28 Questions
What is generated from an operon?
Polycistronic transcript
Which sigma factor is most commonly associated with recognizing promoter regions in bacteria?
Sigma 70
How do regulatory proteins control gene expression?
Through the binding of small molecules
What is the role of CAP in gene regulation when bound to cAMP?
Enhances efficiency of RNA polymerase entry, binding, and initiation
Which inhibitor of RNA synthesis works by binding to the beta-subunit of RNA polymerase?
Rifamycin
How do bacteria respond to the presence of lactose in the medium with respect to beta-galactosidase production?
Beta-galactosidase is produced at high levels
Which of the following statements is true about the lifespans of synthesized RNA?
mRNA is unstable and has a half-life of 2 minutes.
Why is the error frequency higher in RNA synthesis compared to DNA replication?
RNA polymerase lacks 3’-5’ exonuclease proof-reading activity.
What is the difference between a CORE ENZYME and a HOLOENZYME?
HOLOENZYME includes α_2, β, β’, and σ subunits.
Which sequence is located upstream of the transcription start site in prokaryotes?
Pribnow box
What is the role of the σ factor in bacterial transcription?
To allow the core RNA polymerase to specifically recognize promoters.
How does termination of transcription occur at rho-independent sites?
A stable GC-rich hairpin followed by 6 uracils causes RNA polymerase to dissociate.
What event occurs after the RNA polymerase releases the σ subunit?
RNA-DNA duplex is broken, and polymerase continues elongation.
Which component is necessary for the opening of the DNA strands around the start site?
Open complex
What is the main reason why RNA polymerase is asymmetric?
It has two alpha subunits and one of the other subunits
What is the function of the rho protein in transcription termination?
To unwind the RNA-DNA complex
What is the purpose of the -10 and -35 boxes in prokaryotic promoters?
To provide a binding site for the sigma subunit
What is the consequence of the lack of 3'-5' exonuclease proof-reading activity in RNA polymerase?
Higher error frequency in RNA synthesis
What is the role of the sigma subunit in bacterial transcription?
To bind to the promoter region
What is the characteristic of the hairpin structure at rho-independent termination sites?
It is rich in uracil residues
What is the effect of a strong promoter on gene expression?
It increases the efficiency of transcription
What is the consequence of the closed complex formation between RNA polymerase and the promoter?
The strands of DNA are opened
What characterizes the mRNA produced from an operon?
Polycistronic transcript
Which sigma factor is specifically associated with heat shock response in bacteria?
Sigma 32
What happens to LAC repressor when lactose is bound?
It ceases to function as a repressor
How does actinomycin D inhibit RNA synthesis?
Binding to double-stranded DNA between GC pairs
What effect does cAMP binding have on the CAP protein in bacterial gene regulation?
It enhances RNA polymerase binding and initiation
Which environmental condition leads to high levels of beta-galactosidase in bacteria?
Low levels of glucose and high levels of lactose
Study Notes
RNA Synthesis
- A single RNA polymerase synthesizes all types of RNA: rRNA, tRNA, and mRNA
- rRNA and tRNA are stable once synthesized, whereas mRNA is unstable with a half-life of 2 minutes
- RNA synthesis requires a DNA template and riboNTPs
Error Frequency and Proofreading
- Error frequency in RNA synthesis is 1 per 10^4 nucleotides, higher than DNA replication
- This is because RNA polymerase lacks 3'-5' exonuclease proofreading activity and there are no other correction mechanisms
RNA Polymerase Structure
- Core enzyme contains α2, β, and β' subunits
- Holoenzyme contains α2, β, β', and σ subunits
- σ subunits are less abundant than core subunits
- RNA polymerase is asymmetric, having two alpha subunits and only one of the other subunits
Promoters and Transcription Initiation
- Promoters are transcription start sites recognized by a core RNA polymerase associated with a σ factor
- Consensus sequence maximizes homology, including the -10/Pribnow box and -35 box conserved upstream of the start site
- Promoter is asymmetric, matching the asymmetric RNA polymerase structure
- Holoenzyme binds to the promoter without opening DNA strands (closed complex)
- Strands of DNA are opened around the start site (open complex), and selection of NTPs occurs
Transcription Elongation and Termination
- RNA-DNA duplex is broken, and polymerase dissociates
- Rho-independent sites terminate transcription due to a GC-rich hairpin followed by 6 uracils
- Rho-dependent sites have a hairpin but no U tract, preceded by a cytosine-rich region
- Rho (ATP-dependent helicase) binds to the cytosine-rich RNA, unwinding the RNA-DNA complex
Regulation of Gene Expression
- Regulation is partly due to promoter efficiency and regulatory proteins controlling access to RNA polymerase
- Promoters have different efficiencies due to sequence differences
- Operon: a set of genes controlled by one promoter, producing a polycistronic transcript
- Sigma factors recognize different promoter regions, regulating gene expression
- Regulatory proteins: repressors block RNA synthesis, while positive regulators enhance RNA polymerase activity
Examples of Gene Regulation
- Lac repressor and CAP regulator: repressor blocks RNA synthesis when bound to DNA, while positive regulator enhances RNA polymerase activity
- Bacteria change protein expression in response to environmental conditions, such as the induction of β-galactosidase in the presence of lactose
Inhibitors of RNA Synthesis
- Actinomycin D inhibits RNA synthesis by binding to dsDNA between GC pairs
- Rifamycin, an antibiotic, binds to the β-subunit of RNA polymerase, blocking bacterial synthesis and used to treat tuberculosis
RNA Synthesis
- A single RNA polymerase synthesizes all types of RNA: rRNA, tRNA, and mRNA
- rRNA and tRNA are stable once synthesized, whereas mRNA is unstable with a half-life of 2 minutes
- RNA synthesis requires a DNA template and riboNTPs
Error Frequency and Proofreading
- Error frequency in RNA synthesis is 1 per 10^4 nucleotides, higher than DNA replication
- This is because RNA polymerase lacks 3'-5' exonuclease proofreading activity and there are no other correction mechanisms
RNA Polymerase Structure
- Core enzyme contains α2, β, and β' subunits
- Holoenzyme contains α2, β, β', and σ subunits
- σ subunits are less abundant than core subunits
- RNA polymerase is asymmetric, having two alpha subunits and only one of the other subunits
Promoters and Transcription Initiation
- Promoters are transcription start sites recognized by a core RNA polymerase associated with a σ factor
- Consensus sequence maximizes homology, including the -10/Pribnow box and -35 box conserved upstream of the start site
- Promoter is asymmetric, matching the asymmetric RNA polymerase structure
- Holoenzyme binds to the promoter without opening DNA strands (closed complex)
- Strands of DNA are opened around the start site (open complex), and selection of NTPs occurs
Transcription Elongation and Termination
- RNA-DNA duplex is broken, and polymerase dissociates
- Rho-independent sites terminate transcription due to a GC-rich hairpin followed by 6 uracils
- Rho-dependent sites have a hairpin but no U tract, preceded by a cytosine-rich region
- Rho (ATP-dependent helicase) binds to the cytosine-rich RNA, unwinding the RNA-DNA complex
Regulation of Gene Expression
- Regulation is partly due to promoter efficiency and regulatory proteins controlling access to RNA polymerase
- Promoters have different efficiencies due to sequence differences
- Operon: a set of genes controlled by one promoter, producing a polycistronic transcript
- Sigma factors recognize different promoter regions, regulating gene expression
- Regulatory proteins: repressors block RNA synthesis, while positive regulators enhance RNA polymerase activity
Examples of Gene Regulation
- Lac repressor and CAP regulator: repressor blocks RNA synthesis when bound to DNA, while positive regulator enhances RNA polymerase activity
- Bacteria change protein expression in response to environmental conditions, such as the induction of β-galactosidase in the presence of lactose
Inhibitors of RNA Synthesis
- Actinomycin D inhibits RNA synthesis by binding to dsDNA between GC pairs
- Rifamycin, an antibiotic, binds to the β-subunit of RNA polymerase, blocking bacterial synthesis and used to treat tuberculosis
This quiz covers the basics of RNA synthesis, including the role of RNA polymerase, the stability of different types of RNA, and the error frequency of RNA synthesis.
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