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MOL BIO Exam #1- Lo > Lec 07- Transcription and Translation 1 > Flashcards

Lec 07- Transcription and Translation 1 Flashcards

1
Q

Where is hereditary information stored?

A

in DNA

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2
Q

What does genetic instruction consist of?

A

4 letter alphabet

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3
Q

What do the 4 nt do?

A

direct the formation of an organism

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4
Q

What is the function of nt?

A

specify the linear order of amino acids in each protein

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5
Q

What determines biological functions within a cell?

A

properties of proteins

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6
Q

How does DNA control protein synthesis?

A

NOT DIRECTLY

uses RNA as intermediary

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7
Q

What is transcription?

A

when an appropriate piece of DNA (a gene) is copied into RNA

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8
Q

What is translation?

A

When RNA is used as a template to direct the synthesis of protein

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9
Q

What is the central dogma of molecular biology?

A

DNA replication > RNA synthesis (transcription) > Protein synthesis (translation)

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10
Q

How are RNA and DNA similar?

A
  • linear polymers

- made of nt connected by phosphodiester bonds

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11
Q

What are the 4 major differences between DNA and RNA?

A

RNA=

  • single stranded
  • has ribonucleotides instead of deoxyribonucleotides
  • has Uracil instead of Thymine
  • can fold into complex 3D structures allowing some RNAs to have precise structural and catalytic functions
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12
Q

What is the function of mRNA?

A
  • messenger RNA
  • code for proteins
  • coding RNA
  • 3-5% of total cellular RNA
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13
Q

What is the function of rRNA?

A
  • ribosomal RNA
  • form basic structure (core) of the ribosome
  • catalyze protein synthesis
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14
Q

What is the function of tRNA?

A
  • transfer RNA
  • central to protein synthesis as adaptor between mRNA and amino acids (select and hold amino acids during protein synthesis)
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15
Q

What is the function of snRNA?

A
  • small nuclear RNA

- direct splicing of pre-mRNA to form mRNA

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16
Q

What is the function of snoRNA?

A
  • small nucelolar RNA

- help to process and chemically modify rRNAs

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17
Q

What is the function of miRNA?

A
  • microRNA

- regulate gene expression by blocking translation of specific mRNAs and cause their degradation

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18
Q

What is the function of siRNA?

A
  • small interfering RNA
  • turn off EUK gene expression by directing the degradation of selective mRNAs
  • establishment of compact chromatin structures
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19
Q

Many genes have ____ as their final product?

A

RNA

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20
Q

What does non-coding RNA do?

A

serves as enzymatic and structural component for many biological processes

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21
Q

What is PRO RNA pol?

A

a multi-subunit complex

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22
Q

What is the holoenzyme of PRO RNA pol?

A

a2bb’E

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23
Q

What is the function of PRO RNA pol?

A

catalyzes formation of phosphodiester bonds that link nt

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24
Q

Does PRO RNA pol have proof-reading nuclease activity?

A

YES

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25
Q

How can a lower fidelity of RNA synthesis be tolerated by organisms?

A

because mistakes are not transmitted to progeny

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26
Q

What is the start of transcription?

A

binding of pol to promoter on DNA

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27
Q

Once the DNA double helix is unwound, what acts as a template for synthesis of RNA?

A

the other strand

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28
Q

How is nt sequence determined?

A

by complementary base pairing between incoming nt and the DNA template

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29
Q

What kind of bonds covalently link nt?

A

phosphodiester bonds

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30
Q

What catalyzes the transcription reaction?

A

RNA pol

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31
Q

RNA sequence is elongated in what direction?

A

5’&raquo_space; 3’

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32
Q

RNA sequence is _________ to the template strand and ________ to the coding strand

A
  • complementary

- identical

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33
Q

What is the most important step in PRO gene expression?

A

transcription initiation

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34
Q

What is the main regulatory step for PRO?

A

transcription initiation

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35
Q

What does PRO transcription initiation decide?

A

which proteins are produced and at what rate

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36
Q

What does RNA pol assemble into in PT initiation?

A

holoenzyme a2bb’E

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37
Q

After assembling into the holoenzyme, what does the RNA pol do in PT initiation?

A

slides down the DNA until it locates a promoter

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38
Q

What happens when the RNA pol finds a promotor on the DNA in PT initiation?

A

the a-subunit binds to the promotor to form an open promoter complex

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39
Q

What does the open promoter complex make specific contacts with?

A

exposed bases

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40
Q

What is a transcription bubble?

A

an unwound short (17bp) segment of ds DNA in PT initiation

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41
Q

Which DNA strand is accessible for base pairing in PT initiation?

A

template strand

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42
Q

What does the scrunching mechanism do in the beginning of PT?

A

forms a short RNA

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43
Q

What pulls the DNA into the active site during PT initiation?

A

RNA pol that is still bound

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44
Q

What does the stress of the scrunching and the pulling of the DNA into the active site do to the short RNA?

A

causes it to be released by abortive initiation

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45
Q

What provides the energy to form phosphodiester bonds and drive PT initiation forward?

A

Hydrolysis of nucleoside triphosphates

ATP
CTP
UTP
GTP

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46
Q

What are promoters?

A

special sequences of nt

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47
Q

What do promoters do in PT?

A

direct RNA pol to the proper initiation site for transcription

48
Q

What are the 2 common motifs in PRO that are present on 5’ (upstream) side of the transcription start site?

A
  • 35 sequence (TTGACA)

- 10 sequence (TATAAT)

49
Q

When does the PRO elongation phase begin?

A

after formation of nascent RNA with ~10 nt

50
Q

What happens to RNA pol during PRO elongation?

A

it breaks its interaction with the promoter

51
Q

What happens to the sigma factor during PRO elongation?

A

it dissociates from the DNA-RNA complex

52
Q

What happens to the core enzyme during PRO elongation?

A

it binds more strongly to the DNA template

53
Q

How does the RNA pol move during PRO elongation?

A

-moves stepwise along the DNA

54
Q

What is the function of RNA pol during PRO elongation?

A
  • unwinds the helix just ahead of its active site

- exposes new region for complementary base pairing

55
Q

Transcription is __________ during PRO elongation

A

very efficient

56
Q

What does PRO elongation generate?

A

superhelical tension

57
Q

What enzyme eases tension during PRO elongation?

A

DNA gyrase

58
Q

PRO transcription continues until RNA pol meets ______

A

termination signals on the DNA templates

59
Q

What makes the PRO termination signals?

A

a string of AT nt pairs preceded by a 2-fold symmetric DNA sequence

60
Q

What does the RNA transcript of the terminal signal region form in PT termination?

A
  • a self complementary hairpin structure

- a poly U tail

61
Q

What does the hairpin structure do in PT termination?

A

destabilizes the interaction of RNA with RNA pol

62
Q

How many RNA pol synthesize RNA molecules in PRO and EUK?

A

PRO = 1 RNA pol

EUK = 3 RNA pol

63
Q

What does RNA pol II transcribe?

A
  • all protein-coding genes
  • snoRNA
  • miRNA
  • siRNA
  • IncRNA
  • most snRNA
64
Q

What does RNA pol II require during transcription?

A

additional proteins = general transcription factors

65
Q

What kind of packing does EUK transcription need to deal with?

A

higher order packing of DNA

nucleosomes, chromatin, etc…

66
Q

What is unique about RNA pol II?

A

contains a carboxyl-terminal domain (CTD) of the 220kD subunit

67
Q

What regulates the activity of RNA pol II?

A

phosphorylation mainly on Ser residues of the CTD

68
Q

What is the general transcription factor for RNA pol II called?

A

TFII

69
Q

What are the TFIIs denoted as?

A

TFIIA
TFIIB
TFIIC…

70
Q

Where do TFII assemble?

A

at the promoter before transcription

71
Q

What are the 3 functions of TFII?

A
  • help to position RNA pol correctly at promoter
  • aid in pulling apart the 2 strands of DNA to allow transcription to begin
  • release RNA pol from the promoter into the elongation mode once transcription has begun
72
Q

What is the start of ET initiation?

A

binding of TFIID to TATA box

causes distortion in DNA

73
Q

What is the TATA-box-binding protein (TBP)?

A

subunit of TFIID that recognizes TATA

74
Q

After TFIID and TATA bind, what happens next in ET initiation?

A

TFIIB is recruited

Then:
TFIIF is recruited
RNA pol II is recruited
TFIIE is recruited
TFIIH is recruited
75
Q

What factors make up the transcription initiation complex?

A 
TFIIB
TFIIF
TFIIE
TFIIH
RNA pol II
76
Q

What does the RNA pol II do in ET initiation?

A

makes short lengths of RNA

77
Q

What causes RNA pol II do leave the promoter and begin elongation during ET initiation?

A

phosphorylation of CTD by TFIIH

78
Q

What does TFIID do?

A
  • recognizes TATA box
  • recognizes other DNA sequences near the transcription start point
  • regulates DNA-binding by TBP
79
Q

What does TFIIB do?

A
  • recognizes BRE element in promoters

- accurately positions RNA pol at start site of transcription

80
Q

What does TFIIF do?

A
  • stabilizes RNA pol interaction with TBP and TFIIB

- helps attract TFIIE and TFIIH

81
Q

What dies TFIIE do?

A

attracts and regulates TFIIH

82
Q

What does TFIIH do?

A
  • unwinds DNA at transcription start point
  • phosphorylates Ser5 of the RNA pol CTD
  • releases RNA pol from promoter
83
Q

What is the most common promoter sequence for EUK RNA pol II?

A

TATA box

84
Q

What are some additional regulatory sequences besides the TATA box?

A

CAAT box

GC box

85
Q

What happens to RNA pol II during ET elongation?

A

moves along the DNA transcribing RNA along the way, creating superhelical tension

86
Q

What prevents the dissociation of RNA pol II until it reaches the terminal signals during ET elongation?

A

elongation factors

87
Q

What enzyme removes the superhelical tension on the DNA during ET elongation?

A

DNA topoisomerase

88
Q

How is EUK DNA packaged in vivo?

A

packaged into nucleosomes which are arranged in higher order chromatin structures

89
Q

What prevents access to DNA in in vivo transcription initiation?

A

physical barriers

90
Q

What are transcriptional activator proteins?

A

help attract RNA pol II to the transcription initiation start site during in vivo transcription

91
Q

What is a mediator?

A
  • a protein complex

- allows activator proteins to communicate with RNA pol II and the general transcription factors

92
Q

Why are chromatin modifying enzymes recruited during in vivo transcription initiation?

A

to provide greater access to DNA

93
Q

What are the 2 types of chromatin modifying enzymes?

A
  • chromatin remodeling complexes

- histone modifying enzymes

94
Q

What is the immediate product of RNA pol II in ET elongation?

A

pre-mRNA (primary transcript)

95
Q

Does EUK mRNA need to be processed?

A

YES

96
Q

Why are covalent modifications introduced in ET elongation?

A

to allow the cell to assess whether both ends of an mRNA molecule are present before it is exported from the nucleus to cytosol for translation

makes sure message is intact

97
Q

What are the 2 RNA modifications in EUK?

A
  • RNA capping (modification of 5’ end of mRNA) [7-methylguanosine]
  • RNA splicing (removal of non-coding sequences) [intron removal]
  • Poly- A tail (modification of the 3’ end of mRNA)
98
Q

What does the 5’ cap structure consist of?

A

7-methylguanosine joined to the 5’ end of RNA

via a 5’-5’ triphosphate bridge

99
Q

What are the 5’ cap’s functions?

A
  • distinguish mRNA from other RNAs
  • Defines translational start site
  • Stabilizes mRNA by protecting 5’ ends from phosphatases and nucleases
  • helps in RNA processing and export by binding a CBC protein complex (cap binding complex)
100
Q

Why are EUK genes discontinuous?

A

because composed of eons and introns

101
Q

What must be done to form the final mRNA in EUK?

A

-RNA splicing

  • remove introns
  • link exons
102
Q

What assemblies of proteins and snRNA carries out mRNA splicing?

A

spliceosomes

103
Q

What is the 3’ end of an mRNA specified by in EUK?

A

a signal in DNA that is transcribed into the mRNA

104
Q

What are the consensus sequences for poly-a tail?

A
  • AAUAAA
  • GU or U rich sequences
  • CA
105
Q

What recognizes the poly-A tail?

A
  • RNA binding proteins

- RNA processing enzymes

106
Q

What are the 2 important proteins for poly-A tail?

A
  • CPSF: cleavage and polyadenylation specificity factor

- CstF: cleavage stimulation factor

107
Q

What happens to the 2 important poly-A tail proteins when the RNA emerges from the pol?

A

They travel on the RNA pol and then are transferred to the RNA

108
Q

What binds the AAUAAA at the 3’ end of RNA?

A

CPSF

109
Q

What binds the GU rich element beyond the cleavage site?

A

CstF

110
Q

What cleaves RNA at the CA sequence?

A

endonuclease

111
Q

How many A nt does the poly A pol (PAP) add to the 3’ end by cleavage?

A

200 A nt

112
Q

Where does the poly-A tail get the A?

A

from ATP

113
Q

Does PAP require a template?

A

NO

114
Q

What happens after PAP adds 200 A nt?

A

poly A binding proteins assemble

115
Q

Which mRNA is polycistronic, PRO or EUK?

A

PRO

EUK mRNA = monocistronic

116
Q

The 5’ and 3’ ends of ________ mRNA are unmodified

A

PRO

117
Q

Do PRO mRNA have introns?

A

NO

only EUK have introns which are removed by slicing

MOL BIO Exam #1- Lo (8 decks)

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