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Flashcards in finals - gene expression Deck (86):
1

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

polycistronic mRNA

2

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

false

it is unique in bacteria

3

____ preferred carbon source of E. coli

glucose

4

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

false

they are not produced

5

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

true

6

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

catabolite repression

7

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

cAMP

8

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

true

9

_____ the enzyme that catalyzes the formation of cAMP

adenylate cyclase

10

(T/F) the “hunger signal”
for the cell: In the absence of glucose, cAMP levels are low

false

cAMP levels are high

11

(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

12

(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

13

*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

14

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

true

15

(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

16

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

true

17

(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

18

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

isopropylthio-galactoside
(IPTG)

19

(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

20

______ the genes contained in pUC plasmid

LacZ, lacI and bla genes

21

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

true

22

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

23

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

X-gal

24

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

DNA footprinting

25

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

false

bacteria only 1

26

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

27

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

28

(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

29

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 :)

30

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

false

it is -25

31

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!

32

(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

33

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

false

strong Inr = are “TATAless” promoters

34

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

35

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

true

36

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

true

37

____ 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)

38

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

39

*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

40

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

true

41

____ 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

42

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

43

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!

44

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

true

45

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

false

General factors recycle for new round of transcription

46

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

true

recycled!

47

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 :)

48

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

49

______ 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

50

_____ the DNA mechanism done by TFIIH

transcription-coupled repair

51

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

true

52

(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

53

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

Xeroderma Pigmentosum

54

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

false

damage is cumulative and irreversible

55

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

false

Much more complex!

56

(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

57

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!

58

(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

59

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

60

______ 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

61

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

heat shock element

62

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 :)

63

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

cAMP

64

____ the enzyme that degrades cAMP

cAMP phosphodiesterase

65

____ the enzyme that synthesizes cAMP

adenylate cyclase

66

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

true

67

(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

68

____ the molecule activated by the increasing levels of cyclic AMP

protein kinase A or PKA,


also called cyclicAMP-dependent protein kinase

69

(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

70

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

true

71

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

72

_____ CREB

cyclic AMP response element binding protein

73

____ the co activator of CREB

CREB-binding protein (CBP)

74

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

true

75

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

true

76

____ 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

77

_____ are coactivators of CREB

CREB-binding proteins and P300

78

(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

79

______ MAPK

mitogen-activated protein kinase

80

_____ transcription factors phosphorylated by MAPK

AP-1 and Sap-1a

81

(T/F) dopamine can activate activate PKA

true

82

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

83

(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

84

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

true

85

(T/F) CAMK IV can phosphorylate CREB

true

86

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

true