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RNA METABOLISM > ALL THE THINGS > Flashcards

ALL THE THINGS Flashcards

1
Q

What is the coding strand identical to?

A

mRNA strand (except T for U)

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2
Q

What is unique about the template strand?

A

complementary and antiparallel to the mRNA strand

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3
Q

Which strand is the template strand with respect to the DNA double helix?

A

the 3’-5’ strand (bottom strand)

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4
Q

In what direction is the mRNA strand synthesized from the template strand?

A

5’-3’ (but the strand is read in the 3’-5’ direction)

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5
Q

Are there multiple types of RNA polymerases in Bacteria?

A

No. Just one type.

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6
Q

A core RNA polymerase enzyme of how many subunits is required for nucleotide polymerization in Bacteria?

A

5

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7
Q

Can bacterial RNA polymerase proofread?

A

No

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8
Q

What does RNA poly in bacteria need in order to initiate transcription?

A

a promotor sequence ahead of the gene

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9
Q

Describe the DNA sequences that make up promotor sites in Bacterial DNA

A

sequences that extend 70 bp before the transcription start site to 30 bp after the start site

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10
Q

What confers specificity for the promoter site in Bacterial transcription?

A

Sigma Factor binding to the core enzyme of RNA polymerase

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11
Q

What is the complex of the Sigma Factor bound to the core enzyme called?

A

Holoenzyme

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12
Q

Describe the reaction that RNA polymerase catalyzes

A

3’-OH of the nucleotide at the end of the growing strand attacks the 5’-alpha phosphate of the incoming NTP.

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13
Q

What is the driving force for the reaction catalyzed by RNA polymerase?

A

hydrolysis of pyro-phosphate

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14
Q

What is the first nucleotide of the coding strand denoted as?

A

It is the start site and denoted as +1. Anything ahead of it is +2, etc.

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15
Q

What is the nucleotide preceding the start site denoted as?

A

-1

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16
Q

What are the two regions conserved in most bacterial promoter sequences?

A
  • 35 Region

- 10 Region (Pribnow box)

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17
Q

What is unique about the -10 region? E.g. What is there a high concentration of?

A

AT content is high here

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18
Q

Besides binding efficiency, what are the other factors important for determining promoter strength?

A

consensus sequences

spacing between consensus sequences

distance of the consensus sequences from the transcription start site

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19
Q

What can increase the efficiency of promoters?

A

Negative supercoling by topoisomerases

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20
Q

After clearing the promoter, what happens to the RNA poly?

A

undergoes a major conformational chage and cannot revert

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21
Q

How many bp are typically found in bacterial transcription bubbles?

A

15-17 bp

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22
Q

The RNA/DNA hybrid is limited to how many bp in bacterial transcription?

A

7 bp

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23
Q

What is Rho factor involved in?

A

termination of bacterial transcription

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24
Q

What is Rho factor?

A

ATP-dependent helicase which can unwind RNA/DNA hybrids

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25
Q

Where does Rho factor bind?

A

to a CA-rich region in the nascent RNA chain some distance upstream of the termination site

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26
Q

After Rho factor binds the nascent RNA chain, what happens next?

A

it catches up with the RNA polymerase and dissolves the mRNA-DNA-polymerase complex

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27
Q

Describe Rho-factor independent termination of bacterial trancsription

A

termination by combined action of weak U-A bonding in the RNA/DNA hybrid and strong G-C bonding in the nascent RNA

Essentially you form hairpin or stem loop structures in both regions

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28
Q

What affect does RIFAMPIN have on bacterial RNA poly?

A

changes its conformation so that it cannot initiate RNA synthesis

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29
Q

Can Eukaryotic RNA poly bind RIFAMPIN?

A

NO! RNA synthesis is totally unaffected

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30
Q

What kind of DNA does Actinomycin bind to strongly?

A

double stranded DNA (dsDNA)

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31
Q

How is dsDNA affected by Actinomycin?

A

once bound, it is unable to be an effective template for RNA synthesis

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32
Q

What else can Actinomycin inhibit at high concentrations?

A

DNA replication

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33
Q

How does Actinomycin interfere with DNA? How is its action explained?

A

through intercalation; intercalates between two successive GC pairs

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34
Q

How many Eukary RNA poly’s are there?

A

3

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35
Q

Name the Eukary RNA poly’s

A

I
II
III

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36
Q

Where are the different eukary RNA polys located?

A

I - Nucleolus
II - Nucleoplasm
III - Nucleoplasm

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37
Q

What are the products transcribed RNA poly I?

A

18S, 5.8S, and 28S rRNA

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38
Q

What are the products transcribed by RNA poly II?

A

mRNA precursors
snRNA
miRNA

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39
Q

What are the products transcribed by RNA poly III?

A

tRNA and 5S rRNA

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40
Q

What affect does alpha-amantin have on the different Eukary RNA polys?

A

I - insensitive

II - Strongly inhibited

III - inhibited by high concentrations

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41
Q

How do the Eukary RNA polys differ structurally?

A

are differentiated by their C-terminal part; RNA pol II has long C-terminal part

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42
Q

What makes RNA pol II more complex than bacterial RNA poly?

A

12 subunits

long carboxy-terminal domain (CTD) with 52 repeats of Y-S-P-T-S-P-S

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43
Q

What does RNA poly II need to start?

A

general transcription factors

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44
Q

At least how many proteins are needed for eukaryotic RNA transcription?

A

30; functions of the proteins are comparable to Sigma factor

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45
Q

What are the general RNA Pol II promotor elements?

A

BRE - B recognition element

INR - Initiator element

DPE - Downstream promoter element

TBP - TATA binding protein

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46
Q

What are the general transcription factors needed for RNA pol II?

A

TFIIB
TBP
TFIID
TFIID

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47
Q

What transcription factor is associated with BRE?

A

TFIIB - recognizes BRE

48
Q

What transcription factor is associated with TATA?

A

TBP - recognizes TATA box

49
Q

What transcription factor is associated with INR?

A

TFIID

50
Q

What transcription factor is associated with DPE?

A

TFIID

51
Q

What does TFIIH do during transcription?

A

unwinds DNA at the transcription start point; releases RNA poly from the promoter

Also phosphorylates Ser5 of the RNA polymerase CTD

52
Q

After how many nucleotides (nt) are most of the general transcription factors released?

A

60-70 nt

53
Q

What are Elongation factors?

A

become associated with RNA poly so it can read through DNA associated with nucleosomes

54
Q

Describe the functions conferred by Elongation factors associated with RNA poly

A

ATP-dependent complex remodeling that displaces the nucleosome

Histone dimer removal

55
Q

What removes positive supercoils ahead of the RNA polymerase?

A

Topoisomerase

56
Q

How is RNA poly recycled?

A

dephosphorylation

57
Q

When you say “primary transcript,” what are you describing?

A

pre-RNA strand

58
Q

In terms of length, what is the primary transcript equivalent to?

A

full length of DNA transcribed

59
Q

What is the corresponding DNA segment from which the primary transcript is transcribed called?

A

transcription unit

60
Q

What does RNA processing require?

A

a variety of small nuclear RNA’s (snRNAs)

enzymes involved with capping and polyadenylation

61
Q

Is mRNA processed or modified in Bacteria?

A

No because bacterial mRNA is translated as it is being transcribed

62
Q

5’- capping of the nascent RNA chain is carried out by what enzyme?

A

guanylyltransferase

63
Q

Subsequent N7 methylation in the cytosol is carried out by what?

A

guanine-7-methyltransferase

64
Q

What is the point of capping the mRNA?

A

capping protects the mRNA from degradation and is needed for export out of the nucleus and for assembly of a translation complex

65
Q

What types of RNAs aren’t capped?

A

tRNAs and rRNAs

66
Q

What is the Poly-A signal sequence identified by?

A

AAUAAA

67
Q

Where is the Poly-A sequence located?

A

3’- untranslated region (UTR)

68
Q

Where is the nascent mRNA cleaved at the Poly-A sequence?

A

10-40 bp downstream of it

69
Q

What cleaves the Poly-A sequence 10-40 bp downstream from the site?

A

a specialized endonuclease

70
Q

What enzyme carries out the poly-A reaction?

A

polyadenylate polymerase

71
Q

Is the poly-A tail encoded for in the DNA?

A

No

72
Q

Why even have the poly-A tail? What does it do for the mRNA?

A

stabilizes mRNA

needed for nuclear export

needed for assembly of translation complex

73
Q

What happens to the poly-A tail in the cytosol?

A

it is gradually shortened

74
Q

After the processing is complete, what happens to the mRNA next?

A

Splicing happens next

75
Q

What happens during splicing of the processed mRNA?

A

removal of introns splices the flanking exons together into final sequence

76
Q

What is a splicesome?

A

molecular assembly that carries out splicing

77
Q

By what 2 reactions does the splicesome carry out splicing?

A

via 2 transesterifications

78
Q

Describe the splice donor site

A

5’- splice site

border of 3’-end of Exon and 5’-end of Intron

starts with GU

79
Q

Describe the splice acceptor site

A

3’- end of the intron

ends with AG

80
Q

When the intron is removed, describe its structure

A

it resembles a lariat

81
Q

What do snRNAs form when they associate with proteins?

A

snRNPs - small nuclear ribonucleo proteins

82
Q

What do snRNPs do?

A

complex with other proteins to form the splicesome

base pair with the consensus sites involved in splicing and with RNA’s in other snRNPs

83
Q

Which snRNPs are involved in splicing?

A

U1 - U6

84
Q

Splicesome assembly is initiated by —

A

recognition of the 5’-splice site by U1 snRNP

85
Q

What happens after splicesome assembly initiation?

A

U2 snRNP binds to the branch site

86
Q

After interaction with the branch site, what forms the complete splicesome?

A

complex of U4-U5-U6

87
Q

After construction of the complete splicesome, what happens next?

A

U5 interacts with exons on the 5’ and 3’ splice sites and pulls the splice sites together

88
Q

After the splice sites are brought together, what happens next?

A

U6 detaches from U4 and binds to U2

89
Q

After U6 binds to U2 what happens?

A

U6 and U2 snRNP function as ribozymes catalyzing both transesterifications

90
Q

Does splicing require ATP? If so how many molecules are used?

A

Yes. 3 ATP molecules

91
Q

Besides the 3’-UTR, are there any other untranslated regions in processed mRNA?

A

5’UTR where the cap is

92
Q

What are the 3 sources of variant mRNA?

A

Alternative start sites (multiple promotors)

Alternative splicing

Alternative termination sites

93
Q

Intracellular mRNA concentrations are dependent on what?

A

synthesis and degradation

94
Q

Why are bacterial mRNA’s so unstable?

A

short half lives lasting a few minutes

allows the bacteria to rapidly respond to environmental changes

95
Q

What is the half life (roughly) of mRNA in eukaryotes?

A

few minutes to 24 hours depending on the product

96
Q

How is bacterial mRNA degradation carried out?

A

an ENDOribonuclease makes a few cuts in the mRNA followed by 3’ - 5’ EXOribonuclease action

97
Q

In eukary mRNA degradation, what acts a timer for the lifespan of an mRNA strand?

A

natural shortening of the poly-A tail

98
Q

When is eukary mRNA degradation initiated?

A

when the poly-A tail is shorter than ~25A’s

99
Q

How is eukary mRNA degraded?

A

decapping followed by either 5’-3’ or 3’-5’ degradation

100
Q

Where does eukary mRNA degradation occur?

A

specialized regions of the cytoplasm called exosomes

101
Q

How many different rRNAs in Eukary?Prokary?

A

4 - Euk

3 - Pro

102
Q

Where does transcription of rRNA genes and processing of rRNA take place?

A

in the nucleolus

103
Q

How many nucleotides long is the tRNA structure?

A

74-95 nt

104
Q

What two conformations does tRNA exist in?

A

clover-leaf structure

final conformation is L-shaped

105
Q

tRNA’s are derived from longer RNA precursors by —

A

removal of nt’s at both 5’ and 3’ end

106
Q

What do some eukary tRNAs contain that needs to spliced out?

A

an intron

107
Q

Both prokary and eukary tRNAs have —

A

a CCA sequence at the 3’-end

108
Q

How is the CCA sequence in eukary tRNA different from its prokary counterpart?

A

CCA sequence is added post-transcriptionally in eukarys

109
Q

What do modified bases in tRNA allow?

A

better recognition when binding

Inosine (modified adenine) allows for recognizing of multiple codons

110
Q

By what ribozyme are eukary tRNAs processed?

A

RNaseP

111
Q

Our genome contains how many miRNAs?

A

400

112
Q

What are miRNAs transcribed by?

A

RNA Pol II

113
Q

What caps, poly-adenylates, and processes miRNA?

A

Dicer

114
Q

Dicer processes 75 nt long genome encoded RNAs with profound hairpin structures into what?

A

double stranded silencing RNAs (siRNAs)

115
Q

One of the strands of siRNA is incorporated into what?

A

RNA-induced silencing complex (RISC)

116
Q

What is the RISC complex involved in?

A

regulation of the stability and translatability of mRNA’s

RNA METABOLISM (1 decks)

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