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BS209: Molecular Biology > Chapter 10: RNA Processing > Flashcards

Chapter 10: RNA Processing Flashcards

1
Q

RNAs are synthesized from DNA templates that are not functional -> need to be modified to make mature, functional RNA

A

precursor RNAs (pre-RNAs)

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2
Q

alterations of pre-RNAs are known as ()

A

RNA processing

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3
Q

benefits of RNA processing: RNA processing provides:

A
  1. regulation of gene activity
  2. diversity
  3. quality control
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4
Q

tRNA and rRNA transcripts are made as () that must be processed

A

long precursors

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5
Q

an () precursor encodes 3 rRNAs and several tRNAs

A

E. coli

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6
Q

the () precursor encodes 3 rRNAs

A

S. cerevisiae

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7
Q

encoding several RNAs in one precursor ensures that ()

A

similar amounts of each RNA are made

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8
Q

() cleave RNAs into smaller parts

A

ribonucleases

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9
Q

successively remove nucleotides from the end of a transcript; most often in 3’ to 5’, but sometimes in 5’ to 3’

A

exonucleases

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10
Q

exonucleases are not usually (1), and generally act on (2)

A
  1. sequence-specific
  2. single-stranded ends
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11
Q

cleave the DNA within the strand; some are specific for double-stranded RNA, some for single-stranded

A

endonucleases

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12
Q

examples of endonucleases

A

RNase III and RNase P

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13
Q

excision of bacterial rRNAs from longer precursors is performed by (); as well as trimming if some RNAs and tRNAs

A

RNase III

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14
Q

RNase III binds () in the pre-RNAs and cleaves the dsRNAs

A

stem structures (dsRNA)

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15
Q

endonucleases similar to RNase III are involved in many processes, e.g. in eukaryotes, they generate (1) and (2) that inhibit the expression of detrimental genes

A
  1. microRNA (miRNA)
  2. small interfering RNAs (siRNAs)
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16
Q

5’ trimming of tRNAs is done by the endonuclease ()

A

ribonuclease P, RNase P

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17
Q

unlike RNase III, RNase P enzymes have (1) component and (2) components

A
  1. bacterial RNA
  2. protein
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18
Q

in RNase P, the bacterial RNA component alone can cut RNA, thus acting as a ()

A

ribozyme

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19
Q

the () RNase P RNA component cannot cut RNA alone, but is essential for function

A

eukaryotic, archaeal, and mitochondrial

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20
Q

() are present in some tRNAs and rRNAs

A

introns

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21
Q

tRNA splicing is catalyzed by ()

A

protein factors

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22
Q

some rRNAs introns can catalyze their own removal -> they are ()

A

self-splicing

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23
Q

the 3’ ends of mature tRNAs have a conserved () -> attachment site for the amino acid

A

CCA sequence

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24
Q

CCA sequence is mostly added by ()

A

polymerization without template

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25
Q

CCA-adding enzyme takes () in a nucleotide-binding pocket that sequentially changes in size and shape depending on the 3’ end sequence of the bound tRNA

A

CTP or ATP

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26
Q

the presence of CTP or ATP in the nucleotide-binding pocket of the CCA-adding enzyme determines where () is added

A

C or A

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27
Q

additional role of CCA-adding enzyme

A

targeting unstable tRNAs for degradation

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28
Q

CCA-adding enzymes target unstable tRNAs for degradation through the addition of longer ()

A

CCACCA or CCACC tails

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29
Q

tRNA and rRNA nucleotides are often () modified after transcription

A

chemically

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30
Q

t/rRNA modification can be on the (1) or (2)

A
  1. nucleotide base
  2. ribose sugar ring
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31
Q

examples of relatively small t/rRNA modifications

A
  1. addition of H atom
  2. methylation of nitrogen or oxygen
  3. addition of selenium
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32
Q

examples of relatively large t/rRNA modifications

A
  1. incorporation of threonine
  2. multiple independent modifications
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33
Q

modifications in tRNAs:
- contribute overall to (1)
- give tRNAs the ability to (2)
- increase the () of tRNA molecules

A
  1. structural stability
  2. interact with other molecules
  3. repertoire of shapes, structures, and stability
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34
Q

the most common rRNA modifications

A
  1. ribose 2’-O-methylation
  2. pseudouridylation
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35
Q

in eukaryotes and archaea, () guide methylation and pseudouridylation of rRNAs and tRNAs; these molecules guide enzymes to the correct site

A

small nucleolar RNAs (snoRNAs)

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36
Q

snoRNAs associate with a complex of proteins to make ()

A

snoRNP

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37
Q

most vertebrate snoRNAs are made from the introns of ()

A

precursor mRNAs

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38
Q

snoRNAs that direct ribose methylation

A

boc C/D snoRNAs

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39
Q

snoRNAs that direct pseudouridylation

A

H/ACA snoRNAs

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40
Q

5’ ends of eukaryotic mRNAs are capped with (1) via a (2)

A
  1. 7-methylguanine nucleotide
  2. 5’-5’ triphosphate linkage
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41
Q

in the mRNA 5’ cap, the guanine is methylated at ()

A

N7

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42
Q

in more complex eukaryotes, in addition to the 5’ cap, the () of the second and sometimes third base are methylated

A

2’ oxygen

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43
Q

there are () steps in 5’ capping

A

3

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44
Q

proteins in action during 5’ capping in yeast

A

done by different enzymes

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45
Q

proteins in action during 5’ capping in C. elegans and mammals

A

first 2 reactions are done by a single enzyme

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46
Q

the 3’ end of most eukaryotic mRNAs has about 200 adenosines added

A

polyadenosine or polyA tail

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47
Q

mRNAs have () where pre-mRNAs are cleaved and the poly(A) tail is added

A

polyadenylation sites

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48
Q

mRNAs encoding () are exceptions and do not have poly(A) tails

A

metazoan histones

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49
Q

functions of poly(A) tail

A
  1. protects mRNA from degradation by exonucleases
  2. involved in initiation of protein synthesis
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50
Q

multiple polyadenylation sites are found in some mRNAs, and these can participate in regulation

A

alternative polyadenylation sites (APA)

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51
Q

polyadenylation at the distal site of cyclin D mRNA () regulatory sequences

A

retains multiple

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52
Q

polyadenylation at the proximal site of cyclin D mRNA () regulatory sequences

A

eliminates

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53
Q

functions of alternative polyadenylation sites

A
  1. regulate protein synthesis
  2. expand range of proteins products from a single mRNA
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54
Q

mRNA stability and translation are often regulated by ()

A

3’ untranslated regions (3’ UTR)

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55
Q

the variable 3’ UTR lengths specified by () can determine what regulatory sequences will be included

A

different polyadenylation site selections

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56
Q

polyadenylation at the 3’ end of eukaryotic mRNAs starts with an ()

A

intial cleavage

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57
Q

the initial cleavage in polyadenylation usually occurs after a (1) that lies between a (2) and a (3)

A
  1. CA
  2. conserved AAUAAA hexamer
  3. U or GU-rich region
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58
Q

after the initial cleavage in polyadenylation, ~200 adenosines are added by ()

A

poly(A) polymerase

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59
Q

a (smaller/larger) protein complex is required for polyadenylation that for 5’ capping

A

larger -> more complex to recognize different polyadenylation sites in different mRNAs

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60
Q

metazoan histones carry highly conserved () that recruit proteins of similar functions to those that bind poly(A) tails

A

stem-loop structures

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61
Q

5’ capping and 3’ polyadenylation are linked with each other and with other RNA polymerization processes via ()

A

RNA pol II

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62
Q

() is needed to allow RNA pol II to continue elongation

A

5’ capping

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63
Q

() is needed for efficient transcription termination

A

polyadenylation

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64
Q

the () is the largest subunit of RNA pol II

A

C-terminal domain (CTD)

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65
Q

at the CTD of RNA Pol II, () is responsible for mediating mRNA processing

A

RPB1

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66
Q

CTD becomes () on transcription initiation and recruits capping enzyme

A

partially phosphorylated

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67
Q

elongation leads to more phosphorylation of CTD, which recruits ()

A

splicing machinery

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68
Q

recruitment of splicing machinery leads to recruitment of ()

A

cleavage and polyadenylation complex

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69
Q

transcription and processing of eukaryotic mRNA occurs in the ()

A

nucleus

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70
Q

protein factors needed for mRNA transport to cytoplasm are loaded onto the mRNA during transcription, but () is needed before the RNA-protein complex can be released from the transcription complex

A

polyadenylation

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71
Q

Some mRNAs are located in specific regions of the cytoplasm –> this requires “()”, usually found at the 3′ end. They also regulate translation.

A

localization elements

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72
Q

most introns do not themselves contain genes and are excised and degraded; but there are exceptions:

A

snoRNAs and miRNAs

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73
Q

mechanism of intron removal

A

transesterification reactions

74
Q

introns are far more prevalent in (1) than in (2)

A
  1. eukaryotes
  2. bacteria
75
Q

introns allow for (), where exons are exchanged and reordered via recombination, allowing evolution of different genes

A

exon shuffling

76
Q

() of introns gives different transcripts from the same gene

A

differential removal

77
Q

2 steps of transesterifications

A
  1. intron is detached from exon 1
  2. exon 1 reacts with exon 2
78
Q

most eukaryotic introns are removed by a complex called the (1), but some (including some introns in bacteria) are (2)

A
  1. spliceosome
  2. self-splicing
79
Q

a reaction wherein a single phosphodiester bond is broken, and replaced by another phosphodiester bond of similar energy

A

transesterification reactions

80
Q

similar energy of the 2 bonds involved in transesterification reactions means that ()

A
  1. reaction is ATP-independent
  2. reaction is easily reversible
81
Q

insertion of introns into DNA; may have played a role in intron dispersal and genome evolution

A

reverse splicing of introns

82
Q

Group () introns are found in bacteria, viruses, lower eukaryotes, and plants -> these introns excise themselves (i.e. ribozymes) from primary transcript and are ~120-145 nucleotides long

A

I (one)

83
Q

in the 1st transesterification reaction of group I introns, a () attacks and detaches the 5’ end from exon 1

A

free guanosine

84
Q

() are defined by the 3D structure of the intron by recognition of a conserved G-U wobble pair (for both group I and II introns)

A

splice sites

85
Q

group () introns are in bacteria and in genes in the organelles of plants and fungi; ~400-1000 nucleotides long

A

II (two)

86
Q

in the first transesterification reaction of group II introns, () within the intron attacks the exon1-intron junction

A

2’ OH of a specific A within the intron

87
Q

in the second transesterification reaction of group II introns, the () of the newly released exon attacks the intron-exon2 junction

A

terminal 3’ OH

88
Q

once released, a group II intron forms a branched ()

A

lariat intermediate

89
Q

group II introns can also act as () by reverse splicing; they often have open reading frames within the introns that assist splicing

A

mobile genetic elements

90
Q

most eukaryotic splicing is mediated by the spliceosome, which is made of several ()

A

small nuclear riboproteins (snRNPs)

91
Q

a spliceosome catalyzed splicing is similar to that of group (I/II) introns

A

II

92
Q

splice sites in mRNA are recognized by spliceosomes are defined by short sequence motifs:

A
  1. 5’ and 3’ splice sites
  2. branch-point nucleotide w/in intron
  3. polypyrimidine tract before 3’ splice site
93
Q

usually, introns have (1) and (2) at their ends

A
  1. GU
  2. AG
94
Q

the spliceosome has 5 snRNPs:

A

U1, U2, U4, U5, U6

95
Q

each snRNP has a () of about 100-300 nucleotides, plus proteins

A

small nuclear RNA (snRNA)

96
Q

the snRNAs in snRNPs work as the () of the snRNPs by forming base pairs

A

recognition part

97
Q

a protein involved in splicing; found near the active site of the assembled spliceosome and thought to be important in catalysis

A

PRP8

98
Q

proteins involved in splicing; probably help with structural rearrangements and promote lariat and mRNA release after processing

A

ATPases

99
Q

the () is a component of the human spliceosome that marks the transcript as processed -> allows transcript to eventually be recognized by translational machinery for export and translation

A

exon-junction complex

100
Q

() provide insights into the mechanistic details of splicing by the spliceosome

A

high-resolution cryoEM structures

101
Q

majority of pre-mRNA introns have GU and AG dinucleotides at their termini and are recognized by () spliceosome

A

major

102
Q

some introns in multicellular organisms are processed by ()

A

minor, or U12-dependent spliceosome

103
Q

the minor/U12-dependent spliceosome includes the same U5 component but 4 different snRNPs

A

U11, U12, U4atac, U6atac

104
Q

certain introns spliced by the minor spliceosome have () splice sequences

A

unusual (e.g. AU and AC at the intron termini)

105
Q

() splicing is where exons in the same molecule are joined together

A

Cis

106
Q

() splicing is unusual, and joins exons from different RNA molecules

A

Trans

107
Q

in trans splicing, a short RNA (1), is joined to different mRNAs

A

spliced leader RNA, SL RNA

108
Q

in trans splicing, SL RNA replaces the (), and interacts with other snRNPs at the 3’ splice site

A

U1 snRNP

109
Q

majority of genes in eukaryotes undergo () where different combinations of exons are used

A

alternative splicing

110
Q

possible outcomes of alternative splicing: use of (4)

A
  1. different combinations of exons
  2. alternative splice sites
  3. alternative transcriptional starts
  4. different termination sites
111
Q

alternative splicing is important for (), such as in the Drosophila dscam gene

A

genetic diversity

112
Q

The sequences defining intron-exon junctions are simple, so they can occur elsewhere by chance–these are ()

A

cryptic splice sites

113
Q

2 broad conceptual models for how the spliceosome recognizes only true splice sites

A
  1. exon definition
  2. intron definition
114
Q

() definition is thought to occur in mammals; 5’ and 3’ ends of an exon are brought together by interactions between U1 and U2 complex

A

exon

115
Q

the exon is typically marked with (1), and the introns are bound with (2), which masks cryptic splice sites

A
  1. SR proteins
  2. hnRNPs
116
Q

in () definition, introns are defined by interactions between 5’ and 3’ bound factors

A

intron

117
Q

mutations at a 5’ splice site cause:

  • in exon definition: (1)
  • in intron definition (2)
A
  1. exon exclusion
  2. intron inclusion
118
Q

in both intron and exon definition, the 5’ and 3’ splice sites are marked as they are (), facilitated by RNA pol and splicing components

A

transcribed (i.e. co-transcriptionally)

119
Q

in both exon and intron definition, the final splicing complex must be one in which the ()

A

5’ and 3’ complexes interact with each other acroos the intron

120
Q

needed in exon definition, but not in intron definition

A

reorganization of splicing intermediates

121
Q

non-splice site regulatory sequences that strongly affect spliceosomal function

A
  1. splicing enhancers - positively affect splicing
  2. silencer sequences - mask splice sites or block spliceosome activity
122
Q

splicing enhancers can be (2)

A
  1. intronic splicing enhancer sequences (ISE)
  2. exonic splicing enhancer sequences (ESE)
123
Q

silencer sequences can be (2)

A

(intronic, exonic) splicing silencer sequences - ISS, ESS

124
Q

() proteins appear to bind ESE sequences and can be important for exon definition

A

SR

125
Q

an example of a silencer protein is (), which binds to intron elements and silences neighboring weak introns -> works in c-src mRNA

A

polypyrimidine tract binding protein (PTB)

126
Q

alternative splicing is found in the (1), which encodes SRC tyrosine kinase -> positive and negative inputs regulates inclusion of (2) in the final mRNA product

A
  1. c-src mRNA
  2. neural-specific N1 exon
127
Q

in neuronal cells, () binds to either side of the N1 exon in c-src mRNA and doesn’t repress its inclusion

A

PTBP2

128
Q

additional modifications of mRNA () further enhances the range of molecules that can be produced

A

RNA editing

129
Q

in RNA editing, specific nucleotides can be ()

A

modified, inserted, or deleted

130
Q

nucleotide insertions can be (1) or (2)

A
  1. 1-2 nucleotides
  2. more extensive
131
Q

example of a gene that undergoes extensive editing

A

Trypanosoma brucei NADH dehydrogenase 7 gene

132
Q

3 main common RNA edits

A
  1. deamination of adenosine -> inosine
  2. deamination of cytidine -> uridine
  3. methylation of adenosine
133
Q

most common RNA edit in more complex eukaryotes

A

deamination of adenosine to inosine

134
Q

inosine is interpreted as (), thus changing the coding region and can change the final protein sequence

A

guanosine

135
Q

() catalyze the deamination of adenosine to inosine by targeting double-stranded RNA regions

A

adenosine deaminases that act on RNA (ADARs)

136
Q

RNA edit that has been found mainly but not exclusively in plant mitochondrial and chloroplast mRNAs

A

deamination of cytidine to uridine

137
Q

RNA edit that was revealed by deep sequencing

A

methylation of adenosine

138
Q

cytidine to uridine deamination is also observed in the mRNA that makes human (), which is involved in the binding and transport of lipids throughout the human body

A

apolipoprotein B

139
Q

reversible methylation of adenosine is mediated by () proteins in the nucleus

A

writer and eraser

140
Q

methylated adenosines are read by () proteins in the cytoplasm

A

reader

141
Q

binding proteins of ‘reader’ proteins to methylated adenosines in () may be involved in regulation of translations

A

5’ untranslated regions (UTRs)

142
Q

in uridine addition, 20-50 nucleotide () bind to mRNAs and define insertion and deletion locations

A

guide RNAs

143
Q

uridine addition is catalyzed by (1), while uridine deletion is mediated by (2)

A
  1. 3’ terminal uridylyl transferase
  2. 3’ tp 5’ exonuclease
144
Q

RNAs need to be (), removing RNAs that are no longer needed and recycling the nucleotides

A

degraded

145
Q

RNA stability is described as (), the time in which the amount of RNA is reduced by half

A

RNA half-life

146
Q

RNA stability is affected by several factors

A
  1. structures at the 5’ and 3’ ends (5’ cap, 3’ poly(A) tail)
  2. stem-loop structures
  3. other RNA processes (splicing, transport, translation, etc)
147
Q

the 5’ cap in eukaryotic mRNAs protects against ()

A

exonuclease digestion

148
Q

in bacterial, a 3’ poly(A) tail (1) stability, while it (2) stability in eukaryotic mRNA

A
  1. decreases
  2. increases
149
Q

elements like () that remove poly(A) tails in eukaryotes decrease stability

A

AU-rich elements (ARE)

150
Q

3’ stem-loop in bacteria (incl. those formed in Rho-independent termination) protect against ()

A

3’ to 5’ exonuclease activity

151
Q

() in vertebrates encodes an ARE-containing short-lived transcription factor that promotes cellular growth

A

c-fos

152
Q

some tumor causing viruses in vertebrates express (), which does not have ARE -> transcript is not degraded properly, leading to excessive cell growth

A

v-fos

153
Q

in bacterial mRNAs, degradation is often initiated by an (1), often (2)

A
  1. endonuclease
  2. RNase E
154
Q

products of the first digestion of bacterial mRNAs are then degraded by ()

A

3; to 5’ exonucleases

155
Q

RNase E is part of the (), which also has an RNA helicase and a 3’ to 5’ exonuclease

A

degradosome complex

156
Q

species lacking RNase E use (), which has 5’ to 3’ exonuclease as well as endonuclease activity

A

RNase J

157
Q

a 5’ triphosphate inhibits RNase E activity -> this is converted to a monophosphate by ()

A

RppH

158
Q

3’ poly(A) tails hinder rather than aid in degradation in eukaryotes -> first step in degradation is often tail shortening by a ()

A

deadenylase

159
Q

mammalian cells respond to (1) levels -> partially regulated by the (2)

A
  1. iron
  2. transferrin receptors (allow import of transferrin-bound iron)
160
Q

when cellular iron is low, transferring receptor mRNA is protected from degradation by (1) that bind to stem-loop (2)

A
  1. iron regulatory proteins (IRP1, IRP2)
  2. iron response elements (IRE)
161
Q

Foreign nucleic acids are removed by (1) in eukaryotes and (2) in bacteria.

A
  1. RNA interference (RNAi)
  2. CRISPR interference
162
Q

recognition and degradation of foreign (double-stranded) RNAs was termed (1) in C. elegans and (2) in plants

A
  1. RNA interference (RNAi)
  2. post-transcriptional gene silencing (PTGS)
163
Q

in RNAi/PTGS, double-stranded RNA is first cleaved into small fragments by ()

A

Dicer

164
Q

in RNAi/PTGS, double-stranded fragments are loaded onto the () and one strand is released

A

RNA-induced silencing complex (RISC)

165
Q

in RNAi/PTGS, the remaining guide strand directs RISC to complementary full-length RNAs, which are cleaved by the () within RISC

A

Argonaute protein

166
Q

In bacteria and archaea, () are involved in degradation of foreign DNA; foreign DNA is integrated into the () loci

A

clustered regularly interspaced palindromic repeats (CRISPR)

167
Q

in eukaryotic cells, defective mRNAs are removed by (3)

A
  1. nonsense-mediated decay (NMD)
  2. non-stop decay (NSD)
  3. no-go decay (NGD)
168
Q

defective () are removed by specific decay mechanisms

A

endogenous RNAs

169
Q

in eukaryotes, ribosomes on defective RNAs are marked by interaction with proteins such as the (), which recruit RNases to degrade the RNA

A

EJC

170
Q

in bacteria, stalled ribosomes are recognized by a complex containing (), an RNA that acts both as a tRNA and as an mRNA

A

tmRNA

171
Q

to mediate precise RNA-protein interactions, proteins have specific ()

A

RNA-binfing motifs

172
Q

examples of RNA-binding motifs

A
  1. RRM
  2. KH
  3. PAZ
173
Q

most common RNA-binding motif is the (), which has alpha helices and 4 beta sheets in a sandwich -> adaptable and can bind RNAs with different structures

A

RNA-recognition motif (RRM)

174
Q

the RRM is also known as ()

A

RNA-binding domain (RBD) or ribonucleoprotein (RNP) domain

175
Q

() domains also bind single-stranded RNA

A

KH and PAZ

176
Q

() domains have an RNA-binding groove formed by 2 alpha helices and 1 beta strand

A

KH

177
Q

() domains have a pocket formed from beta strands and an alpha helix; this pocket interacts with the single-stranded overhangs of siRNA

A

PAZ

178
Q

PAZ domains are found in many (1) proteins, like (2)

A
  1. RNAi
  2. Dicer
179
Q

RNase III family enzymes have (); these proteins have an alpha helix and 2 loop regions that interact with 3 grooves on dsDNA

A

double-stranded RNA-binding domains (dsRBDs)

180
Q

interacting grooves in RNase III family enzymes

A

1 major, 2 minor grooves

181
Q

RNA-binding proteins often have (1/ >1) binding motif

A

> 1

BS209: Molecular Biology (8 decks)

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