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QUIZ 4 > RNA Metabolism > Flashcards

RNA Metabolism Flashcards

1
Q

transcribed strand

A

template/antisense/-

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2
Q

nontranscribed strand

A

nontemplate, coding, +; identical to RNA except RNA will have U’s instead of T’s

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3
Q

requirements for transcription

A

template, all four NTPs, divalent metal ion, no primer

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4
Q

E. coli RNA polymerase

A

DNA-dependent RNA polymerase; only one type for synthesis of all RNAs

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5
Q

Why is RNA not proofread?

A

it is quickly degraded

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6
Q

RNA polymerase holoenzyme

A

core enzyme + sigma factor; must be in holoenzyme form for polymerization

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7
Q

sigma factor

A

transcription initiation factor that recognizes promoter regions in DNA and facilitates core enzyme to start transcription

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8
Q

promoter

A

where RNA polymerase binds on DNA

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9
Q

consensus sequence

A

the most common nucleotides at a particular position; practice on slide 25 if forgot

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10
Q

prokaryote consensus sequences

A

-35 (TTGACA) and -10 (TATA box)

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11
Q

elongation in prokaryotes

A

sigma factor dissociates, core enzyme proceed along DNA and EF factors bind

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12
Q

topoisomerase I (prokaryotes)

A

rewinds DNA behind the transcription bubble

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13
Q

topoisomerase II (prokaryotes)

A

releases tension ahead of the transcription bubble

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14
Q

quinolone antibiotics

A

inhibit gyrase, interfering with both DNA replication and transcription

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15
Q

polycistronic mRNAs

A

specify more than one protein; only in prokaryotes

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16
Q

termination in prokaryotes

A

Rho dependent or Rho independent

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17
Q

Rho independent

A

palindrome sequence at the end of a gene allows folding of newly transcribed RNA into a hairpin loop –> poly U stretch will pull RNA away from the DNA (not paired strongly)

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18
Q

Rho dependent

A

rho protein will bind the RNA and use its ATPase activity to separate DNA-RNA hybrid

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19
Q

Where does transcription occur in eukaryotes?

A

nucleus

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20
Q

mRNA

A

carries genetic information from DNA to ribosome, where it specifies amino acid sequence; synthesized in nucleus

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21
Q

rRNA

A

structural RNAs; synthesized in nucleolus; 80% of RNA is in cells

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22
Q

tRNA

A

transport amino acids to ribosomes for incorporation into a polypeptide undergoing synthesis; synthesized in nucleus

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23
Q

miRNA

A

small RNA molecule, which functions in transcriptional and translational regulation of gene expression

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24
Q

RNA polymerase I

A

transcribes genes in nucleolus; makes 45S for rRNAs

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25
45S precursor becomes _
5.8, 18, and 28 (major subunit of ribosome)
26
RNA polymerase III
transcribes small stable RNAs, 5S rRNA, tRNAs
27
RNA polymerase II
transcribes mRNA precursors and miRNA
28
eukaryotic promoter
TATA box, located 25-35bp upstream of transcription start site
29
general TFs
minimal requirements for recognition of promoter; recruitment of RNA polymerase II to promoter, and initiation of transcription
30
sequence specific TFs
bind to proximal or distant position --> interact with core factors to modulate transcription
31
pre-initiation complex
TFIID binds to DNA --> kinks DNA at each end of TATA box --> other core finders bind
32
TFIID
TATA binding protein and TATA associated factors
33
TFIIH
helicase activity
34
steps in initiation
TFIID binds --> TFIIH has helicase activity to open DNA and phosphorylate TFIIF (RNA polymerase II)
35
xeroderma pigmentosa
defective TFIIH; can not perform nucleotide excision repair --> skin extremely sensitive to UV light
36
termination in eukaryotes
poly A complex binds to pol II and scans RNA for a polyadenylation site
37
noncoding genes
make up 67% of all genes
38
noncoding RNAs
housekeeping ncRNAs and regulatory RNAs
39
housekeeping RNAs
rRNA, tRNA, snRNA, snoRNA
40
regulatory RNAs
short ncRNAs (siRNA, miRNA) and long ncRNAs
41
RNA interference
dsRNA enters cell --> Dicer cleaves dsRNA into siRNA duplex --> siRNA recruited by RISC complex --> siRNA unwinds and forms protein-siRNA complex with RISC --> complex binds to target mRNA --> mRNA is cleaved at specific site and then degraded
42
Where does dsRNA come from?
RNA viruses, siRNA, endogenous dsRNA, miRNA, added exogenously
43
miRNA regulates gene expression in 3 ways
1. can be incorporated into an RISC and cause degradation 2. can be incorporated into an RISC and cause translational silencing 3. can be incorporated into an RNA and cause silencing
44
RNA-induced transcriptional silencing
miRNA/siRNA trigger down regulation at specific gene --> histones modify by methylation --> heterochromatin formation
45
Patisiran (RNAi drug)
accumulates in livers and targets mutant transthyretin which impairs heart and nerve function
46
possible therapeutical uses of RNAi
antiviral therapies (knockdown host receptors), treatment for neurodegenerative diseases (reduce mutant protein levels), cancer (knockdown oncogenes)
47
acridine
inhibits all RNA polymerase; anti-septin | **can not be used for cancer treatment because it is too toxic to humans
48
alpha-amanitin
specific for polymerase II, very toxic and specific for eukaryotes
49
actinomycin D
inhibits all RNA polymerases; antibiotic and anti-cancer agent
50
rifampicin
inhibits bacterial RNA polymerase; antibiotic
51
antiseptic
used on the skin, contain microorganisms to deter development of bacteria and viruses
52
antibiotics
used inside body and only effective against bacterial infections (not viral!)
53
actinomycin D mechanism
binds DNA by intercalation causing DNA damage --> blocks DNA and RNA pol movement, inhibiting both transcription and replication
54
How can actinomycin D insert into DNA?
it has a conjugated bond and flat structure
55
mitochondrial transcription
monomeric RNA polymerase that has 3 promoters; creates polycistronic transcripts
56
mRNA processing (transcription)
5' capping and 3' poly A tail and splicing
57
5' cap function
regulation of nuclear export, prevention of degradation by exonucleases, promotion of translation, and promotion of 5' proximal intron excision
58
5' cap reaction
phosphohydrolase cleaves gamma subunit of triphosphate --> guanylyltransferase adds a GTP --> there is now a 5' - 5' triphosphate linkage --> 7-methyl guanosine is added
59
polyadenylation
CPSF binds the RNA tail --> endonuclease cleaves 10-30 nt downstream of poly A sign, adding an -OH --> polyadenylate polymerase synthesizes poly A tail with adenyl groups coming from ATP
60
polyadenylation functions
increases mRNA stability, facilitate exit from nucleus, aids in translation
61
pre-mRNA splicing
premature RNA splices out introns to aid in formation of mature RNA
62
conserved splice site sequences
upstream splice site (GU), downstream splice site (AG), branch site
63
snRNPs
use RNA as guide to find special splicing sequence; snRNA + protein
64
spliceosomes
complexes of snRNPs that aid in splicing
65
splicing mechanism
snRNP bring the pre-mRNA, bringing sequence of neighboring exons into correct alignment --> 2' OH group of branch site in the intron attacks the phosphate at the 5' end of the intron --> creates a lariat structure --> 3' OH of exon 1 will not bind 5' at splice acceptor site of exon 2 --> releases intron lariat
66
lupus erythematosus
autoantibodies against the snRNPs; causes fatal inflammatory disease
67
ways of alternative splicing
use alternative cleavage and polyadenylation site or use different splice sites
68
diseases due to defective splicing
familial lipoprotein lipase deficiency, thalassemias, myotonic dystrophy type 1
69
familial lipoprotein lipase deficiency
LPL facilitates the removal of lipoproteins from bloodstream --> mutations causes this lipase to be inactive --> triglyceride levels build up leading to problems with pancreas and liver
70
familial lipoprotein lipase deficiency mutation
mutation at the acceptor site of intron 6 causes deletion of exon 7 and shifts the reading frame
71
familial beta-thalassemia mutation
part of intron 1 remains between exon 1 and exon 2
72
familial beta-thalassemia
body makes less hemoglobin, resulting in inefficient oxygenation of body
73
myotonic dystrophy type 1 (DM1) mutation
expansion of CTG repeats in the 3' UTR of DMPK gene --> these transcripts are not retained in the nucleus, triggering cascade of toxic events
74
processing of tRNA
5' and 3' cleavage, addition of CCA to 3' end
75
tRNA modification
methylation, deamination, reduction
76
mRNA editing
changes to specific nucleotides after RNA has been synthesized; rare event
77
example of mRNA editing
Apo B-100 to Apo B-48; Apo B-100 is in liver and Apo B-48 is edited to be put in intestine

QUIZ 4 (5 decks)

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