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Euk Genes > mRNA Stability and Localization > Flashcards

mRNA Stability and Localization Flashcards

(48 cards)

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1
Q

ORF

A

(open reading frame) protein coding region

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2
Q

AUG

A

Start codon, 1st amino acid

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3
Q

UAG, UGA, UAA

A

Stop codon, no amino acid

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4
Q

mRNP

A

messenger ribonucleoprotein

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5
Q

3’ poly-A, poly(A) polymerase (PAP)

A

enzyme adds stretch of polyadenylic acid to 3’ end of RNA

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6
Q

Hairpin/stem-loop

A

2ndary structure RNA of base-paired region (stem) + terminal loop of ssRNA

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7
Q

Why is mRNA unstable?

A

Ribonucleases

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8
Q

Endoribonuclease

A

Cleaves RNA at internal site(s)

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9
Q

Exoribonuclease

A

Removes terminal ribonucleotides from RNA

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10
Q

Enzyme remains associated with substrate while catalyzing removal of nucleotides

A

Processive nuclease

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11
Q

Enzyme that catalyzes removal of only one or a few nucleotides before dissociating from substrate

A

Distributive nuclease

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12
Q

Bacterial mRNA half-lives

A

Few minutes

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13
Q

Eukaryotic mRNA half-lives

A

10-20 minutes yeast, 2-3 hrs mammals

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14
Q

Importance of differential mRNA stability?

A

mRNA abundance and spectrum of proteins

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15
Q

Steady state

A

Concentration of population of molecules where rates of synthesis and degradation are constant

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16
Q

RBPs

A

(RNA-binding proteins) large number exist, uncharacterized

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17
Q

RNA regulons

A

Overlapping sets of regulatory proteins and mRNAs

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18
Q

Prokaryotic mRNA degradation

A

Before translation. Degradosome (RNAse E, PNPase, helicase & accessory enzyme)

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19
Q

mRNA that is simultaneously being translated by multiple ribosomes

A

Polyribosome

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20
Q

mRNA that codes for one polypeptide

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A

Monocistronic mRNA

21
Q

mRNA that codes for several polypeptides

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A

Polycistronic mRNA

22
Q

Protects mRNA from direct 3’ attack (prokaryotes)

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A

Stem-loop structure

23
Q

Most mRNA degradation occurs via…?

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A

Two deadenylation-dependent pathways

24
Q

PABP

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A

Poly(A) binding protein, binds to 3’ stretch of poly(A) on eukaryotic mRNA

25
Deadenylation-dependent pathways
1) 5’ -> 3’ (Dcp + Xm1) 2) 3’ -> 5’ (exosome) Initiated by deadenylation by poly(A) nucleases
26
Competes with translation intitiation complex for 5' cap binding
Decapping enzyme
27
Exosome
Large protein complex, 9 core subunits, interacts with Ski complex
28
Translationally repressed mRNAs particles (aka mRNP granules)?
Maternal mRNA granules, neuronal granules, stress granules
29
Where degradation may occur in cytoplasm
Processing bodies (PBs)
30
Alternative degradation pathways that target specific mRNAS?
Deadenylation-independent decapping, histone degradation via addition of poly(U)-tail, endonucleotic cleavage, miRNA-mediated silencing
31
Cis-elements that affect rate of degradation in mRNAs
Stabilizing and destabilizing elements
32
Destabilizing element example
AU-rich elements (ARE)
33
Stabilizing element example
Iron-response element (IRE)
34
AREs
No strict sequence conservation, promote rapid deadenylation-dependent exosome degradation
35
Iron-response element (IRE)
Stability or translation of mRNAs regulated by cellular iron concentration, Fe low -> Transferrin mRNA stable and IRP in high-affinity binding state
36
Aberrant nuclear RNAs identified and destroyed by...?
RNA surveillance system
37
Yeast TRAMP Complex
Recruits exosome to aberrant RNAs and facilitates 3' to 5' exonuclease activity
38
Defective RNP examples
Misfolded RNA, missing poly(A) tail
39
CUTs
Cryptic unstable transcripts
40
Cryptic unstable transcripts
Non-protein coding RNAs, majority of RNA Pol II transcripts
41
Nonsense-mediated decay (NMD) targets....
mRNAs with premature stop codons, conserved Upf and SMG proteins
42
Recognition of premature termination codon in mammals?
Presence of downstream exon junction complexes (EJC)
43
Recognition of premature termination codon in most organisms?
Unusual 3/ UTR structure or length
44
Nonstop decay (NSD) targets...
mRNAs lacking an in-frame termination codon, requires conserved SKI proteins
45
No-go decay (NGD) targets...
mRNAs with stalled ribosomes in coding regions
46
Localization of mRNA mechanisms (3)?
Uniform distribution but degradation at all sites except translation, freely diffusible but trapped at translation sites, active transport to translation site
47
Zipcode (localization) signal
Any of mRNA cis-elements involved in directing cellular localization
48
Predominant active transport mechanism of mRNPs?
Cytoskeletal tracks

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