Transcription Flashcards
Transcription, the process of ___ ___ from a DNA template
RNA synthesis
How many phases are there in transcription?
3 phases
Initiation of ___ ___
Polymerization
Elongation of the ____ ___
RNA chain
Termination of ___ ___
strand growth
What are the 3 phases of transcription?
Initiation, elongation, termination
RNA transcription occurs in what direction?
5’ to 3’
what is the primary enzyme in prokaryotic transcription?
RNA polymerase holoenzyme
a2BB’o is the formula of what enzyme
RNA polymerase holoenzyme
what is the part of RNA polymerase holoenzyme that is the core that synthesizes but in unable to bind to promoters
a2BB’
The core polymerase can synthesis RNA but it is unable to ___ to promoters
bind
what is the part if RNA polymerase holoenzyme that binds the holoenzyme to the promoter sequence?
o
what is the part of RNA polymerase holoenzyme that binds to the DNA template?
B’
what is the part of RNA polymerase holoenzyme that binds to the RNA nucleotides?
B
what is the part of RNA polymerase holoenzyme that is essential for assembly of enzyme subunits?
a
what two parts of RNA polymerase holoenzyme contribute to the active site where new RNA nucleotide is added to the end of the growing chain?
BB’
Step 1 of transcription
Binding of RNA polymerase
Step 2 of transcription
Closed promoter complex
Step 3 of transcription
Open promoter complex
Step 4 of transcription
Initiation of synthesis
Step 5 of transcription
Transition to elongation phase
Step 6 of transcription
Release of o subunit
what is the name of the first amino acid of the new growing chain that is synthesized?
n terminal (5’)
what is the name of the last amino acid of the new growing chain that is synthesized?
c terminal (3’)
the first and second RNA nucleotides bind the the RNA polymerase and to the +1 and +2 bases at the transcription start site via ____ bond
phosphodiester
the ____ subunit of RNA polymerase holoenzyme is released to complete initiation
o
what is the name of the transcription start site?
+1
where are the two promoter regions?
-35, -10
what is the sequence of the -35 region?
TTGACA
what is the sequence of the -10 region?
TATAAT
what is the known as the pribnow box?
-10 region
The ___ and ___ region of the prokaryotic promoter bind the o subunit of RNA polymerase haloenzyme in the initiation of transcription
-35 and -10
In elongation, what is the direction of the upper strand (nontemplate strand)?
5’ to 3’
In elongation, what is the direction of the lower strand (template strand)?
3’ to 5’
In elongation, RNA polymerase moves along the ___ ___, producing an RNA copy of the complementary, nontemplate strand
template strand
The RNA transcript is both transcribed and translated in the ____ direction
5’ to 3’
The 5’ end of the transcript corresponds to the ____ end of the polypeptide
N-terminal
3 bases correspond to __ ___ ___
one amino acid
The C-terminal end is synthesized ___
last
In elongation, the core RNA polymerase (α2ββ’) moves along the ___ ____,
synthesizing the RNA chain to the 3’ end
template strand
In elongation, the core polymerase moves along __ ___, the double helix is
unwound, and then rewound behind the advancing ____
the DNA, polymerase
What is the rate that nucleotides are added to the growing RNA chains in elongation?
20-50 nucleotides per second
What is the error rate in incorporating the wrong nucleotides into the RNA chains?
1 in 10,000
To prevent supercoiling of the double helix from slowing transcription,
topoisomerase enzymes act to remove ___ ___ and relax the
DNA ahead of the polymerase.
DNA supercoils
what enzyme acts to remove DNA supercoils and relax the DNA ahead of the polymerase to prevent supercoiling of the double helix and slowing transcription?
topoisomerase enzymes
what are the 2 means of chain termination in prokaryotes?
determined by sequences alone DNA (termination sites), binding of protein termination factor rho (ρ).
Termination of transcription is determined by specific sequences along the DNA called ___ ___
termination sites
Termination of transcription occurs through the binding of a protein termination factor called ___
rho (ρ)
At a termination site at the end of a gene, inverted repeat sequences result in the formation of a ___ ___ or “hairpin” structure in the RNA transcript
stem-loop
The stem-loop structure causes the RNA polymerase to ____, which brings about the spontaneous dissociation of the RNA transcript from the DNA.
pause
what is found at the termination site of prokaryotes
repeated structure (palendrome)
the inverted repeat sequence of the termination sequence in prokaryotes forms what kind of structure?
stem loop “hairpin”
what is the role of the prokaryote stem loop structure?
causes RNA polymerase to pause which brings about dissociation of the RNA transcript from DNA
in rho factor termination, the rho protein moves along the new transcript unit it unwinds what?
RNA:DNA hybrid region
In rho factor-dependent termination, rho factor moves along the new transcript until it
unwinds the RNA:DNA hybrid region behind the advancing __ ___ and
releases the _____
RNA polymerase , transcript
eukaryotes have____ types of RNA polymerase
3
RNA polymerase ____ transcribes major ribosomal RNA genes and is located in the nucleolus
1
RNA polymerase _____ transcribes protein-coding genes and therefore synthesizes mRNA and is the one we need to know for this topic!!!!
2
RNA polymerase ____ transcribes tRNA genes, 5S, rRNA genes, and genes of other small RNAs
3
what two sites are located on the eukaryote core promoter region?
RNA polymerase 2 binding site, bind sites for general transcription factors (GTFs)
the transcription state site on eukaryote is ___
+1
what is the sequence required to define the core promoter in eukaryotes?
TATAAA (box)
in the core eukaryotic promoter, the TATA box binds the ____ subunits of _____
TBP, GTF TFIID
in eukaryote genes that lack a TATA box, they can use____ to initiate transcription
initiator element inr
what is the tail of RNA polymerase 2 called?
CTD
what general transcription factor has the helicase ability to split the DNA strands of eukaryotes?
TF2H
in eukaryote, the ___ _____ binds to general transcription factors and RNA polymerase 2 to bring about initiation
mediator complex (M)
once elongation begins in eukaryote, the ____ _____ dissociates from GTFs and RNA polymerase 2
mediator complex (M)
how many protein subunits are in the mediator complex?
26
for eukaryotes to go from initiation to elongation, _____ of ATP to ADP must occur
phosphorylation
___ enzyme initiates phosphorylation from initiation to elongation
kinase
the octamer motif, GC box, CAAT box, and TATA box are all a part of what?
the full promoter region
what factor binds to the TATA box?
TBP
what factor binds to the CAAT box?
CTF/NF1
what factor binds to the GC box?
SP1
what factors bind to the octamer motif?
OCT1, OCT2
how many molecules per cell are there of CAAT box?
300,000
how many molecules per cell are there of GC box?
60,000
___ __ are regulatory sequences that may be located several thousand nucleotides from the promoter
enhancer elements
How far away are enhancer elements from the promoter?
several thousand nucleotides away
Transcription factors bound at the enhancer active ___
transcription
How do transcription factors bound at the enhancer active transcription?
Through the formation of a DNA loop involving the promoter region
Formation of a DNA loop brings the enhancer-bound activator protein to the ___ ___ positioned at the promoter
RNA polymerase
how is the 5’ end of mRNA molecules processed?
cap derived from GTP is added
how is the 3’ end of mRNA processed?
a polyAtail of 100-200 A residues is added
what is alternative splicing?
some exons being removed to generate transcripts that code for proteins with different amino acid sequences
what does splicing remove?
non-coding intron sequences between the exons that code for proteins
what is the signal sequence of polyA?
AAUAAA
PolyA signal sequence AAUAAA initiates the binding of what 2 proteins?
CPSF (cleavage and polyA specificity factor) and CFs (cleavage factors)
the addition of up to ____ A residues helps protect the 3’ end of exonucleases
200
what is the second, lesser role of the CPSF and CFs in the processing of the 3’ ends of mRNA molecules?
termination of RNA synthesis by destabilizing the RNA polymerase and DNA
mRNA splicing is carried out by _______ which are composed of several RNA protein complexes
spliceosomes
spliceosomes are composed of several RNA protein complexes called _____
snRNPs (small nuclear ribonucleoproteins)
what are the 5 options of snRNAs?
U1,U2,U4,U5,U6
what are the start and stop sequences of introns?
GU (start), AG (end)
what is the branch point of the intron?
A
how many proteins are present in an snRNP?
10
spliceosomes recognize ____ _____ at the 5’ exon/intron junction and the branch site
conserved sequences
in the splicing reaction, a covalently closed loop of RNA called the ____ is formed by the covalent attachment of the 5’ end of an intron to the branch site of A
lariat
what are the products of the splicing reaction?
lariat form of excised intron, united exons
mRNA has a ___ turnover rate
high
what is the first part of mRNA degredation?
shortening of polyA tail by a deadenylase enzyme
what enzyme shortening the polyA tail during mRNA degredation?
deadenylase enzyme
what is the second step of mRNA degredation?
decapping enzyme removes 5’ cap
what is the final step on mRNA degredation?
mRNA is degraded by both ends by 5’ and 3’ exonucleases
in eukaryotic rRNA processing, the initiation transcripts of ____S are converted into smaller units
45
what are the 3 smaller units of the original 45S rRNA?
18S, 5.8S, 28S
snoRNPs (small nucleaolar ribonucleoproteins) consist of ______ and _____
snoRNAs, proteins
what is the role of snoRNPs?
guide modifications of the rRNAs such as the addition of methyl groups
