finals - gene expression Flashcards
____ and mRNA that encodes several different proteins; common in bacteria
polycistronic mRNA
(T/F) polycistronic mRNAs are found in both bacteria and eukaryotes
false
it is unique in bacteria
____ preferred carbon source of E. coli
glucose
(T/F) in presence of both glucose and lactose , structural proteins of lac operon are produced
false
they are not produced
(T/F) Induction of lac operon only occurs when sole carbon source is lactose and no glucose is present
true
_____ the inhibition of lac proteins by glucose which is regulated by regulatory proteins that bind to the promoter, Plac
catabolite repression
____ a a signaling molecule generated from ATP in response to many forms of cell stimulation
cAMP
(T/F) Binding of CAP to the lac promoter depends on the concentration of adenosine-3’,5’-monophosphate (cAMP) in the bacterium
true
_____ the enzyme that catalyzes the formation of cAMP
adenylate cyclase
(T/F) the “hunger signal”
for the cell: In the absence of glucose, cAMP levels are low
false
cAMP levels are high
(T/F) the presence of cAMP-CAP complex bound to promoter, and the inducer, allolactose , RNA pol binding to the promoter is strong and transcription of the structural genes occurs
true
(T/F) in the presence of glucose, cAMP binds to CAP and the complex binds to CAP binding site on promoter
false
occurs in absence of glucose
- which of the ff is not true?
a. In absence of both glucose and lactose the operon is off because the repressor is bound
b. In presence of lactose and glucose CAP is not bound and operon is off
c. In presence of glucose and lactose, repressor is bound to operator and operon off
d. in high cAMP levels and cAMP-CAP complex at CAP site, presence of lactose to remove repressor the operon turned on
C
glucose is present but NOT lactose
(T/F) the presence of glucose inactivates adenylate cyclase
true
(T/F) The CAP site is a silencer element since it binds a transcription factor cAMP-CAP
complex and enhances transcription
false
it is and ENHANCER element
(T/F) CAP functions as a positive regulator (mediates positive regulation of transcription) since RNA pol requires its presence to function effectively
true
(T/F) Plasmids that do not contain the lac Z promoter can be used to drive the expression of
recombinant genes in bacteria
False
plasmids with lac Z
______ the inducer used to express recombinant genes in bacteria in experiments in place of allolactose
isopropylthio-galactoside
IPTG
(T/F) IPTG, like allolactose can be hydrolyzed and broken down by the cell (a
gratuitous inducer)
false
IPTG cannot be hydrolyzed so concentration does not decrease
______ the genes contained in pUC plasmid
LacZ, lacI and bla genes
(T/F) Ligation reaction in recombinant proteins is not 100% efficient so bacteria are transformed with mixture of normal and insert containing
plasmid
true
which of the ff is not incorporated into media for the blue/white screening of plasmids?
a. ampicillin
b. allolactose
c. IPTG
d. X-gal
B
____ the color indicator used in blue/white screening; a colorless reagent but forms blue color when cleaved by
β-gal
X-gal
*_____ a technique used to identify where proteins bind to DNA
DNA footprinting
(T/F) bacteria and eukaryotes have 3 types of RNA pol
false
bacteria only 1
which of the ff is a mismatch?
a. RNA pol I is located in the nucleous
b. RNA pol II is located in the neoplasm
c. RNA pol II transcribes all protein coding, snoRNA and snRNA genes
d. RNA pol III transcribes 5.8S, 18S, and 28S rRNA genes
D
this is for RNA pol 1
whichi of the ff does not apply to eukaryotic transcription?
a. has σ factors to direct enzyme to promoters
b. require a large set of transcriptional factors that assemble at the promoter with the RNA pol to initiate transcription
c. must contend with nucleosomes and higher order
chromatin packing
d. All three RNA pols contain 10 or more subunits
A
do not use sigma factors, uses transcriptional factors instead
(T/F) Structures of RNA pols I, II, and III differ but share 2 common large subunits that share sequence homology to two of the bacterial RNA pol subunits that comprise the catalytic site
true
which of the ff is not a component of Pol II promoter?
a. Enhancers or silencers
b. TATA box
c. Downstream elements
d. Initiator element
none of the above :)
(T/F) the TATA box is located at (+25)
false
it is -25
which of the ff is not found in pol II promoters?
a. TATA box
b. GC box
c. CTTC box
d. CAAT box
C
there’s no such thing!
(T/F) Most Pol II promoters have a TATA box and is necessarry for orienting/guiding pol II
true
TATA box is essential for transcription of some genes
(T/F) Those that contain TATA box typically have “ strong” Inr sequence
false
strong Inr = are “TATAless” promoters
which of the ff is not a function of general transcription factors category?
a. Function in correctly positioning Pol ll at the promoter
b. Regulate release of Pol ll from promoter to begin polymerization of the transcript
c. Enhance the transcription of specific genes
d. Assist in separating DNA strands to allow transcription initiation
C
this is done by gene-specific
transcription factors or activators
(T/F) general transcription factors (TFII) perform function similar to that of σ factor in bacteria
true
(T/F) six interacting TFll proteins comprise the preinitiation complex that starts transcription at most Pol ll promoters
true
____ are TFII subunits that bind TATA box; a universal transcription factor since also required for Pol l and Pol lll-mediated transcription
TATA-binding proteins (TBP)
which of the ff does not apply to TBPs?
a. required for Pol l and Pol lll-mediated transcription
b. are highly conserved among all species of eukaryotes
c. binds to the minor groove of DNA
d. Associated with up to 14 TBP-associated factors (TAFlls)
C
binds to major groove
- which of the ff does not apply to TBPs?
a. consists of a single protein with two similar domains
b. Binding of TBP distorts DNA at TATA box
c. binding creates an 80 degree bend in the DNA
d. Bending introduces 5 kinks in TATA region and separation of DNA strands factors (TAFlls)
D
2 kinks only
(T/F) The physical distortion of the DNA thought to attract the addition of other factors to the promoter
true
____ the transcription factor protein that has DNA helicase activity
TF II H
Uses energy from ATP to separate strands of DNA at transcription start site
which of the ff is false about the priming of pol II for transcription?
a. Pol ll C-terminal domain (CTD) phosphorylated by a phosphatase subunit associated with TFllH
b. Pol ll initially remains at promoter synthesizing short lengths of RNA
c. TF II H Uses energy from ATP to separate strands of DNA
A
this is done by a kinase subunit
which of the ff does not apply to the elongation and termination phases in transcription?
a. after pol II CTD phosphorylation, it changes conformation
b. conformation change strengthen its attachment to the DNA
c. phosphorylated CTD binds other factors which allow it to transcribe entire gene after disengaging
d. As Pol ll and bound TFllF leave promoter, general transcription factors dissociate
from DNA
C
does this without disengaging!
(T/F) factors that will process the newly transcribed RNA are bound to pol II CTD phosphorylated tail
true
(T/F) general factors are degraded after transcription is completed
false
General factors recycle for new round of transcription
(T/F) At termination, Pol ll dissociates, is dephosphorylated and recycles for another round of transcription
true
recycled!
which of the ff is not done by factors that enhance activity of pol II?
a. stimulate pol II activity
b. may alter Pol ll conformation
c. prevents pausing along certain template sequences (pause sites)
d. prevents prematurely terminating transcription
none of the above :)
which of the ff is not a function of TF IIH?
a. repair of thymine dimer formation in DNA
b. synthesizes RNA primers
c. Regulating the cell cycle
d. general role in transcription
B
______ the covalent, intrastrand bonds between carbons 5 and 6 of adjacent thymine rings (forms a cyclobutyl ring) that distort DNA structure and disrupt the passage of both DNA and RNA polymerases; induced by UV light
thymine dimers
_____ the DNA mechanism done by TFIIH
transcription-coupled repair
(T/F) TFIIH regulate the cell cycle through its cyclin-dependent kinaseactivity
true
(T/F) when RNA pol II encounters a thymine dimer, it is released then, TFIIH together with other DNA binding factors, such as proteins of the XP family bind to the lesion and recruit DNA repair enzymes
true
______ the genetic disorder where there’s extreme sensitivity to sunlight,abnormal skin pigmentation, high incidence of skin cancer, neurological defects
Xeroderma Pigmentosum
(T/F) in Xeroderma Pigmentosum, DNA damage can be reversed by DNA repair mechanisms
false
damage is cumulative and irreversible
(T/F) termination of transcription in eukaryotes involve a simple hairpin release mechanism as in bacteria
false
Much more complex!
(T/F) In eukaryotes, the 5’ untranslated end of mRNAs contains the consensus sequence, AAUAAA
false
this is in the 3’ end after the protein coding region
which of the ff is false about the terminating consensus sequence in eukaryotes?
a. the protein coding region is in the 5’ location from the sequence
b. is recognized by specific factors that cleave the transcript downstream from the consensus sequence
c. occurs about 100-1000 bases away from the actual 5’ terminus of the mRNA
d. After cleavage, Pol ll continues to transcribe the template DNA until it dissociates from the template
C
from the 3’ end!
(T/F) In vivo, hundreds of factors enhance or reduce transcription in a genes-pecific manner including the presence of nucleosomes and higher order structure of eukaryotic DNA which all adds to the complexity of transcription
true
which of the ff is false about the initiation of transcription by Pol ll in vivo?
a. Chromatin remodeling complexes and histone acetylases increase accessibility of DNA in chromatin to the transcription machinery
b. Protein mediators or coactivatorsact as
bridges between activators, pol II and other TF
c. Gene-specific transcriptional activators bind to enhancers or silencers to increase or decrease transcription
d. Enhancers strenghtens the binding of Pol ll to promoter regions in the presence of nucleosomes and higher order chromatin structure
D
Enhancers can help attract Pol ll to promoter regions
______ are enhancers that respond to environmental conditions/ metabolic factors and bind specific activators that are produced in response and activate a set of genes
response elements
_____ an example of a response element that binds to heat-specific transcription factors that are produced by elevated temperatures
heat shock element
which of the ff is not true about heat shock elements?
a. are not contiguous
b. not regulated by the same promoter
c. are similar to bacterial operons
d. one transcription activator can bind to the same response element in multiple genes that each have unique promoters and activate them all
C
they differ from operons because of A, B and D :)
____ a second messenger that are produced by cells in response to stimulation by various types of hormones
cAMP
____ the enzyme that degrades cAMP
cAMP phosphodiesterase
____ the enzyme that synthesizes cAMP
adenylate cyclase
(T/F) hormones such as thyroid-stimulating hormone and glucagon induce the production of cyclic AMP
true
(T/F) heat shock elements differ from operons because they are contiguous and are regulated by same promoter
false
HSE are NOT any of these things, but operons are
____ the molecule activated by the increasing levels of cyclic AMP
protein kinase A or PKA,
also called cyclicAMP-dependent protein kinase
(T/F) both the regulatory and catalytics subunits of PKA are activated by cAMP then activate CREB
false
only the catalytic subunits are activated, then activates
(T/F) activation in CREB in the nucleus is through phosphorylation by PKA
true
which of the ff is not true about PKA?
a. is activated in the nucleus
b. is a kinase
c. Activated catalytic subunits of PKA separate from the regulatory subunits
d. activated by cAMP
A
in the cytosol
_____ CREB
cyclic AMP response element binding protein
____ the co activator of CREB
CREB-binding protein (CBP)
(T/F) activated CREB recruits CBP before inducing gene transcription
true
(T/F) in the absence of phosphorylation, CBP does not bind CREB and transcription does not occur
true
____ are examples of cell processes that are regulated by the cAMP signaling pathways
1) hormone synthesis in endocrine cells and the 2)synthesis of new proteins associated with long term
memory
_____ are coactivators of CREB
CREB-binding proteins and P300
(T/F) CREB-CBP complex can activate most transcription factors signaling in many different signaling pathways
false
other complexes such as CREB-P300 activate other pathways
______ MAPK
mitogen-activated protein kinase
_____ transcription factors phosphorylated by MAPK
AP-1 and Sap-1a
(T/F) dopamine can activate activate PKA
true
which of the ff is in the correct order?
a. activated PKA- D1 dopamine receptor activated-dopamine - cAMP cascade
b. activated PKA- D1 dopamine receptor activated - cAMP cascade - dopamine
c. dopamine - D1 dopamine receptor activated - cAMP cascade - activated PKA
d. dopamine - D1 dopamine receptor activated- activated PKA- cAMP cascade
C
(T/F) glutamate is a neurotransmitter that activates NMDA receptor and leads to the influx of cAMP
false
influx of Ca2+, the rest is true
(T/F) calcium/calmodulin dependent protein kinase type IV (CAMK IV) is activated by Ca2+ influx
true
(T/F) CAMK IV can phosphorylate CREB
true
(T/F) CREB is involved in gene expression in neurons
true
