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Genetics > L4 Gene Regulation > Flashcards

L4 Gene Regulation Flashcards

1
Q

example of prokaryotes

A

bacteria and archaea

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2
Q

examples of eukaryotics

A

plants, animals, fungi

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3
Q

where is the main site of control for most genes in pro and eukaryotes?

A

transcription

in eukaryotes - post transcriptional and posttranslational modifications are also involve in gene regulation

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4
Q

in bacteria, when do transcription and translation occur?

A

simultaneously - geared for speed -

DNA is just free floating in cytoplasm

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5
Q

how are genes regulated in prokaryotes?

A
  • transcription*** mainly used
  • mRNA processing
  • translation
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6
Q

the amount of what dictates protein synthesis in bacteria?

A

mRNA - short half life - the amount of transcription taking place dictates how much protein is produced

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7
Q

what are constitutive genes?

A 
house keeping genes
low level
happens continuously
always on
essential metabolic functions
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8
Q

what are regulated genes?

A

only expressed under certain conditions

can be turned on and off

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9
Q

what are the 2 main types of regulatory proteins in bacteria?

A
  • negative regulation
  • positive regulation

*genes can use both types of regulation

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10
Q

what is negative regulation?

A

repressors bind to operator = will prevent RNA polymerase initiation of transcription

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11
Q

what is an operator?

A

DNA element which is found upstream of a gene

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12
Q

what is positive regulation?

A

activators bind to operator = allow RNA polymerase to initiate transcription

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13
Q

what has a rapid response to the presence or absence of lactose?

A

lac operon

glucose is the preferred energy source of bacteria, but they can also use lactose!

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14
Q

when lactose is absent, lac genes are ____

A

repressed - repressor protein binds to the operator and blocks transcription

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15
Q

when lactose is present, the enzymes responsible for lactose metabolism are ___

A

induced - lac operon is induced

repressor proteins undergoes a conformational change and can’t bind the operator DNA

RNA polymerase is not blocked = transcription

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16
Q

define positive control

A

lactose is present AND glucose is absent

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17
Q

what are the components of the lac operon?

A

proteins coded - structural genes = polycistronic

  • lac Z
  • lac Y
  • lac A

control regions

  • lac O
  • lac P

regulatory proteins
-Lac I

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18
Q

what does lac Z do?

A

beta-galatosidase - breaks 1-4 glycosidic link in lactose dissacharide

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19
Q

what does lac Y do?

A

lactose permease - helps lactose move around cell

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20
Q

what does Lac A do?

A

transacetylase - unknown function - maybe detox of beta galactosides

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21
Q

what does Lac O do?

A

operator - main “switch” - binds repressor protein

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22
Q

what does Lac P do?

A

promoter - binds RNA polymerase

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23
Q

what does Lac I do?

A

lac repressor - turns structural genes off

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24
Q

define negative control:repression?

A

transcription occurs only when the repressor FAILS to bind to the operator region

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25
Q

why is glucose the preferred energy source of bacteria?

A

more efficient metabolism
bacteria will multiply faster with glucose

using lactose, it takes the bacteria longer to divide

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26
Q

when glucose is present is the lac operon expresseD?

A

NO - positive regulation by glucose

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27
Q

what is the role of cAMP?

A

hunger signal that allows the expression of genes that break down other sugar including lactose

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28
Q

what does cAMP bind to and activate?

A

catabolite gene activator protein (CAP)
aka
cAMP regulatory protein

active cAMP-CAP binds to lacP and = transcription activation

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29
Q

when are cAMP levels increased?

A

in the absence of glucose, presence of lactose

results in cAMP-CAP = transcription

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30
Q

what is the role of glucose?

A

inhibit adenyl cyclase = decrease in cAMP

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31
Q

when is there low transcription of structural genes?

A

when glucose is present and lactose is present because glucose is preferred - but the glucose is inhibiting the cAMP which is cutting out the transcription using lactose

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32
Q

what happens if the bacteria produces unneeded proteins?

A

slows the rate of bacterial cell division

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33
Q

what protein makes up a sizeable fraction in bacteria?

A

beta galatosidase

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34
Q

E coli and other bacterias are often in competitive environments so…they need to be good at what?

A

growing quickly and monopolizing resources

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35
Q

what does ‘ mean

A

mutations in genes that results in non-functional proteins - cannot perform function!

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36
Q

what happens if Lac I’ is present?

A

non-functional repressor - transcription always ON! because its unable to bind to operator to shut it off

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37
Q

what happens if LacI s is present?

A

repressor is unable to bind to allolactose and will not dissociate from operator - system always OFF

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38
Q

what is teh trp operon?

A

code for the production of tryptophan

unlike lac operon - trp operon is inhibited by tryptophan

trp level low = ON to produce more!
trp levels high = OFF

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39
Q

is the trp operon an example of negative or positive regulation?

A

negative

-operator is blocked by repressor protein when trp is around = no transcription

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40
Q

of the several potential sites for regulation of gene expression in eukaryotes, what is the most important point of control for eukaryotic gene regulation?

A

initiation of transcription

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41
Q

what modulates gene expression?

A

DNA binding proteins = TF

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42
Q

what are the 2 types of regulatory sequences?

A

regulated and basal cis element factors

43
Q

what are DNA sequences required for basal transcription?

A

promoter regions

44
Q

what do basal TF bind to?

A

TATA box – binding of RNA polymerase II

45
Q

what regulates gene expression in repsonse to hormones and chemicals?

A

enhancers and response regions

46
Q

what are the basal cis TF in eukaryotic promoters?

A

TATA box
CAAT box
GC box

47
Q

what are the two kinds of TFs?

A

basal and enhancer TFs

48
Q

what does basal transcription require?

A

RNA pol II
TFs - 2A, B, D, E, F, H
TF 2D has TATA binding protein

49
Q

what do enhancer TF need?

A

bind to specific DNA sequences (cis elements) to activate or repress transcription

50
Q

what does it mean that TFs are trans acting factors?

A

transcribed at a different location on the genome
translated in the cytosol
bind to DNA at the cis elements

51
Q

what are cis regulatory elements

A

DNA binding sites

i.e. TF binding sites, enhancer binding sites

52
Q

what are trans regulatory elements

A

TFs or enahcner binding PROTEINS

53
Q

what are the 3 modes of action of TFs acting as repressors?

A

competition - bind enhancer sequence on DNA and compete with enhancer proteins = reduce transcription

quenching - bind to enhancer protein and block DNA binding site

blocking - bind to enhancer proteins activating domain and prevent enhancer binding to general TFs

54
Q

where is there competition?

A

for enhancer sequence binding between activator and repressor proteins

55
Q

repressor protiens reduce transcription levels through ___

A

competition

56
Q

what occurs during quenching

A

the activator cannot bind to enhancer sequence

57
Q

repressor proteins can bind to and block the DNA binding domain fo an _____

A

activator protein

58
Q

what occurs during blocking

A

repressor proteins block the activation domain of a TF

59
Q

repressor proteins can bind to and block the activation domain of an activator protein adn prevent it from interacting with the _____

A

basal transcription machinery

60
Q

different genes possess ____ cis regulatory sequences

A

similar

61
Q

different genes providing similar cis regulatory sequences provides what how?

A

spatial and termporal coordination of gene regulation

by expressing TF in specific cells, particular times during embryonic development, or under certain environmental conditions

  1. embryonic development
  2. tissue specific expression
  3. response to external stimuli
62
Q

what are the hypoxia response elements?

A

HIF 1 alpha

HIF 1 beta

63
Q

under normal conditions, HIF1a is degraded in the cytoplasm by

A

oxygen dependent prolyl hydroxylase domain (PHD) and factor inhibiting HIF1 (FIH) hydroxylases

64
Q

when are PHD and FIH inactive

A

under hypoxic conditions

65
Q

what occurs with the HIFs during hypoxia

A

alpha binds to beta = inducing binding to DNA of target genes carrying a hypoxia-response element (HRE)

66
Q

HRE allow coordination gene expression in response to ?

A

anoxia

67
Q

what type of TF is glucocorticoid receptor

A

zinc finger

68
Q

what is the function of the glucocorticoid receptor

A

up regs the expression of antiinflammatory proteins in nucleus

represses the expression of pro-inflammatory proteins in hte cytosol

69
Q

where are HREs found? what is significant about this

A

promoter and regulatory sequences of many genes

allows for coordinated gene regulation at many sites in genome

70
Q

what is the myc/max system role?

A

regulatory mechanism for switching between gene activation or repression

71
Q

when does gene activation occurs wrt myc/max

A

when both myc/max are made in cells

72
Q

what does Max prefer as a partner

A

myc

73
Q

myc/max are always ___ dimers

A

hetero (if possible)

74
Q

when does gene repession (non proliferating cells) result wrt myc/max

A

when only the max polypeptide is made in the cell

75
Q

there are ___ dimers when there is no myc

A

homo= inhibit the transcription of genes

76
Q

describe the myc?

A

transactivation domain

cannot form homodimers or bind DNA

77
Q

describe max?

A

can form homodimers and bind dan

has no transactivation domain

78
Q

what is the only heterodimer that can bind DNA and transactivate it

A

myc-max

79
Q

overexpression of ___ occurs in many tumors

A

myc

80
Q

overepxression of myc disrupts the equilibrium between

A

activation and repression of genes

81
Q

what mutations are a cause of hereditary pheochromocytoma

A

max

82
Q

what acts as a candidate therapeutic target in the treatment of metastatic pheochromocytoma

A

myc

83
Q

how is iron storage regulated

A

by regulation of mRNA and translation or stability

84
Q

what is an iron storage protein

A

ferritin

85
Q

when does ferritin mRNA translation is blocking allowing free iron

A

in low iron

86
Q

when is ferritin protein made and excess iron is stored

A

in high iron

87
Q

what is an iron transport protein

A

transferrin

88
Q

when is transferrin mRNA more stabilized to allow translation of more transferrin

A

in low iron

89
Q

when is transferrin mRNA degraded to reduce protein level

A

in high iron

90
Q

what happens without an iron storage mechanism

A

free iron can facilitate the formation of ROS

91
Q

what is the iron responsive element

A

particular haripin sutrcture located int he 5’ untranslated region or in the 3’ untranslated region of various mRNAs coding for proteins involved in cellular iron metabolism

92
Q

what are IREs recognized by

A

trans-acting proteins known as iron regulatory proteins that control mRNA translation rate and stability

93
Q

there is competition between IRPs and what

A

40S ribosome for binding to mRNA

94
Q

binding of what to IRE preventing binding of ribosome

A

IRP-1 or IRP-2

no protein is produced and iron is not stored and is free for use in the cell

95
Q

low iron requires increase in free iron
transferrin receptor expression —
ferritin expression –

A

on

off

96
Q

high iron requires the prevention of accumulation of toxic levels of free iron
transferrin receptor expression—
ferritin expression –

A

off

on

97
Q

what is RNAi

A

RNA interface

98
Q

what does RNAi include

A

miRNA and siRNA

99
Q

what processes long pre-mRNAs to mature miRNAs hairpin structures

A

Drosha

100
Q

what processes the miRNA hairpin structures to single stranded RNA and initiates the formation of the RNA-induced silencing complex (RISC)

A

Dicer

101
Q

microRNAs regulate gene epxression by binding to sequence elements in hte ___

A

3’ UTR

102
Q

in cancer tumors what happens to genes that encode miRNas

A

amplified - their DNA sequence is duplicated

103
Q

what play an essential role in heart development

A

miRNA

104
Q

you can force a cell to make what using recombinant tech

A

siRNA

slience CCR5 gene in HIV
Bcl-2 in cancer

Genetics (15 decks)

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