RNA structure & Processing (Post-Transcription)

Question 1

What is the chemical structure of RNA?

Answer 1

Mostly single stranded but can base-pair with complementary sequence within itself.

Question 2

What are coding RNAs?

Answer 2

Messenger RNAs (mRNA) that code for synthesis of proteins

Question 3

Match the following non-coding RNAs to their definitions:

1) Ribosomal RNAs (rRNA)
2) Transfer RNAs (tRNA)
3) Small nuclear RNAs (snRNA)
4) Small nucleolar RNAs (snoRNA)
5) Micro RNAs (miRNA)
6) Short interfering RNAs (siRNA)
7) Piwi-interacting RNAs (piRNA)
8) Long non-coding RNAs (lncRNA)

A) Important in protein synthesis; adapter between mRNA and amino acids with a complex tertiary structure

B) Regulate gene expression by blocking translation of specific mRNAs (can also increase degradation)

C) Scaffolds for chromatin folding; X-chromosome inactivation and more. Controversial.

D) 1) primary component of the ribosome & 2) catalyze protein synthesis

E) Involved in pre-mRNA splicing (attach to proteins to form snRNPs - snRiboNucleoProtein /splicesome). There is various kinds; U1, U2, U4, U5, U6 snRNA

F) Processing and chemical modification of rRNAs (increase stability, half life and optimal function)

G) Regulate gene expression by blocking translation of specific mRNAs (can also increase degradation)

H) Bind to piwi proteins and protect the germ line from transposable elements.

Answer 3

Ribosomal RNAs (rRNA): 1) primary component of the ribosome & 2) catalyze protein synthesis

Transfer RNAs (tRNA): Important in protein synthesis; adapter between mRNA and amino acids with a complex tertiary structure

Small nuclear RNAs (snRNA): Involved in pre-mRNA splicing (attach to proteins to form snRNPs - snRiboNucleoProtein /splicesome). There is various kinds; U1, U2, U4, U5, U6 snRNA

Small nucleolar RNAs (snoRNA): Processing and chemical modification of rRNAs (increase stability, half life and optimal function)

Micro RNAs (miRNA): Regulate gene expression by blocking translation of specific mRNAs (can also increase degradation)

Short interfering RNAs (siRNA): Regulate gene expression by blocking translation of specific mRNAs (can also increase degradation)

Piwi-interacting RNAs (piRNA): Bind to piwi proteins and protect the germ line from transposable elements.

Long non-coding RNAs (lncRNA): Scaffolds for chromatin folding; X-chromosome inactivation and more. Controversial.

Question 4

Which non-coding RNAs are important for regulating gene expression?

Answer 4

Micro RNAs (miRNA)
Short interfering RNAs (siRNA)

Question 5

What does post-transcriptional gene control involve?

Answer 5

1) Processing of Eukaryotic Pre-mRNA
2) Regulation of Pre-mRNA processing
3) Transport of mRNA across the nuclear envelope
4) Processing of rRNA and tRNA

Question 6

What is the difference between pre-mRNA and mRNA?

Answer 6

pre-mRNA: mRNA precursor containing introns and not cleaved at the poly(A) site

mRNA: fully processed mRNA with 5’cap, introns removed by RNA splicing and a poly(A)tail

Question 7

Where do the properly processed mRNAs go from the nucleus? What happens to the improperly processed mRNA?

Answer 7

Properly processed mRNAs - exported to the cytoplasm so they can be translated by ribosome

Improperly processed mRNAs = blocked from export to the cytoplasm, degraded by the EXOSOME complex that has lots of ribonucleases. This complex can also modify the mRNA to make it functional.

Question 8

Briefly describe the processing of eukaryotic pre-mRNA.

Answer 8

Pre-mRNA is capped, polyadenylated, spliced, and associated with RNPs (ribonucleoproteins) in the nucleus before export to the cytoplasm.

Splicing is done by a large ribonucleoprotein splicesome complex through two TRANSESTERIFICATION reactions.

Question 9

A network of interactions between SR (serine-arginine rich) proteins, snRNPs, and splicing factors form a ______-____ recognition complex that specifies correct _____ sites.

Answer 9

Cross-exon

Splice

Question 10

What are lariat RNAs?

Answer 10

The introns spliced out of the mRNA that are circular molecules with a short tail.

Question 11

What is the G value paradox? How is it explained?

Answer 11

The number of protein-coding genes does not correlate with biological complexity.

It is in part due to differential processing of pre-mRNAs! (One protein coding gene can yield multiple protein isoforms?)

Question 12

What are the different forms of alternative splicing? Briefly describe them.

Answer 12

1) Constitutive splicing: remove all introns, stitch all exons together

2) Exon skipping: an exon is skipped and still yields a functional protein

3) Intron retention: can have an intron retained as a “pseudo exon.” can be used to suppress protein activity.

4) Mutually exclusive exons: some exons never together; one or the other. Could be due to having different substrates of isoforms or having opposing catalytic activity.

5) Alternative 5’ splice site: what’s at the beginning of the mRNA is different

6) Alternative 3’ splice site: what’s at the end of the mRNA is different

Question 13

Is the largest human gene the human gene with most exons?

Answer 13

No! The largest gene (Contactin-associated protein like 2 gene) has 24 exons spanning millions of base pairs, while the human gene with most exons (TTN gene) has 346 exons spanning 300,000 base pairs.

Question 14

What is the difference between prokaryotic and eukaryotic mRNA?

Answer 14

Prokaryotic mRNA:
- no 5’ cap
- no polyA tail
- several genes of an operon transcribed into one mRNA
- one mRNA leads to multiple proteins

Eukaryotic mRNA:
- 5’ cap
- polyA tail
- one gene transcribed into one mRNA
- one mRNA leads to one protein (not considering alternative splicing)

Question 15

What does RNA processing produce in eukaryotes?

Answer 15

RNA processing produces functional mRNA.

Question 16

Where does RNA polymerase start transcription, where does it end?

Answer 16

RNA polymerase starts transcription at gene nucleotide +1, which is upstream (“before”) of the codon that encodes the first amino acid.

RNA polymerase stops transcription downstream (“after”) of the translation STOP codon.

Question 17

What are the 5’ and 3’ untranslated regions (UTRs) of the mRNA?

Answer 17

These regions are transcribed into mRNA but will not be translated into proteins by the ribosome.

5’ UTR is recognized by the ribosome to bind and initiate translation.

3’ UTR is after the STOP codon.

Question 18

Match the steps of RNA processing:

1) Step 1
2) Step 2
3) Step 3
4) Step 4

A) Endonuclease cleaves primary transcript (downstream of the STOP codon) at the poly(A) site

B) POLY(A) POLYMERASE adds 100-200 A residues

C) For short primary transcripts with few introns, splicing occurs after step 3.
For long primary transcripts with multiple introns, introns spliced out at the nascent RNA during transcription.

D) Nascent RNA 5’ end capped with 7-METHYLGUANYLATE during formation of the RNA transcript. Transcription terminated at one of multiple termination site downstream from the poly(A)site

Answer 18

Step 1: Nascent RNA 5’ end capped with 7-METHYLGUANYLATE during formation of the RNA transcript. Transcription terminated at one of multiple termination site downstream from the poly(A)site

Step 2: Endonuclease cleaves primary transcript (downstream of the STOP codon) at the poly(A) site

Step 3: POLY(A) POLYMERASE adds 100-200 A residues

Step 4: For short primary transcripts with few introns, splicing occurs after step 3.
For long primary transcripts with multiple introns, introns spliced out at the nascent RNA during transcription.

Question 19

What is the function of the poly(A) tail?

Answer 19

• Stabilizes the mRNAs in the nucleus and cytoplasm
• Involved in mRNA translation
• Protects mRNA from being degraded by exonucleases

Question 20

What is the function of 5’ Methylated cap?

Answer 20

• Protects mRNA from enzymatic degradation
• Assists export of the mRNA to the cytoplasm
• Bound by a protein factor required by ribosome to begin translation

Question 21

(T/F) 5ʹ→5ʹ Linkage of 7-methylguanylate to the initial nucleotide of the mRNA molecule and methyl group addition to the 2ʹ hydroxyl of the ribose of base 1 occur in all animal and most plant cells.

Answer 21

True!

Question 22

(T/F) The methyl group can only be added to the 2ʹ hydroxyl of the ribose of base 1.

Answer 22

False! It can be added in base 2 as well.

Yeasts cells lack methyl group on base 1, but have it on base 2. While, vertebrate cells have methyl on both bases.

Question 23

Match the steps of the synthesis of the 5’cap on eukaryotic mRNA:

1) Step 1
2) Step 2
3) Step 3
4) Step 4

A) GUANYLYL TRANSFERASE links GMP residue from GTP to the 5ʹ diphosphate of the transcript, creating a guanosine 5ʹ-5ʹ triphosphate structure.

B) 2’-O-METHYL TRANSFERASE – transfers methyl group from
S-adenosylmethionine to the 2ʹ oxygens of riboses of the first one or two RNA nucleotides (base 1/base 2)

C) PHOSPHOHYDROLASE removes the γ phosphate, while α and β phosphates remain associated with the cap

D) GUANYLYL-7-METHYL TRANSFERASE transfers methyl
group from S-adenosylmethionine to the guanine N7 position

Answer 23

Step 1: PHOSPHOHYDROLASE removes the γ phosphate, while α and β phosphates remain associated with the cap (all attached to the first base of pre-mRNA)

Step 2: GUANYLYL TRANSFERASE links GMP residue from GTP to the 5ʹ diphosphate of the transcript, creating a guanosine 5ʹ-5ʹ triphosphate structure.

Step 3: GUANYLYL-7-METHYL TRANSFERASE transfers methyl
group from S-adenosylmethionine to the guanine N7 position

Step 4: 2’-O-METHYL TRANSFERASE – transfers methyl group from
S-adenosylmethionine to the 2ʹ oxygens of riboses of the first one or two RNA nucleotides (base 1/base 2)

Question 24

What is S-adenosylmethionine?

Answer 24

Methyl donor - gives methyl to the 5’ cap and to the 2ʹ hydroxyl of the ribose of base 1 or base 2 of the mRNA.

Question 25

What is the RNA recognition motif (RRM)?

Answer 25

Most common RNA-binding domain in heterogeneous nuclear ribonuclearprotein proteins (hnRNP proteins) and other RNA-binding proteins. It is composed of two α helices and four β strands. It has highly conserved RNP1 and RNP2 regions, which are located in the two central β strands.

Question 26

What are the sex-lethal RNA recognition motif (RRM) domains?

Answer 26

Two RRM domains in Drosophila melanogaster Sex-lethal (Sxl) protein. The domains are oriented with the β sheets of the RRMs facing toward each other. The domains, together, bind a nine-base sequence in transformer pre-mRNA to the surfaces of the positively charged β sheets.

Question 27

What are the intron splice site invariant bases (flanking bases found at frequencies higher than expected for a random distribution)?

Answer 27

5' GU: splice donor 3' AG: splice acceptor Branch point adenosine *Most conserved + important regions for splicing *10/10 times, there is gonna GU at that 5' site, there is gonna AG at that 3' site and Adenosine in the branch point. *This is what the two transesterification reactions involve

Question 28

What is the polypyrimidine tract in the pre-mRNA? What is the central region?

Answer 28

Polypyrimidine tract: found in most introns near the 3' end Central region: 40 bases-50kilo bases long. Not conserved, can be varied. Regulatory regions.

Question 29

How many nucleotides at each end of an intron are necessary for splicing to occur at normal rates?

Answer 29

30-40 nucleotides

Question 30

Match the following step of the two transesterification reactions that result in the splicing of exons in pre-mRNA: 1) Reaction 1 2) Reaction 2 A) 3' Oxygen of EXON 1 binds to the 5' Phosphate of EXON 2, breaking the ester bond between the phosphate of EXON 2 and the INTRON's 3' oxygen. B) 5' Phosphorus of the INTRON binds to 2' Oxygen of BRANCH POINT A (ester bond) by breaking its bond with the 3' Oxygen of EXON 1 (ester bond).

Answer 30

Reaction 1: 5' Phosphorus of the INTRON binds to 2' Oxygen of BRANCH POINT A (ester bond) by breaking its bond with the 3' Oxygen of EXON 1 (ester bond). Reaction 2: 3' Oxygen of EXON 1 binds to the 5' Phosphate of EXON 2, breaking the ester bond between the phosphate of EXON 2 and the INTRON's 3' oxygen. The two exons are joined, the intron is released as a LARIAT stricture. *look at slide 20 to fully understand

Question 31

What are the key oxygens in the two two transesterification reactions that result in the splicing of exons in pre-mRNA?

Answer 31

1) 3' oxygen of exon 1 2) 2' oxygen of branch point A 3) 3' oxygen of intron

Question 32

snRNAs base pair with the pre-mRNA during splicing. Match the following snRNAs to what they base pair. 1) U1 snRNA 2) U2 snRNA A) Base pairs with sequence surrounding the branch point A B) Base pairs across 5' splice site exon-intron junction

Answer 32

snRNAs base pair with the pre-mRNA. U1 snRNA: base pairs across 5' splice site exon-intron junction U2 snRNA: base pairs with sequence surrounding the branch point A. *U cause they are rich in uracil!

Question 33

Why is branch point A not base paired but only its surroundings by U2 snRNA?

Answer 33

So that it can bulge out to allow the 2' OH to participate in the first transesterification reaction.

Question 34

What happens if there is a mutation in the pre-mRNA 5' splice site and U1 snRNA can no longer base pair to it? How is this restored?

Answer 34

Splicing is blocked! U1 RNA has a compensating mutation, that restores the base pairing, that restores the splicing.

Question 35

What is a spliceosome? What is it composed of?

Answer 35

A massive complex machinery that carries out splicing. It is composed of over 200 proteins in eukaryotes and 5 snRNAs (U1, U2, U4, U5, U6).

Question 36

How much introns does each splicing event remove?

Answer 36

One intron is removed in each splicing event.

Question 37

Fill in the blanks: All eukaryotic mRNAs have a 3' poly (A) tail, except for ______ mRNAs. 3' cleavage and polyadenylation of pre-mRNAs are _______ _______.

Answer 37

Histone! Tightly coupled

Question 38

Match the following steps of cleavage and polyadenylation of pre-mRNAs in mammalian cells: 1) Step 1 2) Step 2 3) Step 3 4) Step 4 A) PAP (Poly(A) polymerase) stimulates cleavage at a poly(A) cleavage site (typically 15–30 nucleotides 3ʹ of the upstream poly(A) signal). B) Cleavage factors are released; the downstream RNA cleavage product rapidly degraded. SLOW ADENYLATION: PAP adds 12 A residues (from ATP) at a slow rate to the 3' hydroxyl group generated by cleavage reaction. C) RAPID ADENYLATION: PABPN1 (Nuclear poly(A)-binding protein) binds to the initial short poly(A) tail and accelerates the rate of addition by PAP. D) CPSF (Cleavage and polyadenylation specificity factor) binds to the upstream AAUAAA poly(A) signal. Then, CStF (Cleavage Stimulation Factor) interacts with a downstream GU- or U-rich sequence and with bound CPSF, forming a loop in the RNA. Lastly, CFI (cleavage factor I) and CFII bind to stabilize the complex.

Answer 38

Step 1: CPSF (Cleavage and polyadenylation specificity factor) binds to the upstream AAUAAA poly(A) signal. Then, CStF (Cleavage Stimulation Factor) interacts with a downstream GU- or U-rich sequence and with bound CPSF, forming a loop in the RNA. Lastly, CFI (cleavage factor I) and CFII bind to stabilize the complex. Step 2: PAP (Poly(A) polymerase) stimulates cleavage at a poly(A) cleavage site (typically 15–30 nucleotides 3ʹ of the upstream poly(A) signal) Step 3: Cleavage factors are released; the downstream RNA cleavage product rapidly degraded. SLOW ADENYLATION: PAP adds 12 A residues (from ATP) at a slow rate to the 3' hydroxyl group generated by cleavage reaction. Step 4: RAPID ADENYLATION: PABPN1 (Nuclear poly(A)-binding protein) binds to the initial short poly(A) tail and accelerates the rate of addition by PAP.

Question 39

What signals PAP to stop adding As after 200-250 A residues have been added?

Answer 39

PABPN1 - Nuclear poly(A)-binding protein

Question 40

Match the following factors of cleavage and polyadenylation of pre-mRNAs in to the steps they are involved in: 1) Step 1 2) Step 2 3) Step 3 4) Step 4 A) PAP B) PABN1 C) CPSF, CStF, CFI, CFII D) PAP, cleavage factors removed

Answer 40

Step 1: CPSF (Cleavage and polyadenylation specificity factor), CStF (Cleavage stimulation factor), CFI, CFII Step 2: PAP (Poly(A) polymerase) Step 3: PAP, cleavage factors removed Step 4: PABN1 (Nuclear poly(A)-binding protein)

Question 41

What does alternative polyadenylation lead to?

Answer 41

Different poly(A) structures. Due to different regulations in polyadenylation -> poly(A) sites.

Question 42

What yields different mRNAs from the same gene?

Answer 42

1) Alternative promoters 2) Alternative splicing 3) Cleavage at different poly(A) sites (alternative polyadenylation)

Question 43

Which proteins regulate alternative splicing?

Answer 43

RNA-binding proteins that bind to specific sequences near splice sites

Question 44

(T/F) Rare RNA editing of mRNA sequences in the nucleus have important consequences by altering the amino acid encoded by an edited codon.

Answer 44

True! Octopus can edit their mRNA!

Question 45

SR (Serine-Argine-rich) proteins contribute to exon definition in ____ pre-mRNAs.

Answer 45

Long

Question 46

How many bases are exons usually composed of? How many bases are introns usually composed of?

Answer 46

Exon - 150 bases Introns - 3500 bases, but longest exceed 500 kb

Question 47

What do SR proteins do?

Answer 47

They interact with EXONIC SEQUENCE ENHANCERS (ESE) within exons. And they promote cooperative binding of U1 snRNP to a 5' splice site and U2 snRNP to a branch point through a network of PROTEIN-PROTEIN interactions that span an exon!

Question 48

SR proteins bound to ESE promote cooperative binding of U1 snRNP to a 5' splice site of the ________ intron. Also promote U2 snRNP binding to a branch point of the _______ intron.

Answer 48

Downstream Upstream

Question 49

(T/F) SR proteins do not interact with each other.

Answer 49

False! They interact with each other.

Question 50

What is the difference between Fibroblast fibronectin and Hepatocyte fibronectin?

Answer 50

Fibroblast fibronectin splice includes EIIA and EIIB exons that encode domains that bind to specific fibroblast membrane proteins. Hepatocyte fibronectine splice out the EIIA and EIIB exons and their flaking introns. This leads them to not be able to bind to fibroblasts, but rather circulate in the bloodstream and form blood cots through fibrin-binding domains.

Question 51

How do individual hair cell neurons respond most strongly to a specific sound frequency?

Answer 51

By expressing a mixture of calcium activated potassium channel isoforms. These isoforms are encoded by alternatively spliced mRNAs produced from the SAME primary transcript.

Question 52

(T/F) Alternative exons used at eight regions in the mRNA leads to 576 possible potassium channel isoforms, which respond to different frequencies by opening at different calcium concentrations.

Answer 52

True! *8 possible splice sites *Calcium concentration at which the channel opens determines the frequency of membrane potential oscillation - frequency to which the cell is tuned.

Question 53

What is the most extreme example of regulated alternative RNA processing yet discovered?

Answer 53

Drosophila Dscam gene! It has the most number of isoforms!

Question 54

(T/F) Dscam isoform expression in Drosophila neurons helps to specify tens of millions of different specific synaptic connections between neurons in the Drosophila brain.

Answer 54

True!

Question 55

(T/F) Out of the 38,016 possible peptides possible from the Drosophila Dscam gene, the ones we have studied so far are very important for branching of the species.

Answer 55

True!

Question 56

(T/F) Sex-lethal protein and the transformer protein are only expressed in female Dosrophilas because they induce a pre-mature stop codon in males.

Answer 56

True! Pre-mature stop codon results in a dysfunctional protein.

Question 57

How are the sex lethal protein and the transformer protein related? Do both sexes express this protien?

Answer 57

Functional Sxl protein influences the splicing of the Tra gene. It blocks exon 1-2 splicing in the tra gene, which would result in a premature stop codon. Because females have the sex-lethal protein, their exon 1-2 splicing is blocked; Tra protein expressed Males do not have the sex-lethal protein, their exon 1-2 splicing is not blocked. Due to exon 2 having a premature codon, this leads to a dysfunctional protein. Males DO NOT express this protein!

Question 58

How is tra protein related to Dsx protein? Do both sexes express this protein?

Answer 58

The Tra protein activates 3 and 4 exon splicing in the female Dsx protein. Males lack functional Tra protein so exon 3 is bound to exon 5. But because there is no premature stop codon, it is functional. Both sexes express the Dsx protein.

Question 59

(T/F) The female Dsx isoform activates genes with Dsx transcription factor binding sites, including genes that induce development of female characteristics, while the male Dsx isoform represses expression of the same target genes with Dsx binding sites.

Answer 59

True! *go over the slides and the pics!

Question 60

Fill in the blanks: The most common and extensively conserved type of alternatively spliced exons in the central nervous system (CNS) are called _______ because they are unusually short ___ to ____ bases long. They are in multiples of _____ to maintain the _______ _______ of up- and downstream of exons of more typical longer lengths.

Answer 60

microexons; 3-27 three; reading frames

Question 61

How many patients with autism exhibit low levels of microexon splicing in the CNS?

Answer 61

1/3rd! *low levels of microexon splicing: reading frame of other exons not maintained

Question 62

Where do the short stretches of amino acids encoded by microexons (1-9 amino acids) reside on? What are their functions?

Answer 62

They reside on PROTEIN SURFACES that participate in PROTEIN-PROTEIN interactions. They are enriched in genes with critical functions in SYNAPTIC BIOLOGY.

Question 63

What is SRRM4? In which patients is it expressed in low levels? What does this tell us?

Answer 63

SRRM4 is a neuron-specific SR protein. Patients with autism expressed low levels of the SRRM4 mRNA! Frequency of micro-exon skipping correlated with degree in the reduction of SRRM4 levels! (low levels of SRRM4: low levels of microexon splicing)

Question 64

(T/F) Spinal Muscular Dystrophy is a neuromuscular disease that affects 1 in 10,000 people and is the result of a mutation in the survival of motor neuron 1 (SMA1).

Answer 64

True!

Question 65

What happens without a functional SMN (survival motor neuron) protein?

Answer 65

The motor neurons in the spinal cord and brain stem degenerate, resulting in MUSCLE WEAKNESS and ATROPHY.

Question 66

(T/F) A paralog of SMN1 in the human genome, SMN2, encodes an identical SMN protein. However, its pre-mRNA undergoes aberrant splicing, with 90% of mature SMN2 transcripts lacking exon 7 and producing a truncated, unstable polypeptide.

Answer 66

True! SMN1 is the stable protein; very important 4 muscle and spinal formation SMN2 is the unstable protein that gets degraded

Question 67

In an healthy individual, the SMN1 protein is ______, while the SMN2 protein i s________.

Answer 67

Active; inactive

Question 68

If the SMN1 gene has a mutation, where the expression of the healthy protein is disrupted and an unstable or inactive protein is made, what are the two possible treatment options?

Answer 68

1) Fix the mutation in SMN1 2) Change the splicing pattern of SMN2 to make it look like SMN1

Question 69

What is SPINRAZA (Nusinersen)? How does it work?

Answer 69

A treatment for spinal muscular dystrophy. It is an antisense oligonucleotide that binds to intron 7 and prevents splicing repressors from binding, resulting in inclusion of exon 7 in SNM2. Whereas normally it would have been spliced out. This results in a SMN1 like functional + stable protein!

Question 70

Do pre-mRNAs still bound to spliceosomes get exported?

Answer 70

No! This ensures only the mature mRNAs to reach the cytoplasm.

Question 71

What do mRNP exporters do?

Answer 71

Transport mRNPs (messenger ribonucleoprotein - mRNA bound with proteins) through the NUCLEAR PORE COMPLEX (NPC)

Question 72

Large NXF1 (nuclear export factor) subunit and a small NXT1 (nuclear export transporter) make a ________, that helps export mRNPs in and out of the nucleus.

Answer 72

HETERODIMER *mRNP is the heterodimer composed of NXF1 with REF and NXT1.

Question 73

(T/F) NXF1 binds RNA and proteins in the mRNP complex with proteins including REF (RNA export factor), a component of the exon-junction complexes.

Answer 73

True!

Question 74

mRNP exporter associates with ___ proteins that are bound to exonic splicing enhancers.

Answer 74

SR

Question 75

While some mRNP proteins dissociate from nuclear mRNP complexes before export to the cytoplasm, which mRNPs remain associated?

Answer 75

CBC - Cap binding complex NXF1/NXT1 PABPN1 (nuclear polyA-binding protein)

Question 76

What happens to the mRNP proteins that get exported with the mRNP?

Answer 76

They dissociate from the mRNP in the cytoplasm and are shuttled back into the nucleus through a Nuclear Pore Complex (NPC).

Question 77

For mRNP in cytoplasm: The translation initiation factor ______ replaces the CBC (cap binding complex) bound to the 5' cap. _________ (cytoplasmic poly(A)-binding protein) replaces PAPBN1.

Answer 77

elF4E PAPBC1

Question 78

(T/F) Stability of most mRNAs is controlled by poly(A) tail length and binding of various proteins to 5' UTR sequences.

Answer 78

False! Stability of most mRNAs is controlled by poly(A) tail length and binding of various proteins to 3' UTR (untranslated region) sequences.

Question 79

Fill in the blanks: mRNA translation can be regulated by ________ and RNA interference by ________ and various degradation, cytoplasmic splicing, and polyadenylation mechanisms.

Answer 79

Micro-RNAs siRNAs

Question 80

Many mRNAs are transported to specific subcellular locations by sequence specific _____ ______ proteins that bind ___ UTR localization sequences

Answer 80

RNA binding 3'

Question 81

What are the three pathways for degradation of eukaryotic mRNAs?

Answer 81

1) Deadenylation-dependent mRNA decay 2) Deadenylation-independent mRNA decay 3) Endonuclease-mediated mRNA decay They all degrade mRNA so it can't get translated!

Question 82

What is the most common pathway for degradation of eukaryotic mRNAs?

Answer 82

Deadenylation-dependent mRNA decay

Question 83

How does Deadenylation-dependent mRNA decay work?

Answer 83

First, DEADENYLASE complex shortens poly(A) tail to ≤20 A residues. This destabilizes the cytoplasmic poly(A)-binding proteins (PABPC1), which directly affects the 3' end but also the 5' end by weakening the interactions between the 5'cap and translation initiation factors. This deadenylated mRNA can either: 1) be capped by the DCP1/DCP2 (decapping enzymes) deadneylation complex and degraded by XRN1(EXORIBONUCLEASE 1), a 5' -> 3' exonuclease or 2) be degraded by 3' -> 5' exonucleases in cytoplasmic exosomes

Question 84

What are exosomes?

Answer 84

Multiprotein complex that degrade unprotected RNAs in the nucleus and cytoplasm.

Question 85

How does the deadenylation-independent mRNA decay pathway work?

Answer 85

mRNAs decapped before deadneylation and are degraded by XRN1 5' --> 3' exonuclease.

Question 86

How does the endonuclease-mediated mRNA decay pathway work?

Answer 86

mRNAs are cleaved INTERNALLY by an endonucleases, yielding in 2 unprotected ends, one without a 5' cap and one without a poly(A) tail. The mRNA fragment without the polyA tail gets degraded by a cytoplasmic exosome 3' --> 5' The mRNA fragment without the cap gets degraded by the XRN1 exonuclease 5' --> 3'.