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Mbg 2040 > Transcription and RNA processing > Flashcards

Transcription and RNA processing Flashcards

1
Q

On the ribose sugar of RNA, the 2’ carbon bears a ___________ _________

A

hydroxyl group

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2
Q

How can the structure and function of RNA resemble proteins

A

has tertiary structure
may interact as functional units (quaternary structure)

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3
Q

How is RNA unstable

A

the presence of the unique 2’ OH group in ribose causes it to react intramolecularly with the 3’ OH site resulting in phosphate bond breakage

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4
Q

Why use RNA if it is unstable?

A

since RNA is single stranded, it is able to take on many forms and has tertiary structure associated with it for many functions

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5
Q

What types of RNA are transcribed in both prokaryotes and eukaryotes

A

mRNA, rRNA, and tRNA

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6
Q

What types of RNA are only produced in prokaryotes

A

CRISPR RNA

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7
Q

What does it mean when saying transcription and translation are coupled

A

they occur simultaneously

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8
Q

Transcription in prokaryotes takes on a Christmas tree like structure; the longest strands would be the ______________ in age, and the shortest would be the ________________ in age

A

longest = oldest
shortest = newest

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9
Q

Why are ribonucleoside triphosphates used in RNA instead of deoxyribonucleoside triphosphates

A

not deoxy because its RNA - has the hydroxyl group

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10
Q

What is the RNA polymerase in prokaryotes

A

holoenzyme

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11
Q

What is the function of the alpha subunit of holoenzyme (there are 2 of these per holoenzyme)

A

assembly of tetrameric core

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12
Q

What is the function of the beta subunit of holoenzyme

A

contains ribonucleoside triphosphate binding site

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13
Q

What is the function of the beta prime subunit of holoenzyme

A

contains the DNA template binding region

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14
Q

What is the function of the omega subunit of holoenzyme

A

stabilizes tetrameric core

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15
Q

What is the function of the sigma subunit of holoenzyme

A

binds to the RNA polymerase tetrameric core and assists in the correct initiation of transcription (these allow for specificity)

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16
Q

What is the tetrameric core of holoenzyme comprised of

A

two alpha subunits, a beta subunit, and a beta prime subunit

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17
Q

Is transcription of RNA in prokaryotes sequence dependent or independent

A

sequence dependant

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18
Q

Is transcription of RNA in prokaryotes primer dependent or primer independent

A

primer independent

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19
Q

What are the important sequences needed for transcription of RNA in prokaryotes

A

-35 consensus (TTGACA)
-10 consensus (TATAAT)

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20
Q

What factor recognizes and binds to the -35 and -10 consensus sequences

A

sigma factor

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21
Q

Why is the -10 promoter sequence prone to unwinding

A

weak H-bonding (AT rich)

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22
Q

How does the initiation of RNA transcription occur in prokaryotes

A
  • The sigma factor of holoenzyme first recognizes and binds to the consensus factors on the DNA sequence
  • then RNA poly is positioned above the +1 site (start) and has unwound DNA to produce a single strand
  • RNA poly binds, unwinds, and joins the first 2 nucleotides
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23
Q

Does RNA synthesis in prokaryotes require a primer

A

no

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24
Q

How does elongation of RNA transcription occur in prokaryotes

A
  • holoenzyme binds tightly and unwinds the double strand
  • rNTP complementary to the first base pair on +1 site serves as the first nucleotide
  • two phosphate groups are cleaved from the subsequent rNTP, creating a nucleotide that is added to the 3’ end of the growing RNA molecule
  • sigma factor is released as RNA poly moves beyond the promoter
  • complementary bases are continually added
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25
Q

How does termination of RNA transcription occur in prokaryotes

A
  • RNA poly reaches a terminator region, but this occurs upstream of where termination actually takes place
  • newly synthesized RNA as well as RNA poly are released
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26
Q

What are the two terminators possessed by bacterial cells

A

Rho-dependant (requires Rho) and Rho-independant (intrinsic terminator)

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27
Q

What are the 2 sequence features of Rho dependant termination

A
  1. sequence causes polymerase to pause
  2. DNA sequence upstream of terminator encodes a stretch of RNA that is C rich
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28
Q

What is the C rich sequence upstream of the Rho dependant termination site called

A

the rut site

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29
Q

Where does Rho bind in Rho dependant termination

A

the rut site

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30
Q

What activity does Rho factor have

A

helicase activity (unwinds the DNA RNA hybrid)
- ends transcription

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31
Q

What are the 2 features of Rho independent termination

A
  1. contains inverted repeats
  2. string of 6-9 A’s follows the inverted repeats
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32
Q

What occurs in Rho independent termination

A

the poly A sequence is transcribed into a poly U tail after the hairpin is transcribed which causes polymerase to pause
- the hairpin forms an destabilizes the DNA/RNA hybrid
(assisted by weak A U pairing)

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33
Q

What is the purpose of “puffs” (balbani rings) in eukaryotic transcription

A

make a lot of protein/enzyme

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34
Q

What are the most important polymerases to know in eukaryotic transcription

A

poly 1 2 and 3

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35
Q

What is the main polymerase for making proteins in RNA

A

poly 2

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36
Q

Transcription in eukaryotes is still sequence dependant and primer independent, but what is different about initiation of eukaryotic transcription

A

requires transcription factors

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37
Q

How is eukaryotic transcription initiation specific

A

accessory proteins recognize specific promoters (specific to each protein) and notify the appropriate polymerase (ie. transcription initiation is dependant on the promoter sequence and the accompanying accessory proteins)

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38
Q

What makes promoters on eukaryotes more complex

A

has a core promoter and a regulatory promoter

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39
Q

Instead of sigma factor, what completes the step involving initiation in eukaryotes

A

polymerase 2

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40
Q

What does polymerase 2 create in the initiation of eukaryotic transcription

A

transcription factors of poly 2 (TFII)

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41
Q

What allows assembly of the TATA box in relation to poly 2

A

TATA-binding protein (TBP)

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42
Q

What is the preinitiation complex (PIC)

A

the complex that initiates transcription in eukaryotes (poly 2, TFIIs, TBP)

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43
Q

What is the more complex transcriptional regulation complex that permits interactions with other activator/repressor proteins

A

mediator

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44
Q

What is meant by the term basal transcriptional machinery

A

the components required for promoter interaction in eukaryotic transcription

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45
Q

Why does the DNA strand loop around in the initiation of eukaryotic transcription

A

so the transcription factors bound to enhancing sequences can interact with the basal transcription apparatus

46
Q

Why does the transcription factor stay bound to the DNA as DNA poly synthesizes RNA in eukaryotic transcription

A

so new initiation can occur at the promoter

47
Q

How long is the transcription bubble in the elongation stage of eukaryotic transcription

A

8 nucleotides

48
Q

What is the function of RNA poly 1 in eukaryotic transcription

A

requires a termination factor (similar to Rho in prokaryotes)

49
Q

What is the function of RNA poly 3 termination in eukaryotic transcription

A

transcribes a terminator sequence of U’s downstream of a hairpin

50
Q

What is the function of RNA poly 2 in eukaryotic transcription termination

A

continues transcribing past the termination sequence (RNA is cleaved at a consensus sequence in the RNA)

51
Q

How does termination in eukaryotic RNA transcription work

A

cleavage occurs at the 3’ coding region in the transcribed RNA, Rat1 exonuclease attaches to the 5’ end of trailing RNA and degrades it as it moves toward RNA poly, once it reaches RNA poly transcription is terminated

52
Q

What is the main difference between Rho and Rat1

A

Rho binds and doesn’t chew up
Rat1 binds and chews up

53
Q

What is the purpose of the regulatory promoter region in eukaryotic RNA transcription

A

binds transcription factors that positively or negatively influence transcription

54
Q

What type of RNA does RNA poly 2 transcribe in eukaryotes

A

mRNA

55
Q

What type of RNA does RNA poly 1 transcribe in eukaryotes

A

large RNAs

56
Q

What type of RNA does RNA poly 3 transcribe in eukaryotes

A

rRNAs and tRNAs

57
Q

What is colinearity when referring to RNA

A

the sequence of the gene directly determines the amino acid sequence - they are collinear

58
Q

What sequence is seen in the RNA processing of prokaryotic RNA

A

Shine Dalgarno sequence

59
Q

What is the 5’ untranslated region (5’UTR)

A

before the start codon, doesn’t code for amino acids but binds to the ribosomal complex

60
Q

What is the protein coding region

A

comprises of codons that code for specific amino acids (begins w start codon and ends w stop codon)

61
Q

What is the 3’UTR

A

does not code for amino acids, affects the stability of the mRNA and regulates its translation

62
Q

What does it mean when saying in eukaryotes gene expression is often ‘interrupted’

A

exons (protein coding) are often accompanied by introns (non coding)

63
Q

What must happen with introns in a sequence

A

must be removed

64
Q

Where does splicing of introns occur in the cell

A

the nucleus

65
Q

What is required for splicing

A

spliceosomal complex that contains smaller nuclear RNAs (snRNAs) and proteins

66
Q

What are the three main processing steps in eukaryotic nuclear pre-mRNA

A
  1. addition of 7 methyl guanosine cap (5’ cap)
  2. addition of poly A tail
  3. removal of introns
67
Q

Where are methyl groups added to form the 5’ cap

A
  • 7’ position of the terminal guanine
  • 2’ OH groups of the sugar of the first (& sometimes second) nucleotide
  • to adenine if it is the second nucleotide (sometimes)
68
Q

What is the formation of the poly A tail

A

50-250 A’s added to the 3’ end (polyadenylation)
- polyadenylation signalled by the poly A consensus sequence 11 to 30 nucleotides upstream (AAUAAA)

69
Q

What is the poly A consensus sequence that signals polyadenylation

A

AAUAAA

70
Q

What does the addition of poly A tail facilitate (think movement)

A

export out of the nucleus

71
Q

What is RNA splicing

A

removal of introns from pre-mRNA

72
Q

Every intron has ___ conserved sequences that are required for precise removal

A

3

73
Q

What are the 3 conserved sequences required for precise intron removal

A

5’ splice site, 3’ splice site, an branch point

74
Q

What are the steps of RNA splicing

A
  1. pre-mRNA is cut at 5’ splice site and the 5’ end of the intron attaches to branch point
  2. cut is made at 3’ splice site and simultaneously the 3’ end of exon 1 attaches to 5’ end of exon 2
  3. intron is released as a lariat and degraded
75
Q

What is a spliceosome

A

an RNA/protein structure that contains five small nuclear RNAs (snRNAs) designated U1, U2, U4, U5 and U6
- these snRNAs associate with about 300 small proteins to form small nuclear ribonucleoproteins (snRPSs)

76
Q

Where does U1 attach

A

5’ splice site

77
Q

Where does U2 attach

A

branch point

78
Q

Where do U4 U5 and U6 go

A

form a complex and join the spliceosome

79
Q

What is the function of the U4 U5 and U6 complex

A

conformational change in the sequence that folds it and brings the 5’ end close to the branch point

80
Q

What happens after U4 U5 and U6 complex folds 5’ end to the branch point

A

U1 and U4 are released, and base pairing occurs between U2 and U6, as well as between U6 and the 5’ splice site (now all in close proximity)
- exons are joined together and the intron is released as a lariat

81
Q

What is alternative splicing

A
  • pre-mRNA is processed in different ways to produce alternative types of mRNA
  • alternative exons are used
  • results in different proteins from the same DNA sequence

in essence - all exons can be included or only some, resulting in different products depending on what is included

82
Q

What occurs in multiple 3’ cleavage sites

A

can generate a shorter or longer exon
occurs at the last exon
could produce a different protein
(*not the same as 3’ splice site - this is the U rich cleavage site previously covered)

in essence - exons have multiple cleavage sites so they vary in length and create different products as a result

83
Q

How is alternate splicing and multiple 3’ splice sites important

A

increases diversity of proteins created

84
Q

What is a real life application of alternate splicing

A

different tissues of the body produce different variations of exon strands to give rise to variability in the proteins created

85
Q

How often do genes go through alternate splicing

A

95%

86
Q

How often do genes have multiple 3’ cleavage sites

A

50%

87
Q

What is RNA editing

A

information in the RNA strand is altered

88
Q

What are gRNAs (think RNA editing)

A

guide RNAs - direct insertion of uridine bases in mRNA (by a repair polymerase)

89
Q

What does the function of gRNAs result in

A

permanently modifies the mRNA by making new codons that specify new amino acids in the protein

90
Q

What are apoplipoproteins

A

blood proteins that carry lipids

91
Q

What enzyme contributes to RNA editing changing C to U

A

cytidine deaminase

92
Q

What is the point of cytidine deaminase

A

convert a normal glutamine codon (CAA) to a termination codon (UAA) which ends the protein and gives rise to a different function

93
Q

What are the steps of tRNA modification

A
  1. precursor tRNA is cleaved to produce just the individual tRNA molecule
  2. introns are removed via splicing
  3. bases are added to the 3’ end
  4. modification of several bases produce mature tRNA
94
Q

What enzymes contributes to modifying tRNA

A

tRNA modifying enzymes

95
Q

What is different about the removal of introns in tRNA

A

no spliceosomes required

96
Q

What makes up a ribosome

A

a large and small subunit

97
Q

What are the protein amounts associated with prokaryotic ribosomes

A

large subunit: 50S
small subunit: 30S
(come together to form 70S)

98
Q

What are the protein amounts associated with eukaryotic ribosomes

A

large subunit: 60S
small subunit: 40S
(come together to form 80S)

99
Q

How many genes and products in prokaryotic ribosomes

A

1 gene: 3 products (16S, 23S, and 5S)

100
Q

How many genes and products in eukaryotic ribosomes

A

2 genes (large and small on separate): 4 products (18S, 5.85S, 28S on large, 5S on small)

101
Q

Where is the site of rRNA synthesis in prokaryotes

A

cytoplasm (no nuclear envelope)

102
Q

Where is the site of rRNA synthesis in eukaryotes

A

nucleolus

103
Q

What are snRNAs

A

small nuclear RNAs - spliceosomes

104
Q

What are snoRNAs

A

small nucleolar RNAs - ribosomal

105
Q

What is the role of snRNAs (spliceosomes)

A

play roles in post-transcriptional processing (ie. splicing)

106
Q

What is the role of snoRNAs (ribosomal)

A

in eukaryotes, guide enzymatic modifications of ribosomal RNAs, transfer RNAs, and small nuclear RN

107
Q

What are siRNA and miRNA

A

found in eukaryotes and act as short complementary sequences that bind to complementary sequences in mRNA
- control gene expression in various ways

108
Q

What is CRISPR RNA

A

found in prokaryotes and works with Cas9 to cleave foreign DNA that enters a host cell (bacterial defense system)

109
Q

What are LncRNAs

A

long non-coding RNAs
- function in eukaryotic cells to regulate and control gene expression at the level of transcription of translation
OR
- bind and recruit proteins involved in DNA modification

110
Q

What initially binds to the TATA box on the DNA template in eukaryotes

A

TFIID

111
Q

When eukaryotic mRNA is hybridized to the complementary DNA, loops of unhybridized DNA are seen, what do they mean

A

they correspond to non coding regions of the gene and demonstrate that genes and proteins are not collinear

Mbg 2040 (13 decks)

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