Section 2 pt 3

Question 1

cll is a transcriptional regulator. It activates expression of __ (the repressor) and __ (integrate)

Answer 1

cl
int

Question 2

cl protein function:

Answer 2

turns off all the replication and lysis genes, activates its own expression

Question 3

integrase

Answer 3

protein recombines the genome into the host genome

Question 4

Integration happens by recombination between the __ (attachment phage) and the ___(attachment bacterium) sites which are homologues sequences in the two DNA molecules

Answer 4

attP
attB

Question 5

The organization of genes integrated is different than that in the linear virion form.

Answer 5

Genes that were next to each other in the circular form are now at opposite ends

Question 6

cl, the only gene expressed and the only protein made in the lysogenic state.

cl is a ____-_____ protein that is only able to bind DNA as a dimer (binds to diff sites w diff affinities)

Answer 6

DNA-binding

Question 7

regulatory proteins that bind to DNA will bind to their recognition sequences and variants of them at different affinity
SO occupancy of the sequences depends of concentration of the protein

Answer 7

Low amount of protein: only strong sites bound

A lot of protein: all sites bound

Question 8

cl binds to 6 different sites on DNA: operators: (3) ________ which overlap promotors: (2) _____________

and operators: (3)________ which overlap promotor: (1)________

Answer 8

OR1,2,3 overlap PR and PRM

OL1.2.3 overlap PL

Question 9

when there is ___ _____, PR and PL are left free and active so it allows for late gene expression Replication, structural, lysis

Answer 9

no cl

Question 10

when there is __ ___ ___, all 6 sites are occupied and PRM, PR, PL are all off so no expression

Answer 10

a lot of cl

Question 11

when there is cl, the cl proteins on the two sets of O sequences interact forming ____ _______ and makes the binding even stronger

Answer 11

DNA loops around

Question 12

preference for binding of cl is OR1>OR2>OR3 where ____ and ____ adjacent dimers interact and have a synergistic cooperate binding effect even stronger

Answer 12

OR1 and OR2

Question 13

The _____ is the weakest of all 6Os, last to be occupied and it overlaps PRM “Promotor for Repressor Maintenance”

Answer 13

OR3

Question 14

if cl levels decrease OR3 is the first to be vacant, frees up ____ and activates cl transcription

Answer 14

PRM

This cells cell in lysogenic state

Question 15

cells carrying lambda integrated as a prophage are protected from super-infection by other lambda particles (and similar things) as there is a lot of ___ protein that can prevent expression of all incoming phage genes

Answer 15

cl

Question 16

lambda (and other prophages) can be included to enter lytic cycle by _____ of the cl protien from its DNA and prevention of its binding
HOW??

Answer 16

REMOVAL OF cl protein TO ENTER LYTIC

Question 17

induction of the lytic cycle occurs when the cl protein is degraded by the bacterial protease ____

Answer 17

RecA
cleaves and inactivates cl preventing its binding to DNA

Question 18

how does RecA work: (2 things)

Answer 18

• happens in response to hosts SOS response (bacteria response to stress such as DNA damaging agents)
• cleaves and inactivates cl preventing its binding to DNA

Question 19

RecA is normally a _______ _____ but in response to DNA damage it becomes active as a protease

Answer 19

recombination enzyme

Question 20

RecA targets cellular repressors and removes them especially ______ which triggers the SOS response

Answer 20

LexA

Question 21

LexA normally inhibits expression of _____ _____ so when its removed all the DNA damage stress genes get expressed

Answer 21

stress genes

Question 22

LexA and cl look alike so RecA recognizes it by mistake and it is a way the phage co-opted the cell’s damage control system as a cue for activating its lytic replication AKA:

Answer 22

things are going bad for this cell lets get out

Question 23

removal of cl repressor exposes PR and allows for transcription of cro protein

Answer 23

Right promotor

Question 24

Cro turns on expression of early lytic genes and inhibits ___ transcription

Answer 24

cl

Question 25

upon induction ______ occurs, where the phages genome comes out of its integrated into the cells chromosome state into a circle

Answer 25

excision

Question 26

integration requires ____ and excision requires __ and ____ both are translated from the mRNA at the end of the integrated genome

Answer 26

int int and xis (excisionsase)

Question 27

The genome must be in circular excised from for the lytic pathway to :(2 things)

Answer 27

1. replicate the DNA 2. express late genes

Question 28

During the lytic cycle: Integration into the host genome is prevented by a phenomenon called _____

Answer 28

retroregulation

Question 29

Retroregulation: anti termination by N allows PL transcription to proceed past int and xis to ____

Answer 29

sib

Question 30

sib does not encode a protein, so what does it do?

Answer 30

has a sequence that gets targeted by the cellular RNase enzymes, which degrade the mRNA in a 3' to 5' direction

Question 31

due to sib, more xis gets translated before the RNase makes it to it as compared to int, this disproportionate ratio keeps lambda DNA out of the chromosome ONLY WHEN

Answer 31

its in the excised circular form

Question 32

when its inside the chromosome to begin with, sib isn't downstream of int cuz of the attp, so int and xis get transcribed to allow excision, then sib prevents int translation so that the genome can't reintegrate

Question 33

why must the genome be In circular form for the lytic cycle?

Answer 33

1. cuz the structure gene promoter is at the other end of the linear version of the genome that is inside visions 2. cuz the mechanism for DNA replication for phage lambda is the rolling circle replication of a long concatemer that joins at cos sites

Question 34

phage genomes are made up of sets of genes called _____ that are located together and transcribed together, each having diff functions

Answer 34

modules

Question 35

phages can be put together from modules with _______ evolutionary backgrounds (mix and match modules A&B blue and red)

Answer 35

different

Question 36

exchangeable modules are _______ than complete structural or functional units

Answer 36

smaller

Question 37

Plasmid prophages: (ex P1)

Answer 37

temperate phages that do not integrate into the bacterial genome but rather exist as circular plasmid prophages

Question 38

Plasmid prophages: because its not actually integrated into the genome it does tricks to get passed down to daughter cells: (2tricks)

Answer 38

1. has partition genes that make each daughter cell get 1 copy 2. plasmid addiction module that kills the cell if plasmid is lost (HOW?)

Question 39

how does plasmid addiction module work in plasmid prophages?

Answer 39

has two proteins Doc: toxin protein (STABLE alone) PhD: toxin inhibitor (unstable) if plasmid goes away PhD degrades and the stable doc protein gets freed to kill the cell

Question 40

Another plasmid prophage: N15 half of its genome like lambda but the other half is very diff allows it to exist as a ____ plasmid and replicate as a ______ plasmid

Answer 40

exist as linear replicate as circular

Question 41

Linear DNA circularizes at cos sites after entering the cell then ____

Answer 41

circular form re-linearizes but with different organization than in the virus particle (linearized DNA in host cell has hairpin ends called telomeres)

Question 42

Satellite phages (ex. P4)

Answer 42

depend on another phage for replication P4 can only replicate in a cell thats also infected by P2 integrated into its genome as a prophage

Question 43

P4: - Does not _____ - turns off _____ and activates just - makes a protein ___

Answer 43

- Does not encode its own structural or lysis genes - P2 prophage genes and activates just the late lytic genes - sid "side determination" that alters the structure of P2 cased to make the head smaller that only packages P4

Question 44

P4 is a _____ and a satellite prophage as it integrates into host genome if P2 is not there (waits for it to come infect a P4 lysogen so that P4 becomes activated

Answer 44

temperate

Question 45

SaPIs are

Answer 45

Staphylococcus aureus pathogenicity islands

Question 46

diff SaPIs are present in diff Staphylococcus aureus strains to encode various _____ factors that contribute to bacterial pathogenicity

Answer 46

virulence

Question 47

SaPIs are normally not active but they are induced for replication by ______ _____ that have a protein that induces SaPIs to make a protein that hijacks the phage capsid protein and packaging machinery (makes phages with shrunken heads and SaPI DNA)

Answer 47

replicating phages

Question 48

lysed cell releases SaPIs ____ _____and some of the original helper phage ____ _____

Answer 48

smaller heads larger heads

Question 49

released SaPI can

Answer 49

1- go and infect other cells 2- Integrate SaPI DNA into cells genome (recombination at att sites like lambda) 3- SaPI inactive for replication until helper gene comes Results in transfer of virulence factors from cell to cell

Question 50

SaPI encode repressor protein that keeps them inactive ____ (acts as sensor to see if helper is there) when helper phage comes, it encodes the antirepressor protien and SaPI is activated

Answer 50

Stl

Question 51

SaPI proteins inhibit

Answer 51

helper Phage gene replication shrink the head alter the terminase packaging enzymes so that SaPI genes get packaged

Question 52

SaPIs were the first to be discovered, now there is a lot of PICIs "___"

Answer 52

phage-inducible chromosomal islands