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Prokaryotic Regulation - Coggle Diagram

- - - - AKA: Transcription Factors
- - - - increases chances of forming open complex
      - increases chances of promoter escape
  - - - eukaryotes have chromatin that represses and co-repressors also repress
  - - - function of gene product
      - affinity of RNAP for promoter
      - accessibility of DNA (chromatin-structure-dependent)
- - - - a DNA binding protein
      - repressor/operator - prevents lactose metabolism
      - binds to allolactose and changes conformation
        
        LacI is released from DNA
        
        allolactose is the effector
        
        That's why there's always a little LacY in the cell
      - LacI is a homotetramer
      - has a lot of affinity for operator 1 followed by operator 3 and operator 2
      - LacI binds to the operator which leads to
        
        hiding of the promoter region which leads to
        
        LacY repression which leads to
        
        lactose can't get into the cell
        
        Note: there's always a little bit of LacY just in case
      - sometimes binds two operators at once
    - - 100 bp upstream of +1
    - - prevents promoter escape
    - - a weak promoter
      - can be made strong when glucose levels are low with the help of an activator (CRP)
    - - beta-galactosidase
        
        breaks down lactose
        
        lactose -> glucose + galactose
        
        Sometimes isomerizes lactose making allolactose
      - Operator 2 is 400bp into the LacZ ORF
    - - a permease
        
        allows lactose into the cell
    - - sugar modifier
  - - - increased cAMP -> CAP binds to DNA
      - low allolactose -> bound LacI
      - No Lac expression
    - - Repressor (LacI) is bound
      - Low cAMP
      - No Lac expression
    - - decreased cAMP
      - Low Lac expression because LacI floats away
      - Low Lac expression
    - - increased cAMP -> CAP binding -> activation
      - derepression of LacI and full activation
      - Lac operon highly expressed
    - - Lac operon would always be repressed because LacI is always stuck to the DNA
    - - Lac operon would always be derepressed becuase if LacI thinks it's stuck to allolactse (even if it's not actually stuck), Then it can't bind to DNA
        
        Lac operon is not necessarily activated because CAP-cAMP are required for activation
        
        Remember CAP-cAMP depends on glucose
    - - If O1 is mutated to the point of not being function, then LacI would move on to O3 first, then O2.
        
        Less repression overall
- - - - binds transcription factors and allows binding or repulsion from the operator
  - - - effector = tryptophan
        
        high tryptophan -> off state
    - - trpE
      - trpA
      - trpB
      - trpC
      - trpD
    - - ORF's 2 and 3 or 3 and 4 can make a hairpin
        
        2/3 -> transcription
        
        preferred pairing
        
        3/4 -> termination
      - Has 4 sites on the small regulatory RNA is encodes
  - - - transcription
        
        transcription stops at polyU sequence downstream of site 4
      - 3/4 hairpin loaded by the ribosome
      - no stalling -> 3/4 hairpin formation
    - - stalling at site 1 (contains two TRP codons) because it's waiting for correct tRNA to come along -> 2/3 hairpin formation
      - RNAP is not kicked off therefore downstream genes are transcribed
      - Tryptophan can be synthesized de novo
    - - tryptophan binds to operator preventing transcription
- - - - promotes LexA cleavage from DNA
      - responds to excessive amounts of damage
      - a co-protease
    - - TLS (translesion) polymerases
      - SulA
        
        a cell division promoter
      - UVR - nucelotide excision repair (NER genes)
        
        UVRA
        
        UVRB
        
        UVRC
        
        UVRD
- - - - cro represses PRM
  - - - First, CI must be reduced so PR and PL can be turned back on
        
        RecA stimulates Autoproteolysis of CI
        
        Autoproteolysis = self cleavage
      - Second, LexA autocleaves when stimulated by RecA
      - Third, SOS signaling leads to PRM deactivation
      - Finally, PR makes cro
    - - PR and PL are on initially but are turned off by CI
  - - - regulatory region
      - genes for DNA replication
      - lysis genes
      - head/tail genes
        
        Head genes code for capsid
        
        Tail genes code for everything else
      - excisionase - cuts prophage from the genome
      - integrase genes/attP site
        
        site-specific integration
  - - - transcribes left up to and including CI
      - promotes repressor establishment
    - - an ORF
      - lambda (lytic cycle) repressor, binds operator
      - represses PR and PL
      - activates PRM when bound to O1 and O2
      - Represses PRM when CI is high and O3 is bound
      - Represses PR when O2 and O2 are bound
      - Prefers O1 followed by O2 and O3
      - If levels are too high, binding to O3 turns off PRM
    - - an ORF
      - a transcription factor
      - establishes CI activator
      - Lysogenic pathway
    - - an ORF
      - homologous to CII
    - - PL is located at O2
        
        PL is a strong constitutive promoter - does not require activation
        
        transcribes left
    - - PRM is located at O3
        
        Promoter repressor maintenance
        
        activated by CI
        
        very weak promoter without CI activation
      - PR is located at O2
        
        PR is a strong constitutive promoter - does not require activation
        
        transcribes right of CI
    - - an ORF
      - a transcription factor
      - prefers O3 -> PRM repression
  - - - CII is required for CI
      - Leads to lytic cycle
      - PRM repressed by cro
    - - CI repressor established
      - CII accumulates and binds to PR
      - degradation of CIII also leads to CII accumulation