Molecular Bio (Exam 4): Regulatory RNA

RNA functions as a regulator by forming secondary structure that changes properties of a _________ _________ (DNA or RNA).

target sequence.

Regulatory RNA can regulate what 3 things?

transcription, translation, and mRNA stability.

Group I introns undertake self-splicing by what process?

transesterification.

What are the only factors required for autosplicing in vitro by group I introns?

metal ions and guanine nucleotide/side.

Pre-mRNA splicing likely shares the mechanism with group __ autocatalytic introns.

II.

Secondary structures within the catalytic site of group __ introns are similar to those formed by snRNAs in pre-mRNA splicing.

II.

Protein factors are not required for group ___ intron splicing.

II.

Transesterification reactions in nuclear introns and group ___ introns are very similar.

II.

Group I/II introns are found in what?

organelles and bacteria.

Group I and II introns splice themselves without function of _________, and do not require ATP.

proteins.

Viroids and virusoids form _________ secondary structure that has self-cleaving activity.

hammerhead.

Hammerhead ribozymes do not require a _________.

protein.

Hammerhead ribozymes have high _________ value.

translational.

What is an RNA whose activity is controlled by the metabolite product or another small ligand?

riboswitch.

In a riboswitch, an element in the ___’ UTR of mRNA can assume alternate base pairing configurations → secondary structure, that can control its own transcription termination or translation.

5.

What is a DNA/RNA or polypeptide region that binds a specific target molecule?

aptamer.

Ligand-binding to aptamer in _________ can result in a conformational change in the RNA.

riboswitch.

What is an RNA element on mRNA that binds a small molecule and regulates translation by own mRNA?

riboswitch.

In most riboswitches, _________ _________ determine the on or off state of the switch.

conformational changes.

In the NMT1 gene, low TPP results in _________ mRNA being produced.

functional.

In the NMT1 gene, high TPP results in a _________ mRNA being produced.

non-functional.

TPP binds to _________ in the intron and regulates the availability of donor.

riboswitch.

What results in individual bases being changed or added at particular positions within an mRNA?

RNA editing.

Result of edited RNA sequence is different from what?

DNA template.

Apoplioprotein-B and glutamate receptors have _________-_________ deaminations catalyzed by cytidine deaminases (APOBECs) and adenosine deaminases (ADARs)

site-specific.

RNA editing can be directed by _________ RNAs.

guide.

Extensive RNA editing in trypanosome mitochondria occurs by insertions or deletions of _________.

uridine.

What is a small RNA whose sequence is complementary to the edited RNA?

guide RNA.

Guide RNA base-pairs with substrate RNA where?

on both sides of region to be edited.

Guide RNA provides a template for the addition or _________.

uridines.

Editosome comprises of:

endonuclease, TUTase, 3’-5’ exoUase, RNA ligase.

What are RNAs that do not contain an open reading frame and therefore do not produce proteins?

ncRNAs.

What is RNA that has a complementary sequence to a target RNA? (artificial or endogenous).

antisense RNA.

ncRNAs form RNA _________ by base pairing with target RNAs, which can occur in the nucleus and cytoplasm.

duplex.

An RNA duplex from ncRNA and target RNA can cause mRNA _________, or inhibition of transcription, processing, transport, and translation.

degradation.

What RNAs regulate transcription, translation, and mRNA stability in bacteria?

sRNA (small).

Which RNA are NOT generated by processing of larger dsRNA precursors, and instead are encoded in their final form by small genes?

sRNAs.

Most sRNAs work by _________ base pairing with complementary target antisense RNA. which is usually aided by Hfq protein.

imperfect.

sRNA in bacteria can _________ or _________ translation.

activate or repress.

What degrades target DNA in CRISPR?

Cas nuclease.

What are widespread regulators in eukaryotes?

MicroRNA.

What is the process by which short antisense RNAs, derived from longer RNAs, inhibit gene expression by translation inhibition, mRNA degradation, or heterochromatin formation?

RNA interference (RNAi).

What results from the RNAi precursor that can be exogenous and endogenous, transposons, and is long dsRNA?

siRNA (short interfering).

What results from the RNAi precursor that is endogenous, short hairpin RNA transcripts?

microRNA (miRNA).

Which results from the RNAi precursor that is endogenous, long single-stranded RNA?

piRNA.

What folds into double-stranded hairpin structures, usually with imperfect base pairing?

pri-miRNA.

What is processed by Drosha in the nucleus?

Pri-miRNA.

What is further processed by Dicer in cytoplasm?

Pre-miRNA.

Double-stranded miRNA products are loaded onto _________, of which Ago proteins are subunits.

RISC.

RISC degrades _________ strand (strand that is not used) and delivers miRNA (guide strand) to target mRNA.

passenger.

RISC degrades passenger strand and delivers miRNA (_________ strand) to target mRNA.

guide.

Drosha and Dicer are both RNase III _________ that process double-strands.

endonuclease.

_________ mainly functions in the nucleus to repress expression of transposons, preserve genome integrity, and control heterochromatic formation.

piRNA.

MicroRNAs regulate gene expression by base pairing with complementary sequences in_________ mRNAs.

target.

miRNA triggers _________ inhibition or degradation of target mRNAs.

translation.

Whether miRNA triggers translation inhibition or degradation depends on the degree of _________ _________ between the target mRNA and miRNA.

base pairing.

miRNA target sequences are usually found in the __’ UTR of mRNAs.

3.

An mRNA can be targeted by multiple _________, and a _________ can target multiple mRNAs.

miRNA.

What can cause general silencing of host genes in mammalian cells if it is longer than 26 nucleotides?

dsRNA.

Long dsRNA activates _________, which inactivates eIF2a by phosphorylation = no translation intiiation.

PKR.

Long dsRNA activates 2’5’ oligoadenylate _________, whose products activates RNase L degrading all RNAs in a cell.

synthase.

Heterochromatin formation requires _________.

siRNAs.

RITS is a form of RNAi in which _________ are used to downregulate transcription by modification and remodeling chromatin.

siRNAs.

Constitutive heterochromatin consists primarily of repeats in simple sequences, that can be transcribed to organize _________.

heterochromatin.

Transcripts are replicated by RNA-dependent RNA _________, forming dsRNA.

polymerase.

dsRNA is processed by _________, incorporated into RITS complex, and loaded to target site.

Dicer.

RITS complex recruits _________ _________ proteins (ex. H3K9 methyltransferase).

histone modification.