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BIOL 240 > Module 8 > Flashcards

Module 8 Flashcards

Regulation

1
Q

define: replication

A

DNA copies itself

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2
Q

define: transcription

A

DNA converts to RNA

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3
Q

define: translation

A

proteins are synthesized from RNA

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4
Q

how does RNA polymerase recognize the genes it will transcribe

A

has both a core enzyme and a sigma factor

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5
Q

describe the modularity of sigma factors

A
  • they can be exchanged for one another
  • each sigma factor is responsible for a number of relevant genes
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6
Q

what is the purpose of sigma factors

A

they recognize and initiate transcription of genes, guide RNA polymerase to promoter regions

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7
Q

define: holoenzyme

A

RNA polymerase + sigma factor

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8
Q

what are the two mechanisms of transcription termination in bacteria

A
  • rho-dependent
  • rho-independent
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9
Q

describe rho-dependent termination

A
  • a rho protein follows RNA pol
  • when the protein catches up it removes RNA pol from the DNA strand
  • happens when the pol reaches the GC-rich termination sequence
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10
Q

describe rho-independent termination

A
  • termination sequence leads to RNA hairpin loop formation, causing RNA pol to disassociate from the DNA
  • hairpin duplex restricts forward movement of RNA pol
  • hairpin made of guanines & cytosines
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11
Q

what is the high-GC hairpin region followed by

A

a row of adenosines

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12
Q

what does the Shrine-Dalgarno sequence do

A

orients the ribosome on the mRNA strand

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13
Q

what does it mean for a mRNA strand to be polycistronic

A

it can code for more than one gene

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14
Q

what allows an mRNA strand to be polycistronic

A

multiple Shrine-Dalgarno sequences

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15
Q

why can transcription and translation occur simultaneously in bacteria

A

there’s no nucleus separation

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16
Q

why do genes need to be regulated

A

expressing all genes is too expensive, allows microorganisms to respond to environmental stimuli

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17
Q

define: inducible genes

A

genes subject to regulation

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18
Q

define: constitutive genes

A

genes that are always on

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19
Q

what are some levels of regulation

A
  • level of mRNA production
  • conversion of mRNA to proteins during translation
  • level of protein activity (modifications to proteins)
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20
Q

what are 2 modifications at the post-translational level

A
  • covalent modifications
  • allosteric regulation
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21
Q

describe how covalent modifications work

A
  • proteins can be phosphorylated, acetylated, methylated, or glycosylated
  • their conformations get changed
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22
Q

how does allosteric regulation work

A
  • involves an effector molecule binding to a protein and changing its activity
  • binds to a second site of the enzyme, not the active site
  • can either activate or inhibit
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23
Q

which form of post-translational protein regulation are multi-step synthesis pathways usually associated with

A

allosteric regulation

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24
Q

what often serves as an effector molecule in multi-step synthesis pathways

A

end product of the pathway, inhibits the first enzyme of the pathway

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25
Q

what parts of the bacterial mRNA are regulatory elements

A
  • activator binding site
  • promoter
  • operator
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26
Q

what regions are in an operon aside from the regulatory elements

A

structural genes

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27
Q

what is the relationship between an operon and mRNA

A

an operon is a DNA structure that gives rise to mRNA

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28
Q

what does negative control of transcription involve

A
  • allosteric protein preventing mRNA synthesis
  • blocking RNA polymerase from proceeding
  • repression or induction of transcription
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29
Q

what does repression of transcription look like

A
  • repressor protein is “ON”
  • repressor protein binds to the operator
  • RNA pol is blocked
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30
Q

what enzymes are usually associated with repression of transcription

A

anabolic enzymes (e.g. amino acid synthesis) [minority of enzymes]

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31
Q

what does induction of transcription look like

A
  • repressor protein can’t bind to the operator
  • repressor is removed
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32
Q

what enzymes are usually associated with induction of transcription

A

catabolic enzymes

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33
Q

define: co-repressor

A

effector molecule that changes repressor shape to enable it to bind to the operator

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34
Q

define: co-inducer

A

effector molecule that changes repressor shape so that it falls off the operator

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35
Q

which region of the operon does postivite control of transcription involve

A

activator binding site

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36
Q

describe the process of positive control of transcription

A
  • effector molecule binds to an allosteric activator protein
  • activator binds to activator binding site
  • transcription is initiated
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37
Q

where is positive control located on the operon

A

upstream of the promoter, doesn’t have to be directly upstream

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38
Q

what is an example where positive control would be used

A

use of an alternative carbon source (e.g. maltose)

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39
Q

why are an activator and activator binding site required for positively controlled promoters

A

the promoters only weakly bind RNA polymerase, the activate changes DNA structure to inscrease the binding affinity

40
Q

since activator proteins are allosteric proteins, what do they require

A

co-activate effector molecule

41
Q

can bacterial genes and operons use multiple methods of regulation

A

yes, they can use either one or both

42
Q

what does the lac operon encode

A

the ability to use lactose as a carbon source

43
Q

define: diauxic growth

A

two phases of growth

44
Q

why is the lac operon regulated

A

the use of glucose is favored above the use of lactose

45
Q

what does the lacZ gene encode

A

the β-galactosidase that cleaves lactose into glucose and galactose

46
Q

what does the lacY gene encode

A

a permease, enables lactose to enter the cell

47
Q

what does the lacA gene encode

A

β-galactoside transacetylase, function unknown

48
Q

what is the repressor protein involved in negative control of the lac operon

A

Lacl

49
Q

what happens with the lac operator under “normal” conditions - sufficient glucose

A

Lacl repressor is bound to the lac operator

50
Q

what is produced in addition to glucose & galactorse when β-galactosidase cleaves lactose

A

allolactose, an isomer of lactose

51
Q

what type of effector molecule does allolactose act as in terms of negative control of transcription

A

a co-inducer, binds to Lacl & removes it from the operator or prevent binding in the first place

52
Q

when is cyclic AMP prevented from being produced

A

when glucose is present

53
Q

what type of effector molecule does cAMP act as and what does it act on

A

acts as a co-activator to the lac operon’s activator protein (cAMP receptor protein, CRP)

54
Q

describe the conditions needed for both controls of the lac operon to be activated

A

negative control - presence of lactose
positive control - absence of glucose

55
Q

what is an example of negative control - repression

A

the tryptophan (trp) operon which is responsible for make the amino acid tryptophan

56
Q

what acts as the co-repressor for the trp operon

A

tryptophan itself

57
Q

define: attenuation

A

a form of transcriptional regulation that interrupts transcription after it starts but before its termination

58
Q

in the tryptophan operon, what’s the first region transcribed

A

the leader sequence (trpL)

59
Q

why can’t attenuation occur in eukaryotes

A

the ability for transcription and translation to occur simulatenously is required

60
Q

what happens when there sufficient tryptophan in the cell [attenuation]

A
  • region 1 is rapidly processed by ribosome (requires tryptophan)
  • regions 1 and 2 are occupied by the ribosome
  • regions 3 and 4 form a stable “hairpin” - terminator loop for rho-independent termination
  • RNA polymerase falls off
61
Q

what happens when there is not enough tryptophan in the cell [attenuation]

A
  • the ribosome is stalled in region 1
  • region 2 and 3 form a stronger hairpin
  • this hairpin prevents terminator loop from forming
  • RNA polymerase continues to transcribe structural genes
62
Q

define: quorum sensing

A

how a group of individuals assess whether there are sufficient individuals (i.e. a quorum) in order to carry out some process of interest

63
Q

how do bacteria assess sufficient population density

A

through chemical signalling

64
Q

define: autoinducer molecules

A

chemicals released for quorum sensing purposes that act as co-activator effector molecules

65
Q

describe how quorum sensing is positive feedback

A

detecting autoinducers => increase of some autoinducers by increased gene expression of signalling genes

66
Q

what is the purpose of quorum sensing

A

to coordinate expensive processes

67
Q

what is an example of the use of quorum sensing

A

Bobtail Squid and Aliivibrio fischeria

68
Q

what are the components in two-component regulatory systems

A
  • sensing component
  • response component
69
Q

what is the purpose of the sensing component [two-component regulatory systems]

A

membrane-associated protein that detects environmental signals

70
Q

what does the response component do [two-component regulatory systems]

A

changes gene expression & possibly other phenotypic behaviours in response to the signal

71
Q

what is the mechanism of signalling in two-component regulatory systems

A

via chemical signal transduction

72
Q

what type of protein are membrane-associated sensor proteins

A

histidine protein kinase (HPK)
- “kinase” - adds phosphate groups to itself or has phosphate groups added
- “histidine” - the histidine residue is phosphorylated

73
Q

what is the signal in a two-component regulatory system

A

phosphorylation event

74
Q

what does the response regulator receive from the HPK

A

it receives a phosphate, attached to an aspartate residue

75
Q

how is the ability of the response regulator limited

A

the phosphate group can be removed

76
Q

what is autophosphatase activity

A

ability for a protein to desphosphorylate themselves [context or response regulators]

77
Q

what are ways to remove phosphate groups

A
  • autophophatase activity
  • instability of the phophate-aspartate bond
  • use of other proteins
78
Q

what form of transcription regulation are two-component regulatory systems responsible for

A

negative control, positive control, or both

79
Q

what does Agrobacterium tumefaciens regulate through a two-component regulatory system

A

it’s virulence

80
Q

when are vir genes found on the Ti plasmid expressed [Agrobacterium tumefaciens]

A

conditions similar to a plant wound site

81
Q

what proteins are required for expression of the other virulence genes in Agrobacterium tumefaciens

A

VirA - sensor kinase
VirG - response regulator

82
Q

what is chemotaxis an example of in terms of regulation

A

modification of a two-component regulatory system

83
Q

what are the 3 steps to chemotaxis

A
  1. response to an attractant or repellant signal
  2. control of flagellar rotation
  3. adaptation
84
Q

what are the membrane-associated proteins in chemotaxis

A

methyl-accepting chemotaxis proteins (MCPs)
they aren’t kinases themselves, instead they’re associated with sensor kinases

85
Q

define: regulon

A

set of genes that are coordinated together and respond to the same regulatory system

86
Q

define: catabolite repression

A

shutdown of several systems that utilize various nutrients when glucose is present

87
Q

define: SOS response system

A

multigene system for wide-scale DNA repair in response to serious DNA damage

88
Q

what are the most important proteins regulating the SOS response regulon

A

RexA and LexA

89
Q

describe: LexA

A
  • repressor protein responsible for negative control of transcription
  • normally bound to different genes & operons (over 40 different inducible genes)
  • normally present at low levels sufficient to prevent the transcription of these genes
90
Q

describe: RecA

A
  • always present at low concentrations in a cell
  • binds to single-stranded DNA
  • has the ability to cleave LexA
91
Q

what happens when LexA is cleaved by RecA

A
  • LexA can no longer bind to operators
  • results in high levels of SOS-gene expression that produces repair proteins and polymerases
92
Q

what is DNA polymerase made up of (holoenzyme)

A

the polymerase enzyme and its associate sigma factors

93
Q

what is the default sigma factor of RNA polymerase in E. coli

A

sigma-70, recognizes most of the promoters

94
Q

what is the purpose of sigma-54

A

regulation of nitrogen utilization genes

95
Q

what is the purpose of sigma-32

A

heat shock protein gene regulator

96
Q

what is the purpose of sigma-38

A

general stress response gene regulator

BIOL 240 (12 decks)

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