Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
74 Cards in this Set
- Front
- Back
|
hnRNA stands for...
|
heterogeneous nuclear RNA
|
|
|
What does T1 Rnase do?
|
cuts up RNA by cleaving on the 3’ side of G residues.
|
|
|
What does Pancreatic Rnase do?
|
cleaves on the 3’ side of U and C residues.
|
|
|
How was it found out that mRNA is poly adenylated?
|
the mRNA was treated with T1 Rnase and Pancreatic Rnase and instead of small fragments as a result, there were large portions of just Adenine.
|
|
|
How many A's make up the polyadenylated tail?
|
150-200
|
|
|
What was the result of the Darnell Experiment?
|
mRNA molecules somehow start large in the
nucleus, but become smaller by the time they get to the cytoplasm (they are spliced) |
|
|
Are bacterial mRNAs routinely spliced and polyadenylated?
|
no
|
|
|
What is oligo-dT cellulose chromatography?
|
A way of separating mRNAs from the other RNAs by sending them through a column with lots of T's, then the polyadenylated tail base pairs with the T's and is separated from rRNA and tRNA.
|
|
|
What end of mRNA is polyadenylated?
|
3 prime end
|
|
|
What end of mRNA is capped?
|
5 prime end
|
|
|
Describe the 5’-m7G cap.
|
The 5 prime end has three phosphates attached to it which in turn attaches to the 5 prime end of a sugar with a 7-methyl guanine attached
|
|
|
What is the difference between mRNA in the cytoplasm and hnRNA in the nucleus.
|
hnRNA is heavier than mRNA because it hasn't had its introns spliced out yet.
|
|
|
When is the 5’-m7G cap added?
|
just after transcription initiation, just as the 5’ end of the mRNA emerges from the pol II elongation complex.
|
|
|
how did Pierre Chambon put the ovalbumin mRNA into a plasmid?
|
He Reverse transcribed the mRNA using oligo-dT primer (on the polyadenylated tail) then used DNA pol I to synthesize top strand
|
|
|
What is cDNA?
|
it is a ds Nucleic Acid made by polymerizing a complement strand to mRNA.
|
|
|
What does EcoRI have to do with ovalbumin mRNA?
|
When Chambon sequenced ovalbumin cDNA, there were no EcoRI sites. However, treating the genomic DNA with EcoRI showed breaks. This led to the discovery of splicing out introns.
|
|
|
Explain Chambon's experiment.
|
-Get ovalbumin mRNA
-insert it into plasmid -sequence it to see that it has no EcoRI sites -treat genomic ovalbumin DNA with EcoRI and southern blot it to see that it does have EcoRI sites -synthesize ss chromosomal DNA and hybridize to ovalbumin mRNA -take electron microscopic photo to see introns |
|
|
Pre-mRNA
|
mRNA before splicing
|
|
|
Mature mRNA
|
mRNA after splicing
|
|
|
Alternative splicing
|
genes encode different proteins depending on how introns are spliced out according to their alternate splice sites.
|
|
|
spliceosome
|
The complete assembly of snRNPs and other proteins that participate in splicing
|
|
|
What are involved in splicing?
|
The U1-6 (skip 3) snRNAs and their corresponding snRNPs
|
|
|
The Intron sequence is almost always what?
|
GU…AG
|
|
|
Branching nucleotide
|
(always A) is a sequence-based landmark to guide splicing, usually 15-40 nt from 3’ splice site
|
|
|
Transesterfication
|
the reaction that connects the 5 prime splice site to the branching nucleotide and the two exons together to perform splicing.
|
|
|
Laureate
|
the structure caused by transesterfication of the 5 prime splice site to the branching site (makes a loop)
|
|
|
Co-transcriptional process
|
process that happens at the same time as transcription. Splicing is a Co-transcriptional process.
|
|
|
Primary transcript
|
pre-mRNA, mRNA before it is spliced
|
|
|
Poly-A polymerase (PAP)
|
polyadenylates eukaryotic mRNA as triggered by the sequence AAUAAA
|
|
|
Riboregulation
|
(regulation by RNA)
|
|
|
attenuator
|
a 3/4 hairpin that terminates transcription
in trp operon regulation |
|
|
antiterminator
|
a 2/3 hairpin that prevents the attenuator from forming, allowing transcription to continue
in trp operon regulation |
|
|
riboswitches
|
cis-acting RNA elements that directly detect small molecule ligands and turn genes off in there presence
|
|
|
What are the three categories of small molecule ligands.
|
amino acids, vitamins, or even specific metals
|
|
|
sRNAs
|
small, non-coding RNA molecules
function to regulate gene expression by base-pairing to RNAs transcribed from other locations in the genome |
|
|
2/3 hairpin
|
prevents the attenuator from forming, allowing transcription to continue
antiterminator in trp operon regulation |
|
|
3/4 hairpin
|
terminates transcription
attenuator in trp operon regulation |
|
|
Pyrimidine rich tract
|
a section of intron that is between the branch site and 3 prime splice site.
|
|
|
What chemistry goes on in transesterification?
|
the OH groups attack.
|
|
|
TrpL
|
short leader peptide involved in Trp Opereron Regulation
|
|
|
When and why does trp repressor bind?
|
When trp levels are high, some trp binds to the trp repressor causing it inhibit transcription of the trp synthesis genes so you don't get too much trp.
|
|
|
How do sRNAs function to regulate gene expression?
|
by base-pairing to RNAs transcribed from other locations in the genome
|
|
|
What are Mr. Fire and Mr. Mello known for?
|
Eukaryotic RNA interference
|
|
|
Why does only dsRNA have the effect of gene interference?
|
Because dicer can use it to make mature RISC
|
|
|
What does dicer do?
|
it cleaves dsRNA leaving 3 prime overhangs, then makes RISC loading complex to produce mature RISC with antisense strand as guide strand
|
|
|
miRNAs
|
micro RNAs that are dsRNAs produced by the organism in order to regulate its gene activity through dicer processing.
|
|
|
Howard Dintzis Experiment
|
-to find what direction translation occurs
-pulse reticulocytes with 3H-leu -lyse cells and isolate completed peptides -separate on paper with electrophoresis -measure radioactivity |
|
|
In what direction does protein synthesis proceed?
|
N->C
|
|
|
explain the Nirenberg Matthaei experiment
|
-to figure out what bases code for what amino acids
-prepare cell-free protein synthesis soln. -dump in UUUUU and see what amino acid you get |
|
|
Explain the Crick Experiment
|
-to determine how many bases are required to code for an amino acid.
-noticed that bacteriophages with 3 frameshift mutations had normal phenotypes |
|
|
3’ acceptor stem
|
the CCA sequence that all tRNAs have in common, it sticks out over the 5 prime end and is what holds the proteins.
|
|
|
Amino acids are attached to tRNA molecules by what?
|
aminoacyl-tRNA synthetases
|
|
|
if the codon is GCC, the anticodon is what?
|
GGC
|
|
|
What two bases can pair unconventionally because of "wobble"?
|
G and U
|
|
|
The A site of a Ribosome
|
is where aminoacylated tRNAs enter
|
|
|
The P site of a Ribosome
|
is the site of peptidyl transfer
|
|
|
The E site of a Ribosome
|
is for tRNA exit
|
|
|
the Shine-Dalgarno sequence
|
a purine-rich sequence just upstream of the AUG
|
|
|
A strong Shine-Dalgarno sequence is...
|
AGGAGGNNNNNAUG
|
|
|
Ribosome binding site (RBS)
|
Shine-Dalgarno sequence
|
|
|
16S rRNA
|
a type of rRNA that makes up the 30S subunit and binds to the shine-delgarno sequence
|
|
|
What are the Initiation factors?
|
IF1
IF2 IF3 help position initiator fMet-tRNAfMet at the P-site |
|
|
Initiator fMet-tRNA
|
it is only involved in translation initiation, it's positioning in the p-site recruits the 50S subunit
|
|
|
EF-Tu
|
introduces tRNAs to the A site
|
|
|
EF-G
|
stimulates translocation
|
|
|
what are the Elongation factors?
|
EF-Tu
EF-G |
|
|
Peptidyltransferase center
|
place where the peptides are connected
|
|
|
Ribosome Recycling Factor (RRF)
|
In cooperation with factors EF-G and IF3, it stimulates disassembly of the ribosome, liberating free mRNA and tRNA molecules, and free 30S and 50S ribosomal subunits.
|
|
|
Do eukaryotes have a shine-delgarno sequence?
|
no
|
|
|
Kozak sequence
|
(CCACCAUGG) is known to be quite efficient for translation initiation in mammalian cells
|
|
|
In Eukaryotes, is the initiator tRNA charged with Met or fMet?
|
Met
|
|
|
Where are the proteins on the ribosome?
|
on the outside
|
|
|
siRNA
|
the product of dsRNA being chopped by dicer (has the 3 prime overhangs)
|
|
|
How is translation different in Eukaryotes?
|
-no shine-delgarno sequence (special IF)
-AUG is usually used in Kozak sequence -Met, not fMet is used |
