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BS209: Molecular Biology > Chapter 8: Transcription > Flashcards

Chapter 8: Transcription Flashcards

1
Q

the copying of one strand of the DNA (the coding strand) into an RNA molecule (transcript)

A

transcription

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2
Q

enzyme that transcribes DNA into RNA

A

RNA polymerase

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3
Q

RNA polymerase copies the coding strand of DNA by using the ()

A

complementary (template/non-coding) strand

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4
Q

RNA polymerase separates the DNA strands and allows () to base pair with template strand

A

ribonucleoside triphosphates

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5
Q

types of RNAs that are produced

A
  1. mRNA (encode proteins)
  2. non-coding RNAs (regulatory, catalytic, or structural roles)
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6
Q

3 stages of transcription

A
  1. initiation
  2. elongation
  3. termination
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7
Q

transcription starts when RNA polymerase binds to DNA sequence just preceding the gene: (); signifies start site for transcription

A

promoter

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8
Q

first base to be transcribed; denoted +1

A

transcription start site (TSS)

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9
Q

if RNA is transcribed in the 5’ to 3’ direction, the template must be read in the () direction

A

3’ to 5’

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10
Q

on the RNA, bases 3’ of a site are (1), while bases 5’ of a site are (2)

A
  1. downstream
  2. upstream
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11
Q

during initiation, RNA polymerase separates DNA strands to make a ()

A

transcription bubble

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12
Q

during initiation, the first few ribonucleoside triphosphates are added while ()

A

RNA polymerase is still at promoter

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13
Q

RNA polymerase moves past promoter and changes conformation to be more stably associated with DNA when RNA is ()

A

a sufficient size

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14
Q

transcription stage where RNA polymerase moves along the DNA, adding ribonucleotides

A

elongation

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15
Q

how is the transcription bubble maintained during transcription elongation

A

DNA re-pairs behind RNA polymerase as the enzyme unwinds DNA ahead

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16
Q

elongation continues until the polymerase meets a DNA sequence called a () that signals RNA synthesis to cease

A

terminator

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17
Q

in chromatin-packaged DNA, () prevent transcription machinery binding to DNA

A

nucleosomes

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18
Q

3 additional types of enzymes required in eukaryotic transcription

A
  1. nucleosome remodeling enzymes
  2. histone chaperones
  3. enzymes that reversibly modify histone proteins
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19
Q

enzymes that reposition histones away from DNA to be transcribed; can also work to block transcription

A

nucleosome remodeling enzymes

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20
Q

enzymes that disassemble and reassemble the histone octamer

A

histone chaperone

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21
Q

some enzymes can reversibly modify histone proteins; these modified proteins ()

A

recruit specific proteins to certain DNA regions

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22
Q

eukaryotes have 3 RNA polymerases

A

RNA polymerase I to III

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23
Q

eukaryotic RNA polymerase that transcribes large ribosomal RNA (rRNA) genes

A

RNA Pol I

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24
Q

eukaryotic RNA polymerase that transcribes messenger RNA (mRNA) genes

A

RNA Pol II

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25
Q

eukaryotic RNA polymerase that transcribes a variety of RNAs including transfer RNAs (tRNAs) and 5S ribosomal RNA

A

RNA Pol III

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26
Q

() have a 4th RNA polymerase that transcribes regulatory RNAs

A

plants

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27
Q

number of polymerases in bacteria and archaea

A

1

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28
Q

all RNA polymerases have a core enzyme that (1), but this cannot act alone and relies on extra proteins; same basic core structure is conserved between (2)

A
  1. catalyzes RNA synthesis
  2. 3 domains of life
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29
Q

(1) polymerase is the smallest polymerase, with 5 subunits: (2)

A
  1. bacrterial
  2. 2 alpha, 1 beta, 1 beta’, 1 omega
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30
Q

the () subunits of bacterial RNA polymerase form a jaw-like structure

A

beta and beta’

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31
Q

the () subunit of bacterial RNA polymerase has an N-terminal domain and C-terminal domain joined by a flexible linker

A

alpha

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32
Q

additional function of RNA Pol II in eukaryotic and archaeal transcription

A

couples transcription to the processing of the RNA transcript

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33
Q

the () of Poll II is crucial to the coupling of transcription to RNA transcript processing

A

C-terminal domain (CTD)

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34
Q

core bacterial RNA polymerase requires an extra subunit called () directly contacts (and directs enzyme to) the promoter

A

sigma factor

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35
Q

in bacterial RNA polymerase, core enzyme + sigma factor = ()

A

holoenzyme

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36
Q

type of bacterial sigma factor that recognizes promoter sequence for housekeeping genes as well as promote their transcription

A

primary sigma factor

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37
Q

type of bacterial sigma factor that recognizes promoters for genes whose expression is regulated in response to specific signals or stress conditions

A

alternative sigma factor

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38
Q

2 elements of bacterial promoters

A

-35 and -10 elements

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39
Q

some bacterial promoters have extra recognition sequences, like ()

A

AT-rich UP element

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40
Q

some bacterial promoters have sub-optimal (shorter or nonexistent) -35 elements, which results in ()

A

extended -10 element

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41
Q

factors that promote sigma factor’s specificity -> regulates bacterial transcription

A

each sigma factor has preferred binding sequence and preferred spacing element between -35 and -10 elements

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42
Q

in the RNA polymerase holoenzyme, there are 3 sigma domains that are positioned to recognize specific promoter elements

A
  1. Domain 2
  2. Domain 3
  3. Domain 4
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43
Q

RNA polymerase holoenzyme domain that recognizes the -10 element and performs promoter melting

A

Domain 2

44
Q

separation of duplex DNA performed by Domain 2 of the RNA polymerase holoenzyme

A

promoter melting

45
Q

RNA polymerase holoenzyme domain that recognizes the 2 bases of the extended -10 element

A

Domain 3

46
Q

RNA polymerase holoenzyme domain that recognizes the -35 element

A

Domain 4

47
Q

Domain 4 of the bacterial holoenzyme is attached to the flexible part of the core enzyme, which allows it to ()

A

accommodate different -35 to -10 spacings

48
Q

some bacterial sigma factors are regulated in response to () conditions

A

environmental or developmental

49
Q

bacterial sigma factors can be regulated at the transcriptional or translational level by altering their ()

A

mRNA or protein stability

50
Q

one way to regulate sigma factors is by the use of (), which have inhibitory domains that must be cleaved before the sigma factor can associate with the core enzyme

A

pro-sigma factors

51
Q

proteins that bind to sigma factors and inhibit their function

A

anti-sigma factors

52
Q

in S. typhimurium, the sigma factor () is needed for the expression of genes late in the assembly of the flagellar motility motor

A

sigma F (alternative sigma factor)

53
Q

in S. typhimurium, the housekeeping sigma factor () is required for transcription of genes for initial hook and FlgM

A

sigma 70

54
Q

in S. typhimurium, anti-sigma factor () binds to sigma F, preventing it from binding to the holoenzyme while proteins that form the flagellum base are being synthesized

A

FlgM

55
Q

eukaryotic and archaeal analogs to bacterial sigma factors

A

general transcription factors

56
Q

general transcription factor () complex works with RNA Pol II

A

TFII

57
Q

TFII proteins assemble at promoters with the core polymerase to form the () -> analogous to bacterial holoenzyme

A

pre-initiation complex (PIC)

58
Q

all eukaryotic polymerases need the (1) to initiation transcription (part of 2)

A
  1. TATA-binding protein (TBP)
  2. TFIID
59
Q

eukaryotic promoters have () that direct binding of pre-initiation complex (PIC) -> analogous to -35 and -10 domain of bacterial promoters

A

core promoter elements

60
Q

sequence ~25-20 bp upstream of transcription start in RNA Pol II promoters

A

TATA box

61
Q

TFIIB recognition element in RNA Pol II promoters

A

BRE

62
Q

initiator element in RNA Pol II promoters

A

INR

63
Q

promoter element found downstream of transcription start in RNA Pol II promoters

A

downstream promoter elements (DPE)

64
Q

other subunits of TFIID, called (), mediate recognition of other promoter elements like INR and DPE during PIC assembly

A

TBP-associated factors (TAFs)

65
Q

an additional large protein complex, called () is needed to activate many Pol II transcribed genes in in vivo transcription

A

mediator

66
Q

specific transcription factors for eukaryotic upstream regulatory sequences

A

activators

67
Q

Pol I uses other proteins to initiate transcription; it binds to a promoter with a core element recognized by TBP and an ()

A

upstream control element (UCE)

68
Q

once RNA polymerase is in position, the RNA-promoter complex is called a ()

A

closed complex

69
Q

once transcription bubble is formed, the RNA polymerase bound to an open region of DNA is called the ()

A

open complex

70
Q

which RNA polymerases (eukaryotic/archaeal) require ATP

A
  • require ATP: Pol II
  • don’t require ATP: Pol I and III (unwinding of DNA is spontaneous)
71
Q

exception () RNA polymerase requires energy

A

sigma 54

72
Q

the non-template strand is held away from template strand by the () regions in RNA Pol

A

lid, zipper, rudder

73
Q

similar to DNA replication elongation, () are present at the active site to catalyze addition of ribonucleotides to elongating RNA chain

A

2 Mg2+ ions (nucleophilic attack mechanism)

74
Q

(): RNA pol frequently fails to make a full-length RNA on a first attempt -> leads to release of short RNAs (2-9 nucleotides)

A

abortive initiation

75
Q

both bacterial sigma factor and eukaryotic TFIIB (involved in abortive initiation) have a () that extends into the RNA pol active site region that must be removed for transcription to continue

A

loop

76
Q

process of displacing the loop of sigma factor/TFIIB loop in RNA pol; thought to help the polymerase break away from the promoter

A

promoter clearance

77
Q

during promoter clearance, RNA pol undergoes a () that associates it very stably with DNA, and loosens its grip on initiation factors

A

conformational change

78
Q

eukaryotic Pol II becomes (1) by the action of (2) as it converts to the elongating complex

A
  1. phosphorylated
  2. TFIIH
79
Q

once RNA polymerase has transitioned to the (), transcription is highly processive

A

elongation complex

80
Q

because the most recently added 9 ribonucleotides are still within the transcription bubble, a () exists within the bubble and associates with Pol to contribute to stabiltiy

A

RNA-DNA hybrid

81
Q

RNA polymerase sometimes pauses due to physical obstructions

A

transcriptional pausing

82
Q

transcriptional pausing can occur when:

A
  1. hairpin forms in RNA transcript (due to short complementary sequences present)
  2. presence of a weak DNA-RNA hybrid within the bubble (caused by AU-rich sequence or base mispairing)
83
Q

pausing can be relieved or enhanced by ()

A

elongation factors

84
Q

occurs when the polymerase cannot resume RNA synthesis

A

transcriptional arrest

85
Q

because the resulting molecule synthesized by RNA Pol II isn’t the final active form, it is called the (), which must be processed

A

pre-mRNA

86
Q

the phosphorylated () of RNA Pol II is involved in mRNA processing

A

CTD region of the Rpb1 subunit

87
Q

occurs when RNA Pol II is paused at 30-60 bp downstream of +1 and only resumes efficient transcription with the assistance of other proteins

A

promoter proximal pausing

88
Q

TFIIH phosphorylates (1) in the (2) as RNA Pol II clears the promoter region -> leads to binding of several negative elongation factors

A
  1. fifth serine (Ser-5)
  2. CTD heptad repeat
89
Q

addition of guanosine cap to 5’ end of mRNA leads to phosphorylation of (1) in the CTD heptad repeat by (2), which causes the polymerase to resume elongation (after pausing to add the guanosine cap)

A
  1. second Serine (Ser-2)
  2. p-TEFb
90
Q

the elongation complex can () when there is a pause in RNA synthesis -> allows most recently made RNA to protrude from the front of the complex

A

backtrack

91
Q

() chop off the 3’ protruding RNA when the elongation complex backtracks

A

transcription cleavage factors

92
Q

transcription cleavage factors chop off 3’ end of mRNA by enhancing ()

A

endonuclease activity of RNA pol

93
Q

examples of transcription cleavage factors are (1) in E. coli and (2) in eukaryotes

A
  1. GreA and GreB
  2. TFIIS
94
Q

histone chaperones include:

A

FACT, Asf1, and Spt6

95
Q

2 main classes of bacterial terminators

A
  1. intrinsic
  2. Rho-dependent
96
Q

bacterial terminators that end transcription in the absence of any other factors

A

intrinsic (or simple) terminators

97
Q

2 main features of bacterial intrinsic terminators

A
  1. inverted repeated sequence that results in a stem-loop in the RNA
  2. a string of 8-10 residues that is so unstable it causes Pol to arrest and transcription bubble to collapse
98
Q

at () terminators, DNA sequence alone is not enough for terminators -> other protein factors are needed

A

enzymatic

99
Q

in E. coli, certain genes need the (1) protein to terminate transcription -> called (2); those that do not require the protein are called (3)

A
  1. Rho
  2. Rho-dependent terminators
  3. Rho-independent terminators
100
Q

in eukaryotes, intrinsic terminator sites are recognized by (1); these have stretch of (2), which is thought to destabilize the DNA-RNA hybrid in the same way as E. coli intrinsic terminators

A
  1. RNA Pol III
  2. As
101
Q

Termination for Pol I requires add’l proteins: (1) in yeast and (2) in mice

A
  1. Reb1p
  2. TTF1
102
Q

termination of Pol II genes is coupled to the processing of the () of the mRNA

A

3’ end

103
Q

most eukaryotic mRNAs have a poly-A tail resulting from ()

A

polyadenylation

104
Q

2 main models of transcription termination by RNA Pol II

A
  1. allosteric
  2. torpedo
105
Q

RNA processing proteins associate w processing signals and CTD; cleavage/recognition of the processing proteins causes conformational changes that lead to dissociation of Pol II from DNA

A

allosteric model of transcription termination by Pol II

106
Q

after cleavage, RNA downstream of poly(A) side is digested by Rat1 endonuclease (5’ to 3’) -> disrupts polymerization and causes Pol II to dissociate from DNA

A

torpedo model

107
Q

in the torpedo model, () acts as the torpedo that degrades nascent RNA until it runs into the RNA pol

A

Rat1 endonuclease

BS209: Molecular Biology (8 decks)

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