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Genetics 380 > Gene Regulation In Prokaryotes > Flashcards

Gene Regulation In Prokaryotes Flashcards

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1
Q

constitutive genes

A

“on” all the time aka housekeeping genes; their proteins perform functions that are necessary for basic function, vitality, and maintenance of the cell

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2
Q

regulated genes

A

aka inducible/repressible genes; increased/decreased as cell’s needs change (ex: lac operon and trp operon)

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3
Q

Pribnow box

A

specific regulatory sequence in a promoter region; #s indicate position relative to transcription start sites

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4
Q

sigma factor

A

allows RNA polymerase to bind to DNA; several different types; each one interacts w different promoters & turns of different genes

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5
Q

cis-operating factors

A

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)

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6
Q

every copy of a gene has…

A

…its own promoter region as well as coding sequence

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7
Q

trans-operating factors

A

molecules that bind to regulatory sequences; made by genes on main chromosome and diffuse over

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8
Q

activator proteins

A

trans-operating; bind to sigma factor & inc. transcription

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9
Q

repressor proteins

A

trans-operating; decrease binding of sigma factor and decrease transcription

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10
Q

operon

A

enable organism to activate or inhibit expression of several proteins in response to one regulatory molecule

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11
Q

inducible operons

A

usually off; get turned on when cell needs their proteins (ex: operons that encode enzymes that catabolize nutrient molecules)

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12
Q

repressible operons

A

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)

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13
Q

operon contains:

A

structural genes; promoter; operator; regulator gene

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14
Q

structural gene in operon

A

encodes the proteins

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15
Q

promoter in operon

A

site where molecules that control activity in operon bind; must be bound by RNA polymerase for transcription to occur

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16
Q

operator in operon

A

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

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17
Q

regulator gene in operon

A

not contiguous w operon - it lies at a variable distance from operon; makes a protein that regulates whether operon is on or off

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18
Q

negative control

A

regulator protein is a repressor; when repressor bind to operator of operon, it prevents RNA polymerase from binding to operon’s promoter

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19
Q

positive control

A

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

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20
Q

negative inducible operon

A

regulatory gene makes repressor protein which is made in active form; inducer induces transcription by inactivating repressor and preventing it from binding to operator

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21
Q

positive inducible operon

A

regulatory gene makes activator protein which is made in inactive form; inducer induces transcription by activating activator

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22
Q

negative repressible operon

A

regulatory gene makes repressor protein which is made in inactive form; corepressor represses transcription by activating repressor and enabling it to bind to operator

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23
Q

positive repressible operon

A

regulatory gene makes activator protein which is made in active form; repressor represses transcription by inactivating activator

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24
Q

lac operon

A

negative and positive control; contains structural genes lacZ, lacY, and lacA; inducible: not needed unless lactose is present

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25
Q

lacZ

A

encodes beta-galactosidase which breaks lactose into glucose and galactose

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26
Q

lacY

A

encodes permease which transport lactose into the cell

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27
Q

lacA

A

encodes transacetylase (function unknown)

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28
Q

lacI

A

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

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29
Q

allolactose

A

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

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30
Q

Jacob and Monod

A

discovered mechanism for gene regulation in lac operon using E. coli strains that had mutations in different portions of lac operon

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31
Q

E. Coli experiment

A

using partial diploids w plasmid w own copy of lac operon ; during conjugation donor bacterium gives recipient plasmid copy of lac operon

32
Q

lacY and lacZ

A

work independently; Jacob and Monod

33
Q

lacZ+ lacY- or lacZ- lacY+

A

these genotypes could make both beta-galactosidase and permease; Jacob and Monod

34
Q

mutation in one copy of beta-galactosidase or permease

A

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

35
Q

Z, Y and A genes

A

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

36
Q

mutation in lacI (Jacob and Monod)

A

caused repressor protein to be inactive so transcription was always on (lacI- genotype)

37
Q

lacI+ lacZ-/lacI- lac Z+

A

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

38
Q

superrespressor mutations

A

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

39
Q

lacIs lacZ+/lacI+ lacZ+ or lacIs lacZ+/ lacI- lacZ+

A

does not produce beta-galactosidase even when lactose is present

40
Q

lacOc genotype

A

discovered by Jacob and Monod; prevented repressor from binding - transcription was always on

41
Q

lacOc lacZ+/lacO+ lacZ+

A

produces beta-galactosidase all the time even when lactose is absent because the repressor cannot bind the operator

42
Q

lacI+ lacO+ lacZ-/lac+ lacOc lacZ-

A

produces beta-galactosidase all the time even when lactose is absent bc plasmid’s Oc mutation drives transcription of plasmid’s Z+ gene

43
Q

lacI+ lacO+ lacZ+/lacI+ lacOc lacZ-

A

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

44
Q

cis-acting element

A

lacP- genotype; promoter mutations that prevent the RNA polymerase from binding to the promoter

45
Q

lacI+ lacP+ lacZ+/lacI+ lacP- lacZ+

A

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

46
Q

positive control

A

when glucose is present the bacterium will prefer to use it for energy vs. lactose and will shut down the lac operon

47
Q

activator binding site

A

little way upstream from lac operon

48
Q

glucose present

A

cAMP is low there is little CRP -cAMP complex to bind to activator binding site and transcription stops

49
Q

glucose drops

A

cAMP rises allowing CRP and cAMP to bind resulting in activation of the lac operon

50
Q

trp operon

A

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

51
Q

tryptophan

A

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

52
Q

regulon

A

group of operons that are controlled by activators and repressors that diffuse throughout nucleoid

53
Q

2nd means of negative control of trp

A

can be attenuated

54
Q

leader gene (trpL)

A

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

55
Q

region 1 in trp operon

A

in leader sequence - contains 2 consecutive tryptophan codons

56
Q

regions 2, 3, and 4 in trp operon

A

region 3 can form stem loop structure by binding w region 2 or region 4 but not both (prefers to bind to region 2)

57
Q

region 4

A

RNA polymerase binds just after region 4 to transcribe structural genes

58
Q

regions 3 and 4

A

bind together stem loop blocks RNA polymerase binding site

59
Q

regions 2 and 3

A

bind region 4 is open and RNA polymerase can bind and transcribe the structural genes

60
Q

high tryptophan levels

A

ribosome has no trouble reading through two tryptophan codons bc there is plenty of tryp

61
Q

low tryptophan

A

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

62
Q

archaeal transcription factors

A

can activate and repress transcription (ex: pyrococcus furiosus)

63
Q

TrmBL1 protein

A

represses genes that make transport proteins for other sugar and activates genes for gluconeogenesis (synthesis of glucose)

64
Q

TrmBL1

A

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

65
Q

TrmBL1 uses

A

one binding site to repress transcription and a different binding site to induce transcription

66
Q

signal transduction pathways (2 component regulatory systems) activate transcription factors

A

(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

67
Q

microbes activate genes via quorum sensing

A

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

68
Q

quorum sensing

A

uses diffusible transcription activators

69
Q

virulence factors are activated via quorum sensing

A

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

70
Q

stringent response in bacteria

A

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)

71
Q

translation regulated by antisense RNAs

A

have sequences complementary to certain genes’ mRNAs can bind to these mRNAs and increase/decrease translation depending on which mRNA

72
Q

enabling translation by altering 2ndary structure of mRNA

A

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

73
Q

translation regulation by antisense RNAs

A

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

74
Q

riboswitches

A

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

75
Q

ribozymes and end product inhibition

A

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

Genetics 380 (11 decks)

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