Gene Regulation In Prokaryotes Flashcards
constitutive genes
“on” all the time aka housekeeping genes; their proteins perform functions that are necessary for basic function, vitality, and maintenance of the cell
regulated genes
aka inducible/repressible genes; increased/decreased as cell’s needs change (ex: lac operon and trp operon)
Pribnow box
specific regulatory sequence in a promoter region; #s indicate position relative to transcription start sites
sigma factor
allows RNA polymerase to bind to DNA; several different types; each one interacts w different promoters & turns of different genes
cis-operating factors
affect activity on same DNA molecule in which they reside (ex: promoter sequences bind sigma factor more efficiently than others aka strong promoters which produces higher rate of transcription)
every copy of a gene has…
…its own promoter region as well as coding sequence
trans-operating factors
molecules that bind to regulatory sequences; made by genes on main chromosome and diffuse over
activator proteins
trans-operating; bind to sigma factor & inc. transcription
repressor proteins
trans-operating; decrease binding of sigma factor and decrease transcription
operon
enable organism to activate or inhibit expression of several proteins in response to one regulatory molecule
inducible operons
usually off; get turned on when cell needs their proteins (ex: operons that encode enzymes that catabolize nutrient molecules)
repressible operons
usually on; get turned off when their proteins are no longer needed (ex: operons that encode enzymes that synthesize amino acids or other important molecules)
operon contains:
structural genes; promoter; operator; regulator gene
structural gene in operon
encodes the proteins
promoter in operon
site where molecules that control activity in operon bind; must be bound by RNA polymerase for transcription to occur
operator in operon
site to which molecules that control activity in operon bind; where the repressor can bind to prevent transcription or activator can bind to promote transcription
regulator gene in operon
not contiguous w operon - it lies at a variable distance from operon; makes a protein that regulates whether operon is on or off
negative control
regulator protein is a repressor; when repressor bind to operator of operon, it prevents RNA polymerase from binding to operon’s promoter
positive control
regulator protein is activator; RNA polymerase bind promoter weakly; binding of the activator protein to activator binding site enables RNA polymerase to bind to the promoter
negative inducible operon
regulatory gene makes repressor protein which is made in active form; inducer induces transcription by inactivating repressor and preventing it from binding to operator
positive inducible operon
regulatory gene makes activator protein which is made in inactive form; inducer induces transcription by activating activator
negative repressible operon
regulatory gene makes repressor protein which is made in inactive form; corepressor represses transcription by activating repressor and enabling it to bind to operator
positive repressible operon
regulatory gene makes activator protein which is made in active form; repressor represses transcription by inactivating activator
lac operon
negative and positive control; contains structural genes lacZ, lacY, and lacA; inducible: not needed unless lactose is present
lacZ
encodes beta-galactosidase which breaks lactose into glucose and galactose
lacY
encodes permease which transport lactose into the cell
lacA
encodes transacetylase (function unknown)
lacI
controller of inducibility encodes lac repressor which bind the operator and prevents transcription; lies at a distance from operon so repressor is trans-acting factor
allolactose
lactose is converted to allolactose which bind to repressor and prevent it from binding to operator; transcription occurs proteins are made lactose gets catabolized; when level of lactose drops repressor represses transcription again
Jacob and Monod
discovered mechanism for gene regulation in lac operon using E. coli strains that had mutations in different portions of lac operon
E. Coli experiment
using partial diploids w plasmid w own copy of lac operon ; during conjugation donor bacterium gives recipient plasmid copy of lac operon
lacY and lacZ
work independently; Jacob and Monod
lacZ+ lacY- or lacZ- lacY+
these genotypes could make both beta-galactosidase and permease; Jacob and Monod
mutation in one copy of beta-galactosidase or permease
does not affect protein production from other copy of that gene (cis acting factor); cell had one working copy of each gene and could metabolize lactose; Jacob and Monod
Z, Y and A genes
not completely independent of each other; translation of Z is stopped in mRNA Y and A mRNAs will not get translated; nonsense mutation in one of operon’s genes can cause no translation of any of the downstream genes
mutation in lacI (Jacob and Monod)
caused repressor protein to be inactive so transcription was always on (lacI- genotype)
lacI+ lacZ-/lacI- lac Z+
does not produce beta-galactosidase in absence of lactose which means repressor protein from main chromosome’s I gene could diffuse to bind other copy o f operon in plasmid (repressor is trans-acting factor); doesn’t produce BG only when lactose is present bc functional repressor molecules that are made by main chromosome’s I gene must be inactivated by allolactose in order for there to be transcription
superrespressor mutations
prevents inducer (allolactose) from binding to repressor leaving repressor always active and inducer unable to induce transcription (genotype = lacIs); trans acting factor will repress both copies of operon even in presence of lactose
lacIs lacZ+/lacI+ lacZ+ or lacIs lacZ+/ lacI- lacZ+
does not produce beta-galactosidase even when lactose is present
lacOc genotype
discovered by Jacob and Monod; prevented repressor from binding - transcription was always on
lacOc lacZ+/lacO+ lacZ+
produces beta-galactosidase all the time even when lactose is absent because the repressor cannot bind the operator
lacI+ lacO+ lacZ-/lac+ lacOc lacZ-
produces beta-galactosidase all the time even when lactose is absent bc plasmid’s Oc mutation drives transcription of plasmid’s Z+ gene
lacI+ lacO+ lacZ+/lacI+ lacOc lacZ-
produces beta-galactosidase only when lactose is present bc plasmid Z- gene will not make function beta-galactosidase under any conditions this nullifies the Oc mutation’s effect on beta-galactosidase production
cis-acting element
lacP- genotype; promoter mutations that prevent the RNA polymerase from binding to the promoter
lacI+ lacP+ lacZ+/lacI+ lacP- lacZ+
produces beta-galactosidase normally when lactose is present (from the main chromosome); promoter mutation in the plasmid doesn’t prevent transcription in the main chromosome - promotor is a cis acting element
positive control
when glucose is present the bacterium will prefer to use it for energy vs. lactose and will shut down the lac operon
activator binding site
little way upstream from lac operon
glucose present
cAMP is low there is little CRP -cAMP complex to bind to activator binding site and transcription stops
glucose drops
cAMP rises allowing CRP and cAMP to bind resulting in activation of the lac operon
trp operon
contains 5 structural genes that work together to synthesize the amino acid tryptophan; needed for cell to be active except in presence of ample tryptophan; regulatory gene makes repressor protein which is made in inactive form; negative repressible operon
tryptophan
corepressor of trp operon; when present it binds the repressor and allows repressor to bind operator transcription stops until the level of tryptophan decreases; concentration of tryptophan determines if ribosome can smoothly translate leader mRNA which determines if structural genes of trp operon get transcribed
regulon
group of operons that are controlled by activators and repressors that diffuse throughout nucleoid
2nd means of negative control of trp
can be attenuated
leader gene (trpL)
trp operon; lies between operator and five structural genes whose proteins synthesize tryptophan; RNA polymerase transcribes leader mRNA + ribosomes translate leader mRNA creating leader peptide
region 1 in trp operon
in leader sequence - contains 2 consecutive tryptophan codons
regions 2, 3, and 4 in trp operon
region 3 can form stem loop structure by binding w region 2 or region 4 but not both (prefers to bind to region 2)
region 4
RNA polymerase binds just after region 4 to transcribe structural genes
regions 3 and 4
bind together stem loop blocks RNA polymerase binding site
regions 2 and 3
bind region 4 is open and RNA polymerase can bind and transcribe the structural genes
high tryptophan levels
ribosome has no trouble reading through two tryptophan codons bc there is plenty of tryp
low tryptophan
ribosome stalls as it tries to translate the leader peptide bc it has trouble finding the tryptophan-tRNAs it needs; this allows step loop to form between regions 2 ad 3 which allows RNA polymerase to bind around region 4 and transcribe the structural genes of the trp operon
archaeal transcription factors
can activate and repress transcription (ex: pyrococcus furiosus)
TrmBL1 protein
represses genes that make transport proteins for other sugar and activates genes for gluconeogenesis (synthesis of glucose)
TrmBL1
binds downstream of B recognition element and TATA box of the genes that encode maltodextrin and maltose/trehalose and prevents RNA polymerase from transcribing them; also binds to site upstream of B recognition element and TATA box of genes that encodes enzymes that synthesize glucose and recruits TBP, TFB, and RNA polymerase to the site activating transcription
TrmBL1 uses
one binding site to repress transcription and a different binding site to induce transcription
signal transduction pathways (2 component regulatory systems) activate transcription factors
(1) molecules from environment bind to extracellular domain of transmembrane protein that sensor kinase - when signal molecule binds sensor kinase phosphorylates itself (autophosphorylation) (2) phosphate group is transferred to response regulator which is a transcription factor that is activate by phosphorylation (3) response regulator then activates/inhibits its target genes
microbes activate genes via quorum sensing
glowing bacteria; secrete activator AHL which can activate several genes to make fluorescent protein called luciferase; when only a few bacteria AHL diffuses into environment and doesn’t enter bacterial cells; once enough bacteria AHL concentration in envir. gets high enough for AHL to diffuse into bacterial cells and AHL turns on the genes that make luciferase bacteria glow
quorum sensing
uses diffusible transcription activators
virulence factors are activated via quorum sensing
staphylococcus aureus causes serious wound infections + pneumonia - quorum sensing enables them to secrete their toxins; make inducer AIP transport out of cell w enough bacteria AIP binds to sensor kinase ArgC causing it to autophosphorylate; phosphate transferred to transcription activator ArgA which induces activity in genes that encode virulence proteins that help bacterium adhere to/invade your cells and secrete toxins
stringent response in bacteria
low concentration of nutrients in environment; synthesis of rRNA and tRNA and ribosomes stops; amino acid synthesize increase which enables synthesis of new proteins to compensate for lack of certain nutrients in environment (ex: enzymes to synthesize amino acids that are now no longer available)
translation regulated by antisense RNAs
have sequences complementary to certain genes’ mRNAs can bind to these mRNAs and increase/decrease translation depending on which mRNA
enabling translation by altering 2ndary structure of mRNA
RpoS mRNA has 2ndary structure near 5’ end that gets cleaved by RNAse making impossible for ribosome to translate mRNA; DsrA siRNA binds to 5’ end of RpoS mRNA changing mRNA’s 2ndary structure and changing cut site for RNAse enabling translation
translation regulation by antisense RNAs
ex: decreasing translation - ompF gene encodes channel that allows water and ion to pass into cell when environment has high osmolarity micF gene (encodes mRNA interfering complementary RNA: iRNA) is activated micF RNA binds to 5’ region of ompF mRNA inhibiting ribosome binding and translation which prevents cells from accumulating too high ion concentration
riboswitches
region where proteins and other molecules can bind and control if translation takes place or not; product inhibition - end product of synthetic pathway is regulatory molecules when it binds this inhibits ribosome binding to mRNA and inhibits protein production
ribozymes and end product inhibition
regulates translation; RNAs contain region where molecules can bind and cause mRNA to cleave itself (ribozymes); RNAs make genes that synth. various molecules when too high
concentration of product molecule it binds to ribozyme and causes mRNA to cleave itself
