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Biochemistry module 8 > Lecture RNA synthesis > Flashcards

Lecture RNA synthesis Flashcards

0
Q

RNA is a polymer composed of alternating units of ribonucleotides connected through a

A

3-5 phospodiester bond

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1
Q

RNA is a polymer composed of alternating units of

A

Ribonucleosides

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2
Q

In contrast with DNA, ribonucleotides contain

A

hydroxyl groups on the 2’-carbonof the ribose sugar •

the base uracilin place of thymine

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3
Q

The “working copies” of DNA •Expresses the master plan contained in DNA

A

Significance of RNA

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4
Q

80% of the total RNA

A

Ribosomal RNA

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5
Q

smallest of the 3 major RNA species (excluding the small RNAs), make up 15%

A

Transfer RNA

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6
Q

2-5%, but is the most heterogenousin terms of size and base sequence

A

Messenger RNA

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7
Q

involved in mRNA splicing and gene regulation

A

Small RNA’s

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8
Q

Prokaryotic rRNA

A

23S, 16S, 5S

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9
Q

Eukaryotic rRNA

A

28S, 18S, 5.8S, 5S

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10
Q

measure of size based upon the molecular sedimentation rate during ultracentrifugation

A

Svedberg unit “S”

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11
Q

Similarities between DNA and RNA

A

Both have the general steps of initiation, elongation, and termination with 5’ to 3’ polarity (synthesized in a 5’ 3’ direction, antiparallelto the DNA template strand which is read in a 3’  5’ direction) •Both have large, multicomponentinitiation complexes •Both adhere to Watson-Crick base-pairing rules

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12
Q

RNA

DNA

A

Ribose

Deoxyribose

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13
Q

complementary base pair for A in RNA

A

U instead of T (for DNA)

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14
Q

not involved in RNA synthesis

A

Primer

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15
Q

Only a portion of the genome is transcribed or copied

A

RNA

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16
Q

entire genome must be copied

A

DNA

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17
Q

always read in the 3’ to 5’ direction (RNA)

A

Template strand

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18
Q

The opposite strand is called the (RNA)

A

Coding strand

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19
Q

The enzyme responsible for the polymerization of ribonucleotidesinto a sequence complementary to the template strand of the gene

A

DNA dependent RNA polymerase

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20
Q

DNA DEPENDENT RNA POLYMERASE attach to the ______ on the ______

A

Promoter

Template strand

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21
Q

corresponds to the 5’ nucleotide of the mRNA

A

Starting point of transcription

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22
Q

The numbers increase as the sequence proceeds

A

Downstream

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23
Q

The nucleotide in the promoter adjacent to the transcription initiation site is designated -1, and these negative numbers increase as the sequence proceeds

A

Upstream

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24
Q

defined as that region of DNA that includes the signals for transcription: initiation, elongation, and termination

A

Transcription unit

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25
Q

A transcription unit includes a

A

Promoter
RNA coding region
Terminator

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26
Q

The RNA product, which is synthesized in the 5’ to 3’ direction, is the

A

Primary transcript

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27
Q

with its 4 subunits responsible for 5’ 3’ RNA polymerase activity

A

Core enzyme

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28
Q

Core enzyme cannot recognize the promoter on the DNA template

A

Lack specificity

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29
Q

contains the sigma subunit or sigma factor (that enables RNA polymerase to recognize promoter regions on the DNA

A

Holoenzyme

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30
Q

An auxiliary protein of RNA polymerase

A

Termination factor

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31
Q

Some regions of DNA that signal the termination of transcriptionare recognized by

A

RNA polymerase

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32
Q

Others are recognized by specific termination factors, an example of which is the

A

rho factor of ecoli

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33
Q

The primary transcripts generated by RNA polymerase II(one of three nuclear DNAdependent RNA polymerases in eukaryotes) are promptly capped by

A

7 methylguanosine triposphate

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34
Q

These caps are necessary for the subsequent processing of the primary transcript to mRNA, for the translation of the mRNA, and for protection of the mRNA against exonucleolyticattack

A

7 methylguanosine triposphate

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35
Q

Involves binding of the RNA polymerase holoenzymeto a promoter region

A

Initiation

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36
Q

Pribnowbox and -35 sequence •Highly conserved •Recognized by prokaryotic RNA polymerase sigma factors

A

Consensus nucleotide sequences

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37
Q

A stretch of 6 nucleotides (5’-TATAAT-3’) centered around 8 to 10 nucleotides to the left of the transcription start site that codes for the

A

Initial base of mRNA

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38
Q

A stretch of 6 nucleotides (5’-TATAAT-3’) centered around 8 to 10 nucleotides to the left of the transcription start site that codes for the initial base of mRNA

A

Pribnow box

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39
Q

A second consensus nucleotide sequence centeredaround 35 bases to the left of the transcription start site

A

-35 sequence

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40
Q

A mutationin either the Pribnowbox or -35 sequence can affect the transcription of the gene controlled by the

A

Mutant promoter

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41
Q

Once the promoter has been recognized by the holoenzyme, RNA polymerase (RNAP) begins to synthesize a transcript of the DNA sequence

A

Elongation

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42
Q

Elongation usually beginning with a

A

Purine

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43
Q

Unlike DNA polymerase, RNA polymerase does not require a

A

primer and has no endoor exonucleaseactivity (No repair capability

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44
Q

longation by addition of ribonucleotidesto the

A

3-OH end

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45
Q

3’-OH acts as a __________, attacking the -phosphate of the incoming ribonucleosidetriphosphate and releasing ___________

A

Nucleophile

Pyrophosphate

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46
Q

Alternatively, can recognize termination regions on the DNA template

A

tetramericRNA polymerase

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47
Q

may be required for the release of the RNA product

A

Rho factor protein

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48
Q

Requires Rho factor protein

A

RHO dependent termination

49
Q

Rho factor binds to a _________ near the 3’ end of the newly synthesized RNA, and migrates along behind the___________ in the 5’ to 3’ direction until the termination site is reached

A

C rich region

RNA polymerase

50
Q

Rho factor that hydrolyzes ATP, and uses the energy to unwind the 3’ end of the transcript from the template

A

ATP-dependent RNA-DNA helicase

51
Q

At the termination site, rho factor displaces the DNA template strand, facilitating the

A

Dissociation of the RNA molecule

52
Q

slows down the progress of RNA polymerase and causes it to pause temporarily

A

Hairpin turn

53
Q

A hairpin turn complementary to a region of the DNA template near the termination region that exhibits 2-fold symmetry as a result of the presence of a

A

Palindrome

54
Q

In addition to RNAP recognizing the promoter region and initiating RNA synthesis, several supplemental _____________bind to DNA in eukaryotes

A

Transcription factors

55
Q

For RNAP and the TFs to recognize and bind to the specific DNA sequence, the double helix must assume a loose conformatonand dissociate temporarily from the

A

Nucleosome core

56
Q

Most actively transcribed genes are found in a relaxed form of chromatin

A

Euchromatin

57
Q

Most inactive btranscribe genes segments are in a highly condensed

A

Heterochromatin

58
Q

The interconversionof active and inactive forms of chromatin is called

A

Chromatin modeling

59
Q

Genes that are inactive contain more

A

MethylatedDNA (5-methylcytosine

60
Q

When _________become acetylated, the chromatin structure becomes looser

61
Q

composed of a variety of different cis sequence elements which recruit some of these trans-acting factors through DNA-protein interactions

A

Eukaryotic promoters

62
Q

also occur and account for many of the multi-component complexes found at eukaryotic promoters

A

Protein protein interactions

63
Q

utilize a small number of ubiquitous transcription factors

A

Pol 1 and 3

64
Q

Used Large number of ubiquitous transcription factors

65
Q

in order to specifically bind to a promoter and initiate transcription

A

Transcription factors

66
Q

2 identical subunits of the Upstream Binding Factor

A

Upstream Core eEement

Core Promoter eEement

67
Q

consists of four subunits

A

Selectively factor 1

68
Q

Initiation at RNA Pol 1 promoters

A

Upstream binding factor
Protein interactions
Selectively factor 1
RNA pol1

69
Q

Initiation at RNA Pol 3 promoters (tRNA)

A

TFIIIC- A and B sites
TFIIIB- upstream
RNA polymerase 3- initiates transcription

70
Q

Initiation at RNA polIII promoters (5s rRNA)

A

Same to tRNA except TFIIIA binds the C box

71
Q

A sequence of DNA nucleotides that is almost identical to the Pribnowbox is usually found centeredabout 25 nucleotides upstream of the initial base of the transcription start site for an mRNA molecule •This consensus sequence is the

A

TATA or Hogness box

72
Q

The consensus sequence of TATA or hogness box

A

TATAAAA

so it resembles the TATAAT sequence of the prokaryotic -10region

73
Q

The TATA box appears to be more important for selecting the start point of transcription (i.e. positioning the enzyme) than for

A

Defining the promoter

74
Q

which binds to the TATA box promoter element, is the only transcription factor capable of binding to specific sequences of DNA

75
Q

TFIID consist of

A

TATA binding protein (TBP) and 14 TBP-associated factors (TAFs

76
Q

A second consensus sequence called the.

-found upstream from the transcription start site

A

CAAT Box(70-80 nucleotides

77
Q

CAAT box

78
Q

is a common element in eukaryotic class II promoters. Its consensus sequence is GGGCGG

79
Q

binds to the GC box

A

Transcription factor Sp1

80
Q

Special cis-acting DNA sequences

A

increase the rate of initiation of transcription by RNAP II

81
Q

Special cis-acting DNA sequences that increase the rate of initiation of transcription by RNAP II •Must be on the same chromosome as the gene whose transcription they stimulate •They can be located upstream (to the 5’ side) or downstream (to the 3’ side) of the transcription start site

82
Q

They can be close to or thousands of base pairs away from the promoter •They can occur on either strand of the DNA

83
Q

Enhancers contain DNA sequences called ____________that bind specific transcription factorscalled_________

A

Response elements

Activators

84
Q

similar to enhancers in that they act over long distances to reduce the level of gene expression

85
Q

recognizes and binds to the TATA box

86
Q

binds and stabilizes TFIID binding

87
Q

possibly in a stepwise manner -to form a preinitiationcomplex

A

RNA polymerase II holoenzyme

88
Q

Formation of the PreInitiation Complex (PIC) for polII on a TATA promoter •The order of assembly of transcription factors may be

A

TFIID-> TFIIA-> TFIIB-> (TFIIF + RNAPII) -> TFIIE ->TFIIH

89
Q

differs from its prokaryotic counterpart in that it has a series of heptad repeats with consensus sequence Tyr-Ser-ProThr-Ser-Pro-Serat the carboxyl terminal of the largest polII subunit

A

Eukaryotic pol 2

90
Q

both a substrate for several kinases, including the kinasecomponent of TFIIH, and a binding site for a wide array of proteins

A

Carboxyl Terminal Repeat Domain (CTD

91
Q

are the ultimate targets of cell-signalling pathways

A

Trnscriptions factors

92
Q

inhibits transcription initiation by binding to the beta subunit of prokaryotic RNA polymerase, preventing phosphodiesterbond formation

A

Rifampicin

93
Q

used for tumortherapy; it binds to the DNA template and interferes with the movement of RNA polymerase along the DNA

A

Dactinomycin(ActinomycinD

94
Q

intercalate between successive G=C base pairs in duplex DNA-inhibit transcriptional elongation in proand eukaryotes

A

ActinomycinD, acridine

95
Q

binds the subunit of bacterial RNA polymerase-blocks promoter clearance (elongation

A

Rifampicin

96
Q

produced by fungus Amanita phalloides (death cap mushroom)-potent inhibitor of RNA polII and weak inhibitor of RNA polIII

A

Alpha amanitin

97
Q

the linear copy of the transcription unit

A

Primary transcript

98
Q

The primary transcripts of both prokaryotic and eukaryotic RNA are post-transcriptionally modified by cleavage using

A

Ribonucleases

99
Q

generally identical to its primary transcript

A

Prokaryotic mRNA

100
Q

extensively modified after transcription

A

Eukaryotic mRNA

101
Q

ribosomal RNA of prokaryotes

A

23S, 16S, and 5S

102
Q

Eukaryotic rRNA

A

28S, 18S, 5.8S

103
Q

synthesized by RNAP III and modified separately

A

Eukaryotic 5s rRNA

104
Q

The preribosomalRNAsare cleaved by ____________ to yield intermediate-sized pieces of rRNA, which are further trimmed to produce the required rRNAspecies

A

Ribonucleases

105
Q

tRNAis transcribed by

A

RNA polymerase III

106
Q

The additional nucleotides at the 5’-end are removed by an unusual RNA containing enzyme called

A

Ribonuclease P

107
Q

Some tRNAprecursors contain an _____ located in the anticodonarm Intronsare spliced out during processing of the tRNA

108
Q

These three bases are not coded for by the tRNAgene. Instead, these nucleotides are added during processing of the pre-tRNAtranscript (by replacing UU residues at the 3’ end

A

CCA at the 3 end

109
Q

The enzyme responsible for the addition of the CCA-end is

A

tRNA nucleotidyl transferase

110
Q

The collection of all the precursor molecules for mRNAis known as

A

Heterogenous nuclear RNA

111
Q

is attached to the 5’ end of the mRNA

A

7 methyl guanosine

112
Q

GTP addition is catalyzed by guanylyl transferasein the nucleus •This is followed by methylationof the terminal guanine in the cytosol, catalyzed by

A

Guanine 7 methyl transferase

113
Q

is the source of the methyl group

114
Q

Most eukaryotic mRNAs have a chain of 40 to 200 adenine nucleotides attached to the 3’ end •Not transcribed from DNA but addedby the nuclear enzyme

A

Polyadenelate polymerase

115
Q

found near the 3’ end signals that poly-A-tail must be added to stabilize RNA and facilitate its exit from the nucleus

116
Q

Removal of RNA sequences that do not code for proteins (intervening sequences) from the primary transcript •The remaining EXONS are spliced together by

A

Spliceosome

117
Q

The Intronloops out as __________) bind to form the spliceosome

A

snRNPs(small nuclear ribonucleoproteinparticles or snurps, which are complexes of snRNAsand proteins

118
Q

Removal of intronsfrom pre-mRNA transcripts involves cleavage at the 5’-end of the intronby attack of a specific

A

2oh group, the branch site

119
Q

This forms a phosphodiesterbond with the 5’phosphate of the intron, creating a

A

Lariat structure

120
Q

results from an autoimmune response where the patient produces antibodies against host proteins, including snRNPs

A

Systemic Lupus Erythematosus(SLE

121
Q

Mutations that cause the incorrect splicing of beta-globinmRNA are responsible for some cases of

A

Beta thalassemia

Biochemistry module 8 (4 decks)

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