Term
| Nucleotide excision repair |
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Definition
"dark repair"
UvrAB recognizes damage, UvrC cuts DNA, UvrD removes cut strand, DNAPI & Ligase fill gap |
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Term
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Definition
Nucleotide excision repair
recognize DNA damage |
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Term
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Definition
Nucleotide excision repair
cuts DNA 7-8bp us & 3-4bp ds from damage |
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Term
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Definition
Nucleotide excision repair
removes cut strand
similar to MMR & VSPR |
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Term
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Definition
Excessive DNA damage halts replication
RecA activated by damage, binds to ssDNA
LexA repressor of DNA repair enzymes, activated by RecA to autocleave
DNAPIV mutagenic, replicates across errors |
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Term
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Definition
SOS Response
Activated by DNA damage
Binds to ssDNA to activate LexA
Also involved in homo recombo |
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Term
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Definition
SOS Response
Transcription repressor of DNA repair enzymes
Autocleaves when activated by RecA |
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Term
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Definition
SOS Response
coded by umuDC
mutagenic-> replicates across errors but with a high error rate
null mutation-> less cell survive w/ less mutations |
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Term
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Definition
proteins that bind to specific DNA seq to reg transcription
Repressors, activators, anti-repressors, anti-activators
Sigma factors (RNAP), Rho (RNA term), UP Element (DNA seq binds TF)
Regulated by small molecules-> corepressors (products of anabolic paths), inducers (substrates of catabolic paths), coactivators, anti-activators |
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Term
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Definition
TF bind between -35 & +1
Neg reg
DnaA, SeqA, LexA |
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Term
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Definition
TF bind before -35
Pos reg
Ada, LuxOD47E |
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Term
| Electrophoretic Mobility Shift Assay |
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Definition
Studies TF binding
1. PCR w/ fluorescent probes
2. expose to diff conc. conditions-> probe, probe + low [protein], probe + high [protein]
3. electrophoresis-> bigger size if protein bound, probe + low will have a short & long band |
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Term
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Definition
catabolic
lacO operator binds LacI
LacI repressor
LacZ for B-galactosidase
LacY permeate
LacA unclear function |
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Term
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Definition
operator
binds LacI repressor
lacO(c) mutation has constitutive phenotype, dominant & cis-> lacO not recognized by LacI |
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Term
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Definition
repressor
binds to lacO operator
LacI(-) mutation has constitutive phenotype, recessive & trans-> LacI doesn't bind lacO
LacI(s) mutation has - phenotype, dominant & trans-> LacI can't be released by inducer
LacI(-d) has c phenotype, dominant & trans-> inactive dimer
LacI(rc) has - phenotype, dominant & trans-> binds to lacO only when inducer present |
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Term
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Definition
B-galactosidase breaks down lac to galactose & glucose
LacZ(-) mutation has - phenotype, recessive & trans-> B-galactosidase inactivated |
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Term
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Definition
Permease, transports lac across membrane
LacY(-) mutation has - phenotype, recessive & cis-> doesn't transport lac |
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Term
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Definition
Lac- phenotype
Recessive & cis
Promotor not recognized by sigma70 |
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Term
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Definition
Xgal: blue/white screening
IPTG: non-metabolized inducer
Merodiploids: Jacob & Monad |
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Term
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Definition
1965
1st insights into gene regulation by studying lac operon
Searched for 3 phenotypes-> Lac+ (WT), Lac- (never use lac), Lac(c) (always use lac)
Generated merodiploids by conjugating cell w/ lac operon on chr & cell w/ lac operon knockout on chr but lac on F plasmid
Discovered which mutations were dominant/recessive & cis/trans |
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Term
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Definition
Cis: only affects seq it's on
Trans: affects all genes in cell |
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Term
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Definition
Presence of glucose represses us of other sugars
Adenylate cyclase makes cAMP, inactive when glucose present
cAMP coactivates CAP
CAP activates lac operon
PtsG glucose importer
IIA-Glu prevent lac use when dephosphorylated, promotes use when phosphorylated |
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Term
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Definition
Makes cAMP from ATP
Activated by phosphorylated IIA-Glu when no glucose present |
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Term
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Definition
aka CRP
activator of lac operon
cAMP is coactivator |
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Term
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Definition
Dephorphorylated by glucose
Dephosphorylated form when glucose present, inducer exclusion inhibits LacY
Phosphorylated by glycolysis
Phosphorylated form when no glucose, activates adenylate cyclase |
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Term
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Definition
Negative control
Anabolic, arginine biosynthesis
ArgR repressor (transcription)
Arginine corepressor |
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Term
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Definition
Common negative control mechanism
Galactose-> 2 operators on both sides of promotor
GalR repressor forms tetramer that loops DNA
Galactose inducer |
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Term
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Definition
Disproved idea that all regulation is negative
Arabinose |
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Term
| Arabinose gene regulation |
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Definition
Positive control
araBAD transcribed when arabinose present & glucose absent
AraC regulator has opposite mechanism of LacI (AraC- = Ara-), activated by arabinose
AraC(c) constitutive allele
C(c) + C+ merodiploid gives Ara+ phenotype
AraC forms N-terminal loop when arabinose not present |
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Term
| Tyrptophan gene regulation |
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Definition
1) Transcription initiation: negative regulation by TrpR repressor & tryptophan corepressor
2) Transcription termination: attenuation
Transcription of us leader peptide controls termination
Low tryptophan-> anti-terminator forms when 2 & 3 region base pair, no charged tRNA for trp causes ribosome to stall at 1 region, allowing RNAP to continue transcribing operon
High tryptophan-> terminator (stem loop + U's) forms when 3 & 4 region base pair b/c ribosome efficiently translates leader peptide |
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Term
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Definition
non-coding regulators of transcription or translation
Bind to mRNA, facilitated by Hfq
dsrA & sgrS |
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Term
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Definition
RNA chaperone
stabilizes sRNA-mRNA interactions |
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Term
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Definition
sRNA positively regulates translation of RpoS (sigma s)
Binds to 5'-UTR to prevent stem loop blocking RBS |
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Term
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Definition
Binds to PtsG mRNA, causes degradation
Has ORF to code for sm peptide
sgrR is transcription activator
sgrT inhibits PtsG, binding prevents glucose transport |
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Term
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Definition
Regulation of ds gene in response to sm molecule or signal
Cis
Highly Structured
Usually in 5'-UTR
Aptamer: RNA structure that binds signal
Expression platform: structure controlling ds translation |
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Term
| tRNA synthase gene regulation |
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Definition
Transcription termination regulated by riboswitch
tRNA signal
Uncharged tRNA turns gene on transcription when specifier loop bp w/ anticodon & anti terminator bp w/ CCA
Charged tRNA creates stem loop + U's terminator |
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Term
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Definition
Chemical communication
Density-dependent gene regulation
Avery, MacLeod, McCarty
1st discovered in S. pneumoniae (competence) & V. fisheri (lux) |
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Term
| V. fischeri counterlumination |
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Definition
LuxI: autoinducer synthase activated by high density
LuxR: AHL receptor, TF
Squid expels 95% vf every night b/c high cost to make light & prevents dark mutant proliferation
LuxIR systems common in G- |
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Term
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Definition
V. fischeri quorum sensing
autoinducer synthase
acyl homoserine lactone (AHL)
activated by high density |
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Term
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Definition
sensing environment, quorum sensing
Kinase homodimers: controlled by signal, phosphorylated at His
Response regulator: gets phosphorylated at Asp for output
ATPase: phosphorylates proteins using ATP |
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Term
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Definition
G+, uses peptide as AI
Causes switch from adhesive state to spreading
Positive feedback
ArgA: response regulator that activates promotor
ArgB: transports & processes ArgD
ArgC: kinase that phosphorylates ArgA
ArgD: peptide, pre-AI that acts was signal
RNAIII sRNA synthesized; inhibits adhesion & promotes secreted factors, proteases, & toxins |
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Term
| V. harveyi quorum sensing |
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Definition
G+/G- hybrid quorum sensing
Phosphorelay pathway: similar to 2-component system, but more components
At low cell density, phosphate flows into system so LuxR not made
At high cell density, receptors bind AI switch & become phosphates so LuxR made
LuxN: AI-1 adds phosphate to LuxU His
LuxPQ: AI-2: adds phosphate to LuxU His
LuxU: adds phosphate to LuxO Asp
LuxO: phosphorylated form allows transcription of Qrr sRNAs the inhibit LuxR mRNA |
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Term
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Definition
control many genes
quorum sensing, heat shock, & 2nd messengers |
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Term
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Definition
Vh quorum sensing
Autoinducer 1
Recognizes AHL
His gets phosphorylated
Phosphorylates LuxU |
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Term
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Definition
Vh quorum sensing
Autoinducer 2
Recognizes inter-species signal
His get phosphorylated
Phosphorylates LuxU |
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Term
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Definition
Vh quorum sensing
Transcription activated by phosphorylated LuxO
Uses sigma 54
Inhibits LuxR mRNA when low cell density |
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Term
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Definition
Cells exposed to pulse of heat can better survive extended heat
Pulse induces chaperones & proteases to degrade misfiled proteins
RpoH (sigma H) activates chaperones & proteases, accumulates at high T (>45C), low translation at lower T
Pnak protease degrades RpoH at 30-37C |
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Term
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Definition
RNA structure that senses T
ex. rpoH mRNA has stem loop blocking RBS that melts at high T |
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Term
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Definition
Sense environment
Often derived from purine nucleotides |
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Term
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Definition
Activates CAP-> lactose utilization, biofilm formation
Adenylate cyclase: coded by cydA, synthesizes cAMP from ATP
CdpA: breaks down cAMP into AMP
Inverse relationship w/ glucose |
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Term
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Definition
Transcription factor
AHL receptor in Vf quorum sensing
Inhibits biofilm formation |
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Term
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Definition
stringent response
Mike Cashell
activates RNAP-DKSA-> stress response
RelA: synthesizes ppGpp from GTP & ATP when uncharged tRNA enter ribosome A site (starvation conditions)
SpoT: synthesizes & degrades (to GDP) ppGpp |
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Term
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Definition
Activated by ppGpp
Stress response-> inhibited growth, ribosome synthesis, & replication; activated rpoS
DksA: similar structure to GreAB, needed for ppGpp to interact w/ RNAP |
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Term
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Definition
Can synthesize (from GTP & ATP) and degrade (to GDP) ppGpp
Null mutant is lethal b/c ppGpp toxic buildup (live if RelA or DksA knockout) |
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Term
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Definition
Regulates biofilms & motility
Rediscovered in 2004
CGDEF: synthesizes c-di-GMP from 2 GTP
EAL or HDGYPs: breakdown c-di-GMP to 2 GMP
Synthesis & breakdown controlled by environmental signal
Interacts w/ TFs, riboswitches, & proteins |
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Term
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Definition
Controls cell wall physiology
Responds to osmolarity changes
Discovered 2008
Mostly G+ |
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Term
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Definition
Rodospirillium
Common in eukaryotes
Secreted
Cell encystment |
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Term
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Definition
Membrane remodeling
Newest discovered
V. cholerae
Binds & activates phospholipase |
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Term
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Definition
Plasmid origin of replication
Controls copy #, plasmid compatibility, replication mechanisms, & host range |
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Term
| Mechanisms of plasmid replication |
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Definition
Theta (oriV)
Rolling Circle |
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Term
| Rolling Circle Replication |
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Definition
Plasmid replication
Rep: nicks double stranded origin-> attaches to 5' end-> pulls off strand as replication follows-> rejoins completed strand
On pulled strand, stem loop forms at single stranded origin-> RNAP makes primer directly ds-> replication |
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