Chapter 8 Flashcards
(91 cards)
1
Q
what is additional to make RNA different
A
hydroxyl group
2
Q
purine
A
A and G
3
Q
pyrimidine
A
U and C
4
Q
RNA synthesis
A
- 5’ to 3’ direction
- when add nucleotide, need to bring in tri-phosphate
- polymerase will be different
5
Q
How does RNA polymerase work
A
catalyzes addition of each ribonucleotide to 3’end and forms phosphodiester bonds
6
Q
mRNA
A
- main RNA
- short lived between DNA and protein
- only type that undergoes translation
7
Q
how is mRNA produced
A
by protein producing genes
8
Q
don’t encode for proteins
A
functional RNA’s
9
Q
function of rRNA
A
combines proteins to form ribosomes
10
Q
tRNA’s function
A
responsible for binding an amino acid and depositing it into a growing protein chain
11
Q
telomerase RNA
A
provides template for synthesis of repetitive DNA telomerase sequences
12
Q
snRNA
A
- plays role in mRNA processing
- small nuclear RNA
13
Q
miRNA and siRNA
A
active in plant and animal cells
14
Q
what are the four stages to Bacterial Transcription
A
- promoter recognition: recognize where we are
- transcription initiation: getting process started
- chain elongation: adding on next RNA
- chain termination: where we need to stop
15
Q
transcription
A
synthesis of single stranded RNA by RNA polymerase
16
Q
promoter
A
- upstream to start of transcription
- controls access of RNA polymerase to gene
17
Q
coding region
A
- has info that will be translated into functional protein
18
Q
termination region
A
regulates end of transcription
19
Q
where is termination region located
A
downstream (3’) to coding segment
20
Q
where does the RNA polymerase bind
A
promoter sequence
21
Q
where does transcription start
A
+1
22
Q
upstream
A
before +1
23
Q
downstream
A
after +1
24
Q
how is the sigma subunit made
A
pentameric RNA polymerase core that binds a sixth subunit
25
what forms the holoenzyme
binding RNA polymerase core with sigma subunits
26
what is the core enzyme composed of
- two alpha subunits
two beta subunits
- w subunit
27
what is the function of the core enzyme
transcribe RNA from DNA template
28
what is the holoenzyme more efficient at
binding to promoter regions
29
sigma 70 function
- helper protein
- do majority of transcription
- most abundant at binding to RNA polymerase
- find promoter region and makes sure RNA polymerase binds correctly
30
bacterial promoter structure
- double stranded DNA that is RNA polymerase binding site
- upstream
31
how is RNA polymerase attracted to promoters
presence of consensus sequences
32
structure of consensus sequences
- single stranded
- (-35) consensus sequence
- (-10) consensus sequence
33
-35 consensus sequence
these regions are very important bc they help RNA polymerase identify where a gene is going to be
34
what stops transcription
termination
35
what do stop codons stop
translation
36
what are the actual coding regions
start to stop codons
37
UTR
untranslated regions
- makes shape that helps to bind ribosome
- not used in translation
38
transcription initiation
- closed promoter complex made
- open promoter complex made
- holoenzyme moves downstream to initiate RNA synthesis at +1
39
how are closed promoter complex made and what is it
- holoenzyme makes loose attachment to promoter sequence
- DNA stays closed
- binds to DNA
40
how are open promoter complex made and what is it
- holoenzyme unwinds
- DNA has been opened and there is movement
41
when and why is the sigma protein released
- once there are a couple nucleotides
42
what happens when you reach termination sequence
RNA polymerase is released and then you have RNA transcript
43
how does intrinsic termination work
forming hairpin loop structure and poly U tail by mRNA pulling back
44
how does intrinsic termination function
- cause RNA polymerase to slow down
- DNA will close
45
what do rho dependent termination need
rho protein to bond mRNA and catalyze separation of mRNA from RNA polymerase
46
what does the rho protein attached to
rut site
47
rho protein function
- moves faster than RNA polymerase
- bind to net sequence
- chases and catches up to RNA polymerase and pulls mRNA off enzyme
48
what are some of the major differences in eukaryotic transcription
- DNA stuck in nucleus
- genes are longer
- lot of diversity
- structure of polymerase is different
49
what do eukaryotic genes carry
introns and exons
50
RNA pol 1
transcribes ribosomal RNA genes
51
RNA pol II
transcribes protein coding genes
52
RNA pol III
transcribes tRNA genes, one small nuclear gene, and one ribosomal gene
53
most common promoter in eukaryotes
TATA box
- (-25) position
54
why are consensus sequences important
for binding of transcription factors
55
what aids RNA pol II in recognizing and binding to promoter consensus sequences
transcription factors
56
what binds the TATA box sequence
a multi subunit protein containing TATA binding protein and subunits of protein TBP-associated factor
- TFID
57
what lead to differential expression and regulation of genes
enhancer sequences
silencer sequences
58
what is the main job of enhancer sequences
enhance transcription levels
- promoters combined with enhancers drive gene expression
59
what is the main job of silencer sequences
reduce or eliminate transcription of particular gene
60
how do enhancers work
- upstream of TATA box/promoter
- bind proteins with proteins bound to gene promoters
- bind activator proteins and coactivators to protein bridge to link transcription complex at promoter
61
what does the protein bridge in enhancers do
bends DNA so proteins are brought close together so interaction will increase RNA pol II efficiency
62
what do silencers bind
proteins that induce bends in DNA
63
how do silencers work
the bends they create in DNA reduce transcription of target gene by shielding DNA from RNA pol II activity
64
what does the level of chromatin affect
accessibility if RNA pol II and transcription factors
65
nucleolus
nuclear organelle containing rRNA and multiple copies of genes encoding rRNA
66
core element
needed for initiation of transcription
67
what is the purpose of the upstream control element
increase level of transcription
68
in which organisms is transcription most stable
eukaryotes
69
what are the modifications of mature mRNA compared to pre-mRNA
1. 5'capping
2. 3' polyadenylation
3. intron splicing
70
functions of 5' cap
1. protection of mRNA from degradation
2. facilitating transport of mRNA out of nucleus
3. facilitating intron slicing
4. enhance translation efficiency
71
what are the three steps to capping 5'
1. the y phosphate is removed at 5' end
2. guanine added loses 2 phosphates to become monophosphate
3. guanine monophosphate joins 5' mRNA end by 5'-5' triphosphate linkage
72
what are the functions of polyadenylation
1. facilitate transport of mature mRNA to cytoplasm
2. protect mRNA from degradation
3. enhance transcription
73
steps to polyadenylation
1. cleavage and polyadenylation action complex formed
2. pre mRNA cleaved leaving PAP at 3'
3. 3' fragment degraded in nucleus
4. PAP adds new adenines to 3'
5. PABII molecules bind to increase rate of polyadenylation
74
what is the torpedo model of eukaryotic transcription termination
- "chomps" up the uncapped parts of transcription
- causes RNA polymerase to disassociate from DNA
75
what are introns removed from and how
pre-mRNA by spliceosome complex
76
group 1 introns
slef splicing
77
group 2 introns
self splicing
78
pre-mRNA introns
spliceosome
79
split genes
presence of intron and exon sequences
80
what does spliceosome do
- form lasso structure
- remove intron and leave exon
81
how does alternative intron splicing work
take same initial transcript and splice different regions of introns out but give different products
82
group 1 introns
- self splicing
- have binding portions within intron back to actual exon
- after connection is made, 3D shape is what is more different
83
group 2 introns
- self splicing takes place in lasso structure
- form complex secondary structure
84
what is RNA editing responsible for
posttranscriptional substitutions of nucleotide sequencewhat of some mRNA's
85
what helps uracil to be added
guide RNA
86
TFIID
needs to bind directly to prompter region
87
TFIIA, IIB, IIF
get RNA polymerase secured to DNA
88
PAP job
add poly A tail
89
what are the three parts to the intron
1. 5' splice site that is start
2. branch site that use A to loop back 5' end to form lasso
3. 3' splice site which is end
90
what forms the loop structure
U4, U5, U6
91
snRNP's
- made of RNA and proteins
- make up spliceosome
