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BChem Transcription

For my final

Question	Answer
Genetic information encoding protons and structural RNAs is contained in _ genes flanked by _ sites	structural, regulatory
Direct the initiation and termination of transcription.	regulatory sites
In prokaryotes, most structural genes are found in _	operons
In prokaryotes, genes that encode molecules with common functions are transcribed as ____	single RNA/polycistronic RNA
Eukaryotes utilized single genes with complex _ _ and often introns (_ _).	control signals, intervening sequences
In eukaryotes, introns are removed from the _ _	primary transcript
The sense strand of the DNA has the same sequence as ___	mRNA
The mRNA is complementary to the _ strand of DNA	antisense
mRNA contains _	codons
tRNA contains _	anticodons
_ are translated into polypeptides	anticodons
Does RNA polymerase contain proofreading?	no
Mg2+ (A) promotes _ of the 3' OH of the primer base	deprotonation
During 2 metal ion catalysis, the O- on what phosphate is nucleophilically attacked?	alpha
Mg 2+ B orients the incoming _ by interacting with the β & γ phosphates.	base
Mg2+ B facilitates the formation of the _ _ and ultimately for the departure of _	transition state, Ppi
E. coli RNAP _ is a large 450 kD complex	holoenzyme
The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the σ subunit do?	recognize the promoter sequence
The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the α subunit do?	recognized the promoter sequence (UP element)
The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the β subunit do?	catalytic domain
The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the β' subunit do?	DNA binding domain
By using different sigma factors, the cell can regulate different classes of _	genes
Which are the regions recognized by sigma factors in bacteria?	-35,-10
In E. Coli,_. _ has many different sigma factors, many involved in sporulation	B. subtilus
σ factors are speciﬁc for phage genes, shuts off host gene transcription	bacteria phage
σ factors are used for the rapid scanning of the DNA for _	promoters
After transcription initiation in bacteria, these are released.	sigma factors
in bacteria, the holoenzyme has a _ affinity for DNA	low
How the holoenzyme moves along the DNA in bacterial transcription initiation	diffusion
Bacterial transcription initiation: the enzyme binds to the promotor region, approximately _ bp 5' to start site	40
Bacterial transcription initiation: enzyme binds to promotor sequence with _ affinity	high
How many faces of the DNA does the enzyme bind in bacterial transcription initiation?	1
The bacterial transcription initiation enzyme binds one face of the DNA, so the complex is _	closed
Bacterial Transcription Initiation: enzyme melts DNA at _ region (_-->_)	-10,-9,2
Bacterial Transcription Initiation: enzyme melts DNA to create a _ complex	open
Bacterial Transcription Initiation: the open complex formation: the conformational change in _ guides the strand into the _ _ _	sigma, active site tunnel
Bacterial Transcription Initiation: after the strand is in the active site tunnel, the initiating nucleotides _ and _	bind, join
What step of bacterial transcription initiation sees a lot of aborted transcription>	open complex formation
Bacterial transcription always begins with the coupling of 2 __	NTPs
The first of the NTP pair in bacterial transcription is almost always a _	purine
Does the bacterial transcription initiation process, where 2 NTPs bind, require a primer?	No
Bacterial Transcription Initiation: Promoter escape is the transition between _ and _	initiation, elongation
Besides in open complex formation, where are there a lot of aborted transcripts in bacterial transcription initation?	promoter escape
In E. coli promoter escape, the first _ occurs and the _ subunit is released. A tight binding of the ternary complex occurs.	translocation, sigma
Bacterial transcription elongation: _ and _ of DNA, both thought to be passive processes (no energy input)	unwinding, re-annealing
During transcription elongation, the active site has a short region of _	RNA:DNA hybrid
The incoming nucleotides during bacterial elongtation basepair with template in _ base pairs	WC
The two types of transcription terminators in bacteria	Rho-dependent, Rho-independent
Rho dependent terminators contain a region of _ symmetry and a string of >6_ in DNA	dyad, A
In E. coli transcription Rho-independent termination, _ _ _ and _’s in mRNA reduces DNA:RNA contacts and causes the polymerase to fall off.	RNA secondary structure,UUUU
In Rho independent termination, the incorporation of _ and/or 5 _ decreases termination	I,BrU
I:C_G:C	<
Rho dependent terminators – contain region of dyad symmetry in DNA, which causes RNA polymerase to _. It also acts as a barrier to _	dyad, pause, nucleases
Rho is what?	helicase
Rho can unwind _:_ and _:_ double helices	DNA:RNA, RNA:RNA
Rho binds specific sequences in RNA, like multiple _ or _ _	C, CA
Rho hydrolyzes _ to propel it along the RNA 5'-->3' until it catches the _ _	NTP, RNA polymerase
How does Rho destabilize the RNA polymerase:DNA interaction?	It unwinsd the RNA-DNA hybrid
Rho may also bind _ and cause a conformational change that enhances __.	polymerase, termination
The Rho protein is __, so it has 6 identical subunits	hexameric
the Rho protein is an ATP-_ helicase	dependent
In prokaryotes, Rho-dependent termination: 3’-end of transcript contains a _-rich sequence known as _ for Rho utilization.	CA, rut
Eukaryotes contain _ distinct RNAP activites that are responsible for synthesizing different types of RNA	three
Where is RNAP I located?	Within the nucleoli
RNA polymerase is also known as	RNAP I
What does RNAP I do?	synthesizes precursors of most rRNAs
RNAP I sees _-specific promoter recognition	species
RNAP I: __-> ___ required for high level expression. Binds transcription factors.	-187,-107
RNAP I: _->_ required for proper initiation	-31, +6
Where is RNAP II located?	nucleoplasm
What does RNAP II do?	synthesizes mRNA recursors, recognizes promoters
What does RNAP II depend on?	transcription factors
Promoters contain a large number of _ _ for different factors	binding sites
TATA (-25)	helps determine start site
CCAAT (-70-->-90)	increases rate of transcription initation
GGGCGG	found in housekeeping genes, increases rate of initation
Enhancers- work at a distance in either orientation to increase __.	RNA II
Where is RNAP III located?	Within the nucleoplasm
What does RNAP III do?	synthesizes precursors of 5S rRNAs, tRNAs, and other small nuclear and cytosolic RNAs
Where are organelle polymerases found?	chloroplast, mitochondria
Organelle polymerases are similar to what?	RNA polymerases
Eukaryotic polymerases are large and complex, with at least _ subunits	10
Eukaryotic polymerases have a large number of _ factors, _ factors and _ factors.	initiation, elongation, termination
Eukaryotic Transcription Initiation: what two things affect the formation/transition of both the initiation and elongation complexes?	chromatin structure and DNA seuqence
Eukaryotic Transcription Initiation: these proteins remodel the chromatin by moving nucleosomes, as well as control transcription activity	SWI, SNF, NURF
How do SWI, SNF, and NURF control transcriptional activity?	Pre-initiation complex assembly, promoter escape and early elongation stages.
TFIIB	Binds TBP and recruits Pol II and TFIIF
TFIIF-Pol II	Adapter between Pol II and TFIIB
TFIIE	Recruits TFIIH
TFIIH	helicase, unwinds DNA at promoter, PO4 Pol II CTD
TBP	specifically regonzines the TATA box
Pol II	catalyzes RNA synthesis
What's the inchworm model of elongation presume>	Two DNA binding sites can move independent of one another.
RNA is held to polymerase by the two __ binding sites in the inchworm model	RNA
E Elongation: the catalytic site is located at upstream edge of __	DNA binding site I
E Elongation: the catalytic site adds _ nucleotides as it moves along DNA site I	about 10
While the catalytic site moves along DNA site I, DNA site I is __ and DNA site II is __ with the catalytic site	fixed, moving
E Elongation: at the end of nucleotide addition, RNA and DNA sites _ become ﬁxed and DNA binding site _ translocates 10 bases to start again.	II, I
In E. Elongation, Crystal structure suggests that _ portion of enzyme undergoes a conformational change after each addition step to move the enzyme down the DNA	bridge
Why are inhibitors useful in elongation?	chemotherapy and mechanistic studies
Name 4 elongation inhibitors.	intercalating agents, amatoxins, rifamycis, cordycepin
Inercalating agents contain __ aromatic rings that fit between base pairs, blocking what?	planer, DNA and RNA synthesis
Give examples of intercalating agents.	Daunomycin, Adriamycin, Actinomycin D, EtBr, Proﬂavin
Amatoxins are one of the poisons in _	mushrooms
a-amanitin is a bicyclic octpeptide that binds 1:1 with _ and inhibits elongation	Pol II, Pol III
Rifamycins only inhibit what kind of polymerases?	prokaryotic.
Rifamycins They bind pol and block elongation from _ to _ nuc.	second, third
What happens if rifamycins are added later?	Rifamycins do not block initiation or later elongation
What does late addition rifamycin indicate?	confomrational difference
What does cordycepin, a 3'deoxyadenosine, do?	When incorporated into growing chain,causes termination.
Which inhibitor indicated elongation is 5' to 3"?	cordycepin
During transcription, a DNA sequence is read by an RNA polymerase, producting an RNA strand that is both __ and __	complementary, antiparallel

Created by: ScarlettRose

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BChem Transcription

For my final

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