Week 2 Flashcards
What is negative regulation?
A form of gene regulation in which the binding of a repressor protein inhibits transcription by preventing RNA polymerase from accessing the promoter.
What is positive regulation in prokaryotes?
Positive regulation involves an activator protein recruiting RNA polymerase to the promoter, leading to transcription activation.
Where are gene regulatory elements found?
typically close to the transcriptional start site of the prokaryotic genes
but they can also be found
- far upstream of the gene (left)
- downstream of the gene (right; most common in eukaryotes)
- within gene (intro; only in eukaryotes)
What is an example of a gene regulatory element that is distant from the transcriptional start site and influences transcription?
- NtrC protein is a transcriptional activator
- DNA looping allows NtrC to directly interact with RNA polymerase to activate transcription from a distance
What mechanism allows the bacteriophage lambda to switch between lifestyles?
Positive and negative regulatory mechanisms work together to regulate the lifestyles of bacteriophage lambda.
What is bacteriophage lambda
virus that infects bacterial cells, specifically E. coli. It can exist in two states: the prophage state and the lytic state.
What are the two main regulatory proteins involved in the switch between the prophage and lytic states of bacteriophage lambda?
the lambda repressor protein (cI) and the Cro protein. They repress each other’s synthesis.
What occurs during the prophage state of bacteriophage lambda?
the lambda repressor occupies the operator, blocking the synthesis of Cro, activating its own synthesis (2 functions), and preventing the transcription of most bacteriophage DNA.
What happens during the lytic state of bacteriophage lambda?
the Cro protein occupies the operator, blocking the synthesis of the lambda repressor, allowing its own synthesis (no activator needed), and leading to extensive transcription of bacteriophage DNA, replication, packaging, and release of new bacteriophage through host cell lysis.
What triggers the switch from the prophage to the lytic state?
The switch to the lytic state is triggered by the host’s response to DNA damage, which inactivates the lambda repressor. This is called the induction event
How does the lambda repressor maintain the prophage state?
Under favorable growth conditions, the lambda repressor protein turns off Cro and activates its own synthesis in a positive feedback loop, maintaining the prophage state.
What is a transcriptional circuit?
a regulatory mechanism that controls gene expression through interactions between different regulatory proteins and DNA, exemplified by the prophage-lytic control in bacteriophage lambda.
What is a positive feedback loop in transcriptional circuits?
a regulatory mechanism where the product of a gene enhances its own production, creating a self-amplifying cycle that can lead to stable states or cell memory.
What is a negative feedback loop in transcriptional circuits?
a mechanism where the product of a gene inhibits its own production, helping to maintain homeostasis and prevent overexpression.
What is a feed-forward loop in transcriptional circuits?
a regulatory network where one gene (A) regulates another gene (B), and both A and B are required to activate a third gene (Z). This allows the circuit to measure the duration of a signal.
How do transcriptional circuits contribute to cellular memory?
Transcriptional circuits, particularly through positive feedback loops, can create stable states that allow cells to “remember” past signals, influencing future behavior.
What is synthetic biology in the context of transcriptional circuits?
Synthetic biology involves the design and construction of new biological parts and circuits, allowing scientists to create artificial regulatory networks and study their behavior in cells.
How do transcriptional circuits in eukaryotic cells differ from those in prokaryotic cells?
Eukaryotic transcriptional circuits are typically more complex due to the presence of multiple regulatory elements, introns, and the ability to integrate signals from various pathways.
What is the Repressilator?
a synthetic biology construct that functions as a simple gene oscillator using a delayed negative feedback circuit involving three genes.
What are the components of the Repressilator?
A: Lac repressor
B: Tet repressor (responds to antibiotics)
C: Lambda repressor
How does the Repressilator work?
- A is expressed and represses B.
- B is expressed and represses C.
- C is expressed and represses A.
This creates a feedback loop that results in oscillations of gene expression.
What is the predicted outcome of the Repressilator’s design?
the delayed negative feedback will give rise to oscillations in the expression of the repressor genes.
What was observed when the Repressilator was introduced into bacterial cells?
The introduction of the Repressilator into bacterial cells resulted in increasing amplitude due to bacterial growth
What type of feedback loop does the Repressilator utilize?
utilizes a delayed negative feedback loop, which is essential for generating oscillatory behavior in gene expression.
What is the role of circadian clocks in gene regulation?
Circadian clocks use negative feedback loops to control gene expression in a rhythmic manner, typically on a 24-hour cycle, allowing organisms to synchronize their biological processes with environmental changes.
What is transcriptional attenuation?
a regulatory mechanism that leads to the premature termination of transcription, preventing the synthesis of RNA molecules.
How does transcriptional attenuation occur?
It occurs when RNA adopts a structure that interferes with RNA polymerase, leading to the cessation of transcription.
What role do regulatory proteins play in transcriptional attenuation?
Regulatory proteins can bind to RNA and interfere with the process of attenuation, influencing whether transcription continues or terminates.
What are riboswitches?
short RNA sequences that change conformation when bound by a small molecule, regulating gene expression.
Give an example of how riboswitches function in prokaryotes.
In prokaryotes, a riboswitch regulating purine biosynthesis can detect guanine levels: low guanine allows transcription to proceed, while high guanine levels cause the riboswitch to change shape and terminate transcription.
What happens to transcription of purine biosynthetic genes when guanine levels are low?
When guanine levels are low, transcription of purine biosynthetic genes is on, allowing for the synthesis of necessary enzymes.
What happens to transcription of purine biosynthetic genes when guanine levels are high?
When guanine levels are high, guanine binds to the riboswitch, causing a conformational change that leads to RNA polymerase to terminate transcription. Transcription of purine biosynthetic genes if off.
Why are transcriptional attenuation and riboswitches considered ancient forms of gene control?
They are thought to represent some of the earliest mechanisms of gene regulation, allowing organisms to respond rapidly to changes in their environment.
How is DNA made into RNA?
DNA is transcribed into RNA by the enzyme RNA polymerase
What kind of RNA do cells make?
several types (mRNA,rRNA,tRNA) which are present in eukaryotes and prokaryotes but eukaryotes have more
