Lecture RNA synthesis Flashcards
(122 cards)
0
Q
RNA is a polymer composed of alternating units of ribonucleotides connected through a
A
3-5 phospodiester bond
1
Q
RNA is a polymer composed of alternating units of
A
Ribonucleosides
2
Q
In contrast with DNA, ribonucleotides contain
A
hydroxyl groups on the 2’-carbonof the ribose sugar •
the base uracilin place of thymine
3
Q
The “working copies” of DNA •Expresses the master plan contained in DNA
A
Significance of RNA
4
Q
80% of the total RNA
A
Ribosomal RNA
5
Q
smallest of the 3 major RNA species (excluding the small RNAs), make up 15%
A
Transfer RNA
6
Q
2-5%, but is the most heterogenousin terms of size and base sequence
A
Messenger RNA
7
Q
involved in mRNA splicing and gene regulation
A
Small RNA’s
8
Q
Prokaryotic rRNA
A
23S, 16S, 5S
9
Q
Eukaryotic rRNA
A
28S, 18S, 5.8S, 5S
10
Q
measure of size based upon the molecular sedimentation rate during ultracentrifugation
A
Svedberg unit “S”
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
12
Q
RNA
DNA
A
Ribose
Deoxyribose
13
Q
complementary base pair for A in RNA
A
U instead of T (for DNA)
14
Q
not involved in RNA synthesis
A
Primer
15
Q
Only a portion of the genome is transcribed or copied
A
RNA
16
Q
entire genome must be copied
A
DNA
17
Q
always read in the 3’ to 5’ direction (RNA)
A
Template strand
18
Q
The opposite strand is called the (RNA)
A
Coding strand
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
20
Q
DNA DEPENDENT RNA POLYMERASE attach to the ______ on the ______
A
Promoter
Template strand
21
Q
corresponds to the 5’ nucleotide of the mRNA
A
Starting point of transcription
22
Q
The numbers increase as the sequence proceeds
A
Downstream
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
24
defined as that region of DNA that includes the signals for transcription: initiation, elongation, and termination
Transcription unit
25
A transcription unit includes a
Promoter
RNA coding region
Terminator
26
The RNA product, which is synthesized in the 5' to 3' direction, is the
Primary transcript
27
with its 4 subunits responsible for 5’ 3’ RNA polymerase activity
Core enzyme
28
Core enzyme cannot recognize the promoter on the DNA template
Lack specificity
29
contains the sigma subunit or sigma factor (that enables RNA polymerase to recognize promoter regions on the DNA
Holoenzyme
30
An auxiliary protein of RNA polymerase
Termination factor
31
Some regions of DNA that signal the termination of transcriptionare recognized by
RNA polymerase
32
Others are recognized by specific termination factors, an example of which is the
rho factor of ecoli
33
The primary transcripts generated by RNA polymerase II(one of three nuclear DNAdependent RNA polymerases in eukaryotes) are promptly capped by
7 methylguanosine triposphate
34
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
7 methylguanosine triposphate
35
Involves binding of the RNA polymerase holoenzymeto a promoter region
Initiation
36
Pribnowbox and -35 sequence •Highly conserved •Recognized by prokaryotic RNA polymerase sigma factors
Consensus nucleotide sequences
37
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
38
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
Pribnow box
39
A second consensus nucleotide sequence centeredaround 35 bases to the left of the transcription start site
-35 sequence
40
A mutationin either the Pribnowbox or -35 sequence can affect the transcription of the gene controlled by the
Mutant promoter
41
Once the promoter has been recognized by the holoenzyme, RNA polymerase (RNAP) begins to synthesize a transcript of the DNA sequence
Elongation
42
Elongation usually beginning with a
Purine
43
Unlike DNA polymerase, RNA polymerase does not require a
primer and has no endoor exonucleaseactivity (No repair capability
44
longation by addition of ribonucleotidesto the
3-OH end
45
3’-OH acts as a __________, attacking the -phosphate of the incoming ribonucleosidetriphosphate and releasing ___________
Nucleophile
| Pyrophosphate
46
Alternatively, can recognize termination regions on the DNA template
tetramericRNA polymerase
47
may be required for the release of the RNA product
Rho factor protein
48
Requires Rho factor protein
RHO dependent termination
49
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
C rich region
| RNA polymerase
50
Rho factor that hydrolyzes ATP, and uses the energy to unwind the 3’ end of the transcript from the template
ATP-dependent RNA-DNA helicase
51
At the termination site, rho factor displaces the DNA template strand, facilitating the
Dissociation of the RNA molecule
52
slows down the progress of RNA polymerase and causes it to pause temporarily
Hairpin turn
53
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
Palindrome
54
In addition to RNAP recognizing the promoter region and initiating RNA synthesis, several supplemental _____________bind to DNA in eukaryotes
Transcription factors
55
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
Nucleosome core
56
Most actively transcribed genes are found in a relaxed form of chromatin
Euchromatin
57
Most inactive btranscribe genes segments are in a highly condensed
Heterochromatin
58
The interconversionof active and inactive forms of chromatin is called
Chromatin modeling
59
Genes that are inactive contain more
MethylatedDNA (5-methylcytosine
60
When _________become acetylated, the chromatin structure becomes looser
Histones
61
composed of a variety of different cis sequence elements which recruit some of these trans-acting factors through DNA-protein interactions
Eukaryotic promoters
62
also occur and account for many of the multi-component complexes found at eukaryotic promoters
Protein protein interactions
63
utilize a small number of ubiquitous transcription factors
Pol 1 and 3
64
Used Large number of ubiquitous transcription factors
Pol 2
65
in order to specifically bind to a promoter and initiate transcription
Transcription factors
66
2 identical subunits of the Upstream Binding Factor
Upstream Core eEement
| Core Promoter eEement
67
consists of four subunits
Selectively factor 1
68
Initiation at RNA Pol 1 promoters
Upstream binding factor
Protein interactions
Selectively factor 1
RNA pol1
69
Initiation at RNA Pol 3 promoters (tRNA)
TFIIIC- A and B sites
TFIIIB- upstream
RNA polymerase 3- initiates transcription
70
Initiation at RNA polIII promoters (5s rRNA)
Same to tRNA except TFIIIA binds the C box
71
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
TATA or Hogness box
72
The consensus sequence of TATA or hogness box
TATAAAA
| so it resembles the TATAAT sequence of the prokaryotic -10region
73
The TATA box appears to be more important for selecting the start point of transcription (i.e. positioning the enzyme) than for
Defining the promoter
74
which binds to the TATA box promoter element, is the only transcription factor capable of binding to specific sequences of DNA
TFIID
75
TFIID consist of
TATA binding protein (TBP) and 14 TBP-associated factors (TAFs
76
A second consensus sequence called the.
| -found upstream from the transcription start site
CAAT Box(70-80 nucleotides
77
CAAT box
CTF
| NF1
78
is a common element in eukaryotic class II promoters. Its consensus sequence is GGGCGG
GC box
79
binds to the GC box
Transcription factor Sp1
80
Special cis-acting DNA sequences
increase the rate of initiation of transcription by RNAP II
81
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
Enhancers
82
They can be close to or thousands of base pairs away from the promoter •They can occur on either strand of the DNA
Enhancer
83
Enhancers contain DNA sequences called ____________that bind specific transcription factorscalled_________
Response elements
| Activators
84
similar to enhancers in that they act over long distances to reduce the level of gene expression
Silencer
85
recognizes and binds to the TATA box
TFIID
86
binds and stabilizes TFIID binding
TFIIA
87
possibly in a stepwise manner -to form a preinitiationcomplex
RNA polymerase II holoenzyme
88
Formation of the PreInitiation Complex (PIC) for polII on a TATA promoter •The order of assembly of transcription factors may be
TFIID-> TFIIA-> TFIIB-> (TFIIF + RNAPII) -> TFIIE ->TFIIH
89
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
Eukaryotic pol 2
90
both a substrate for several kinases, including the kinasecomponent of TFIIH, and a binding site for a wide array of proteins
Carboxyl Terminal Repeat Domain (CTD
91
are the ultimate targets of cell-signalling pathways
Trnscriptions factors
92
inhibits transcription initiation by binding to the beta subunit of prokaryotic RNA polymerase, preventing phosphodiesterbond formation
Rifampicin
93
used for tumortherapy; it binds to the DNA template and interferes with the movement of RNA polymerase along the DNA
Dactinomycin(ActinomycinD
94
intercalate between successive G=C base pairs in duplex DNA-inhibit transcriptional elongation in proand eukaryotes
ActinomycinD, acridine
95
binds the subunit of bacterial RNA polymerase-blocks promoter clearance (elongation
Rifampicin
96
produced by fungus Amanita phalloides (death cap mushroom)-potent inhibitor of RNA polII and weak inhibitor of RNA polIII
Alpha amanitin
97
the linear copy of the transcription unit
Primary transcript
98
The primary transcripts of both prokaryotic and eukaryotic RNA are post-transcriptionally modified by cleavage using
Ribonucleases
99
generally identical to its primary transcript
Prokaryotic mRNA
100
extensively modified after transcription
Eukaryotic mRNA
101
ribosomal RNA of prokaryotes
23S, 16S, and 5S
102
Eukaryotic rRNA
28S, 18S, 5.8S
103
synthesized by RNAP III and modified separately
Eukaryotic 5s rRNA
104
The preribosomalRNAsare cleaved by ____________ to yield intermediate-sized pieces of rRNA, which are further trimmed to produce the required rRNAspecies
Ribonucleases
105
tRNAis transcribed by
RNA polymerase III
106
The additional nucleotides at the 5’-end are removed by an unusual RNA containing enzyme called
Ribonuclease P
107
Some tRNAprecursors contain an _____ located in the anticodonarm Intronsare spliced out during processing of the tRNA
Intron
108
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
CCA at the 3 end
109
The enzyme responsible for the addition of the CCA-end is
tRNA nucleotidyl transferase
110
The collection of all the precursor molecules for mRNAis known as
Heterogenous nuclear RNA
111
is attached to the 5’ end of the mRNA
7 methyl guanosine
112
GTP addition is catalyzed by guanylyl transferasein the nucleus •This is followed by methylationof the terminal guanine in the cytosol, catalyzed by
Guanine 7 methyl transferase
113
is the source of the methyl group
SAM
114
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
Polyadenelate polymerase
115
found near the 3’ end signals that poly-A-tail must be added to stabilize RNA and facilitate its exit from the nucleus
AAUAAA
116
Removal of RNA sequences that do not code for proteins (intervening sequences) from the primary transcript •The remaining EXONS are spliced together by
Spliceosome
117
The Intronloops out as __________) bind to form the spliceosome
snRNPs(small nuclear ribonucleoproteinparticles or snurps, which are complexes of snRNAsand proteins
118
Removal of intronsfrom pre-mRNA transcripts involves cleavage at the 5'-end of the intronby attack of a specific
2oh group, the branch site
119
This forms a phosphodiesterbond with the 5'phosphate of the intron, creating a
Lariat structure
120
results from an autoimmune response where the patient produces antibodies against host proteins, including snRNPs
Systemic Lupus Erythematosus(SLE
121
Mutations that cause the incorrect splicing of beta-globinmRNA are responsible for some cases of
Beta thalassemia
