the following could be a correct interpretation?
The reaction is either blocked by constraints or not needed for the objective under that condition
The reaction is essential for growth
The stoichiometric coefficients are all zero
The model has crashed
Explanation - Zero flux can arise from thermodynamic restrictions, lack of substrates, or the optimization not requiring that pathway.
Correct answer is: The reaction is either blocked by constraints or not needed for the objective under that condition
Q.100 Which of the following is a typical way to incorporate 'regulatory' information into a constraint‑based model?
Adding Boolean rules that turn reactions on/off based on gene expression levels
Changing the stoichiometric coefficients to reflect regulation
Removing the biomass reaction
Increasing the size of the stoichiometric matrix arbitrarily
Explanation - Regulatory FBA (rFBA) uses logical constraints to mimic transcriptional regulation.
Correct answer is: Adding Boolean rules that turn reactions on/off based on gene expression levels
Q.101 In a model where the objective is to maximize the secretion of lactate, which reaction would typically be assigned the highest coefficient in the objective function?
The lactate exchange reaction
The glucose uptake reaction
The ATP maintenance reaction
The biomass reaction
Explanation - Giving the lactate export reaction the largest weight drives the optimizer to secrete more lactate.
Correct answer is: The lactate exchange reaction
Q.102 When a model contains 'or' relationships in its GPR rules, it means:
Any one of the listed genes can encode a functional enzyme for the reaction
All listed genes must be present simultaneously
The reaction is irreversible
The reaction is a transport step
Explanation - An OR relationship captures isoenzymes where any one gene product can catalyze the reaction.
Correct answer is: Any one of the listed genes can encode a functional enzyme for the reaction
Q.103 Which of the following statements is true about 'Flux Balance Analysis' when applied to a non‑growing (stationary) cell culture?
The biomass reaction is typically set to zero, and alternative objectives such as maintenance ATP are used
The model cannot be solved because growth is required
All exchange reactions must be closed
The stoichiometric matrix must be inverted
Explanation - In stationary phase, models often focus on maintenance or product formation rather than growth.
Correct answer is: The biomass reaction is typically set to zero, and alternative objectives such as maintenance ATP are used
Q.104 A 'parsimonious' solution in the context of FBA is preferred because:
It minimizes the total enzymatic effort, reflecting biological economy
It maximizes the number of active reactions
It always yields the highest possible growth rate
It removes all reversible reactions
Explanation - Parsimony aligns with the observation that cells often use the simplest pathways that satisfy their needs.
Correct answer is: It minimizes the total enzymatic effort, reflecting biological economy
Q.105 In a constraint‑based model, the 'biomass reaction' is usually:
A pseudo‑reaction that consumes precursor metabolites to produce a unit of biomass
A transport reaction moving glucose across the membrane
A reversible reaction converting ATP to ADP
An exchange reaction for oxygen
Explanation - The biomass equation aggregates the building blocks required for cell growth into a single sink.
Correct answer is: A pseudo‑reaction that consumes precursor metabolites to produce a unit of biomass
Q.106 Which of the following is a typical use of 'COBRApy' in constraint‑based modeling?
Building, simulating, and analyzing metabolic models in Python
Performing molecular dynamics simulations
Designing printed circuit boards
Analyzing astronomical spectra
Explanation - COBRApy provides a Python implementation of the COBRA toolbox functions for metabolic analysis.
Correct answer is: Building, simulating, and analyzing metabolic models in Python
Q.107 When a model includes a reaction that produces a metabolite not present in any other reaction, this metabolite is classified as:
A dead‑end product
A core metabolite
A reversible metabolite
A transport metabolite
Explanation - If the metabolite cannot be consumed elsewhere, it becomes a dead‑end, indicating a possible gap.
Correct answer is: A dead‑end product
Q.108 In the context of metabolic engineering, the term 'product yield' is defined as:
The amount of desired product formed per unit of substrate consumed
The total number of reactions in the model
The speed of the computer solving the LP
The electrical power generated by the cell
Explanation - Yield quantifies efficiency of converting feedstock into the target compound.
Correct answer is: The amount of desired product formed per unit of substrate consumed
Q.109 Which of the following best describes the 'dual' of a linear programming problem in FBA?
A problem that provides shadow prices for each metabolite and indicates how the objective changes with constraint variations
A second FBA run with a different objective
A simulation of metabolite concentrations over time
A random sampling of flux distributions
Explanation - The dual problem yields the sensitivity information (shadow prices) associated with each primal constraint.
Correct answer is: A problem that provides shadow prices for each metabolite and indicates how the objective changes with constraint variations
Q.110 Which of the following is an example of a 'hard' bound that can be applied to a transport reaction for glucose uptake?
Upper bound = -10 mmol·gDW⁻¹·h⁻¹ (maximum uptake rate)
Objective coefficient = 1
Preference for high ATP yield
Soft penalty for high flux
Explanation - Setting a numeric bound restricts the maximum rate at which glucose can be taken up.
Correct answer is: Upper bound = -10 mmol·gDW⁻¹·h⁻¹ (maximum uptake rate)
Q.111 In a constraint‑based model, a reaction that is designated as 'blocked' means:
It cannot carry any flux under any feasible condition
It always carries the maximum possible flux
It is part of the biomass equation
It is reversible
Explanation - Blocked reactions are identified by algorithms that test feasibility across the solution space.
Correct answer is: It cannot carry any flux under any feasible condition
Q.112 When integrating proteomics data using the 'GECKO' workflow, the model is enriched with:
Enzyme capacity constraints derived from measured protein abundances and kcat values
Additional exchange reactions for all metabolites
A new objective function based on ATP consumption
Randomly generated reaction fluxes
Explanation - GECKO adds enzyme constraints (ecFBA) to link protein levels with metabolic capacities.
Correct answer is: Enzyme capacity constraints derived from measured protein abundances and kcat values
Q.113 Which of the following is a common approach to predict the effect of a nutrient limitation on growth?
Restrict the upper bound of the corresponding nutrient's exchange reaction and re‑run FBA
Delete all reactions that involve the nutrient
Increase the biomass coefficients for all metabolites
Set all reaction lower bounds to zero
Explanation - Limiting nutrient uptake directly tests its impact on the optimal growth rate.
Correct answer is: Restrict the upper bound of the corresponding nutrient's exchange reaction and re‑run FBA
Q.114 In a constraint‑based model of a eukaryotic cell, compartments are indicated by suffixes such as '[c]' and '[m]'. What do these suffixes denote?
'[c]' = cytosol, '[m]' = mitochondria
'[c]' = carbon source, '[m]' = membrane
'[c]' = concentration, '[m]' = mass
'[c]' = calcium, '[m]' = magnesium
Explanation - Compartment tags allow the model to differentiate metabolites located in different cellular spaces.
Correct answer is: '[c]' = cytosol, '[m]' = mitochondria
Q.115 Which of the following statements about 'thermodynamic feasibility' constraints is FALSE?
They guarantee that every reaction proceeds in the direction of decreasing Gibbs free energy
They can be represented as linear inequalities using transformed ΔG values
They always require integer programming to solve
They can prevent artificial energy‑generating cycles
Explanation - Thermodynamic constraints can be expressed as linear constraints, keeping the problem within linear programming.
Correct answer is: They always require integer programming to solve
Q.116 A model includes an artificial 'sink' for acetate. This is typically used to:
Allow acetate to be removed from the system without specifying a transport mechanism
Force the cell to produce acetate
Increase the flux through the TCA cycle
Represent a gene knockout
Explanation - Sink reactions provide a way to balance metabolite accumulation when the true pathway is unknown.
Correct answer is: Allow acetate to be removed from the system without specifying a transport mechanism
Q.117 When a model uses 'binary variables' in MILP to represent gene knockouts, what does a value of 0 for a binary variable typically indicate?
The associated reaction is disabled (knocked out)
The reaction operates at maximum flux
The reaction is reversible
The reaction has infinite bounds
Explanation - Binary variables are used to turn reactions on (1) or off (0) in mixed‑integer formulations.
Correct answer is: The associated reaction is disabled (knocked out)
Q.118 Which of the following best captures the purpose of 'Flux Coupling Analysis' (FCA)?
To classify relationships among reactions based on their co‑dependency in feasible flux distributions
To compute the exact concentrations of metabolites
To model electrical circuits within cells
To simulate the time course of gene expression
Explanation - FCA identifies fully, directionally, and partially coupled reactions, revealing network structure.
Correct answer is: To classify relationships among reactions based on their co‑dependency in feasible flux distributions
Q.119 In a model of a photosynthetic organism, which of the following reactions would typically have a positive flux direction under light conditions?
Photon uptake (light) exchange reaction
Oxygen uptake exchange reaction
CO₂ secretion exchange reaction
NADH oxidation reaction
Explanation - Photons are imported from the environment, so the exchange reaction carries a positive (import) flux.
Correct answer is: Photon uptake (light) exchange reaction