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Euk Genes > mRNA Stability and Localization > Flashcards

mRNA Stability and Localization Flashcards

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

A

Monocistronic mRNA

21
Q

mRNA that codes for several polypeptides

A

Polycistronic mRNA

22
Q

Protects mRNA from direct 3’ attack (prokaryotes)

A

Stem-loop structure

23
Q

Most mRNA degradation occurs via…?

A

Two deadenylation-dependent pathways

24
Q

PABP

A

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

25
Q

Deadenylation-dependent pathways

A

1) 5’ -> 3’ (Dcp + Xm1)
2) 3’ -> 5’ (exosome)
Initiated by deadenylation by poly(A) nucleases

26
Q

Competes with translation intitiation complex for 5’ cap binding

A

Decapping enzyme

27
Q

Exosome

A

Large protein complex, 9 core subunits, interacts with Ski complex

28
Q

Translationally repressed mRNAs particles (aka mRNP granules)?

A

Maternal mRNA granules, neuronal granules, stress granules

29
Q

Where degradation may occur in cytoplasm

A

Processing bodies (PBs)

30
Q

Alternative degradation pathways that target specific mRNAS?

A

Deadenylation-independent decapping, histone degradation via addition of poly(U)-tail, endonucleotic cleavage, miRNA-mediated silencing

31
Q

Cis-elements that affect rate of degradation in mRNAs

A

Stabilizing and destabilizing elements

32
Q

Destabilizing element example

A

AU-rich elements (ARE)

33
Q

Stabilizing element example

A

Iron-response element (IRE)

34
Q

AREs

A

No strict sequence conservation, promote rapid deadenylation-dependent exosome degradation

35
Q

Iron-response element (IRE)

A

Stability or translation of mRNAs regulated by cellular iron concentration, Fe low -> Transferrin mRNA stable and IRP in high-affinity binding state

36
Q

Aberrant nuclear RNAs identified and destroyed by…?

A

RNA surveillance system

37
Q

Yeast TRAMP Complex

A

Recruits exosome to aberrant RNAs and facilitates 3’ to 5’ exonuclease activity

38
Q

Defective RNP examples

A

Misfolded RNA, missing poly(A) tail

39
Q

CUTs

A

Cryptic unstable transcripts

40
Q

Cryptic unstable transcripts

A

Non-protein coding RNAs, majority of RNA Pol II transcripts

41
Q

Nonsense-mediated decay (NMD) targets….

A

mRNAs with premature stop codons, conserved Upf and SMG proteins

42
Q

Recognition of premature termination codon in mammals?

A

Presence of downstream exon junction complexes (EJC)

43
Q

Recognition of premature termination codon in most organisms?

A

Unusual 3/ UTR structure or length

44
Q

Nonstop decay (NSD) targets…

A

mRNAs lacking an in-frame termination codon, requires conserved SKI proteins

45
Q

No-go decay (NGD) targets…

A

mRNAs with stalled ribosomes in coding regions

46
Q

Localization of mRNA mechanisms (3)?

A

Uniform distribution but degradation at all sites except translation, freely diffusible but trapped at translation sites, active transport to translation site

47
Q

Zipcode (localization) signal

A

Any of mRNA cis-elements involved in directing cellular localization

48
Q

Predominant active transport mechanism of mRNPs?

A

Cytoskeletal tracks

Euk Genes (13 decks)

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