Lecture 1 - RNA Gene Regulation Flashcards
When can gene regulation occur?
at every stage of gene expression
RNA can fold into structures that what?
…that perform diverse biological functions
* for ribosomes its a ribozyme
* gene regulation (trp leader)
etc
What directionality does RNA have?
5’ to 3’ directionality (like DNA)
On the ribose sugar, what is located on the 2’?
a 2’ hydroxyl
What is RNA synthesized as?
a single-stranded polymer
Does RNA stay single-stranded?
No, it forms structures… for example, like the transcription terminator hairpin
What is the ribosome?
it is a ribozyme… ribosomal RNA catalyzes peptide bond formation
What is tRNA?
the adapter for translating the genetic information into a polypeptide
What are tRNA’s processed into?
they are processed into a mature form by a ribozyme called RNase P, which is present in all domains of life
What does the spliceosome do?
it catalyzes RNA splicing… it is also a ribozyme
What is a riboswitch?
they are cis-acting RNA chemical sensors
What small molecules and ions can riboswitches sense?
small molecules: purines, amino acids, vitamins etc.
Ions: flourine, iron, manganese, magnesium
What percentage of bacterial genes are thought to be regulated by riboswitches?
3-5%
Riboswitches can control gene expression at several different levels… Name the levels:
transcription, translation, rna stability and rna splicing
In transcription, what does the riboswitch control?
the riboswitch controls whether a terminator hairpin forms
* more rarely, some riboswitches control rho dependent transcription termination
During translation, what does the riboswitch control?
it controls whether the ribosome can bind a Shine-Dalgarno sequence to initiate translation
In RNA stability, what does the riboswitch control?
controls whether an RNA cleaves itself
*self cleavage causes RNA degradation
During RNA splicing, what does the riboswitch control?
whether RNA splicing occurs
What is the riboswitch aptamer?
a chemical sensor that can bind a ligand
What does the expression platform control?
it controls the gene expression based on whether the aptamer bound to its ligand
* it tells the cell to turn gene expression on or off
Without a ligand, what happens to the structure?
only one structure forms
If the ligand is there what happens to the structure then?
both the structures form
In the absence of a metabolite, the terminator hairpin does what and are the genes expressed or not?
- the terminator hairpin terminates transcription before the downstream genes are transcribed
- the genes are not expressed
Give a real life example of of a riboswitch.
the ZTP riboswitch that controls purine biosynthesis
What is an antisense RNA?
an antisense RNA is an RNA strand that is complementary to a segment of an mRNA sequence
Are riboswitch RNA’s cis or trans acting?
cis-acting
Are antisense RNA’s cis or trans acting?
trans-acting
What can antisense RNA’s do?
they can inhibit or activate translation
What is strategy 1 of gene regulation by antisense RNA’s?
the antisense RNA sequesters the ribosome binding site and/or start codon, which blocks translational initiation
What is strategy 2 of gene regulation by antisense RNA’s?
the ribosome binding site and/or start codon is sequesteres by a structure in the mRNA, the antisense RNA opens this structure which permits translation initiation to occur.
How are bacterial promoters recognized?
by sigma factors
Cells need strategies to regulate what?
to regulate gene expression in response to changes in temperature
What does bacteria use to cause a global change in transcription in response to heat shock?
a heat shock sigma factor
What is the RNA thermometer used for?
to control translation of a heat shock sigma factor
The RNA thermometer blocks translation at what temperature?
low temperature
* the AUG start codon is sequestered by RNA secondary structure
The RNA thermometer allows translation at what temperature?
high temperature
* at high temps, the RNA secondary structure is less stable and the AUG codon becomes accessible, therefore allowing the ribosome to bind and initiate translation efficiently
