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Biochem 2 > finals - gene expression > Flashcards

finals - gene expression Flashcards

1
Q

____ and mRNA that encodes several different proteins; common in bacteria

A

polycistronic mRNA

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2
Q

(T/F) polycistronic mRNAs are found in both bacteria and eukaryotes

A

false

it is unique in bacteria

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3
Q

____ preferred carbon source of E. coli

A

glucose

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4
Q

(T/F) in presence of both glucose and lactose , structural proteins of lac operon are produced

A

false

they are not produced

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5
Q

(T/F) Induction of lac operon only occurs when sole carbon source is lactose and no glucose is present

A

true

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6
Q

_____ the inhibition of lac proteins by glucose which is regulated by regulatory proteins that bind to the promoter, Plac

A

catabolite repression

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7
Q

____ a a signaling molecule generated from ATP in response to many forms of cell stimulation

A

cAMP

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8
Q

(T/F) Binding of CAP to the lac promoter depends on the concentration of adenosine-3’,5’-monophosphate (cAMP) in the bacterium

A

true

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9
Q

_____ the enzyme that catalyzes the formation of cAMP

A

adenylate cyclase

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10
Q

(T/F) the “hunger signal”

for the cell: In the absence of glucose, cAMP levels are low

A

false

cAMP levels are high

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11
Q

(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

A

true

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12
Q

(T/F) in the presence of glucose, cAMP binds to CAP and the complex binds to CAP binding site on promoter

A

false

occurs in absence of glucose

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13
Q
  • 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
A

C

glucose is present but NOT lactose

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14
Q

(T/F) the presence of glucose inactivates adenylate cyclase

A

true

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15
Q

(T/F) The CAP site is a silencer element since it binds a transcription factor cAMP-CAP
complex and enhances transcription

A

false

it is and ENHANCER element

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16
Q

(T/F) CAP functions as a positive regulator (mediates positive regulation of transcription) since RNA pol requires its presence to function effectively

A

true

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17
Q

(T/F) Plasmids that do not contain the lac Z promoter can be used to drive the expression of
recombinant genes in bacteria

A

False

plasmids with lac Z

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18
Q

______ the inducer used to express recombinant genes in bacteria in experiments in place of allolactose

A

isopropylthio-galactoside

IPTG

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19
Q

(T/F) IPTG, like allolactose can be hydrolyzed and broken down by the cell (a
gratuitous inducer)

A

false

IPTG cannot be hydrolyzed so concentration does not decrease

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20
Q

______ the genes contained in pUC plasmid

A

LacZ, lacI and bla genes

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21
Q

(T/F) Ligation reaction in recombinant proteins is not 100% efficient so bacteria are transformed with mixture of normal and insert containing
plasmid

A

true

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22
Q

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

A

B

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23
Q

____ the color indicator used in blue/white screening; a colorless reagent but forms blue color when cleaved by
β-gal

A

X-gal

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24
Q

*_____ a technique used to identify where proteins bind to DNA

A

DNA footprinting

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25
Q

(T/F) bacteria and eukaryotes have 3 types of RNA pol

A

false

bacteria only 1

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26
Q

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

A

D

this is for RNA pol 1

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27
Q

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

A

do not use sigma factors, uses transcriptional factors instead

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28
Q

(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

A

true

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29
Q

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

A

none of the above :)

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30
Q

(T/F) the TATA box is located at (+25)

A

false

it is -25

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31
Q

which of the ff is not found in pol II promoters?

a. TATA box
b. GC box
c. CTTC box
d. CAAT box

A

C

there’s no such thing!

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32
Q

(T/F) Most Pol II promoters have a TATA box and is necessarry for orienting/guiding pol II

A

true

TATA box is essential for transcription of some genes

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33
Q

(T/F) Those that contain TATA box typically have “ strong” Inr sequence

A

false

strong Inr = are “TATAless” promoters

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34
Q

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

A

C

this is done by gene-specific
transcription factors or activators

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35
Q

(T/F) general transcription factors (TFII) perform function similar to that of σ factor in bacteria

A

true

36
Q

(T/F) six interacting TFll proteins comprise the preinitiation complex that starts transcription at most Pol ll promoters

A

true

37
Q

____ are TFII subunits that bind TATA box; a universal transcription factor since also required for Pol l and Pol lll-mediated transcription

A

TATA-binding proteins (TBP)

38
Q

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)

A

C

binds to major groove

39
Q
  • 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)
A

D

2 kinks only

40
Q

(T/F) The physical distortion of the DNA thought to attract the addition of other factors to the promoter

A

true

41
Q

____ the transcription factor protein that has DNA helicase activity

A

TF II H

Uses energy from ATP to separate strands of DNA at transcription start site

42
Q

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

A

this is done by a kinase subunit

43
Q

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

A

C

does this without disengaging!

44
Q

(T/F) factors that will process the newly transcribed RNA are bound to pol II CTD phosphorylated tail

A

true

45
Q

(T/F) general factors are degraded after transcription is completed

A

false

General factors recycle for new round of transcription

46
Q

(T/F) At termination, Pol ll dissociates, is dephosphorylated and recycles for another round of transcription

A

true

recycled!

47
Q

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

A

none of the above :)

48
Q

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

A

B

49
Q

______ 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

A

thymine dimers

50
Q

_____ the DNA mechanism done by TFIIH

A

transcription-coupled repair

51
Q

(T/F) TFIIH regulate the cell cycle through its cyclin-dependent kinaseactivity

A

true

52
Q

(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

A

true

53
Q

______ the genetic disorder where there’s extreme sensitivity to sunlight,abnormal skin pigmentation, high incidence of skin cancer, neurological defects

A

Xeroderma Pigmentosum

54
Q

(T/F) in Xeroderma Pigmentosum, DNA damage can be reversed by DNA repair mechanisms

A

false

damage is cumulative and irreversible

55
Q

(T/F) termination of transcription in eukaryotes involve a simple hairpin release mechanism as in bacteria

A

false

Much more complex!

56
Q

(T/F) In eukaryotes, the 5’ untranslated end of mRNAs contains the consensus sequence, AAUAAA

A

false

this is in the 3’ end after the protein coding region

57
Q

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

A

C

from the 3’ end!

58
Q

(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

A

true

59
Q

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

A

D

Enhancers can help attract Pol ll to promoter regions

60
Q

______ are enhancers that respond to environmental conditions/ metabolic factors and bind specific activators that are produced in response and activate a set of genes

A

response elements

61
Q

_____ an example of a response element that binds to heat-specific transcription factors that are produced by elevated temperatures

A

heat shock element

62
Q

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

A

C

they differ from operons because of A, B and D :)

63
Q

____ a second messenger that are produced by cells in response to stimulation by various types of hormones

A

cAMP

64
Q

____ the enzyme that degrades cAMP

A

cAMP phosphodiesterase

65
Q

____ the enzyme that synthesizes cAMP

A

adenylate cyclase

66
Q

(T/F) hormones such as thyroid-stimulating hormone and glucagon induce the production of cyclic AMP

A

true

67
Q

(T/F) heat shock elements differ from operons because they are contiguous and are regulated by same promoter

A

false

HSE are NOT any of these things, but operons are

68
Q

____ the molecule activated by the increasing levels of cyclic AMP

A

protein kinase A or PKA,

also called cyclicAMP-dependent protein kinase

69
Q

(T/F) both the regulatory and catalytics subunits of PKA are activated by cAMP then activate CREB

A

false

only the catalytic subunits are activated, then activates

70
Q

(T/F) activation in CREB in the nucleus is through phosphorylation by PKA

A

true

71
Q

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

A

in the cytosol

72
Q

_____ CREB

A

cyclic AMP response element binding protein

73
Q

____ the co activator of CREB

A

CREB-binding protein (CBP)

74
Q

(T/F) activated CREB recruits CBP before inducing gene transcription

A

true

75
Q

(T/F) in the absence of phosphorylation, CBP does not bind CREB and transcription does not occur

A

true

76
Q

____ are examples of cell processes that are regulated by the cAMP signaling pathways

A

1) hormone synthesis in endocrine cells and the 2)synthesis of new proteins associated with long term
memory

77
Q

_____ are coactivators of CREB

A

CREB-binding proteins and P300

78
Q

(T/F) CREB-CBP complex can activate most transcription factors signaling in many different signaling pathways

A

false

other complexes such as CREB-P300 activate other pathways

79
Q

______ MAPK

A

mitogen-activated protein kinase

80
Q

_____ transcription factors phosphorylated by MAPK

A

AP-1 and Sap-1a

81
Q

(T/F) dopamine can activate activate PKA

A

true

82
Q

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

A

C

83
Q

(T/F) glutamate is a neurotransmitter that activates NMDA receptor and leads to the influx of cAMP

A

false

influx of Ca2+, the rest is true

84
Q

(T/F) calcium/calmodulin dependent protein kinase type IV (CAMK IV) is activated by Ca2+ influx

A

true

85
Q

(T/F) CAMK IV can phosphorylate CREB

A

true

86
Q

(T/F) CREB is involved in gene expression in neurons

A

true

Biochem 2 (13 decks)

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