Lecture 14 Flashcards
(52 cards)
1
Q
RNA is more reactive than DNA because
A
it has a hydroxyl group on the 2’ carbon atom of its sugar component, whereas DNA has a hydrogen atom
2
Q
rRNA
A
structural and function components of the ribosome
3
Q
mRNA
A
carries genetic code for proteins
4
Q
tRNA
A
helps incorporate amino acids into polypeptide chain
5
Q
snRNA
A
processing of pre-mRNA
6
Q
snoRNA
A
processing and assembly of rRNA
7
Q
miRNA
A
inhibits translation of mRNA
8
Q
siRNA
A
trigger degradation of other RNA molecules
9
Q
template for transcription
A
a single strand of DNA.
10
Q
transcription of a gene takes place
A
only on one strand
11
Q
template strand
A
strand used for transcription
12
Q
transcriptional unit
A
a stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription
13
Q
three components of transcriptional unit
A
promotor, RNA-coding sequence, and terminator
14
Q
promotor
A
- DNA sequence that the transcription apparatus recognizes and binds
- indicates which of the DNA strands is to be read as the template, and direction of transcription
- determines the transcription start site
- located next to the transcription start site BUT NOT TRANSCRIBED
15
Q
transcription start site
A
the first nucleotide that will be transcribed into RNA
16
Q
RNA-coding region
A
a sequence of DNA that is copied into an RNA molecule
17
Q
terminator
A
- a sequence of nucleotides that signals where transcription is to end.
- usually part of RNA-coding sequence; transcription stops only after the terminator has been copied into RNA
18
Q
nucleotides upstream/downstream of the start sites are assigned what numbers?
A
upstream - negative
downstream - positive
19
Q
direction of transcription synthesis
A
5’ to 3’
20
Q
RNA synthesis does not require a
A
primer
21
Q
RNA synthesis is performed by
A
RNA polymerases
22
Q
accessory proteins
A
enhance RNA polymerases
23
Q
core RNA polymerase
A
- composed of multiple polypeptides and has the enzymatic activity for RNA elongation
- without sigma factor will randomly transcribe DNA
24
Q
sigma factor
A
- controls the binding of RNA polymerase to the promotor for bacterial RNA polymerase
25
RNA polymerase holoenzyme
the sigma factor plus the RNA core polymerase
26
transcription in prokaryotes performed by
a single RNA polymerase
27
RNA polymerase I transcribes
rRNA
28
RNA polymerase II transcribes
pre-mRNA
29
RNA polymerase III transcribes
tRNA
30
examples of accessory proteins
- transcription factors
| - activator proteins
31
consensus sequences
- short stretches of common sequence in the promotor
| - implies that the sequence is associated with an important function
32
-10 consensus sequence
- most common consensus sequence found in almost all bacterial promotors
- centered 10 bp upstream of the start site
33
prokaryotic promotors contain
two sequences that the RNA polymerase holoenzyme will recognize and bind
- indicated on the nontemplate strand
34
-35 consensus sequence
- lies approximately 35 nucleotides upstream of the start site
35
RNA transcription is initiated when
core RNA polymerase binds to the promotor with the help of the sigma factor
36
Termination of bacterial transcription
- RNA polymerase must stop synthesis
- RNA molecule must be released from the RNA polymerase
- the newly made RNA must dissociate fully from the DNA
- RNA polymerase must detach from the DNA template
- occurs as rho-dependent and rho-independent
37
prokaryotic types of terminators
- rho-dependent
| - rho-independent
38
inverted repeat (palindrome)
- leads to hairpin on the RNA during transcription
| - in rho independent
39
rho independent termination
- inverted repeats form a hairpin secondary structure
- a string of 7-9 adenine residues follows the inverted repeat. their transcription produces a string of uracil
- the string of uracil causes the RNA polymerase to pause, allowing the formation of the hairpin
- destabilized DNA-RNA pairing, causing RNA to separate from DNA and stopping transcription
40
rho dependent termination
- DNA sequences produce a pause in transcription
- DNA sequences encodes a stretch of RNA upstream of the terminator that is devoid of secondary structures
- unstructured RNA serves as a binding site for Rho, which binds to the RNA and moves to the 3' end, following RNA pol
- When RNA polymerase encounters terminator sequence in DNA, it pauses, allowing rho to catch up.
- the rho protein has helices activity which unwinds the RNA-DNA hybrid causing transcription to stop
41
promotor recognition in eukaryotic transcription
carried out by accessory proteins that bind to a specific promotor and recruit the appropriate type of RNA polymerase
42
basal transcription apparatus
- formed by general transcription factors and RNA polymerase.
- assembles near the start site and initiates minimal levels of transcription.
43
transcriptional activator proteins
bind to specific sequences to bring about higher levels of transcription by stimulating the assembly of the basal transcription apparatus at the start site
44
two parts of promotor for RNA polymerase II
- core promotor
| - regulatory promotor
45
core promotor
- the site to which the basal transcription apparatus binds.
- located just upstream of the gene
- includes one or more consensus sequences
- most common is the TATA box
46
TATA box
- consensus sequence TATAAA
| - located -25 to -30 bp upstream of start site
47
regulatory promotor
- located immediately upstream of core promotor
| - variety of different consensus sequences found
48
transcriptional activator proteins
binds to the regulatory consensus sequences and either directly or indirectly make contact with the basal transcription apparatus and affect the rate and which transcription is initiated
49
enhancers
- distant sequences that transcriptional activators bind to regulate transcription
- The DNA between an enhancer and the promoter loops out, so transcriptional activators can interact with the basal transcription machinery at the core promoter.
50
Eukaryotic transcription initiation
- initiated through assembly of the transcriptional assembly on the promotor
- consists of the RNA polymerase a series of transcription factors
- TATA-binding protein binds to the minor groove of the DNA, bending the DNA and partly unwinding it
- other transcription factors bind to additional consensus sequences and position the RNA polymerase over the transcription start site
- conformation changes take place in DNA and polymerase, which produces a single-strand DNA template
- single strand DNA template positioned within active site of RNA polymerase creating the open complex. After open complex formed RNA synthesis begins
51
RNA polymerase II termination
1. RNA pol transcribes well past coding sequence
2. cleavage near the 3' end of RNA while RNA pol continues transcribing
3. Rat1 exonuclease attaches to 5' end of trailing RNA and moves toward RNA pol, degrading RNA as it goes
4. When Rat1 reaches the polymerase, transcription is terminated
52
rNTP
- substrate for transcription
- nucleotides added to the 3' OH group
- two phosphate groups cleaved.
