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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
Q

45S precursor becomes _

A

5.8, 18, and 28 (major subunit of ribosome)

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26
Q

RNA polymerase III

A

transcribes small stable RNAs, 5S rRNA, tRNAs

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27
Q

RNA polymerase II

A

transcribes mRNA precursors and miRNA

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28
Q

eukaryotic promoter

A

TATA box, located 25-35bp upstream of transcription start site

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29
Q

general TFs

A

minimal requirements for recognition of promoter; recruitment of RNA polymerase II to promoter, and initiation of transcription

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30
Q

sequence specific TFs

A

bind to proximal or distant position –> interact with core factors to modulate transcription

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31
Q

pre-initiation complex

A

TFIID binds to DNA –> kinks DNA at each end of TATA box –> other core finders bind

32
Q

TFIID

A

TATA binding protein and TATA associated factors

33
Q

TFIIH

A

helicase activity

34
Q

steps in initiation

A

TFIID binds –> TFIIH has helicase activity to open DNA and phosphorylate TFIIF (RNA polymerase II)

35
Q

xeroderma pigmentosa

A

defective TFIIH; can not perform nucleotide excision repair –> skin extremely sensitive to UV light

36
Q

termination in eukaryotes

A

poly A complex binds to pol II and scans RNA for a polyadenylation site

37
Q

noncoding genes

A

make up 67% of all genes

38
Q

noncoding RNAs

A

housekeeping ncRNAs and regulatory RNAs

39
Q

housekeeping RNAs

A

rRNA, tRNA, snRNA, snoRNA

40
Q

regulatory RNAs

A

short ncRNAs (siRNA, miRNA) and long ncRNAs

41
Q

RNA interference

A

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
Q

Where does dsRNA come from?

A

RNA viruses, siRNA, endogenous dsRNA, miRNA, added exogenously

43
Q

miRNA regulates gene expression in 3 ways

A
  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
Q

RNA-induced transcriptional silencing

A

miRNA/siRNA trigger down regulation at specific gene –> histones modify by methylation –> heterochromatin formation

45
Q

Patisiran (RNAi drug)

A

accumulates in livers and targets mutant transthyretin which impairs heart and nerve function

46
Q

possible therapeutical uses of RNAi

A

antiviral therapies (knockdown host receptors), treatment for neurodegenerative diseases (reduce mutant protein levels), cancer (knockdown oncogenes)

47
Q

acridine

A

inhibits all RNA polymerase; anti-septin

**can not be used for cancer treatment because it is too toxic to humans

48
Q

alpha-amanitin

A

specific for polymerase II, very toxic and specific for eukaryotes

49
Q

actinomycin D

A

inhibits all RNA polymerases; antibiotic and anti-cancer agent

50
Q

rifampicin

A

inhibits bacterial RNA polymerase; antibiotic

51
Q

antiseptic

A

used on the skin, contain microorganisms to deter development of bacteria and viruses

52
Q

antibiotics

A

used inside body and only effective against bacterial infections (not viral!)

53
Q

actinomycin D mechanism

A

binds DNA by intercalation causing DNA damage –> blocks DNA and RNA pol movement, inhibiting both transcription and replication

54
Q

How can actinomycin D insert into DNA?

A

it has a conjugated bond and flat structure

55
Q

mitochondrial transcription

A

monomeric RNA polymerase that has 3 promoters; creates polycistronic transcripts

56
Q

mRNA processing (transcription)

A

5’ capping and 3’ poly A tail and splicing

57
Q

5’ cap function

A

regulation of nuclear export, prevention of degradation by exonucleases, promotion of translation, and promotion of 5’ proximal intron excision

58
Q

5’ cap reaction

A

phosphohydrolase cleaves gamma subunit of triphosphate –> guanylyltransferase adds a GTP –> there is now a 5’ - 5’ triphosphate linkage –> 7-methyl guanosine is added

59
Q

polyadenylation

A

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
Q

polyadenylation functions

A

increases mRNA stability, facilitate exit from nucleus, aids in translation

61
Q

pre-mRNA splicing

A

premature RNA splices out introns to aid in formation of mature RNA

62
Q

conserved splice site sequences

A

upstream splice site (GU), downstream splice site (AG), branch site

63
Q

snRNPs

A

use RNA as guide to find special splicing sequence; snRNA + protein

64
Q

spliceosomes

A

complexes of snRNPs that aid in splicing

65
Q

splicing mechanism

A

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
Q

lupus erythematosus

A

autoantibodies against the snRNPs; causes fatal inflammatory disease

67
Q

ways of alternative splicing

A

use alternative cleavage and polyadenylation site or use different splice sites

68
Q

diseases due to defective splicing

A

familial lipoprotein lipase deficiency, thalassemias, myotonic dystrophy type 1

69
Q

familial lipoprotein lipase deficiency

A

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
Q

familial lipoprotein lipase deficiency mutation

A

mutation at the acceptor site of intron 6 causes deletion of exon 7 and shifts the reading frame

71
Q

familial beta-thalassemia mutation

A

part of intron 1 remains between exon 1 and exon 2

72
Q

familial beta-thalassemia

A

body makes less hemoglobin, resulting in inefficient oxygenation of body

73
Q

myotonic dystrophy type 1 (DM1) mutation

A

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
Q

processing of tRNA

A

5’ and 3’ cleavage, addition of CCA to 3’ end

75
Q

tRNA modification

A

methylation, deamination, reduction

76
Q

mRNA editing

A

changes to specific nucleotides after RNA has been synthesized; rare event

77
Q

example of mRNA editing

A

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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