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MolCell Mega Class > VEST 1 > Flashcards

VEST 1 Flashcards

1
Q

The addition of a 5’ end 7-methyl G cap to mRNA protects it from degradation by _________.

A

5’ exonucleases

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2
Q

The 5’ end 7-methyl G cap enhances the _________ of the 5’ most exon.

A

splicing

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3
Q

the ________ is necessary for targeting mRNAs for export to the cytoplasm through the nuclear pores.

A

5’ end 7-methyl g cap

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4
Q

In the cytoplasm, the 5’ end 7-methyl G cap interacts with ___________ to form a closed loop structure.

A

poly(A) tail binding proteins (at the 3’ end)

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5
Q

The closed loop structure formed by the 5’ end 7-methyl G cap and poly(A) tail binding proteins recruits the ________ for translation.

A

ribosome

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6
Q

RNA methylation to form N6-methyladenosine (m6A) in pre-mRNA is an abundant internal modification that controls ____________.

A

gene expression

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7
Q

The process of RNA methylation to form N6-methyladenosine (m6A) is referred to as the ______________.

A

epitranscriptome

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8
Q

m6A is found in mRNAs involved with specific _________ and __________.

A

developmental processes, cell differentiation

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9
Q

Most m6A sites are ________ and are similar in different tissues.

A

constitutive

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10
Q

m6A is enriched in the __________ and near _______, but also occurs in the _______ and internally.

A

3’ UTR and near stop codons, 5’UTR

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11
Q

The presence of a __________ is a strong inducer of m6A addition in the transcribed mRNA.

A

long internal exon

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12
Q

m6A addition occurs in the ________ during __________.

A

nucleus, transcription

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13
Q

The m6A writer complex adds the m6A _________.

A

co-transcriptionally

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14
Q

The m6A writer complex contains _________ and ________ proteins.

A

METTL3, METTL14

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15
Q

m6A erasers are mostly found in the _________.

A

nucleus

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16
Q

The main m6A eraser is __________.

A

ALKBHS

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17
Q

In the nucleus, the m6A binds “________”.

A

reader proteins

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18
Q

In the cytoplasm, other “reader proteins” affect ____________.

A

mRNA stability, localization,
and translation of the mRNA

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19
Q

_________ is the regulated removal of intron sequences from pre-mRNA.

A

Splicing

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20
Q

Splicing involves the simultaneous joining (________) of exon sequences together.

A

ligation

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21
Q

Exon sequences contain the _______________________.

A

5’ untranslated regions (UTR), protein coding regions, and the 3’ UTR

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22
Q

________ sequences are exported from the nucleus.

A

Exon

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23
Q

__________ is catalyzed by RNA.

A

Splicing

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24
Q

Pre-mRNA splicing uses the same chemistry as __________ but needs more help.

A

group 2 self-splicing

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25
Q

___________ is the most common type of splicing.

A

Protein-mediated splicing

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26
Q

Protein-mediated splicing needs _______ and ________ to perform the reactions.

A

proteins, RNA-protein complexes

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27
Q

_________ occurs when transcripts from different genes are spliced together.

A

Trans-splicing

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28
Q

Splicing is a highly regulated process that is necessary to remove ________ from the primary transcript.

A

RNA intron sequences

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29
Q

Both ________ and the primary pre-mRNA transcript have both exon and intron sequences.

A

genes (DNA)

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30
Q

Splicing removes the _________ to produce mRNA.

A

intron sequences

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31
Q

The gene includes DNA sequence that codes for all _________________________________________________.

A

all exons, introns, and those
sequences at the beginning and end of the RNA that are not translated into a protein,
including the entire transcription unit

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32
Q

The entire transcription unit includes _______________.

A

the promoter, the RNA coding sequence, and the terminator.

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33
Q

Sequences that direct where splices are made are surprisingly _______-.

A

simple

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34
Q

Splicing sequences include the _________.

A

5’ splice site, 3’ splice site, polypyrimidine tract, and branch point

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35
Q

The 5’ splice site splicing consensus sequence is ___________.

A

GU A/G AGU

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36
Q

The 3’ splice site splicing consensus sequence is ________.

A

CAGG

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37
Q

The branch point splicing consensus sequence is an ___________ approximately 18-40 nucleotides upstream from the 3’ splice site.

A

adenine (A)

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38
Q

The polypyrimidine tract splicing consensus sequence is approximately 10-20 _______ nucleotides.

A

C/U

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39
Q

The spliceosome is comprised of 5 ________ containing ____________.

A

RNA-protein molecules, small nucleolar RNAs (snRNPs)

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40
Q

The spliceosome contains up to ________ accessory proteins.

A

300

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41
Q

The _________ binds to the 5’ splice site.

A

U1 snRNP

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42
Q

The ________ binds to the branchpoint.

A

U2 snRNP

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43
Q

The ________ holds the 5’ and 3’ exons in close proximity to each other.

A

U5 snRNP

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44
Q

The _______ interact near the branchpoint.

A

U4-U6 snRNPs

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45
Q

The __________ binds the polypyrimidine tract and helps U2 bind to the branchpoint.

A

U2AF (U2 associated factor)

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46
Q

The U2AF also interacts with the ________.

A

3’ splice site

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47
Q

In addition to the snRNPs, there are at least _____, and perhaps up to ______, additional proteins that comprise the spliceosome and participate in the
splicing reaction.

A

24, 300

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48
Q

Following the release of _______, the 5’ splice site is correctly positioned in the active site due to base pairing between the 5’ end of the intron, the RNA
sequences in U6 snRNP, and interactions with U2 snRNP.

A

U1 snRNP

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49
Q

U2AF is composed of _____ subunits.

A

2

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50
Q

The ________ subunit of U2AF binds the polypyrimidine tract.

A

U2AF-65

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51
Q

The _______ subunit of U2AF binds the AG in the 3’ splice site.

A

U2AF-35

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52
Q

Together U2AF-65 and U2AF-35 recruit _________ to the branchpoint.

A

U2 snRNP

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53
Q

_______ also plays a critical role in positioning the 5’ and 3’ splice sites in the spliceosomal complex.

A

U5 snRNP

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54
Q

Just prior to lariat formation, _____________ all interact with each other to correctly position the RNA substrate for the splicing reaction.

A

U2, U5, and U6 snRNPs

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55
Q

_________ is a process where some exons are skipped and removed from the final mRNA product.

A

Alternative splicing

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56
Q

If something prevents default sequential splicing, then ________ will occur.

A

alternative splicing

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57
Q

Different proteins from the same primary RNA transcript can have markedly _________.

A

different functions

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58
Q

A major deciding factor in alternative splicing and differential protein production is ____________ binding to an RNA G quadruplex near the 5’SS.

A

RBM25

59
Q

___________ elements are recognized by activator proteins.

A

Enhancer

60
Q

__________ elements are bound by repressor proteins, which tend to be members of the ____________ protein family.

A

Silencer, hnRNP

61
Q

Examples of hnRNP proteins include __________.

A

HNRNPI, HNRNPA1,
HNRNPC

62
Q

Activators tend to enhance the binding of ________ to the regulated splice site, while repressors tend to inhibit binding or function of the ___________.

A

spliceosomal components

63
Q

The binding of activator and repressor factors can occur in either ___________ or _________ sequences.

A

exon, intron

64
Q

Alternative splicing is accomplished by regulating the ________ of sequences that direct where splices are made.

A

accessibility

65
Q

_________ stands for exonic splicing enhancer.

A

ESE

66
Q

________ stands for intronic splicing silencer.

A

ISS

67
Q

_______ stands for intronic splicing enhancer.

A

ISE

68
Q

_________ stands for exonic splicing silencer.

A

ESS

69
Q

True or False: There are many forms of alternative splicing.

A

True

70
Q

Polyadenylation requires ________ proteins.

A

50

71
Q

The _______ sequence is canonically AAUAAA.

A

Polyadenylation Sequence (PAS)

72
Q

__________ binds the AAUAAA sequence.

A

CPSF (Cleavage and Polyadenylation Specificity Factor)

73
Q

_____________ binds the GU-rich or U-rich downstream element.

A

CSTF (Cleavage Stimulatory Factor)

74
Q

CPSF and CSTF interact and along with additional cleavage factors, cut the ________.

A

pre-mRNA

75
Q

__________ adds Adenines (A residues) to the 3’ end of the pre-mRNA.

A

PAP (poly-A polymerase)

76
Q

The nuclear _________ binds to the 3’ end of the pre-mRNA.

A

Poly-A binding protein (PABPN1)

77
Q

CPSF has ______ subunits.

A

4

78
Q

CPSF 4 directly contacts the _____________ and recruits Poly A polymerase to the 3’ end.

A

PAS (AAUAAA)

79
Q

CSTF has _____ subunits and binds the U/GU-rich element downstream from both the PAS and cleavage site.

A

3

80
Q

CSTF is required for _________ but not _________-.

A

cleavage, polyadenylation

81
Q

There are _____ CF factors that enhance 3’ end processing and cleavage at the 3’ end.

A

3

82
Q

___________ is a scaffold for cleavage and polyadenylation machinery.

A

SYMPK (symplekin)

83
Q

____________ is a member of the CPSF complex that interacts with and stimulates the activity of PAP.

A

FIP1L1

84
Q

________ is a member of the CPSF complex that recognizes the PAS.

A

WDR33

85
Q

The end to which polyA is to be added is generated by the _________ activity of _________.

A

endonuclease, CPSF2

86
Q

The cleavage event produces _______ ends.

A

two

87
Q

The 3’ end of the cleaved RNA gains a ________.

A

poly A tail

88
Q

The 5’ end of the cleaved RNA recruits _________ or _______-.

A

XRN2, RAT1 (exonucleases that degrade the RNA)

89
Q

When _________ or ____________ catch up with the RNA polymerase, they interact with the
polymerase C-Terminal Domain (CDT)) to cause it to cease transcribing the DNA
into RNA.

A

XRN2, RAT1

90
Q

Cleavage of the RNA occurs approximately 15-30 nt downstream of the _______.

A

PAS

91
Q

Poly A tail addition requires only __________.

A

PAP, CPSF, and PABPN1

92
Q

Initially PAP ________ binds RNA and CPSF.

A

loosely

93
Q

Regular dissociation of PAP only allows the addition of ________-.

A

a few A residues

94
Q

Dissociation of PAP adding a few A residues is referred to as ___________.

A

distributive polyadenylation

95
Q

__________ binding to short poly A sequences stabilizes PAP binding, leading to rapid addition of A residues without PAP dissociation.

A

PABPN1

96
Q

PABPN1 binding to the short poly A sequence and rapidly adding more A residues is referred to as ___________.

A

processive polyadenylation

97
Q

Most mammalian transcripts have a poly A tail of about _________ nucleotides.

A

200

98
Q

The 3’ poly(A) tail protects the 3’ end from degradation by _________.

A

3’ exonucleases

99
Q

The 3’ poly(A) tail is necessary for __________ from the nucleus to the cytoplasm.

A

mRNA transport

100
Q

The 3’ poly(A) tail facilitates _________ by interacting with the 5’ cap.

A

translation

101
Q

There is a link between ___________ and _________ of the 3’ terminal exon.

A

polyadenylation site proteins, splicing factors of the 3’
terminal exon

102
Q

________ and other 3’ end processing proteins have been found to play a role in promoting alternative splicing at internal exon-intron junctions.

A

CPSF

103
Q

Approximately _______% of mammalian mRNA contain more than one PAS.

A

75

104
Q

Alternative PAS usage (_______) dictates the length of the transcript and its ___________.

A

alternative polyadenylation, stability, localization, and translation efficiency

105
Q

Alternative polyadenylation may also impact the _________, leading to the translation of different protein isoforms.

A

coding sequence

106
Q

Adding an extra 3 prime translated region to an mRNA adds a ___________ to the protein.

A

carboxy terminal domain

107
Q

__________ are a subclass of RNAs that lack free 3’ and 5’ ends, thus existing as continuous loop RNAs.

A

Circular RNAs

108
Q

CircRNAs have been identified for _____________ and are regulated in ________ and _______.

A

thousands of genes, developmental stages and pathological conditions

109
Q

They are often expressed in a ________ manner.

A

tissue- or cell-type specific

110
Q

CircRNAs are produced by a process called ________ of linear precursor RNAs.

A

backsplicing

111
Q

CircRNAs are evolutionarily _______ and are found in flies through mammals, including humans.

A

conserved

112
Q

At least _______ circRNAs are thought to exist in humans.

A

32

113
Q

It has been postulated that _________ of RNA circRNA transcripts exist.

A

millions

114
Q

CircRNAs may serve as _______ for certain diseases.

A

biomarkers

115
Q

Examples of diseases for which circRNAs may serve as biomarkers include _________.

A

numerous cancers,
cardiovascular and neurological diseases

116
Q

When splice sites (ss) are joined in a linear order by the pre-mRNA splicing machinery, a canonical _________ is generated that is also capped and polyadenylated.

A

linear mRNA

117
Q

Alternatively, __________ can join a 5′ ss to an upstream 3′ ss, resulting in
production of a circular RNA whose ends
are covalently linked by a 3′-5′
phosphodiester bond and can function via a
number of distinct molecular mechanisms.

A

backsplicing

118
Q

The ends of circular RNA are covalently linked by a _________.

A

3′-5′ phosphodiester bond

119
Q

Primary functions of circRNA include acting as ________ and _________.

A

miRNA sponges, protein sponges, encode novel proteins

120
Q

CircRNA can also ________ using alternative translation initiation mechanisms, such as IRES and m6A residues.

A

encode novel proteins

121
Q

________ gives rise to circRNAs from lariat intermediate structures, which are produced during exon skipping.

A

Lariat-driven circularization

122
Q

__________ is a more direct form of circRNA formation and involves hybridization of flanking introns, which brings splice sites in close proximity.

A

Intron-pairing-driven
circularization

123
Q

A _______ consists of all exon sequence.

A

circRNA

124
Q

A _________ consists of all intron RNA.

A

ciRNA

125
Q

An _______ consists of exon and intron RNA.

A

EIciRNA

126
Q

A 5’ methyl G cap is added to the pre-mRNA during ____________ to protect against 5’ degradation and facilitate translation.

A

transcription

127
Q

Internal methylation in RNA can influence ______, _______, and _________.

A

stability, splicing, translation

128
Q

The ________ (primary transcript) consists of exon (5’ UTR, protein coding region, 3’
UTR) and intron sequences.

A

pre-mRNA

129
Q

________ occurs to remove intron sequences from the primary transcript.

A

Splicing

130
Q

Polymerase II transcripts need _______ (snRNA + specific protein complexes) to splice out introns.

A

snRNPs

131
Q

________ binds to the 5’ splice site.

A

snRNP 1

132
Q

_______ binds to the branchpoint.

A

snRNP 2

133
Q

_______ binds to the polypyrimidine tract.

A

U2AF

134
Q

__________ generates multiple mRNAs and proteins from a single primary transcript.

A

Alternative splicing

135
Q

The poly(A) tail consists of ~ _____- A residues and has multiple functions, including protecting the mRNA from 3’ degradation and enhancing translation.

A

200

136
Q

________ are circular RNAs that regulate expression in multiple ways.

A

circRNAs

137
Q

________ are noncoding sequences that interrupt the coding sequences (exons) of genes.

A

Introns

138
Q

Introns are common in ________, but very rare in _________.

A

eukaryotic cells, bacterial cells

139
Q

An mRNA molecule has 3 primary regions: a ________, a_______, and a ________.

A

a 5’ untranslated region, a protein
coding region, and a 3’ untranslated region

140
Q

_________ is translated immediately after transcription and undergoes little processing.

A

Bacterial mRNA

141
Q

The pre-mRNA of a eukaryotic protein-encoding gene is extensively processed in the following ways: (1) a modified guanine nucleotide and methyl groups, collectively termed a “ BLANK”, are added to the 5’ end of pre-mRNA; (2) introns are removed; and (3) the 3’
end is cleaved, and a poly(A) tail is added.

A

cap

142
Q

Introns are removed from pre-mRNA within a structure called the _______, which is composed of several small nuclear RNAs and proteins.

A

spliceosome

143
Q

Some pre-mRNAs undergo _________, in which different combinations of exons are spliced together, different promoters, and/or different 3’ cleavages sites
are used.

A

alternative processing

144
Q

A cell can generate multiple mRNAs and multiple proteins through ____________.

A

alternative splicing

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