Chapter 15.3: RNA-Mediated Mechanisms of Gene Regulation Flashcards
What are the 3 ways in which sRNAs regulate the translation of mRNAs?
o Most sRNAs are repressive, meaning that they inhibit translation of their target mRNAs by base pairing with the ribosome binding site
o Some sRNAs activate translation of their target mRNAs by disrupting the formation of a stem-loop structure in the leader of the mRNA that would otherwise block the ribosome binding site
o Another way in which certain sRNAs can influence the expression of particular genes is by promoting the degradation of the mRNA: The double-stranded RNA region resulting from sRNA binding to the mRNA causes the mRNA to be degraded by ribonuclease enzymes
What are allosteric RNA leaders that bind small molecule effectors to control gene expression?
riboswitches
What are the 3 ways in which antisense RNAs regulate genes?
o Some antisense RNAs function like the trans-acting sRNAs: they inhibit translation by base pairing with the sense mRNA and blocking the ribosome binding site
o In other cases, the double-stranded RNA formed by base pairing between the sense mRNA and the antisense RNA can be degraded by ribonucleases
o In some cases, it is not the antisense RNA itself, but the act of transcribing it that inhibits expression of the sense gene; that is, antisense transcription can interfere with initiation of transcription of the sense gene
Why is the 3-4 stem loop configuration called a terminator?
because it forms in the trp operon transcript, RNA polymerase contacts it and stops transcription, producing a short, “attenuated” RNA
What’s an aptamer?
• Leaders that act as riboswitches have a region called the aptamer that binds a particular effector directly
Define attenuation
control of gene expression by RNA leader-mediated premature termination of transcription
What are antisense RNAs and what is their function?
o Some bacterial genes are regulated by RNAs that are complementary in sequence to the mRNA because their transcription template is the opposite strand of DNA
These regulatory RNAs are called antisense RNAs; the mRNAs they regulate are sense RNAs
What happens when tryptophan is present in the 3-4 stem loop configuration?
o When tryptophan is present, the ribosome moves quickly past the trp codons in the RNA leader and proceeds to the end of the leader’s codons, allowing formation of the terminator
What is the expression platform?
• Riboswitches also have a second region, called the expression platform, which controls gene expression by altering its stem-loop structures in response to the aptamer configuration
What acts in trans to regulate the translation of mRNAs?
• Regulatory Small RNAs Act in trans to Regulate the Translation of mRNAs
How do RNA leaders form stem or hairpin loops?
Through complementary base pairing, many RNA leaders form secondary structures called stem loops (or hairpin loops)
Define riboswitches
allosteric RNA leaders that bind small molecule effectors to control gene expression
Describe the outcome of Yanofsky TrpR experiments?
- Showed that the trp genes of trpR- mutants are not completely de-repressed (turned on) when tryptophan is present in the growth medium
- The removal of tryptophan from a medium in which trpR- mutants are growing caused expression of the trp genes to increase threefold
- Found that this repressor-independent change in the trp operon expression involves the production of alternative trp operon transcripts
What is the terminator?
o The 3-4 stem loop configuration
What is the antiterminator?
• The alternative RNA structure, called the antiterminator, forms by base pairing between regions 2 and 3
What are sRNAs and their function?
o Bacterial genomes encode many small RNA molecules, or sRNAs, that regulate translation in trans by base pairing with mRNAs
Describe the first conformation (3-4) of the folding of the trp RNA leader
• The first conformation contains two stem-loop structures: Region 1 makes a stem loop with region 2, while region 3 associates with region 4
What does allostery of a protein mean?
changes in their shapes that occur when they bind to small molecules
What is control of gene expression by RNA leader-mediated premature termination of transcription?
attenuation
What act in cis to regulate gene expression?
• Diverse RNA Leader Devices Act in cis to Regulate Gene Expression
What happens in the absence of tryptophan in the 2-3 configuration?
o In the absence of tryptophan, the ribosome stalls at the two trp codons in the RNA leader because of the lack of the charged tRNATrp in the cell. The antiterminator is then able to form, which prevents formation of the terminator. As a result, transcription proceeds through the leader into the structural genes
What is the RNA leader sequence?
o All bacterial mRNAs begin with an untranslated region called the 5’ UTR, or RNA leader sequence
What is the function of stem or hairpin loops?
• The stem loops can terminate transcription of the rest of the mRNA prematurely, or they can prevent translation by blocking access of the mRNA to the ribosome binding site
Why can’t the RNA leader form the terminator in the 2-3 stem loop configuration and what happens as a result?
o The leader RNA cannot form the terminator (because region 3 is no longer available to pair with region 4) and as a result, the transcription machinery continues to produce a full-length mRNA that includes the trp structural gene sequences
What does the allostery of the regulatory protein enable?
• Allostery of the regulatory proteins (changes in their shapes that occur when they bind to small molecules) enables genes to be turned on or off in response to the cellular environment
