Deck 22: Exploring Synthetic Biology: Concepts, Techniques, and Applications

Question 1

Which of the following would be most useful in a synthetic circuit to accelerate a screen for drugs that inhibit the activity of a negative transcription regulator,EthR,from Mycobacterium tuberculosis?

A) translational fusion of VP16 with a reporter gene
B) translational fusion of ethR with the VP16 transcriptional activator
C) translational fusion of ethR with a reporter gene
D) place VP16 under control of the cis-element to which EthR native binds promoter
E) place GFP under control of the cis-element to which EthR native binds promoter

Answer 1

B

Question 2

What is the relationship of Francois Jacob to synthetic biology?

A) One of his quotations was included in the watermark in the first synthetic genome.
B) His discoveries about electrical circuit engineering have been applied to genetic circuits.
C) He led the synthesis of the first synthetic genome.
D) His discoveries about gene regulation facilitated the eventual development of synthetic biology.
E) He led the sequencing of the human genome,which provided models for synthetic genes.

Answer 2

D

Question 3

Which of the following is not a characteristic of synthetic biology?

A) well-defined parts
B) modularity
C) ethics
D) reusable parts
E) random mutagenesis by chemicals

Answer 3

E

Question 4

What is the objective of (Multiplex Automated Genome Engineering)MAGE?

A) parallel synthesis of blocks of genomic DNA for genome assembly
B) site-directed mutagenesis of dozens of sites in a single experiment
C) rapid synthesis of large fragments of genomic DNA
D) replacement of large chromosomal segments by homologous recombination
E) use of artificial intelligence to guide design of synthetic genomes

Question 5

How is a toggle switch different from a repressilator?

A) A repressilator oscillates whereas a toggle switch is bistable.
B) Repressilators encode repressors (e.g.LacI),but toggle switches do not.
C) A repressilator requires a control molecule (e.g.IPTG),whereas a toggle switch does not.
D) Toggle switches encode repressors (e.g.LacI),but repressilators do not.
E) Anhydrotetracycline is an effective regulatory of repressilators,but not of toggle switches.

Question 6

Undergraduates from around the world participate in a synthetic biology competition known as

A) SynBioX
B) iGEM
C) SGI
D) SGVI
E) iDNA

Question 7

In an analogy comparing computer systems to biological systems,which of the following pairs of components is most correct?

A) transistor: tissue
B) computer network: gene
C) resistor: pathway
D) physical layer: pathway
E) computer: cell

Question 8

Which of these would be most useful in building a genetic circuit for memory storage?

A) miRNA
B) promoter
C) toggle switch
D) GFP
E) ssDNA binding protein

Question 9

Which of the following was not a component of the metabolic engineering strategy for artemisinic acid production?

A) a Met-inducible module to increase flux to the artemisinin pathway
B) incorporation of a mutant yeast allele to increase production of an artemisinic acid precursor
C) expression of multiple Artemissia annua genes in yeast
D) a cytochrome P450
E) a TetR repressor system to decrease flux to competing pathways

Question 10

Which of these would be most useful in building a genetically encoded toggle switch?

A) two genes encoding transcription factors
B) two genes encoding repressors
C) one gene encoding a repressor,and one gene encoding a protease
D) three genes encoding proteases
E) three genes encoding transcription factors

Question 11

Through synthetic biology,artemisinin is

A) made toxic to antibiotic resistant strains of Mycobacterium tuberculosis.
B) made into an anti-malarial compound by site directed mutagenesis of the wormwood genome.
C) made toxic to the pathogenic bacterium that cause tumours in immune deficient patients.
D) produced more efficiently in yeast than it can be produced from its natural source in plants.
E) used as a control molecule in a repressilator system than mimics natural chemical rhythms.

Question 12

Given the functional genetic toggle switch shown,what would be the result of treatment with both IPTG and aTc?

A) None of the proteins in the diagram would be expressed.
B) All of the proteins in the diagram would be expressed.
C) Only TetR would be expressed.
D) Only LacI would be expressed.
E) Only GFP would be expressed.

Question 13

Given the functional genetic toggle switch shown,which of the following would result in GFP expression?

A) treatment with IPTG
B) treatment with aTc
C) treatment with aTc followed by removal of aTc from the system
D) deletion of the Pro-2 promoter
E) deletion of the Pro-2 promoter and deletion of the Pro-1 promoter

Question 14

Which of the following is not distributed by the BioBricks Foundation?

A) viral vectors
B) recombinant DNA
C) synthetic genomes
D) promoters
E) transcription factors

Question 15

What does it mean for a synthetic circuit to interface with natural cellular processes?

A) Natural genes can be used as a foundation for design of synthetic circuits.
B) Complete synthetic genomes are transplanted into natural cells.
C) Small fragments of synthetic DNA are incorporated into living cells.
D) The output of a synthetic circuit is controlled by an endogenous signal.
E) Natural metabolic pathways can beengineered by site-directed mutagenesis.

Question 16

Which of the following is not true of a genetically encoded toggle switch?

A) It allows expression of one of two alternative operons.
B) It is bistable.
C) It is controlled by small molecules.
D) Transient exposure to the control molecule is sufficient for stable activation.
E) The native lac operonconstitutes an example of a toggle switch.

Question 17

Which of the following is a synthetic molecule used in MAGE (Multiplex Automated Genome Engineering)?

A) dsRNA
B) cDNA
C) cRNA
D) ssDNA
E) miRNA

Question 18

In Mycobacterium tuberculosis,the ethA gene product confers

A) resistance to phage therapy.
B) the ability to colonize a host.
C) antibiotic resistance.
D) rapid growth.
E) sensitivity to ethionamide.

Question 19

The synthetic killer microbes that have been created to treat Pseudomonas aeruginosa infections

A) respond to the quorum-sensing molecules produced by P.aeruginosa.
B) encode bacteriophage that lyse the pathogenic bacteria.
C) constitutively produce a compound that is toxic to P.aeruginosa.
D) secrete an antibiotic through membrane transporters.
E) have been engineered to produce a stronger toxin than is naturally produced.

Question 20

Given the functional genetic toggle switch shown,what would be the outcome of treatment with IPTG?

A) GFP expression would be turned off,and then would remain off even if IPTG were removed.
B) GFP expression would be turned off,but then would be turned on if IPTG were removed.
C) GFP expression would be turned on,and then would remain on even if IPTG were removed.
D) GFP expression would be turned on,but then would be turned off even if IPTG were removed.
E) IPTG would have no effect on the system.

Question 21

The watermarks in a synthetic genome could be used to distinguish it from a natural genome.

Question 22

Synthetic biology is best described as the combination of molecular biology with principles of synthetic chemistry.

Question 23

Synthetic biology is effectively a synonym for systems biology.

Question 24

What genus was chosen to host the first transplanted synthetic genome,and why?

A) Mycobacterium,because it has a very small genome
B) Mycobacterium,because it is an important pathogen
C) Mycoplasma,because it is an important pathogen
D) Mycoplasma,because it has a very small genome
E) Escherichia,because it is an important pathogen

Question 25

The first successfully transplanted genome was assembled from synthetic ssDNA oligonucleotides.

Question 26

Building artificial systems is an effective way to test our understanding of natural systems.

Question 27

Artemisinin is a natural compound that is an important antimalarial drug.

Question 28

How is Saccharomyces cerevisiae used in genome transplantation?

A) for assembly of large fragments by homologous recombination
B) for site-directed mutagenesis and correction of assembly errors
C) as the final host of the transplanted genome
D) as a host for the viruses into which the genome is transplanted
E) to produce the recombinant lambda-Red ssDNA-binding protein

Question 29

Synthetic biology differs from previous applications of biotechnology only in scale.

Question 30

The leader of the team that created the first synthetic genome is J.Craig Venter.

Question 31

The leader of the team that created the first synthetic genome also led one of the two major human genome sequence projects.

Question 32

In one application of synthetic biology in the human gut,a genetic circuit induces lysis of E.coli to release toxins when it encounters a particular pathogen.

Question 33

Reading is to writing as genome sequencing is to genome synthesis.

Question 34

Why is phage lambda-Red ssDNA-binding protein beta used in MAGE (Multiplex Automated Genome Engineering)?

A) to facilitate phage packaging
B) to inhibit supercoiling
C) to promote supercoiling
D) to promote ligation
E) to promote annealing

Question 35

Synthetic biology includes projects that range in scale from modifying a single gene to synthesizing an entire genome.

Question 36

E.coli cells are chilled to 4°C during MAGE to allow for strand annealing.

Question 37

The world's first synthetic organism is known as Syntheticum venterii.

Question 38

A toggle switch is a necessary component of a cellular clock.

Question 39

The leader of the team that produced artemisinin in yeast is J.Craig Venter.

Question 40

Bistable circuits have only two possible states: ON or OFF.

Question 41

Which of the following is not one of the main questions asked by systems biology?

A) How do perturbations affect the system?
B) What are the emergent properties?
C) What is the molecular function of a specific gene of interest?
D) What are the associations among the components?
E) What are the elements of the system?

Question 42

How can MAGE (Multiplex Automated Genome Engineering)be used to mimic evolution?

Question 43

Which of the following is an example of an emergent property?

A) Functioning of a group of molecules as a bistable switch.
B) Identification of a novel mutation in a developmental pathway.
C) Binding of allolactose to the lac repressor.
D) Reverse transcription of a viral coat protein gene.
E) Binding of allolactose to the lac operator.

Question 44

Why do systems biologists define the lac operon as an AND gate?

A) It has both positive and negative regulatory components.
B) It only functions if two conditions are fulfilled.
C) Its function is additive,depending on stimulus.
D) It operates if glucose is present and lactose is absent.
E) It encodes both a transporter and a catalytic enzyme.

Question 45

Which equation is used in systems biology to model transcription?

A) Y = mbⁿ
B) dY/dt = b - aY
C) Y = b - aⁿ/t
D) dY/dt = bⁿ - a
E) dY/dt = ab/n

Question 46

Which of the following is an example of a bottom-up strategy to systems biology?

A) simulating vein development in Arabidopsis thaliana
B) modeling transcriptional networks in Saccharomyces cerevisiae
C) characterizing the eyeless gene defective in Drosophila eye development
D) creating a catalogue of all expressed human proteins
E) conducting phylogenetic analysis of human ancestors

Question 47

Degenerate oligonucleotide pools are useful in MAGE.

Question 48

Compare synthetic biology to the Human Genome Project,in terms of their respective methods and objectives.

Question 49

How is the rate of transcript degradation generally expressed in systems biology?

A) degradation/production
B) degraded RNA/total RNA
C) transcripts/picogram
D) molecules/millisecond
E) percent/minute

Question 50

An emergent property is

A) any substance that a cell secretes into the extracellular environment.
B) a biochemical function such as galactose utilization,which has to be turned on and off.
C) an effect that occurs when a population becomes too large,such that migration is necessary.
D) a property of a system as a whole,which may be greater than the sum of individual properties of its components.
E) any property of a system that becomes evident only when the system has reached equilibrium.

Question 51

Mutation of what would convert the lac operon to an OR gate?

A) An operator sequence,so that it was constitutive.
B) A cis-element so either inducer was sufficient for transcription.
C) An operon so that only lacZ or lacY was transcribed at any time.
D) The promoter so that it would not bind RNA polymerase.
E) The repressor so that it could not bind allolactose.

Question 52

How is synthetic biology used in production of flu vaccines?

Question 53

Explain the advantages of modularity in synthetic biology.

Question 54

Polymerase cycling assembly is a process useful in genome synthesis.

Question 55

A molecular ratchet

A) allows processes to be reversed after they are initiated.
B) has equal thresholds for activation and inactivation.
C) is used in synthetic biology but not natural systems.
D) requires more stimulation to turn itself on than to keep itself on.
E) is an intrinsic rather than emergent property.

Question 56

Genome transplantation has successfully converted one species into another.

Question 57

What are the advantages of using algae for biofuels?

Question 58

The steady state level of mRNA is

A) invariant across transcripts within a species.
B) invariant across transcripts within a cell type.
C) production rate divided by degradation rate.
D) emergent and cannot be predicted.
E) independent of the rate of transcription.

Question 59

What type of logic gate is represented by this table? $$\begin{array} { | l | l | l | } \hline \text { Input A } & \text { Input B } & \text { Output } \\\hline 0 & 0 & 0 \\\hline 0 & 1 & 1 \\\hline 1 & 0 & 1 \\\hline 1 & 1 & 1 \\\hline\end{array}$$

A) NOT
B) NAND
C) XOR
D) OR
E) AND

Question 60

How is synthetic biology different from biotechnology as practiced in previous decades?

Question 61

A molecule that is present only when a disease is present is called a

A) node.
B) SNP.
C) biomarker.
D) activator.
E) LINE.

Question 62

In the Hill equation,what is the significance of the term "n"?

A) Higher values of n indicate a system that is more switchlike.
B) Higher values of n indicate a system that has higher maximum activity.
C) Lower values of n indicate a system that has higher maximum activity.
D) Higher values of n indicate a system that is more stable.
E) Higher values of n indicate a higher degradation rate.

Question 63

Which system is most likely to produce the stimulus-response curve shown here?
In the systems shown below,the concentration of molecule 3 represents the stimulus,and the concentration of molecule 2 is the response.Molecule 1 is a substrate of molecule 3.Molecule 4 is an inactive form of molecule 3.Molecule 2 activates molecule 5.

A)

B)

C)

D)

E)

Question 64

Systems biology attempts to define all the components of a biological system and understand how they function in conjunction with one another.

Question 65

Which system is most likely to produce the stimulus-response curve shown here?
In the systems shown below,the concentration of molecule 3 represents the stimulus,and the concentration of molecule 2 is the response.Molecule 1 is a substrate of molecule 3.Molecule 4 is an inactive form of molecule 3.Molecule 2 activates molecule 5.

A)

B)

C)

D)

E)

Question 66

Which system is most likely to produce the stimulus-response curve shown here,where T_i is the inhibition threshold,and T_a is the activation threshold?
In the systems shown below,the concentration of molecule 3 represents the stimulus,and the concentration of molecule 2 is the response.Molecule 1 is a substrate of molecule 3.Molecule 4 is an inactive form of molecule 3.Molecule 2 activates molecule 5.

A)

B)

C)

D)

E)

Question 67

What is a distinctive feature of the feed forward motif?

A) It acts as an amplifier.
B) It is a molecular ratchet.
C) It can regulate transcription.
D) It has a maximum of three nodes.
E) It only responds to persistent stimuli.

Question 68

Which system is most likely to produce the stimulus-response curve shown here?
In the systems shown below,the concentration of molecule 3 represents the stimulus,and the concentration of molecule 2 is the response.Molecule 1 is a substrate of molecule 3.Molecule 4 is an inactive form of molecule 3.Molecule 2 activates molecule 5.

A)

B)

C)

D)

E)

Question 69

An emergent property is what happens to a system when it is in a disease state.

Question 70

Studies of complex biological networks would not be possible without high-throughput computational tools.

Question 71

Because of the high degree of genetic variation among individuals,systems biology has little application to medicine.

Question 72

Transcription factors can regulate the expression of other transcription factors.

Question 73

Protein networks are sets of proteins that interact with DNA.

Question 74

Discovery science is used to identify all the elements of a biological system rather than to test a specific hypothesis.

Question 75

What is represented in the stimulus-response graph shown?

A) hysteresis
B) bistability
C) feed back
D) instability
E) incomplete data

Question 76

Why does the Hill function use maximum promoter activity as a parameter?

A) Maximum promoter activity is the best predictor of activator concentration.
B) Maximum promoter activity cannot be measured,so it must be represented as a variable.
C) Transcription rate is limited by factors other than activator concentration.
D) Maximum promoter activity is negatively correlated with activator concentration.
E) Transcription rate is by definition maximal in hysteric systems.

Question 77

Which of the following is the correct Hill function for activation?

A) Y = β(X*)^-1/Kⁿ(X*)ⁿ
B) Y = β(X*)ⁿ/(Kⁿ + (X*)ⁿ)
C) Y = β(X*)ⁿ/Kⁿ
D) Y = β(X*)/Kⁿ
E) Y = β(X*)ⁿ/K(X*)ⁿ

Question 78

Which of the following is not a parameter of the Hill function for activation?

A) K
B) order
C) degradation rate
D) activator concentration
E) maximum promoter activity

Question 79

Prostate-specific antigen (PSA)is

A) a promising drug target.
B) a commercialized drug.
C) an activator.
D) a signalling molecule.
E) produced by normal prostate cells.

Question 80

The stimulus-response graph shown is characteristic of

A) hysteresis.
B) feed forward motifs.
C) random switching.
D) saturation.
E) futile cycling.