MCB Final Flashcards
Lytic Phase Definition
the phage makes more phage and kills its host cell
Lysogenic Phase Definition
the phage establishes a parasitic relationship with its host cell and does not kill its host
Prophage Definition
Phage DNA integrated into host genome
Lysogen Definition
Bacterium with integrated phage DNA
Is lysogeny reversible?
Yes
4 stages of lysogenic phase
- Commitment
- Integration to host chromosome
- Maintenance of lysogeny
- Exit from lysogeny (to lytic state)
What are the 3 transcriptional regulatory proteins?
Cl, Cll, Cro
Cl Repressor does what?
- Represses expression of lytic genes (including cro)
- Tanscriptional activator
PRM stands for what?
Promoter for repressor maintenance
PR stands for what?
Rightward promoter
Cl affinity binding order?
OR1 > OR2 or OR3
What happens when Cl binds?
Binding of Cl to OR1, OR2, OL1, OL2 blocks RNAP from binding @ PL and PR so NO TRANSCRIPTION OF LYTIC GENES OCCURS (INCLUDING CRO)
Are PL and PR weak promoters?
No, they are strong
Expression from PR and PL creates Cro and Cll and they race. What happens if Cll wins?
Cl gets made and represses LYTIC functions (including cro) ; it goes lysogenic
Cll Characteristics
- activator of Cl
- 97 AAs, unstable
How does Cll bind?
Binds to Cll binding site near PRE and recruits RNAP to transcribe Cl
PRE stands for
Promoter for repressor establishment
Is PRE a weak promoter?
Yes
Expression from PR and PL creates Cro and Cll and they race. What happens if Cro wins?
Cl is not made, lytic functions get repressed ; it goes lytic
Cro Characteristics
- repressor of Cl gene
- HTH Motif
Cro affinity binding order?
OR3 > OR1 or OR2
Where does Cro bind?
Cro binds to OR3 which blocks RNAP from binding at PRM so Cl is NOT transcribed
What factors influence the race?
- The stability of Cll
- Nutrient availability
When nutrients are abundant and the cells are growing well, lambda tends to go?
Lytic
- lots of bacteria present, low MOI, FtsH degrades Cll and keeps it at low levels
MOI meaning
the number of phage infecting a bacterial cell
When nutrients are low and the cells are not growing well, lambda tends to go?
Lysogenic
- little bacteria present, high MOI, too much Cll for FtsH to degrade
For integration into the host chromosome to occur, Site- specific recombination needs to occur between
attP and attB ; requires Int and IHF
Cll activates transcription from PRE and PI which makes
Integrase
Potential problem with maintaining lysogeny (doesn’t actually happen)
- as cell grows Cl repressor dilutes and if its too diluted it cannot repress lytic genes/cro so the phage will go lytic
How is Cl maintained in lysogeny?
When bound to OR1/OR2 it activates its own gene expression at PRM
What is prophage induction?
Switch from lysogenic to lytic state
What is prophage induction triggered by?
- DNA Damage
- Spontaneity
What happens in prophage induction?
- Overcome repression by Cl
- Expression of Cro to repress Cl synthesis
- Excision of DNA from chromosome
- Expression of lytic functions
How does lambda exit lysogeny?
RecA senses DNA damage to make RecA filaments that activate autoproteolytic activity of Cl
What happens when Cl gets cleaved when exiting from lysogeny?
It binds to operators with lower affinity and it no longer represses which allows RNAP to transcribe @ PR and PL
Lambda negative control is done by
Cl and Cro
Lambda positive control is done by
Cl and Cll
Lambda cooperativity is done by
Cl monomers, dimers, and tetramers
Lambda Autoproteolysis is stimulated by
RecA*
Lambda protein stability and targeted degradation is done by
Cll and FtsH
Two mechanisms of activation in eukaryotes
- Nucleosome remodeling
- Recruitment of RNA polymerase
Examples of activation by recruitment of RNAP
- Gal activation system in yeast
- CREB system
- Hormone response system
In Gal activation, expression of the gal genes requires
Gal4 which forms dimers that bind to UAS sequence
What are the roles that the Gal4 transcription factor plays
- When it binds to UAS it induces chromatin remodeling to insure GAL1 promoter is exposed
- Recruits transcriptional machinery to the exposed promoter
Gal4 purpose
Transcriptional activator
Gal80 purpose
Anti-activator, binds Gal4
Gal3 purpose
Anti-activator, binds Gal80
What senses galactose?
Gal3
What happens when Gal3 binds galactose?
Gal3-galactose binds Gal80 and causes it to be released from Gal4
Phosphorylation of a protein occurs on
Serine, threonine, tyrosine, or histidine residues
Components of ligand binding hormone systems
- Hormone receptor
- Hormone response element
Mechanisms of ligand binding hormone systems
- Hormone activates receptor in the cytoplasm
- Hormone activates receptor in the nucleus
In prokaryotes, negative control directly blcoks RNAP from binding via
Occlusion
Inactivation of a female X chromosome involves
hypermethylation of its DNA and hypoacetylation of its histones. The inactivated chromosome condenses into heterochromatin (barr body)
Combinatorial control
More than one signal controls expression of a given gene. The more activators that bind, the greater the transcription
Splicing with alternate promoter results
Proteins with different N-terminal sequences
Splicing with alternate polyadenylation sites results
Proteins with different C-terminal sequences
Splicing with intron retaining mode results
Retain intron in some transcripts
Splicing with exon cassette mode results
Internal deletion or insertion in protein
When iron is low, Tfr mRNA is
stable and translated
When iron is high, Tfr mRNA is
unstable and degraded
Iron Response Protein (IRP) is aconitase which is
an iron-containing enzyme
RNA Interference (RNAi) is a mechanism involved in what two processes?
- protecting cells from drRNA viruses
- regulating gene expression
dsRNA triggers RNAi. Where does the dsRNA come from?
- dsRNA virus
- microRNA genes
- transgenes (inadvertent, planned antisense)
What is antisense RNA?
An RNA complementary to an mRNA
Antigen definition
Foreign substances recognized by the body as being different
VDJ Recombination DNA Sites
- Recombination Signal Sequences (RSS)
- Found next to V,D, and J segments
- Bind recombinase
VDJ Recombination Protein Factors
- RAG1/RAG2 (recombination activating gene)
- HMG (DNA bending protein)
