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Genetics - BIO 2306 > Ch 16 Control of Gene Expression in Bacteria > Flashcards

Ch 16 Control of Gene Expression in Bacteria Flashcards

1
Q

the mechanisms and systems that control the expression of genes

A

gene regulation

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2
Q

genes that encode proteins that are used in metabolism or biosynthesis or play a structural role in the cell

A

structural genes

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3
Q

genes that encode RNA or proteins that interact with other DNA sequences and affect transcription/translation of the sequences

A

regulatory genes

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4
Q

structural genes that are not regulated and are expressed continually

A

constitutive genes

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5
Q

genes that are not transcribed; affect the expression of DNA sequences to which they’re physically linked to

A

regulatory elements

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6
Q

processes that stimulate gene expression

A

positive control

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7
Q

processes that inhibit gene expression

A

negative control

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8
Q

list the levels of gene regulations

A

alteration of DNA or chromatin structure
regulation of transcription
mRNA processing
regulation of mRNA stability
regulation of translation
posttranslational modification

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9
Q

why is regulation of transcription important in both bacterial and eukaryotic cells?

A

it allows for limited production of a protein early

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10
Q

functional parts of a protein, usually consisting of 60 to 90 amino acids

A

domains

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11
Q

what part of regulatory proteins are responsible for binding to DNA

A

the domains (functional parts)

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12
Q

what are the most common amino acids within a domain that bind with the DNA?

A

asparagine, glutamine, glycine, lysine, and arginine

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13
Q

how do amino acids within a domain of DNA-binding proteins interact with DNA?

A

by forming hydrogen bonds with the bases or interacting with the sugar-phosphate backbone of DNA

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14
Q

characteristic structures found within the binding domain that allow proteins to bind to DNA

A

motifs

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15
Q

motif characterized by two alpha helices and binds into the major groove of the DNA double helix

A

helix-turn-helix

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16
Q

motif characterized by a loop of amino acids with zinc at base, and binds into the major groove of the DNA double helix

A

zinc finger

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17
Q

motif characterized by two perpendicular alpha helices with zinc surrounded by four cysteines; binds into the major groove and DNA backbone

A

steroid receptor

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18
Q

motif characterized by helix of leucine and a basic arm and two leucines interdigitate; binds into two adjacent major grooved

A

leucine zipper

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19
Q

motif characterized by two alpha helices separated by a loop of amino acids; binds into the major groove of the DNA double helix

A

helix-loop-helix

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20
Q

motif characterized by three alpha helices; binds into the major groove of the DNA double helix

A

homeodomain

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21
Q

how are genes regulated in bacteria?

A

bacterial genes w/ related functions are clustered, controlled, and transcribed together into a single mRNA, by using operons

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22
Q

a group of bacterial structural genes that are transcribed together, along with their promoter and additional sequences that control their transcription

A

operon

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23
Q

which level of gene regulation is the most important in bacteria?

A

transcription

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24
Q

describe and label the structure of an operon

A

promoter: upstream of first structural gene, where RNA polymerase binds and starts transcription
operator: where regulator protein binds
structural genes: genes transcribed into mRNA and translated to produce proteins/enzymes

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25
Q

gene that helps control expression of structural genes by encoding the regulatory protein

A

regulatory gene

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26
Q

is the regulator gene part of the operon?

A

no, it is not part of the operon. it has its own promoter

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27
Q

protein that binds to the operator in operon, affecting the rate of transcription

A

regulatory protein

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28
Q

region of operon where regulatory protein binds and affects whether transcription takes place

A

operator

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29
Q

what are the two types of transcriptional control

A

negative control and positive control

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30
Q

transcription control in which regulatory protein is a repressor, which binds to DNA to inhibit transcription

A

negative control

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31
Q

transcription control in which regulatory protein is an activator, which binds to DNA to stimulate transcription

A

positive control

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32
Q

operon in which transcription is normally off and must be turned on

A

inducible operon

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33
Q

operon in which transcription is normally on and must be turned off

A

repressible operon

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34
Q

what does the regulator gene for a negative inducible operon encode for?

A

an active repressor protein

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35
Q

what does the regulator gene for a negative repressible operon encode for?

A

an inactive repressor protein

36
Q

what does the regulator gene for a positive inducible operon encode for?

A

an inactive activator protein

37
Q

what does the regulator gene for a positive repressible operon encode for?

A

an active activator protein

38
Q

small molecule that binds to repressor protein and inactivates it, therefore protein cannot bind and transcription turns on

A

inducer

39
Q

small molecule that binds to repressor protein and activates it, therefore protein can bind and transcription turns off

A

corepressor

40
Q

how does the binding of an inducer or corepressor to a regulatory protein affect it?

A

it alters the proteins shape

41
Q

in a negative inducible operon, if the inducer is absent, what happens?

A

if the inducer is absent, transcription remains off, due to the repressor protein remaining active and binding to the operator

42
Q

what kind of processes do negative inducible operons usually control?

A

they usually control proteins that carry out degradative processes
the proteins synthesized from the operon break down the substrate

43
Q

in a negative repressible operon, if the corepressor is absent, what happens?

A

if the corepressor is absent, transcription remains on, due to the repressor protein being inactive and cannot bind to the operator

44
Q

what kind of processes do negative repressible operons usually control?

A

they usually control proteins that carry out biosynthesis of molecules needed in the cell
the product produced by the proteins synthesized from the operons are always needed by the cell, and operon is only turned off when there’s an adequate amount of the product present

45
Q

in a positive inducible operon, if the inducer is absent, what happens?

A

if the inducer is absent, transcription remains off, due to the activator protein being inactive and cannot bind to the operator

46
Q

in a positive repressible operon, if the corepressor is absent, what happens?

A

if the corepressor is absent, transcription remains on, due to the activator protein being active, binding to the operator

47
Q

what kind of operon is the lac operon? what does it regulate? what are the structural genes and what do they encode?

A

negative inducible operon
regulates lactose metabolism
structural genes:
lacZ - ß-galactosidase
lacY - permease
lacA - transacetylase

48
Q

what is the purpose of the protein lactose permease?

A

since lactose cannot easily diffuse across cell membranes, permease actively transports it

49
Q

what is the purpose of the enzyme ß-galactosidase?

A

ß-galactosidase catalyzes the reaction that breaks down lactose into glucose and galactose, to use as energy sources
also converts lactose into allolactose

50
Q

how is coordinate induction demonstrated in the lac operon, by the presence of lactose?

A

when lactose is present, the rate of synthesis of the protein produces increases

51
Q

what is the inducer molecule in the lac operon

A

allolactose

52
Q

if the lac operon is repressed and no proteins are being produced, how does lactose get into the cell, convert into allolactose in order to turn on transcription?

A

repression is never fully off; when the repressor is bound, only low levels of transcription are performed, which allows some permease to transports small amounts of lactose in, which is converted to allolactose by some ß-galactosidase, which then inactivates the repressor

53
Q

cells that possess two copies of the lac operon, one on a chromosome and another on an extra piece piece of DNA

A

partial diploid

54
Q

what does it mean when some parts of an operon are cis-acting?

A

they are able to control the expression of genes only on the same piece of DNA

55
Q

what does it mean when some parts of an operon are trans-acting?

A

they are able to control the expression of genes on other DNA molecules

56
Q

what are the effect of lacZ & lacY mutations?

A

they affect structure of the proteins (permease and ß-galactosidase), making them nonfunctional; they don’t regulate the synthesis of them

57
Q

if a partial diploid had: lacZ+ lac Y- / lac Z- lac Y+ , would galactosidase and permease still be synthesized?

A

yes, a single functional lacZ+ and lacY+ (despite presence of mutations) are sufficient to produce ß-galactosidase and permease

58
Q

what are the effect of lacI mutations?

A

they are mutations in the regulatory gene, thus affected regulation of protein production

59
Q

describe the affect of lacI- and how it differs from lacI+

A

lacI- : irregular production; the regulatory protein (repressor) would not be synthesized, therefore transcription remains on and proteins are produced all the time
lacI+ : normal production; repressor is synthesized

60
Q

is lacI+ cis- or trans-acting

A

trans-acting

61
Q

describe superrepressors (lacI s)

A

produce defective repressor proteins that could not be inactivated by an inducer, therefore repressor always remains attached to operator, preventing transcription

62
Q

which is dominant? lacI s or lacI+

A

lacI(s) is dominant over lacI+

63
Q

what are the effect of lacO mutations?

A

operator DNA sequence altered and repressor protein cannot bind, therefore transcription transcription is always on

64
Q

which is dominant? lacOc or lacO+

A

lacOc is dominant over lacO+

65
Q

is lacO cis- or trans-acting?

A

lacO is cis-acting

66
Q

what are the effect of lacP mutations?

A

they interfere with binding of RNA polymerase to the promoter, therefore transcription cannot occur

67
Q

is lacP cis-or trans-acting?

A

lacP is cis-acting

68
Q

why do bacteria prefer to metabolize glucose?

A

glucose requires less energy to metabolize than other sugars

69
Q

explain catabolite repression
what type of control is it?

A

genes that participate in metabolism of other sugars are turned off when glucose is present
positive control - when there are low glucose levels, transcription turns on

70
Q

what is CAP? what does it bind with to form a complex?
explain its importance in catabolite repression

A

CAP - catabolite activator protein
forms a complex with cAMP
must bind to DNA first in order for RNA polymerase to bind efficiently to the promoter

71
Q

describe the relationship of concentration of cAMP to glucose, and how they effect transcription

A

concentration of cAMP is inversely proportional to glucose levels
high concentrations of glucose = low cAMP-CAP complexes that bind to DNA –> little transcription
low concentrations of glucose = high cAMP-CAP complexes that bind to DNA –> lots of transcription

72
Q

what in CAP allows RNA polymerase to have better affinity at the promoter?

A

CAP has a helix-turn-helix DNA-binding motif that when it binds to DNA, the DNA helix bends, enabling RNA polymerase to bind

73
Q

what kind of operon is the trp operon? what does it regulate? what do the structural genes encode?

A

negative repressible operon
regulates biosynthesis of the amino acid tryptophan
structural genes: trp E, trp D, trp C, trp B, and trp A –> produce components to convert chorismate into tryptophan

74
Q

describe the trp operon when there are low and high levels of tryptophan

A

when there are low levels of tryptophan, the repressor molecule is inactive and transcription turns on, increasing tryptophan levels
when there are high levels of tryptophan, the repressor molecule is active and transcription turns off

75
Q

describe attenuation

A

transcription begins at the transcription start site but terminates prematurely, before RNA polymerase reaches the structural genes

76
Q

what kind of operons is attenuation associated with?

A

operons that encode enzymes participating in biosynthesis of amino acids

77
Q

what region of the trp operon is responsible for attenuation?

A

the long 5’ UTR region in the trpE gene

78
Q

describe the four regions in the 5’UTR of the trpE and their complementaries

A

region 1 complementary to region 2
region 2 complementary to region 3
region 3 complementary to region 4

79
Q

explain why tryptophan is required for the translation of the 5’UTR region in the trpE gene and how this relates to attenuation?

A

the ribosome binding site is located upstream of region 1
within the coding sequence of region 1, there are two UGG codons, that specify the amino acid tryptophan
tryptophan must be added to the developing amino acid chain
if there are low levels of tryptophan, transcription proceeds to synthesize more tryptophan

80
Q

describe transcription when tryptophan levels are low

A

ribosome binds to 5’ UTR and begins translation as RNA polymerase transcribes downstream
ribosome stops at region 1 at Trp (UGG) codons, since there are low levels of tryptophan, the ribosome stalls
RNA polymerase continues transcription, and region 2 base pairs with region 3, forming antiterminator, preventing termination
transcription continues, and translation of the mRNA into enzymes synthesizes tryptophan

81
Q

secondary structure formed in 5’ UTR when region 2 base pairs with region 3, preventing termination of transcription

A

antiterminator

82
Q

describe transcription when tryptophan levels are high

A

ribosome binds to 5’ UTR and begins translation as RNA polymerase transcribes downstream
ribosome is able to translate region 1 due to abundant tryptophan and keep up with RNA polymerase
hairpin forms by pairing of regions 1 & 2, and hairpin forms between 3 &4, producing the attenuator, and transcription terminates, causing no additional tryptophan to be synthesized

83
Q

secondary structure formed in 5’UTR when region 3 base pairs with region 4, followed by a string of uracil nucleotides, causing termination of transcription

A

attenuator

84
Q

RNA molecules that control gene expression by binding to complementary sequences on mRNA and inhibiting translation

A

antisense RNA

85
Q

describe how antisense RNA affects gene expression

A

a regulator gene is activated to produce an antisense RNA
the antisense RNA pairs with complementary sequence in 5’UTR of target mRNA to inhibit the binding of a ribosome, therefore preventing translation

86
Q

regulatory sequences in mRNA where regulator molecules can bind and affect gene expression by influencing the formation of secondary structures in mRNA

A

riboswitches

87
Q

describe how riboswitches affect gene expression

A

riboswitches fold into secondary structures within the mRNA molecule
when a regulatory protein binds, it may stabilize the structure, and may lead to premature termination of transcription or prevent initiation of translation
when no regulatory protein binds, the riboswitch changes to another structure that allows transcription/translation

Genetics - BIO 2306 (20 decks)

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