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GN 421 > Basic Transcription Part 4 > Flashcards

Basic Transcription Part 4 Flashcards

1
Q

Anti termination by N

A
  • can cause anti termination at both rho-dependent and independent terminators
  • binds to hairpin to prevent its formation
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2
Q

site to the right of cro allows

A

-polymerase to ignore terminator and enter the delayed early genes

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3
Q

Q utilization site (qut site)

A
  • overlaps late promoter PR’
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4
Q

in absence of Q

A
  • RNA polymerase pauses for several seconds at qut site

- then transcribes to the terminator and stops late transcription

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5
Q

In presence of Q

A
  • Q recognized paused complex and binds qut site
  • Q inhibits hairpin formation
  • Q then binds polymerase and causes it to resume transcription and ignore terminator and continue into late genes
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6
Q

to progress from immediate early to delayed early genes

A
  • requires anti termination by N
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7
Q

to progress from delayed early genes to late genes

A
  • requires anti termination by Q
  • at qut site just downstream of Q
  • Q is a delayed early gene
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8
Q

cI

A
  • encodes lambda repressor protein
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9
Q

2 promoters control the cI gene

A
  • PRM

- PRE

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10
Q

repressor maintenance

A
  • PRM
  • used during lysogeny to provide continual supply of repressor to maintain lysogenic state
  • requires the product of its own product for activity - auto regulation
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11
Q

why PRM cannot be be used to establish lysogeny

A
  • because no repressor present to activate it

- instead PRE is used

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12
Q

PRE

A
  • promoter establishment
  • located to the right of PR and cro
  • directs transcription leftward through cro and then through cI
  • allows cI expression before any repressor is available
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13
Q

PRE transcription

A
  • cro usually transcribed rightward from PR
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14
Q

leftward transcription from PRE

A
  • produces antisense product of cro

- sense product of cI

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15
Q

antisense RNA

A
  • helps establish lysogen by binding to cro mRNA

- cannot be translated

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16
Q

promoting lysogeny

A
  • Cro works against lysogeny

- blocking cro promotes lysogeny

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17
Q

CII

A
  • promotes transcription from a leftward promoter (anti-Q) within Q
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18
Q

cII promotes transcription from a leftward promoter (anti-Q) within Q

A
  • promotes Q antisense RNA - blocks production of Q
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19
Q

What is Q required for

A
  • late transcription in lytic phase

- interfering with its synthesis favors lysogeny

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20
Q

cII function

A
  • can stimulate polymerase to bind only PRE, P1, and anti-Q

- but not other promoters

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21
Q

P1

A
  • promoter for integrase for lysogeny
22
Q

PRE area

A
  • -10 and -35 boxes with no similarities to consensus
23
Q

cII interaction RNA pol

A
  • cII required for transcription for transcription
  • RNA pol can’t bind alone
  • cII can’t bind alone
  • both proteins can bind and form a stable complex around the promoter
24
Q

how do cII and RNA pol bind

A
  • bind cooperatively to the promoter on opposite sides of the helix
25
Q

cIII

A
  • prevents destruction of cII by proteases in the cell (key stop for deciding between lysis or lysogeny)
  • works with cII to establish lysogeny by activating PE and P1
26
Q

lambda repressor binds where to do what

A
  • to both OR and OL

- to turn off further early transcription, interfering with the lytic cycle

27
Q

why is turning off cro important

A
  • stimulate own synthesis (lambda repressor) by activating PRM
  • allows pol to bind further transcribing the repressor which inhibits transcription from left and right
28
Q

OR division

A
  • divided into three parts
  • OR1, OR2, and OR3
  • each can bind repressor
29
Q

OR controls

A
  • leftward transcription of cI

- rightward transcription of cro

30
Q

repressor binds most tightly to

A
  • OR1
  • then OR2
  • and least tightly to OR3
31
Q

how many repressor binding sites in each operator

A

3

32
Q

repressor is a

A
  • dimer

- each subunit has 2 domains

33
Q

first domain of repressor

A
  • DNA binding
34
Q

second domain of repressor

A
  • involved in repressor-repressor interactions
35
Q

repressor dimers bound to both OR1 and O2 close to the binding site for RNA pol at PRM

A
  • inhibit RNA pol from binding to PR but help bring in pol to bind to PRM
  • prevent transcription from PRE
36
Q

how the repressors prevent transcription from PRE

A
  • by blocking cII and cIII transcription from PR and PL
37
Q

what are cII and cIII required for

A
  • required for transcription from PRE
38
Q

during lysogeny lambda repressor does what

A
  • represses transcription from PL and PR

- stimulates transcription from PRM

39
Q

polymerase-repressor interactions

A
  • required for activation of transcription from PRM
40
Q

activation interaction involves

A
  • sigma factor not alpha
41
Q

lambda repressor interacts with which region of sigma factor

A
  • region 4

- substitutes for weakly recognized -35 box

42
Q

maintaining lysogeny

A
  • once lysogeny established, a small amount of repressor is required to maintain it
  • cII and cIII disappear
43
Q

race between cro and cI

A
  • if cI wins, lysogeny results

- cro wins, lytic cycle results

44
Q

cI wins

A
  • cro binds first to OR3 (has highest affinity for)

- cI binds 1, 2, 3

45
Q

cro wins

A
  • if cro binds OR3 prevents cI binding
  • cI transcription from PRM stops
  • OR3 overlaps PRM
  • cro represses PRM
46
Q

cII level

A
  • determines lysis or lysogeny
47
Q

cII will

A
  • activate PRE and help turn on lysogeny program

- work against lysis by making anti-sense cro RNA

48
Q

in a rich medium

A
  • high protease concentration
  • not enough cIII to protect cII
  • lysis
49
Q

most important determinant in lysis versus lysogeny

A
  • concentration of cII
50
Q

switch from lysogeny to lysis

A
  • mutagenic chemicals can do it

- SOS response

51
Q

immunity region

A
  • contains cI, OR, OL, and cro
  • lysogen are immune to superinfection by a phage with the same control region
  • lambda repressor represses new phage DNA from infecting the cell

GN 421 (36 decks)

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