Transcription Flashcards
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’
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’
what direction is the template strand?
3’ to 5’
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?
TCTTGACAT
what is the sequence of the -10 region?
TATAAT
what is the known as the pribnow box?
the -10 region promoter sequence?
Nucleotides are added to the growing RNA chain at a rate of ____ to _____ nucleotides per second
20, 50
the error rate in incorporating the wrong nucleotide into the RNA chains is what?
1/10,000
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
____ synthesis is more accurate than ____ synthesis
DNA, RNA
what are the 2 means of chain termination in prokaryotes?
determined by sequences alone DNA (termination sites), binding of protein termination factor rho
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
how many subunits form the ring of the rho structure?
6
in rho factor termination, the rho protein moves along the new transcript unit it unwinds what?
RNA:DNA hybrid
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
once elongation begins in eukaryote, the ____ _____ dissociates from GTFs and RNA polymerase 2
mediator complex
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
the __ ___ ___ ____ DNA binding protein consists of two perpendicular a helicies connected by a beta turn, and the side chains of one a helix fits into the major groove of DNA
helix turn helix motif
in the helix turn helix motif, the side chains of one ___ ______ fits into the ___ ____ of the DNA
a-helix, major grooves
the ___ ___ _____ DNA binding protein consists of two anti-parallel b strands followed by an a helix, Zn2+ ions are bound to the amino acid side chains, and the a helix inserts into the major groove of the DNA
zinc finger motif
what does the zinc finger motif consist of?
2 anti-parallel b-strands followed by an a-helix
in the zinc finger motif, Zn2+ ions bind to __ ___ ___ ____
amino acid side chains
the __ ______ of the zinc finger motif inserts into the major groove of the DNA
a helix
the ___ ____ ______ DNA binding protein consists of a-helices from two different proteins that formed a coiled coil, and extensions of the a-helices bind to the major groove
leucine zipper motif
what does the leucine zipper motif consist of?
a-helices from two different proteins that form a coiled coil
the extensions of the a-helices of the leucine zipper motif bind to the ___ ___ of the DNA
major groove
___ _____ are regulatory sequences that may be located several thousand nucleotides from the promoter and activator transcription factors can bind
enhancer elements
transcription factors bound to the enhancer activate transcription through the formation of a ___ _____ involving the promoter region
DNA loop
what is the role of the DNA loop formed via transcription factors bound at the enhancer?
brings the enhancer-bound activator protein to the RNA polymerase that is positioned at the promoter
enhancers can be upstream/downstream of promoter regions in introns
both
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
___ ____ adds the GTP to the 5’ end of the mRNA
guanylyl transferase
the GTP is added via ____ to _____ linkage
5’, 5’
what is the purpose of the 5’ 5’ linkage of GTP when processing the 5’ ends of mRNA?
resisting cleavage from 5’ exonucleases
the 5’ to 5’ bond of 5’ end processing are connected by ___ ______
3 phosphates
____ groups are added to the 5’ end of a transcript and signal that this is the 5’ end of the transcript and a ribosome should bind
methyl (between 1-3)
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 3 products of the splicing reaction?
lariat form of excised intron, united exons
what happens to the lariat in the nucleus?
rapidly degraded in the nucleus
at least _____ of human protein coding genes show alternative splicing
95%
what is the most common form of alternative splicing?
exon skipping
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
