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BIOCHEM > Transcription > Flashcards

Transcription Flashcards

1
Q

Transcription, the process of ___ ___ from a DNA template

A

RNA synthesis

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2
Q

How many phases are there in transcription?

A

3 phases

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3
Q

Initiation of ___ ___

A

Polymerization

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4
Q

Elongation of the ____ ___

A

RNA chain

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5
Q

Termination of ___ ___

A

strand growth

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6
Q

What are the 3 phases of transcription?

A

Initiation, elongation, termination

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7
Q

RNA transcription occurs in what direction?

A

5’ to 3’

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8
Q

what is the primary enzyme in prokaryotic transcription?

A

RNA polymerase holoenzyme

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9
Q

a2BB’o is the formula of what enzyme

A

RNA polymerase holoenzyme

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10
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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11
Q

The core polymerase can synthesis RNA but it is unable to ___ to promoters

A

bind

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12
Q

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

A

o

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13
Q

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

A

B’

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14
Q

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

A

B

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15
Q

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

A

a

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16
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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17
Q

Step 1 of transcription

A

Binding of RNA polymerase

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18
Q

Step 2 of transcription

A

Closed promoter complex

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19
Q

Step 3 of transcription

A

Open promoter complex

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20
Q

Step 4 of transcription

A

Initiation of synthesis

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21
Q

Step 5 of transcription

A

Transition to elongation phase

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22
Q

Step 6 of transcription

A

Release of o subunit

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23
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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24
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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25
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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26
Q

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

A

o

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27
Q

what is the name of the transcription start site?

A

+1

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28
Q

where are the two promoter regions?

A

-35, -10

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29
Q

what is the sequence of the -35 region?

A

TTGACA

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30
Q

what is the sequence of the -10 region?

A

TATAAT

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31
Q

what is the known as the pribnow box?

A

-10 region

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32
Q

The ___ and ___ region of the prokaryotic promoter bind the o subunit of RNA polymerase haloenzyme in the initiation of transcription

A

-35 and -10

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33
Q

In elongation, what is the direction of the upper strand (nontemplate strand)?

A

5’ to 3’

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34
Q

In elongation, what is the direction of the lower strand (template strand)?

A

3’ to 5’

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35
Q

In elongation, RNA polymerase moves along the ___ ___, producing an RNA copy of the complementary, nontemplate strand

A

template strand

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36
Q

The RNA transcript is both transcribed and translated in the ____ direction

A

5’ to 3’

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37
Q

The 5’ end of the transcript corresponds to the ____ end of the polypeptide

A

N-terminal

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38
Q

3 bases correspond to __ ___ ___

A

one amino acid

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39
Q

The C-terminal end is synthesized ___

A

last

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40
Q

In elongation, the core RNA polymerase (α2ββ’) moves along the ___ ____,
synthesizing the RNA chain to the 3’ end

A

template strand

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41
Q

In elongation, the core polymerase moves along __ ___, the double helix is
unwound, and then rewound behind the advancing ____

A

the DNA, polymerase

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42
Q

What is the rate that nucleotides are added to the growing RNA chains in elongation?

A

20-50 nucleotides per second

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43
Q

What is the error rate in incorporating the wrong nucleotides into the RNA chains?

A

1 in 10,000

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44
Q

To prevent supercoiling of the double helix from slowing transcription,
topoisomerase enzymes act to remove ___ ___ and relax the
DNA ahead of the polymerase.

A

DNA supercoils

45
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

46
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 (ρ).

47
Q

Termination of transcription is determined by specific sequences along the DNA called ___ ___

A

termination sites

48
Q

Termination of transcription occurs through the binding of a protein termination factor called ___

A

rho (ρ)

49
Q

At a termination site at the end of a gene, inverted repeat sequences result in the formation of a ___ ___ or “hairpin” structure in the RNA transcript

A

stem-loop

50
Q

The stem-loop structure causes the RNA polymerase to ____, which brings about the spontaneous dissociation of the RNA transcript from the DNA.

A

pause

51
Q

what is found at the termination site of prokaryotes

A

repeated structure (palendrome)

52
Q

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

A

stem loop “hairpin”

53
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

54
Q

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

A

RNA:DNA hybrid region

55
Q

In rho factor-dependent termination, rho factor moves along the new transcript until it
unwinds the RNA:DNA hybrid region behind the advancing __ ___ and
releases the _____

A

RNA polymerase , transcript

56
Q

eukaryotes have____ types of RNA polymerase

A

3

57
Q

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

A

1

58
Q

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

A

2

59
Q

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

A

3

60
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)

61
Q

the transcription state site on eukaryote is ___

A

+1

62
Q

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

A

TATAAA (box)

63
Q

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

A

TBP, GTF TFIID

64
Q

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

A

initiator element inr

65
Q

what is the tail of RNA polymerase 2 called?

A

CTD

66
Q

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

A

TF2H

67
Q

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

A

mediator complex (M)

68
Q

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

A

mediator complex (M)

69
Q

how many protein subunits are in the mediator complex?

A

26

70
Q

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

A

phosphorylation

71
Q

___ enzyme initiates phosphorylation from initiation to elongation

A

kinase

72
Q

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

A

the full promoter region

73
Q

what factor binds to the TATA box?

A

TBP

74
Q

what factor binds to the CAAT box?

A

CTF/NF1

75
Q

what factor binds to the GC box?

A

SP1

76
Q

what factors bind to the octamer motif?

A

OCT1, OCT2

77
Q

how many molecules per cell are there of CAAT box?

A

300,000

77
Q

how many molecules per cell are there of GC box?

A

60,000

78
Q

___ __ are regulatory sequences that may be located several thousand nucleotides from the promoter

A

enhancer elements

79
Q

How far away are enhancer elements from the promoter?

A

several thousand nucleotides away

80
Q

Transcription factors bound at the enhancer active ___

A

transcription

81
Q

How do transcription factors bound at the enhancer active transcription?

A

Through the formation of a DNA loop involving the promoter region

82
Q

Formation of a DNA loop brings the enhancer-bound activator protein to the ___ ___ positioned at the promoter

A

RNA polymerase

83
Q

how is the 5’ end of mRNA molecules processed?

A

cap derived from GTP is added

84
Q

how is the 3’ end of mRNA processed?

A

a polyAtail of 100-200 A residues is added

85
Q

what is alternative splicing?

A

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

86
Q

what does splicing remove?

A

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

87
Q

what is the signal sequence of polyA?

A

AAUAAA

88
Q

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

A

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

89
Q

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

A

200

90
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

91
Q

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

A

spliceosomes

92
Q

spliceosomes are composed of several RNA protein complexes called _____

A

snRNPs (small nuclear ribonucleoproteins)

93
Q

what are the 5 options of snRNAs?

A

U1,U2,U4,U5,U6

94
Q

what are the start and stop sequences of introns?

A

GU (start), AG (end)

95
Q

what is the branch point of the intron?

A

A

96
Q

how many proteins are present in an snRNP?

A

10

97
Q

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

A

conserved sequences

98
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

99
Q

what are the products of the splicing reaction?

A

lariat form of excised intron, united exons

100
Q

mRNA has a ___ turnover rate

A

high

101
Q

what is the first part of mRNA degredation?

A

shortening of polyA tail by a deadenylase enzyme

102
Q

what enzyme shortening the polyA tail during mRNA degredation?

A

deadenylase enzyme

103
Q

what is the second step of mRNA degredation?

A

decapping enzyme removes 5’ cap

104
Q

what is the final step on mRNA degredation?

A

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

105
Q

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

A

45

106
Q

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

A

18S, 5.8S, 28S

107
Q

snoRNPs (small nucleaolar ribonucleoproteins) consist of ______ and _____

A

snoRNAs, proteins

108
Q

what is the role of snoRNPs?

A

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

BIOCHEM (16 decks)

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