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genetics > ch 8 RNA transcription, processing, and decay > Flashcards

ch 8 RNA transcription, processing, and decay Flashcards

1
Q

pulse-chase experiment

A

method of labelling molecules with specific markers to determine where they are found
1. pulse label a eukaryotic cell with 32P UTP
2. then chase away the label with an excess of non-radioactive UTP

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2
Q

conclusion of pulse-chase experiment

A

label first appears in nucleus
after chase moves to Cytoplasm
signal is then lost (RNA turnover)

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3
Q

informational RNA

A

RNA which is used as a template for protein synthesis (mRNA)
carries the ‘genetic message’ from genes in the nucleus to the ribosome in the cytoplasm

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4
Q

functional RNA

A

RNA that is functional as an RNA molecule and is not translated into a protein
- tRNA, rRNA, snRNA, miRNA, siRNA

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5
Q

transfer RNA (tRNA)

A

transport of aa to the ribosome

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6
Q

ribosomal RNA (rRNA)

A

component of the ribosome

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7
Q

small nuclear RNA (snRNA)

A

RNA processing

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8
Q

microRNA (miRNA)

A

inhibit gene expression

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9
Q

small interfering RNA (siRNA)

A

genome integrity

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10
Q

gene (molecular terminology)

A

a segment of DNA that can be transcribed into RNA and the regulatory sequence that makes transcription possible

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11
Q

transcription

A

production of any RNA from a DNA template

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12
Q

typical prokaryotic gene

A

transcribed = coding sequence -> RNA -> protein
regulatory regions = promoter and terminator

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13
Q

typical eukaryotic gene

A

transcribed region and regulatory region
transcribed region = introns (noncoding sequence) and exons (coding sequence)

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14
Q

RNA is complementary to the

A

template strand

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15
Q

template strand =

A

non-coding strand

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16
Q

non-template strand =

A

coding strand

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17
Q

3 stages of transcription

A
  1. initiation - binding to template
  2. elongation - synthesis of RNA
  3. termination - release of RNA transcript
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18
Q

RNA polymerase

A

the enzyme which transcribes DNA into RNA

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19
Q

how does RNA polymerase know where to start transcription?

A

consensus sequences
- strong promoters, those with high levels of RNA transcription, are closer matches to the consensus

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20
Q

holoenzyme

A

RNA polymerase binding to promoter

21
Q

sigma factor

A

attached to the holoenzyme
- recognizes and binds to the -35 and -10 regions
- opens helix at the -10 region (AT rich)

22
Q

core enzyme

A

initiation
- no sigma factor
first nucleotide transcribed at +1

23
Q

elongation

A

transcription bubble moves with polymerase
addition of new bases is always to the 3’ end of the growing chain

24
Q

hairpin loop

A

internal base pairing of G and C forms helical stem

25
Q

Poly-U stretch

A

follows the hairpin
- forms spontaneously

26
Q

termination - intrinsic

A

intrinsic - factor-independent
stop point defined by newly synthesized RNA sequence of hairpin loop and ploy-u stretch
hairpin loop destabilizes DNA-RNA hybrid - RNA dissociates from DNA template

27
Q

termination - rho dependent

A
  • rho protein binds to RNA at rut site, moves towards RNA polymerase
  • nearby sequence causes polymerase to pause
  • rho catches up and causes RNA dissociation
28
Q

why does mRNA decay

A

for control - respond to changing environment, pathway feedback

29
Q

how does mRNA decay

A

5’PPP -> 5’P
endonuclease activity to cleave mRNA
exonuclease activity to degrade mRNA, processively 3’ -> 5’

30
Q

activator

A

a protein that binds to a DNA element and activates transcription

31
Q

repressor

A

a protein that binds to a DNA element and prevent transcription

32
Q

operon

A

multigeneic segment of DNA sharing regulatory regions
- predominantly found in prokaryotes

33
Q

transcription of eukaryotes - increased complexity:

A

larger genomes - comprised of chromatin
multicellular organisms
gene composition
- more genes
- significantly longer
- have non-coding regions (introns)

34
Q

3 eukaryotic RNA polymerases

A

RNA pol I - rRNA
RNA pol II - mRNA
RNA pol III - tRNA and 5S rRNA

35
Q

general transcription factors (GTFs)

A

needed bc RNA polymerase complex does not recognize and bind to promoters on its own
- recognize promoter elements
- may modify polymerase activity

36
Q

TATA box

A

initiation site of eukaryotes
similar to -10 region in prokaryotes

37
Q

TFIID

A

multi-protein complex
including TATA box binding protein

38
Q

pre-initiation complex

A

TFIIs recruited
DNA helix opened (TFIIH)
RNA polymerase bound

39
Q

what happens to get from initiation to elongation

A

TFIIH phosphorylates RNA pol II
RNA synthesis begins
transcriptions factors dissociate

40
Q

co-transcriptional modification

A

mRNA processing - within the eukaryotic nucleus
5’ cap = addition pf 7-methylguanosine
removal of introns, splicing together of exons
polyA tail added to 3’ end

41
Q

5’ cap

A

guanylyltransferase adds 7-methylguanosine to the 5’ end

42
Q

poly(A) tail

A

endonuclease recognizes the polyadenylation site (AAUAA)
mRNA is cleaved on the 3’ side of site
50-250 A’s are added by poly
(A) polymerase (PAP)

43
Q

splicing

A

introns, transcribed in the primary transcript, are removed and exons are spliced together

44
Q

branch point

A

conserved sequences
- key nucleotide = A

45
Q

spliceosome

A

an RNA/protein complex responsible for splicing
- composed of snRNA and protein = snRNPs

46
Q

roles of the spliceosome

A
  • recognize the conserved intron sequence
  • help fold the intron into the correct 3d shape
  • regulate the spicing process (alternative splicing)
47
Q

3 steps of the 2 transesterification reactions

A
  1. 2’ OH pf branch point A attacks 5’ splice site, releases 5’ exon (3’ OH exposed)
    first transesterification
  2. A is now involved in 3’-5’ bond and 2’-5’ bond
    second transesterification
  3. 3’ OH of 5’ exon attacks 3’ splice site, joining together the 2 exons
48
Q

2 methods of mRNA decay in eukaryotes

A

both start with deadenylation (poly(A) tail removal)
1. decapping by Dcp1/Dcp2
- 5’ -> 3’ exonuclease
2. 3’ -> 5’ exonuclease
- DcpS releases 5’m2Gp

49
Q

ribozymes

A

RNA with enzymatic activity
- self splicing introns - free GTP attacks phosphodiester bond at 5’ splice site, 5’ exon joins 3’ exon

genetics (9 decks)

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