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MLSCI 480 > Eukaryotic Transcription > Flashcards

Eukaryotic Transcription Flashcards

1
Q

T o F. Not all genes code for proteins, some RNA products are functional

A

T! rRNA and tRNA

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2
Q

RNAP I

A

RNA polymerase I
- transcription of rRNA precursors

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3
Q

RNAP II

A

RNA Pol II
- transcription of mRNA precursors

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4
Q

RNAP III

A

RNA Pol III
- transcription of 5S rRNA, tRNA, and other small RNA precursors

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5
Q

largest subunit of RNAP II

A

Rpb1

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6
Q

phases of transcription

A

assembly
initiation
elongation
termination

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7
Q

cofactors of RNAP II

A

Mg 2+
Zn 2+

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8
Q

transcription factors required to initiate transcription by RNAP II

A

6 general transcription factors
- required for synthesis of all mRNAs
- names begin with TFII; (TF-transcription factor; II-RNAPII)

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9
Q

this binding protein is the first protein to bind to a promoter in initiation

A

TATA binding protein
- part of TFIID along with TBP-associated factors or TAFs
- binding distors the DNA, partially unwinding the duplex
- hydrogen bonding and vDW interactions
- Pol II by itself is unable to bind to a promoter

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10
Q

TFIIH

A

helicase
phosphorylation of CTD

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11
Q

T or F. Eukaryotes lack precise transcription termination sites

A

T!
no identified transcriptional termination sie in eukaryotes

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12
Q

RNA polymerase undergoes selective _____________.

A

inhibition
- rifampicin
- actinomycin D
- alpha-amanitin

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13
Q

Rifampicin

A
  • antibiotic
  • inhibits bacterial B subunit of RNA pol
  • prevents promoter clearance
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14
Q

actinomycin D

A
  • anti-cancer agent
  • inhibits bacterial and eukaryotic RNA pol
  • intercalates into dsDNA preventing movement of RNA and RNA pol along template
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15
Q

alpha-amanitin

A
  • inhibits eukaryotic RNA pol
  • blocks pol II (at higher concentrations, pol III too)
  • does not block bacterial pol or Pol I
  • from poisonous death cap mushrooms
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16
Q

function of 5’ cap

A
  • protects mRNA from ribonucleases (resistant to 5” exonucleases)
  • binds to specific cap-binding complex
  • participates in binding to ribosome to initiate translation
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17
Q

T or F. RNA is synthesized from the coding or sense strand

A

F! RNA comes from the antisense strand

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18
Q

T or F. The coding strand sequence matches the sequence of RNA

A

T! It is used as a reference for the sequence

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19
Q

Additional RNAPs will exist in organelles like ___________ and ______________.

A

mitochondria and chloroplasts
- some subunits are shared b/w I,II, and III
> omega homolog = identical in all 3
> alpha homolog = identical in I and III

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20
Q

carboxy-terminal domain with consensus sequence

A

lots of Ser
- what is phosphorylated
- serines susceptible to covalent modification by phosphorylation (CTD kinase, CTD phosphatase)
- elongation/initiation sensitive to phosphorylation state of CTD

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21
Q

RNAP II active site

A

clamp portion of Rpb2 locks over bound DNA to increase processivity

contacts between RNAP and hybrid duplex are primarily to backbone

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22
Q

what are eukaryotic promoters?

A
  • promotes process; knows where to start!
  • each polymerase has its own associated promoter types
  • accessory proteins identify promoters and recruit RNAP to transcription start site
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23
Q

upstream is …

A

negative (left)
where initiation happens

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24
Q

elements in a pol II promoter

A

TFIIB
TFIID (TATA binding protein)
MTE/PDE elements = used in absence of TATA box

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25
describe the formation of the pre-initiation complex
1. TBP component of TFIID binds to TATA box of promoter 2. TFIIA & TFIIB bind 3. TFIIF binds to RNAP II and escorts it to the complex 4. TFIIE and TFIIH are sequentially recruited, thereby completing the PIC
26
TFIIB interacts with both RNA Pol II via ________ domain and TBP via _______ domain
N-terminal; C-terminal
27
T or F. One RNAP = one mRNA
T!
28
Transcription is iniated after...
pre-initation complex is assembled and then Pol II CTD is phosphorylated
29
TFIIH
- essential for nucleotide-excision repair complex - site of DNA lesion = Pol II halts, TFIIH interacts with lesion => recruits entire nucleotide-excision repair complex - result = repair of damaged DNA more efficient on actively transcribed genes and template stand is repaired more efficiently than non-template strand
30
T or F. There is no transcript stop signal in eukaryotes
T! unlike bacteria; but there is a poly-A tail that exists for translation to occur
31
T or F. Prokaryotic mRNA protein coding is not as tightly processed as eukaryotic coding
T! not usually modified (translation initiates before synthesis is complete in prokaryotes)
32
eukaryotic mRNA primary transcripts are extensively modified here
nucleus
33
T or F. tRNA and rRNA are modified in both prokaryotes and eukaryotes
T
34
this removes introns from primary transcripts
splicing
35
where does eukaryotic transcription occur?
nucleus primary transcripts undergo extensive modification prior to going to cytosol (translation)
36
coding and non-coding eukaryotic transcripts
coding = exons non = intorns
37
function of 5' cap
- protects mrNA from ribonucleases (resistant to 5' exonucleases) - binds to specific cap-binding complex - participates in binding to ribosome to initiate translation
38
describe the 5' cap
7-methyguanosine attached to 5' nucleotide via triphosphate linkage 2-hydroxyls of first and second nucleotides often methylated capping enzymes bound to RNAPII's phosphorylated CTD added early in transcription (after first 20-30 nucleotides)
39
process of added 5' cap
removal of 5' phosphatase - hydrolysis GTP addiiton methylation of G- generating the mature cap
40
synthesis of the 5' cap is carried out by enzymes tethered to the _________ terminal domain of POLII
carboxyl - enzymes synthesize cap are tethered to RNAPOLII CTD -cap remains tethered to CTD by camp-binding complex/CBCC > protects RNA from degradation > involved in transport
41
describe the eukaryotic poly A tail
80-250 residues at 3' end of primary transcript protein binding site (polA binding proteins) protects RNA from degradation (without polY, longevity of RNa greatly reduced) poly A not encoded in the genome - added in a multi step process > recognition of sequence > cleavage > addition of A
42
process of binding polyA tail
- conserved AAUAAA sequence is 10-30 nts upstream of polyA - transcript extend beyond where polyA is added - enzyme complex with endonuclease (polyadenylate polymerase) associated with CTD and binds AAUAAA transcript cleaved by endonuclease A residues are added to free 3'-OH by polyadenylate polymerase - no template required
43
expressed regions
exon
44
intervening/intragenic regions
introns
45
T or F. Introns occur in majority of vertebrate genes
T! - only known vertebrate structural genes that lack introns = histone and interferon genes
46
size of introns vs exons
exons = <1000 bp introns = 50- 20 000 bp NOTE: human genes have more DNA devoted to introns than exons ~80% of typical vertebrae structural gene is composed of introns
47
four general classes of introns
group I and II are self-splicing = auto-catalytic > no proteins involved required in vitro spliceosomal introns = nuclear mRNA primary transcripts and splicing is mediated via a large protein complex unnamed class of introns = certain tRNAs; require ATP and an endonuclease
48
Group I vs II introns
I = nucleus, mitochondria, chloroplast genes (rRNA, mRNA, tRNA) in diverse eukaryotes **not vertebrates**, and in some bacteria II = primary transcripts of organelles (mitochondria and chloroplasts) of fungi, algae, and plants **both do not require ATP; transesterification**
49
largest class of introns
spliceosomal introns
50
where are spliceosomal introns found?
nuclear mRNA primary transcripts - heterogenous nuclear RNA and pre-mRNA
51
mechanism of spliceosomal introns
lariat-forming mechanism (similar to group II introns) - requires large splicing complex - spliceosome made up of RNA-protein complexes (snRNPs - small nuclear ribonucleo proteins) 5 snRNAs = U1, U2, U4, U5, U6 ~50 proteins comparable in size and complexity to the ribosome energy spent!
52
what do spliceosomes do?
recognize and bring two exons together - 5' of U1-snRNA = partially complementary to consensus sequence of 5' splice junctions - U1-snRNP recognizes the 5' splice junction spliceosome is highly dynamic = various components associating and dissociating during specific stages of splicing process
53
spliceosome complexes remove _____ in nuclear ______ primary transcripts
introns; mRNA
54
how do spliceosome complexes remove introns in mRNA primary transcripts?
- U1, U2 recognize exon intron junction > dinucleotide AG , GU flank intron (consensus) > U1 complementary sequence that pairs to consensus 5' splice site > U2 = intron sequence (internal) that contains A residue that will perform nucleophilic attack - base pairing forms bulge around A = activates it > conformation around A is a duplex structure different from other regions - ATP consumed during assembly phase (not during splicing) - transesterification => lariat formation w joining of exon terminal nucleotides
55
T or F. Complexity of organism does not correlate with number of genes
T
56
Poly(A) site choice generates __________ in variable domains of immunoglobulin heavy chains
diversity - polyA affactes stability
57
what does alternative splicing produce in fruit fly development?
3 different forms of myosin heavy chain transcript at different stages of development
58
T or F. rRNAs and tRNAs also undergo processing
T! - made from longer precursors; so must be smaller - contain modified nucleosides; must be inncorporated - tRNAs (40-50 in most cells) > enzymatic removal of 5' & 3' ends of longer precursor > 3'-terminal CCA that attaches to amino acid for protein synthesis is added by tRNA nucleotidyltransferase > base modification (methylation, deamination, reduction)
59
ribozymes
- self-splicing group I and II introns, RNAse P - catalyze 2 rxns = transesterification and hydrolysis of phophodiester bonds - subsrates often RNA, in which case base-pairing can align the substrate for rxn - 3D structure important for function and therefore are inactivated by denaturation = just like proteins
60
RNA stability in eukaryotic cell
average = 3h with 10x turnover within a cell generation - may be seconds, minutes or stable over many generations - 5' and polyadenylation IMPORTANT
61
what degrades RNAs?
ribonucleases
62
RNA degradation in lower eukaryotes
shortening of polyA tail, decapping, mRNA degradation in 5'->3' direction
63
RNA degradation in higher eukaryotes
have 3'->5' degradative pathway

MLSCI 480 (16 decks)

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