A Genetic Switch
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How many base pairs in 1 turn of the helix?
10 base pairs
mRNA is read at what end?
begins reading at the 5' end
Binding of a protein to the operator is dependant on these two factors
- intrinsic affinity
- protein concentration
what triggers a lambda virus to enter to lytic cycle?
cI gene encodes for?
which is stronger: the ionic bond or the hydrogen bond?
Ionic bond is stronger
The lambda repressor is what type of regulator?
both negative and positive. It turns off all genes but turns on its own gene.
Cro protein is responsible for?
promotes and is required for lytic growth
Which gene (cI or cro) can be transcribed without a regulatory protein?
PR promoter (cI gene)
about ____ of the repressor proteins are found as dimers
dimerization of the repressor protein can be increase by:
Repressor dimers use which end to bind to the DNA major groove?
cro exists as a _____ in the cell
dimer (nearly 100% of the time due to high affinity to form a dimer)
How does the principle of exclusion apply to lambda phage?
Repressor at OR2 turns off cro gene by preventing of RNA polymerase to PR
How does repressor act as a positive control?
Repressor at OR2 helps RNA polymerase bind and begin transcription at PRM to transcribe cl (increase in roughly ten-fold)
What would happen if the Gln-Ser sequence in helix 3 of the repressor was altered? What if the same sequence was altered in Cro?
- both of these signals are responsible for the recognition of the promoter.
- Gln recognizes A
- Ser recognizes G
How does repressor/Cro protein distunguish between operator sites?
amino acids other than Gln-Ser
Which characteristics can contribute to the affinity to either Cro or repressor; allow it to distinguish operators?
- the tightness of binding
- interactions between other parts of the protein and DNA
- in lamda represson, the end of it's flexible arm
A characteristic which differs PR from PRM?
- PR has a much better match at -35 and -10 region then PRM , thus it transcribes freely
- PRM needs lambda repressor at OR2
What is the effect of binding at OR1 with either Cro or repressor?
RNA polymerase is excluded from PR because bound protein covers part of the surface of DNA helix that must be copied.
What is the effect when either Cro or repressor binds to OR3?
the protein would block RNA polymerase from transcribing PRM
What is the effect of repressor bound at OR2?
- turns OFF PR by overlapping the DNA surface
- stimulates PRM
Name the effect if Cro is bound at OR2?
- fails to stimulate PRM
- it also lacks the specific amino acids along the contacting surface that would favorably interact with RNA polymerase
What characteristic is paramount to the function of the Lamda switch?
- the overlapping regions of the promoters and the operators
- additionally, the regulation by the proteins
The TATAA box of the promoter is found in what region?
Cro at OR2 blocks polymerase from binding to PR
Which gene does the repressor turn on?
it's own gene cI
the att of the viral circular DNA refers to?
the attachment site
When phage DNA is injected into the bacteria, it is linear. Next it becomes circular. Describe the process of how it becomes circular.
- The DNA has an overhang (lots of C's and G's) that automaically anneal and are joined by a bacterial enzyme
- known as the cos site (cohesive ends)
if the phage enters a lysogenic cycle, only these 2 genes are expressed.
cI and int.
the N protein is a _____ regulator?
The N protein turns on 9 genes. What genes does it not turn on?
head, tail and R genes
N protein only interacts with 1 promoter which turns ON cIII , xis, and int
- While N protein does interact with PL to turn on those genes, it can also interact in the opposite direction with PR and trascribe cro,cII,O,P,Q
What is the importance of the Q protein?
Q protein is an anti-terminator which allows transcription to proceed right and transcribe genes for lysis such as: head and tail
N protein, like Q protein, is also an anti-terminator
True (pg 53)
How does repressor synthesis begin in the absence of repressor?
cI can be transcribed from 2 promoters, one is activated by the repressor, but the other one is activated by CII protein
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