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genetics > chapter 12 part 3 > Flashcards

chapter 12 part 3 Flashcards

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Biology 101 flashcards
1
Q

what happens under heat stress

A

alternative sigma factors are used to activate expression of specialized heat stress response genes

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2
Q

what do heat shock genes encode

A

proteins that protect cells from certain types of heat-induced damage

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3
Q

what does heat shock response in bacteria require?

A

expression of an alternative sigma factor that changes the promoter-recognition ability of the RNA polymerase core enzyme

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4
Q

what gene encodes the sigma factor 32?

A

rpoH

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5
Q

what does the sigma factor 32 recognize?

A

promoters that contain G-C rich sequences at the -10 position
(instead of the usual A-T rish sequence of the Pribnow box)

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6
Q

what is the promoter for rpoH recognized by?

A

sigma 70 containing RNA polymerase when the temperature is elevated

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7
Q

what is also elevated during the heat shock response?

A

third sigma factor 24
-also re3cognizes rpoH gene promoter

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8
Q

what else happens when there is high temperature in heat response?

A

change in chaperone proteins

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9
Q

what do chaperone proteins normally do?

A

several chaperones bind to the small amount of sigma 32 present in the cell to inhibit it from forming holoenzyme RNA polymerase & targets it for degradation by the proteasome

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10
Q

what happens to chaperone proteins at high temperature

A

the chaperones release sigma 32 leaving it free to join RNA polymerase
-the chaperones are redirected to heat-damaged proteins

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11
Q

what is more commonly used: transcriptional regulation of translational regulation?

A

transcriptional regulation

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12
Q

what do translation repressor proteins bind?

A

mRNAs near the Shine-Dalgarno sequence

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13
Q

what do translation repressor proteins do?

A

they interfere with interaction between the mRNA & the 16s rRNA in the small subunit to precent translation of these bound mRNAs

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14
Q

what do complementary antisense RNA do?

A

block mRNA translation

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15
Q

what does the binding of complementary antisense RNA and antisense RNA do?

A

creates a double-stranded region of the message

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16
Q

what is IS10 regulation

A

antisense RNA regulation

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17
Q

how many & what are the promoters that the IS10 sequence contains?

A

there are 2
-PIN: relatively weak & controls transcription of the transposase
-POUT: much stronger

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18
Q

what does pOUT promoter do?

A

its embedded in the transposase gene
-directs transcription of an antisense RNA complimentary to part of the transposase mRNA

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19
Q

where is most transposase mRNA bound?

A

to antisense RNA, so that very little transposase is made, & transpostion is relatively rare

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20
Q

what is a riboswitch

A

occurs when an mRNA binds a small regulatory molecule

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21
Q

what can riboswitches do?

A

-regulate transciption
-affect translation
-can alter mRNA stability

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22
Q

what do riboswitches regulate?

A

transcription of the thiamin (thi) operon, which codes for proteins of the biosynthetic pathway for thiamin pyrophosphate (TPP) production

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23
Q

riboswitch mRNA in Bacillus substilis

A

Low TPP concentration
–TPP wont bind to riboswitch ..leads to antitermination stem loop formation & transcription of operon genes

High TPP concentration
–TPP will bind to riboswitch… generates termination stem loop followed by poly-U sequence
—PREVENTS TRANSCRIPTION

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24
Q

does riboswitch is bacillus subitilis affect transcription or translation?

A

transcription

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25
Q

riboswitch of mRNA in E.coli

A

Low TPP
-shine dalgarno antisequestor stem loop is formed
-start codon may initiate translation of the operon mRNA

High TPP
-tpp binds to riboswitch which makes mRNA stem loop that prevents shine-dalgarno sequence & start codon from initiating translation
-PREVENTS TRANSLARION

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26
Q

in e. coli, TPP proudction by the thiMD operon is regulated by a riboswitch at the level of _________.

A

translation

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27
Q

in B. subtilus, which gene codes for enzyme glutamine:fructose-6-phosphate amidotransferase

A

glm6

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28
Q

what is involved in production of GlcN6P?

A

glm6 which encodes for enzyme glutamine:fructose-6-phosphate amidotransferase

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29
Q

what happens when there are low concentrations of GlcN6P?

A

glmS is expressed

30
Q

what happens when GlcN6P is high?

A

GlcN6P binds to riboswitch sequence in the glmS mRNA, inducing mRNA cleavage & preventing translation
-AFFECTS mRNA STABILITY

31
Q

what are the requirements for successful phage infection?

A

-genetic regulatory switches must be controlled by phage gene expression to redirect action of host genes
-phage gene expression must initiate a sequence of events leading the host cell to participate in expression of phage genetic info (most clearly seen in lambda phage, which can undergo lytic or lysogenic cycle)

32
Q

what is the lambda genome composed of?

A

48 kb of linear double-stranded DNA, encoding nearly 60 genes

33
Q

what does the lambda genome circularize by?

A

joining of the two single-stranded cohesive (cos) ends of about 12 nucleotides in length

34
Q

what is the lambda genome organized as?

A

a series of operons
-expression of some operons begins immediately after circularization

35
Q

immediate early genes

A

expressed shortly after circularizarion

36
Q

delayed early genes

A

expressed after immediate early genes

37
Q

late genes

A

expressed later in the infection cycle

38
Q

what are the immediate early genes?

A

N & cro proteins which compete for control of a genetic switch
-determines whether the phage enters the lytic or lysogenic cycle

39
Q

what are the two promoters where transcription begins?

A

PR- rightward transcription of EARLY GENES needed to establish LYTIC cycle by transcribing CRO protein (a repressor)

PL- leftward transcription of PROMOTER needed to establish the LYSOGENIC cycle by transcribing the N protein (an antiterminator)

40
Q

what does the N protein do?

A

blocks transcription termination allowing expression of delayed early & late genes

41
Q

what does regulation for lysogeny begin with?

A

protein N binding to three transcription terminating DNA sequences: tL, tR1, & tR2

42
Q

what does tL do when unbound?

A

acts to block leftward transcription beyond N

43
Q

what does tR1 & tR2 do when unbound?

A

prevents rightward transcription beyond cro & three other early genes (cII & others)

44
Q

when bound by N, what continues?

A

transcription continues since N protein is an antiterminator
-this allows expression of delayed early genes (integrase, cII, cIII, & cI

45
Q

what are produced by leftward transcription?

A

integrase & cIII protein

46
Q

what is produced by rightward transcription?

A

protein cII

47
Q

what is protein cII stabilized by?

A

binding to cIII

48
Q

what does the cII/cIII complex do?

A

promoter PRE to initiate leftward transcription of the cI gene

-it ALSO binds to Pl to produce additional integrase protein

-THIS STIMULATES LYSOGENY

49
Q

what is the cI gene also called?

A

lambda repressor protein

50
Q

what does the genetic switch for lysis or lysogeny depend on?

A

a balance between cro protein & lambda repressor (cI gene product)

51
Q

what are the operator sequences?

A

OR1, OR2, OR3
-these are between PRM & PR

52
Q

what does entry into the lytic cycle require?

A

transcription of late genes, regulated by late promoters & late operators
-these are genes rightward of PR

53
Q

how many base pairs are each of the target sequences for the operator sequences?

A

17-bp for binding either cro or lambda repressor

54
Q

what is the order of operators for cro as it increases?

A

OR3, OR2, OR1

55
Q

what does cro protein bound at the operator sequence do?

A

it blocks access of RNA polymerase at the PRM preventing production of lambda repressor (cI)

56
Q

what does PRM mean

A

promoter of repressor maintenance

57
Q

what does cro binding stimulate?

A

transcription from pR enhancing transcription of cro

58
Q

what does Q encode

A

Q protein which is a positive regulator of transcription of late genes rightward of PR

59
Q

what do late genes include

A

those needed for production of head & tail proteins & those required for host cell lysis

60
Q

what is the order in which the dimerized lambda repressor binds to the operator sequences?

A

OR1, OR2, then OR3
-it functions as a dimer & spans the 17 bp of DNA at each operator sequence

61
Q

what does lambda repressor protein bound at the operator initiate?

A

positive control at PRM leading to continuous transcription of cI, maintaining repression, it also activates integrase

62
Q

would a large number of phages favor lytic or lysogenic cycle?

A

lysogenic
-prevents wiping out all the host cells in a population

63
Q

would DNA damage to the host such as UV radiation favor lytic or lysogenic cycle?

A

lytic cycle

64
Q

if the host cell population is actively growing, would lytic or lysogenic cycle be favored?

A

lytic cycle
-new phage can easily find new hosts
-cII protein is degraded by proteases

65
Q

if the host cell population is growing poorly, would the lytic or lysogenic cycle be favored?

A

lysogenic
-prophage can remain silent until conditions for continued infection reappear

66
Q

is lysogeny permanent?

A

no, its a semi-permanent state

67
Q

what is the process that brings lysogeny to an end?

A

induction
-it is like a switch & triggered by DNA damage (UV light or other extracellular conditions) that activates DNA repair

68
Q

what protein is part of the DNA repair cascade & what is its role?

A

RecA
-its role is to activate recombination

69
Q

what type of activity does RecA have & what is it activated by?

A

protease activity that is activated by UV light damage to DNA

70
Q

what does RecA do?

A

it targets the lambda repressor monomores & cleaves off the C terminus
-the OR1, OR2, & OR3 sequences are exposed & positive regulation of ci & negative regulation of cro end

71
Q

after RecA does its thing, what happens?

A

cro protein can now bind to the exposed operators
-this leads to expression of Xis which produces enzyme excisionase

72
Q

what does excisionase do?

A

removes the lysogen from its integrated location
-this event triggers the resumption of the lytic cycle

genetics (37 decks)

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