module 3 rna

in the initiation complex (of transcription), the first DNA region that is unwound is

-10 Pribnow box sequence

where is the AT-rich sequence located?

-10 pribnow box sequence

what are the two consensus sequences located in bacterial transcription?

-35, -10

eukaryotic signal recognition particle composed of

7SL RNA

what are two common post-transcriptionally edited bases in RNA?

A to I, C to U

what two nucleotides are most abundant in upstream promoter regions in bacteria?

A, T

what are the intron boundaries of the minor spliceosome? (respectively)

AU, AC

standard base pairs in RNA

AU, GC, GU

changes in the phosphorylation pattern of serine residues in CTD

CTD cycle

what is the correct order of assembly in the cellular factory?

DNA -> RNA -> protein

enhancers are

DNA sequences where activators of transcription bind

which of the following macromolecules can store genetic info?

DNA, RNA

which base is used for the 5' cap of eukaryotic mRNAs?

G

order RNA base pair bonds from strongest to weakest

GC > AU > GU

what are the intron boundaries of the major spliceosome? (respectively)

GU, AG

in eukaryotic cells, what polymerase(s) are responsible for transcribing ribosomal RNA?

I and III

what is the most common mRNA methylation?

N6-methyladenosine (m6A)

according to the RNA world hypothesis, which came first?

RNA

eukaryotic lncRNAs are mainly transcribed by

RNA Pol II

eukaryotic miRNAs are mainly transcribed by

RNA Pol II

what is the main functional difference between RNA and DNA?

RNA carries information and acts on molecules; DNA stores information

which is more error prone? DNA polymerase or RNA polymerase?

RNA polymerase

what can cause pausing during Elongation?

RNA secondary structures, backtracking, limited NTP

what is a riboswitch?

RNA that can adopt two different stable structures

what is the ternary complex made up of?

RNAP, DNA, and RNA

how is RNAi a useful research tool?

RNAi can bind complementary RNA sequences and can be used to inactivate genes

how can RNAi be used to fight cancer?

RNAi can inactivate cancer genes by binding to different mRNAs and target them for degradation

5' ends of the primary tRNAs transcripts are processed by

RNAse P

which basal transcription factor is responsible for recognizing the TATA box?

TFIID - TBP subunit

what is a prion?

a type of protein that can trigger normal proteins in the brain to fold abnormally

what is an operon?

a unit made up of linked genes which is thought to regulate other genes responsible for protein synthesis

what is the function of cAMP in regulation of the lac operon?

activates an activator protein

transcription termination where binding of 3' processing factors leads to rearrangement of elongation complex and termination

allosteric model

what are the three models of Pol II transcription termination?

allosteric, torpedo, combination

what are required for initiation of transcription in eukaryotic cells?

basal transcription factors

mechanism of splicing for group II introns?

branch site A

mechanism of splicing for nuclear pre-mRNA?

branch site A

what do RNAs do in the cell?

carry molecules ratchet up the speed of operations switch cellular machines on and off carry coded messages from the nucleus to the ribosome

gene expression that is expressed all the time

constitutive expression

mechanism of splicing for tRNA introns?

endonuclease, ligase

what do activators bind to upstream of the genes?

enhancers

mechanism of splicing for group I introns

exogenous G

in RNA degradation, what do the 5' cap and 3' tail protect the RNA from?

exonucleases

enhancers are most often

far away from the transcription start site

how many different rRNAs do eukaryotes have?

four

how many different tRNAs do eukaryotes have?

greater than 30

what enzymes catalyze addition of 7 methyl guanine cap to the 5' end?

guanylyl transferase and methyl transferase

the C-terminal domain (CTD) of Rpb1 contains 15-50+ ___ repeats

heptapeptide

in eukaryotic cells, mRNA goes through processing before it can be used as a template for protein synthesis. why don't prokaryotic cells have extensive mRNA processing?

in prokaryotes, transcription is coupled with translation

how do the 5' cap and 3' tail affect mRNA stability?

increase stability

gene expression that is normally off, but can be turned on by an inducer

inducible

which transcription termination depends on the sequence and not additional proteins?

intrinsic termination

what does not occur during mrna processing in eukaryotic cells?

introns are joined together

A-to-I editing in mammalian cells mostly occurs in which system?

nervous system (influences synaptic transmission)

do all transcripts made by Pol II have a polyA tail?

no

three mechanisms of mRNA quality control

nonsense, nonstop, no-go

where does eukaryotic mRNA processing and modifications occur?

nucleus

where does polyadenylation of the mRNA occur?

nucleus, occasionally the cytosol

how many RNA polymerases do bacteria have?

one RNA polymerase and several sigma factors

7mG cap is added to the 5' end of RNAs transcribed by which polymerase(s)?

only Pol II

what signal is necessary for termination of transcription and addition of the 3' modifications?

polyA signals

the lac repressor is what type of molecule?

protein molecule

what is the most common unusual base in RNA?

pseudouracil

what does RNA Pol I transcribe?

rRNAs

which eukaryotic RNAs are processed from a single transcript, similar to bacterial codons?

rRNAs

gene expression that is normally on, but can be turned off by a repressor

repressible

what do scientists think was the first RNA that led to life?

self-replicating RNA

what subunit of bacterial RNA polymerase is responsible for promoter recognition?

sigma

which subunit directs RNA polymerase to the promoter?

sigma factor subunit

couples the synthesis of membrane proteins to their proper membrane localization delivers nascent membrane proteins to ER (in eukaryotes) or plasma membrane (in bacteria)

signal recognition particle

splicing sites are recognized by base-pairing with __?

snRNAs

introns are removed from pre-mRNAs by a process called

splicing

what are the main modifications in eukaryotic mRNA?

splicing, capping, polyA tail

what type of RNA has the most unusual base pairs?

tRNA

unusual bases such as inosine and pseudo-uracil more common in:

tRNA (mRNA for the most part have regular bases)

which RNA carries amino acids to the ribosome and helps translate a coded message?

tRNA (transfer RNA)

what is RNP ribozyme (RNase P) responsible for?

tRNA processing

which transcripts are made by Pol III?

tRNAs

presence of secondary structures in the nascent mRNA chain during transcription can lead to

termination of transcription and/or stalling of the polymerase

The promoter sequence of a bacteria is a perfect match to the consensus sequence for sigma factor. If two adenines in the sequence are mutated to guanines, what would be the most likely outcome?

the gene will be transcribed less because sigma factor will have less affinity for the changed sequence

what steps are the sigma factor present?

the sigma factor is only there for the initiation, but leaves during the elongation process after a couple of nucleotides are laid down

how many nuclear RNA polymerases are present in eukaryotes?

three

what enzyme is responsible for resolving the positive and negative supercoils in bacterial transcription?

topoisomerase

transcription termination where nuclease degrades nascent mRNA from 5' end, catches up with elongation complex and displaces Pol II from DNA

torpedo model

trans-splicing can occur in

trypanosomes

do all transcripts made by Pol II have a cap?

yes

is post-transcriptional A-toI editing performed in mammalian cells?

yes, rarely