Lec 07- Transcription and Translation 1 Flashcards
1
Q
Where is hereditary information stored?
A
in DNA
2
Q
What does genetic instruction consist of?
A
4 letter alphabet
3
Q
What do the 4 nt do?
A
direct the formation of an organism
4
Q
What is the function of nt?
A
specify the linear order of amino acids in each protein
5
Q
What determines biological functions within a cell?
A
properties of proteins
6
Q
How does DNA control protein synthesis?
A
NOT DIRECTLY
uses RNA as intermediary
7
Q
What is transcription?
A
when an appropriate piece of DNA (a gene) is copied into RNA
8
Q
What is translation?
A
When RNA is used as a template to direct the synthesis of protein
9
Q
What is the central dogma of molecular biology?
A
DNA replication > RNA synthesis (transcription) > Protein synthesis (translation)
10
Q
How are RNA and DNA similar?
A
- linear polymers
- made of nt connected by phosphodiester bonds
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
12
Q
What is the function of mRNA?
A
- messenger RNA
- code for proteins
- coding RNA
- 3-5% of total cellular RNA
13
Q
What is the function of rRNA?
A
- ribosomal RNA
- form basic structure (core) of the ribosome
- catalyze protein synthesis
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)
15
Q
What is the function of snRNA?
A
- small nuclear RNA
- direct splicing of pre-mRNA to form mRNA
16
Q
What is the function of snoRNA?
A
- small nucelolar RNA
- help to process and chemically modify rRNAs
17
Q
What is the function of miRNA?
A
- microRNA
- regulate gene expression by blocking translation of specific mRNAs and cause their degradation
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
19
Q
Many genes have ____ as their final product?
A
RNA
20
Q
What does non-coding RNA do?
A
serves as enzymatic and structural component for many biological processes
21
Q
What is PRO RNA pol?
A
a multi-subunit complex
22
Q
What is the holoenzyme of PRO RNA pol?
A
a2bb’E
23
Q
What is the function of PRO RNA pol?
A
catalyzes formation of phosphodiester bonds that link nt
24
Q
Does PRO RNA pol have proof-reading nuclease activity?
A
YES
25
How can a lower fidelity of RNA synthesis be tolerated by organisms?
because mistakes are not transmitted to progeny
26
What is the start of transcription?
binding of pol to promoter on DNA
27
Once the DNA double helix is unwound, what acts as a template for synthesis of RNA?
the other strand
28
How is nt sequence determined?
by complementary base pairing between incoming nt and the DNA template
29
What kind of bonds covalently link nt?
phosphodiester bonds
30
What catalyzes the transcription reaction?
RNA pol
31
RNA sequence is elongated in what direction?
5' >> 3'
32
RNA sequence is _________ to the template strand and ________ to the coding strand
- complementary
| - identical
33
What is the most important step in PRO gene expression?
transcription initiation
34
What is the main regulatory step for PRO?
transcription initiation
35
What does PRO transcription initiation decide?
which proteins are produced and at what rate
36
What does RNA pol assemble into in PT initiation?
holoenzyme a2bb'E
37
After assembling into the holoenzyme, what does the RNA pol do in PT initiation?
slides down the DNA until it locates a promoter
38
What happens when the RNA pol finds a promotor on the DNA in PT initiation?
the a-subunit binds to the promotor to form an open promoter complex
39
What does the open promoter complex make specific contacts with?
exposed bases
40
What is a transcription bubble?
an unwound short (17bp) segment of ds DNA in PT initiation
41
Which DNA strand is accessible for base pairing in PT initiation?
template strand
42
What does the scrunching mechanism do in the beginning of PT?
forms a short RNA
43
What pulls the DNA into the active site during PT initiation?
RNA pol that is still bound
44
What does the stress of the scrunching and the pulling of the DNA into the active site do to the short RNA?
causes it to be released by abortive initiation
45
What provides the energy to form phosphodiester bonds and drive PT initiation forward?
Hydrolysis of nucleoside triphosphates
ATP
CTP
UTP
GTP
46
What are promoters?
special sequences of nt
47
What do promoters do in PT?
direct RNA pol to the proper initiation site for transcription
48
What are the 2 common motifs in PRO that are present on 5' (upstream) side of the transcription start site?
- 35 sequence (TTGACA)
| - 10 sequence (TATAAT)
49
When does the PRO elongation phase begin?
after formation of nascent RNA with ~10 nt
50
What happens to RNA pol during PRO elongation?
it breaks its interaction with the promoter
51
What happens to the sigma factor during PRO elongation?
it dissociates from the DNA-RNA complex
52
What happens to the core enzyme during PRO elongation?
it binds more strongly to the DNA template
53
How does the RNA pol move during PRO elongation?
-moves stepwise along the DNA
54
What is the function of RNA pol during PRO elongation?
- unwinds the helix just ahead of its active site
| - exposes new region for complementary base pairing
55
Transcription is __________ during PRO elongation
very efficient
56
What does PRO elongation generate?
superhelical tension
57
What enzyme eases tension during PRO elongation?
DNA gyrase
58
PRO transcription continues until RNA pol meets ______
termination signals on the DNA templates
59
What makes the PRO termination signals?
a string of AT nt pairs preceded by a 2-fold symmetric DNA sequence
60
What does the RNA transcript of the terminal signal region form in PT termination?
- a self complementary hairpin structure
| - a poly U tail
61
What does the hairpin structure do in PT termination?
destabilizes the interaction of RNA with RNA pol
62
How many RNA pol synthesize RNA molecules in PRO and EUK?
PRO = 1 RNA pol
EUK = 3 RNA pol
63
What does RNA pol II transcribe?
- all protein-coding genes
- snoRNA
- miRNA
- siRNA
- IncRNA
- most snRNA
64
What does RNA pol II require during transcription?
additional proteins = general transcription factors
65
What kind of packing does EUK transcription need to deal with?
higher order packing of DNA
| nucleosomes, chromatin, etc...
66
What is unique about RNA pol II?
contains a carboxyl-terminal domain (CTD) of the 220kD subunit
67
What regulates the activity of RNA pol II?
phosphorylation mainly on Ser residues of the CTD
68
What is the general transcription factor for RNA pol II called?
TFII
69
What are the TFIIs denoted as?
TFIIA
TFIIB
TFIIC...
70
Where do TFII assemble?
at the promoter before transcription
71
What are the 3 functions of TFII?
- 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
What is the start of ET initiation?
binding of TFIID to TATA box
causes distortion in DNA
73
What is the TATA-box-binding protein (TBP)?
subunit of TFIID that recognizes TATA
74
After TFIID and TATA bind, what happens next in ET initiation?
TFIIB is recruited
```
Then:
TFIIF is recruited
RNA pol II is recruited
TFIIE is recruited
TFIIH is recruited
```
75
What factors make up the transcription initiation complex?
```
TFIIB
TFIIF
TFIIE
TFIIH
RNA pol II
```
76
What does the RNA pol II do in ET initiation?
makes short lengths of RNA
77
What causes RNA pol II do leave the promoter and begin elongation during ET initiation?
phosphorylation of CTD by TFIIH
78
What does TFIID do?
- recognizes TATA box
- recognizes other DNA sequences near the transcription start point
- regulates DNA-binding by TBP
79
What does TFIIB do?
- recognizes BRE element in promoters
| - accurately positions RNA pol at start site of transcription
80
What does TFIIF do?
- stabilizes RNA pol interaction with TBP and TFIIB
| - helps attract TFIIE and TFIIH
81
What dies TFIIE do?
attracts and regulates TFIIH
82
What does TFIIH do?
- unwinds DNA at transcription start point
- phosphorylates Ser5 of the RNA pol CTD
- releases RNA pol from promoter
83
What is the most common promoter sequence for EUK RNA pol II?
TATA box
84
What are some additional regulatory sequences besides the TATA box?
CAAT box
| GC box
85
What happens to RNA pol II during ET elongation?
moves along the DNA transcribing RNA along the way, creating superhelical tension
86
What prevents the dissociation of RNA pol II until it reaches the terminal signals during ET elongation?
elongation factors
87
What enzyme removes the superhelical tension on the DNA during ET elongation?
DNA topoisomerase
88
How is EUK DNA packaged in vivo?
packaged into nucleosomes which are arranged in higher order chromatin structures
89
What prevents access to DNA in in vivo transcription initiation?
physical barriers
90
What are transcriptional activator proteins?
help attract RNA pol II to the transcription initiation start site during in vivo transcription
91
What is a mediator?
- a protein complex
| - allows activator proteins to communicate with RNA pol II and the general transcription factors
92
Why are chromatin modifying enzymes recruited during in vivo transcription initiation?
to provide greater access to DNA
93
What are the 2 types of chromatin modifying enzymes?
- chromatin remodeling complexes
| - histone modifying enzymes
94
What is the immediate product of RNA pol II in ET elongation?
pre-mRNA (primary transcript)
95
Does EUK mRNA need to be processed?
YES
96
Why are covalent modifications introduced in ET elongation?
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
What are the 2 RNA modifications in EUK?
- 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
What does the 5' cap structure consist of?
7-methylguanosine joined to the 5' end of RNA
via a 5'-5' triphosphate bridge
99
What are the 5' cap's functions?
- 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
Why are EUK genes discontinuous?
because composed of eons and introns
101
What must be done to form the final mRNA in EUK?
-RNA splicing
- remove introns
- link exons
102
What assemblies of proteins and snRNA carries out mRNA splicing?
spliceosomes
103
What is the 3' end of an mRNA specified by in EUK?
a signal in DNA that is transcribed into the mRNA
104
What are the consensus sequences for poly-a tail?
- AAUAAA
- GU or U rich sequences
- CA
105
What recognizes the poly-A tail?
- RNA binding proteins
| - RNA processing enzymes
106
What are the 2 important proteins for poly-A tail?
- CPSF: cleavage and polyadenylation specificity factor
| - CstF: cleavage stimulation factor
107
What happens to the 2 important poly-A tail proteins when the RNA emerges from the pol?
They travel on the RNA pol and then are transferred to the RNA
108
What binds the AAUAAA at the 3' end of RNA?
CPSF
109
What binds the GU rich element beyond the cleavage site?
CstF
110
What cleaves RNA at the CA sequence?
endonuclease
111
How many A nt does the poly A pol (PAP) add to the 3' end by cleavage?
200 A nt
112
Where does the poly-A tail get the A?
from ATP
113
Does PAP require a template?
NO
114
What happens after PAP adds 200 A nt?
poly A binding proteins assemble
115
Which mRNA is polycistronic, PRO or EUK?
PRO
EUK mRNA = monocistronic
116
The 5' and 3' ends of ________ mRNA are unmodified
PRO
117
Do PRO mRNA have introns?
NO
only EUK have introns which are removed by slicing
