15 Questions
What is the role of Hfq in bacterial small RNA regulation?
Hfq helps sRNA bind mRNA target and stabilizes the binding
What happens when a riboswitch binds to S-adenosylmethionine (SAM)?
It causes rearrangements in the aptamer and expression platform, affecting gene expression
How do riboswitches respond to metabolite binding?
They exhibit protein-like structure diversity
What is the function of regulatory small RNAs (sRNAs) in bacteria?
They can repress levels of one protein and promote another
How do bacterial small RNAs (sRNAs) affect mRNA translation?
They can cause mRNAs destruction by RNase, blocking translation
Riboswitches are only found in eukaryotic cells.
False
Bacterial small RNAs (sRNAs) always repress levels of proteins and never promote them.
False
Riboswitches can bind and respond to uncharged tRNAs.
True
Activated riboswitch structures always block further transcription or translation.
False
Riboswitches exhibit limited structural diversity compared to proteins.
False
Explain the regulatory roles of single stranded RNA in gene transcription and translation.
Single stranded RNA can facilitate regulatory roles by serving as regulators of gene transcription and translation, and small RNAs (sRNAs) can repress levels of one protein and promote another.
Describe the function and mechanism of riboswitches in gene transcripts.
Riboswitches are built-in metabolite sensors that control mRNA translation in response to changes in metabolite amount. They consist of an aptamer region that binds a metabolite and an expression platform that changes conformation in response to metabolite binding. This results in altered transcription, translation, or splicing of RNA.
How do bacterial small RNAs (sRNAs) regulate gene expression and mRNA translation?
Bacterial small RNAs (sRNAs) can regulate gene expression by binding to complementary target mRNAs to form double-stranded RNAs, leading to mRNA destruction by RNase and blocking translation. However, in some cases, sRNAs can also stimulate translation.
Explain the mechanism of attenuation and its effect on RNA Pol transcription and ribosomal translation.
Attenuation causes RNA Pol dissociation, blocking any further RNA Polymerase transcription of the transcript. It can also block ribosomal translation of the transcript by preventing initiation through the formation of a structure with the ribosome binding site (RBS).
How do riboswitches respond to metabolite binding and what are the different outcomes of metabolite binding to riboswitches?
Riboswitches respond to metabolite binding by undergoing conformational changes, which can either activate or prevent transcription termination, block or increase access to ribosome binding site, and alter ribosome interactions. They can bind and respond to various metabolites, each with unique structures.
Study Notes
Eukaryotic Promoters and Transcription Initiation
- Eukaryotic promoters contain subsets of four different sequences
- Prokaryotic σ factor replaced by many eukaryotic general transcription factors (GTFs) that assist RNA polymerase
- Prereplicative complex involves sequential TFII assembly followed by phosphorylation events
- Eukaryotic RNA polymerase II targeted by multiple protein kinases for promoter escape
Mediator Complexes and RNA Polymerase II Activity
- Multisubunit Mediator complexes generally needed for RNA polymerase activity
- RNA polymerase II phosphorylation serves as a switch between initiation and elongation
Elongation and Processing
- Elongation factor proteins accelerate RNA growth by stopping pauses (errors)
- FACT-mediated reversible histone removal and replacement keeps DNA packed and protected
- Proper elongation, termination, and processing require enzyme recruitment
- RNA capped early to protect transcript and ensure proper processing
- RNA 5’ capping needs GTP, S-adenosyl methionine (SAdoMet), and three sequential enzymes
- RNA’s poly-A tail partly encoded by DNA, RNA cleaved, and enzymes add extra A
Transcriptional Termination
- Transcriptional termination models differ in that one needs RNase (torpedo)
RNA Polymerase I and III
- RNA genes transcribing RNA polymerase I and III require specialized GTFs
Regulatory RNAs
- Regulatory RNAs exploit Watson-Crick base-pairing to other RNAs and DNAs, blocking binding and altering RNA structure
Test your knowledge of nucleic acids biochemistry, regulatory RNAs, and examples of prokaryotic and eukaryotic promoters with this quiz. Review the concepts of eukaryotic promoter sequences, the role of sigma factors and general transcription factors, as well as the process of pre-replicative complex assembly and promoter escape.
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