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Questions and Answers
What roles do A, B, and C play in the example of the repressilator?
What is transcription attenuation primarily associated with?
What function do riboswitches serve in gene expression regulation?
How does low guanine levels affect transcription of purine biosynthetic genes?
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What type of organism utilizes riboswitches to regulate gene expression?
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What kind of feedback loops can be associated with transcriptional circuits?
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Which bases are considered purines in DNA/RNA?
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What can interfere with RNA polymerase during transcription attenuation?
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What role does the lambda repressor protein play under good growth conditions?
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What is a characteristic feature of positive feedback loops in transcriptional circuits?
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What is the function of feed-forward loops in biological systems?
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In eukaryotic cells, what is the outcome of combining various regulatory circuits?
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What is the key concept behind synthetic biology as demonstrated by the Repressilator?
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What type of feedback mechanism does the Repressilator rely on?
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What interaction leads to oscillations in the Repressilator circuit?
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Which of the following best describes the relationship between prophage state and lytic state in lambda phage?
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What is the main function of the tryptophan repressor in prokaryotic gene regulation?
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Which mechanism allows the NtrC protein to activate transcription from a distance?
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What role do the lambda repressor and Cro proteins play in bacteriophage lambda?
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In positive regulation during prokaryotic transcription, what is the primary role of the activator protein?
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What is the significance of a helix-turn-helix DNA binding motif in prokaryotic gene regulation?
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What is the primary effect of transcription attenuation on RNA molecules?
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How do regulatory elements influence transcription in prokaryotes?
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Which statement describes the state of the bacteriophage lambda during the lytic phase?
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What triggers the switch between prophage and lytic states in bacteriophage lambda?
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What is the role of riboswitches in gene control?
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In which way do negative feedback loops function in gene expression?
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During the prophage state, what is the role of the lambda repressor protein?
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What determines the specific binding of the tryptophan repressor to DNA?
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Why are gene regulatory elements important in prokaryotic gene expression?
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Study Notes
Prokaryotic Gene Regulation
- Most common DNA binding motif: helix-turn-helix
- Tryptophan repressor protein contains a helix-turn-helix binding motif
- Tryptophan binding induces conformational change
- Tryptophan repressor binds to the major groove of the DNA double helix
Regulation
- Negative Regulation: RNA polymerase competes with repressor proteins for promoter binding sites
- Positive Regulation: Activator proteins recruit RNA polymerase to the promoter and activate transcription
- Regulatory elements are typically close to the transcriptional start site in prokaryotes
- Regulatory elements can also be found far upstream of the gene
- Regulatory elements can be found downstream of the gene
- Regulatory elements can be found within the gene (introns)
NtrC
- NtrC is a transcriptional activator
- DNA looping allows NtrC to directly interact with RNA polymerase
- DNA looping activates transcription from a distance
Bacteriophage Lambda
- Virus that infects bacterial cells
- Two gene regulatory proteins initiate switching between prophage and lytic pathways: lambda repressor protein (cI) and Cro protein
- lambda repressor and Cro repress each other’s synthesis
Prophage State
- Lambda Repressor occupies the operator
- Lambda repressor blocks synthesis of Cro
- Lambda repressor activates its own synthesis
- Most bacteriophage DNA is not transcribed
Lytic State
- Cro occupies the operator
- Cro blocks synthesis of lambda repressor
- Cro activates its own synthesis
- Most bacteriophage DNA is transcribed
- DNA replication occurs
- New bacteriophage is packaged
- Host cell lysis occurs and bacteriophage is released
Prophage to Lytic State Switching
- Host response to DNA damage causes the switch to the lytic state
- The switch inactivates the repressor
Positive Feedback Loop
- Under good growth conditions, lambda repressor protein turns off Cro and activates itself in a positive feedback loop
- This loop maintains the prophage state
Transcriptional Circuits
- Control various biological processes
Positive Feedback Loops
- Create cell memory
Feed-Forward Loops
-
Measure signal duration
-
Both A and B are required for transcription of Z
-
Brief input: B does not accumulate, Z is not transcribed
-
Prolonged input: B accumulates, Z is transcribed
Synthetic Biology
- Scientists construct artificial circuits to examine their behavior in cells
The Repressilator
- Simple gene oscillator using a delayed negative feedback circuit
- Repressors: Lac, Tet, Lambda
- Predicted: delayed negative feedback gives rise to oscillations
- Repressor genes were introduced into bacterial cells and expression was observed
Transcriptional Attenuation
- Premature termination of transcription
- RNA adopts a structure that interferes with RNA polymerase
- Regulatory proteins can bind to RNA and interfere with attenuation
Riboswitches
- Short RNA sequences that change conformation when bound by a small molecule
- Regulate gene expression
- Examples: Prokaryotic riboswitches that regulate purine biosynthesis
Purine Biosynthesis
- Bases in DNA/RNA include purines (A,G) and pyrimidines (C, U, T)
- Low guanine levels: transcription of purine biosynthetic genes is on
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Description
This quiz explores key concepts of prokaryotic gene regulation, including DNA binding motifs, repressor and activator proteins, and the role of regulatory elements. Understand the mechanisms involved in transcriptional activation and repression, with a focus on the interplay between different proteins and DNA structure.
