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BIOC3021 > Transcription > Flashcards

Transcription Flashcards

1
Q

RNA transcription occurs in what direction?

A

5’ to 3’

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2
Q

what is the primary enzyme in prokaryotic transcription?

A

RNA polymerase holoenzyme

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3
Q

a2bb’o is the formula of what enzyme?

A

RNA polymerase holoenzyme

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4
Q

what is the part of RNA polymerase holoenzyme that is the core that synthesizes but in unable to bind to promoters

A

a2bb’

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5
Q

what is the part if RNA polymerase holoenzyme that binds the holoenzyme to the promoter sequence?

A

o

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6
Q

what is the part of RNA polymerase holoenzyme that binds to the DNA template?

A

b’

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7
Q

what is the part of RNA polymerase holoenzyme that binds to the RNA nucleotides?

A

b

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8
Q

what is the part of RNA polymerase holoenzyme that is essential for assembly of enzyme subunits?

A

a

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9
Q

what two parts of RNA polymerase holoenzyme contribute to the active site where new RNA nucleotide is added to the end of the growing chain?

A

bb’

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10
Q

what direction is the template strand?

A

3’ to 5’

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11
Q

what is the name of the first amino acid of the new growing chain that is synthesized?

A

n terminal (5’)

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12
Q

what is the name of the last amino acid of the new growing chain that is synthesized?

A

c terminal (3’)

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13
Q

the first and second RNA nucleotides bind the the RNA polymerase and to the +1 and +2 bases at the transcription start site via ____ bond

A

phosphodiester

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14
Q

the ____ subunit of RNA polymerase holoenzyme is released to complete initiation

A

o

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15
Q

what is the name of the transcription start site?

A

+1

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16
Q

where are the two promoter regions?

A

-35, -10

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17
Q

what is the sequence of the -35 region?

A

TCTTGACAT

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18
Q

what is the sequence of the -10 region?

A

TATAAT

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19
Q

what is the known as the pribnow box?

A

the -10 region promoter sequence?

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20
Q

Nucleotides are added to the growing RNA chain at a rate of ____ to _____ nucleotides per second

A

20, 50

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21
Q

the error rate in incorporating the wrong nucleotide into the RNA chains is what?

A

1/10,000

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22
Q

what enzyme acts to remove DNA supercoils and relax the DNA ahead of the polymerase to prevent supercoiling of the double helix and slowing transcription?

A

topoisomerase enzymes

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23
Q

____ synthesis is more accurate than ____ synthesis

A

DNA, RNA

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24
Q

what are the 2 means of chain termination in prokaryotes?

A

determined by sequences alone DNA (termination sites), binding of protein termination factor rho

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25
Q

what is found at the termination site of prokaryotes?

A

repeated structure (palendrome)

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26
Q

the inverted repeat sequence of the termination sequence in prokaryotes forms what kind of structure?

A

stem loop “hairpin”

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27
Q

what is the role of the prokaryote stem loop structure?

A

causes RNA polymerase to pause which brings about dissociation of the RNA transcript from DNA

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28
Q

how many subunits form the ring of the rho structure?

A

6

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29
Q

in rho factor termination, the rho protein moves along the new transcript unit it unwinds what?

A

RNA:DNA hybrid

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30
Q

eukaryotes have____ types of RNA polymerase

A

3

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31
Q

RNA polymerase ____ transcribes major ribosomal RNA genes and is located in the nucleolus

A

1

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32
Q

RNA polymerase _____ transcribes protein-coding genes and therefore synthesizes mRNA and is the one we need to know for this topic!!!!

A

2

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33
Q

RNA polymerase ____ transcribes tRNA genes, 5S, rRNA genes, and genes of other small RNAs

A

3

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34
Q

what two sites are located on the eukaryote core promoter region?

A

RNA polymerase 2 binding site, bind sites for general transcription factors (GTFs)

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35
Q

the transcription state site on eukaryote is ___

A

+1

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36
Q

what is the sequence required to define the core promoter in eukaryotes?

A

TATAAA (box)

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37
Q

in the core eukaryotic promoter, the TATA box binds the ____ subunits of _____

A

TBP, GTF TFIID

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38
Q

in eukaryote genes that lack a TATA box, they can use____ to initiate transcription

A

initiator element inr

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39
Q

what is the tail of RNA polymerase 2 called?

A

CTD

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40
Q

what general transcription factor has the helicase ability to split the DNA strands of eukaryotes?

A

TF2H

41
Q

in eukaryote, the ___ _____ binds to general transcription factors and RNA polymerase 2 to bring about initiation

A

mediator complex

42
Q

once elongation begins in eukaryote, the ____ _____ dissociates from GTFs and RNA polymerase 2

A

mediator complex

43
Q

how many protein subunits are in the mediator complex?

A

26

44
Q

for eukaryotes to go from initiation to elongation, _____ of ATP to ADP must occur

A

phosphorylation

45
Q

___ enzyme initiates phosphorylation from initiation to elongation

A

kinase

46
Q

the octamer motif, GC box, CAAT box, and TATA box are all a part of what?

A

the full promoter region

47
Q

what factor binds to the TATA box?

A

TBP

48
Q

what factor binds to the CAAT box?

A

CTF/NF1

49
Q

what factor binds to the GC box?

A

SP1

50
Q

what factors bind to the octamer motif?

A

OCT1, OCT2

51
Q

how many molecules per cell are there of CAAT box?

A

300,000

52
Q

how many molecules per cell are there of GC box?

A

60,000

53
Q

the __ ___ ___ ____ DNA binding protein consists of two perpendicular a helicies connected by a beta turn, and the side chains of one a helix fits into the major groove of DNA

A

helix turn helix motif

54
Q

in the helix turn helix motif, the side chains of one ___ ______ fits into the ___ ____ of the DNA

A

a-helix, major grooves

55
Q

the ___ ___ _____ DNA binding protein consists of two anti-parallel b strands followed by an a helix, Zn2+ ions are bound to the amino acid side chains, and the a helix inserts into the major groove of the DNA

A

zinc finger motif

56
Q

what does the zinc finger motif consist of?

A

2 anti-parallel b-strands followed by an a-helix

57
Q

in the zinc finger motif, Zn2+ ions bind to __ ___ ___ ____

A

amino acid side chains

58
Q

the __ ______ of the zinc finger motif inserts into the major groove of the DNA

A

a helix

59
Q

the ___ ____ ______ DNA binding protein consists of a-helices from two different proteins that formed a coiled coil, and extensions of the a-helices bind to the major groove

A

leucine zipper motif

60
Q

what does the leucine zipper motif consist of?

A

a-helices from two different proteins that form a coiled coil

61
Q

the extensions of the a-helices of the leucine zipper motif bind to the ___ ___ of the DNA

A

major groove

62
Q

___ _____ are regulatory sequences that may be located several thousand nucleotides from the promoter and activator transcription factors can bind

A

enhancer elements

63
Q

transcription factors bound to the enhancer activate transcription through the formation of a ___ _____ involving the promoter region

A

DNA loop

64
Q

what is the role of the DNA loop formed via transcription factors bound at the enhancer?

A

brings the enhancer-bound activator protein to the RNA polymerase that is positioned at the promoter

65
Q

enhancers can be upstream/downstream of promoter regions in introns

A

both

66
Q

how is the 5’ end of mRNA molecules processed?

A

cap derived from GTP is added

67
Q

how is the 3’ end of mRNA processed?

A

a polyAtail of 100-200 A residues is added

68
Q

what is alternative splicing?

A

some exons being removed to generate transcripts that code for proteins with different amino acid sequences

69
Q

what does splicing remove?

A

non-coding intron sequences between the exons that code for proteins

70
Q

___ ____ adds the GTP to the 5’ end of the mRNA

A

guanylyl transferase

71
Q

the GTP is added via ____ to _____ linkage

A

5’, 5’

72
Q

what is the purpose of the 5’ 5’ linkage of GTP when processing the 5’ ends of mRNA?

A

resisting cleavage from 5’ exonucleases

73
Q

the 5’ to 5’ bond of 5’ end processing are connected by ___ ______

A

3 phosphates

74
Q

____ groups are added to the 5’ end of a transcript and signal that this is the 5’ end of the transcript and a ribosome should bind

A

methyl (between 1-3)

75
Q

what is the signal sequence of polyA?

A

AAUAAA

76
Q

PolyA signal sequence AAUAAA initiates the binding of what 2 proteins?

A

CPSF (cleavage and polyA specificity factor) and CFs (cleavage factors)

77
Q

the addition of up to ____ A residues helps protect the 3’ end of exonucleases

A

200

78
Q

what is the second, lesser role of the CPSF and CFs in the processing of the 3’ ends of mRNA molecules?

A

termination of RNA synthesis by destabilizing the RNA polymerase and DNA

79
Q

mRNA splicing is carried out by _______ which are composed of several RNA protein complexes

A

spliceosomes

80
Q

spliceosomes are composed of several RNA protein complexes called _____

A

snRNPs (small nuclear ribonucleoproteins)

81
Q

what are the 5 options of snRNAs?

A

U1,U2,U4,U5,U6

82
Q

what are the start and stop sequences of introns?

A

GU (start), AG (end)

83
Q

what is the branch point of the intron?

A

A

84
Q

how many proteins are present in an snRNP?

A

10

85
Q

spliceosomes recognize ____ _____ at the 5’ exon/intron junction and the branch site

A

conserved sequences

86
Q

in the splicing reaction, a covalently closed loop of RNA called the ____ is formed by the covalent attachment of the 5’ end of an intron to the branch site of A

A

lariat

87
Q

what are the 3 products of the splicing reaction?

A

lariat form of excised intron, united exons

88
Q

what happens to the lariat in the nucleus?

A

rapidly degraded in the nucleus

89
Q

at least _____ of human protein coding genes show alternative splicing

A

95%

90
Q

what is the most common form of alternative splicing?

A

exon skipping

91
Q

mRNA has a ___ turnover rate

A

high

92
Q

what is the first part of mRNA degredation?

A

shortening of polyA tail by a deadenylase enzyme

93
Q

what enzyme shortening the polyA tail during mRNA degredation?

A

deadenylase enzyme

94
Q

what is the second step of mRNA degredation?

A

decapping enzyme removes 5’ cap

95
Q

what is the final step on mRNA degredation?

A

mRNA is degraded by both ends by 5’ and 3’ exonucleases

96
Q

in eukaryotic rRNA processing, the initiation transcripts of ____S are converted into smaller units

A

45

97
Q

what are the 3 smaller units of the original 45S rRNA?

A

18S, 5.8S, 28S

98
Q

snoRNPs (small nucleaolar ribonucleoproteins) consist of ______ and _____

A

snoRNAs, proteins

99
Q

what is the role of snoRNPs?

A

guide modifications of the rRNAs such as the addition of methyl groups

BIOC3021 (25 decks)

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