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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
why is glucose the preferred energy source of bacteria?
more efficient metabolism bacteria will multiply faster with glucose using lactose, it takes the bacteria longer to divide
26
when glucose is present is the lac operon expresseD?
NO - positive regulation by glucose
27
what is the role of cAMP?
hunger signal that allows the expression of genes that break down other sugar including lactose
28
what does cAMP bind to and activate?
catabolite gene activator protein (CAP) aka cAMP regulatory protein active cAMP-CAP binds to lacP and = transcription activation
29
when are cAMP levels increased?
in the absence of glucose, presence of lactose results in cAMP-CAP = transcription
30
what is the role of glucose?
inhibit adenyl cyclase = decrease in cAMP
31
when is there low transcription of structural genes?
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
32
what happens if the bacteria produces unneeded proteins?
slows the rate of bacterial cell division
33
what protein makes up a sizeable fraction in bacteria?
beta galatosidase
34
E coli and other bacterias are often in competitive environments so...they need to be good at what?
growing quickly and monopolizing resources
35
what does ' mean
mutations in genes that results in non-functional proteins - cannot perform function!
36
what happens if Lac I' is present?
non-functional repressor - transcription always ON! because its unable to bind to operator to shut it off
37
what happens if LacI s is present?
repressor is unable to bind to allolactose and will not dissociate from operator - system always OFF
38
what is teh trp operon?
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
39
is the trp operon an example of negative or positive regulation?
negative | -operator is blocked by repressor protein when trp is around = no transcription
40
of the several potential sites for regulation of gene expression in eukaryotes, what is the most important point of control for eukaryotic gene regulation?
initiation of transcription
41
what modulates gene expression?
DNA binding proteins = TF
42
what are the 2 types of regulatory sequences?
regulated and basal cis element factors
43
what are DNA sequences required for basal transcription?
promoter regions
44
what do basal TF bind to?
TATA box -- binding of RNA polymerase II
45
what regulates gene expression in repsonse to hormones and chemicals?
enhancers and response regions
46
what are the basal cis TF in eukaryotic promoters?
TATA box CAAT box GC box
47
what are the two kinds of TFs?
basal and enhancer TFs
48
what does basal transcription require?
RNA pol II TFs - 2A, B, D, E, F, H TF 2D has TATA binding protein
49
what do enhancer TF need?
bind to specific DNA sequences (cis elements) to activate or repress transcription
50
what does it mean that TFs are trans acting factors?
transcribed at a different location on the genome translated in the cytosol bind to DNA at the cis elements
51
what are cis regulatory elements
DNA binding sites i.e. TF binding sites, enhancer binding sites
52
what are trans regulatory elements
TFs or enahcner binding PROTEINS
53
what are the 3 modes of action of TFs acting as repressors?
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
where is there competition?
for enhancer sequence binding between activator and repressor proteins
55
repressor protiens reduce transcription levels through ___
competition
56
what occurs during quenching
the activator cannot bind to enhancer sequence
57
repressor proteins can bind to and block the DNA binding domain fo an _____
activator protein
58
what occurs during blocking
repressor proteins block the activation domain of a TF
59
repressor proteins can bind to and block the activation domain of an activator protein adn prevent it from interacting with the _____
basal transcription machinery
60
different genes possess ____ cis regulatory sequences
similar
61
different genes providing similar cis regulatory sequences provides what how?
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
what are the hypoxia response elements?
HIF 1 alpha | HIF 1 beta
63
under normal conditions, HIF1a is degraded in the cytoplasm by
oxygen dependent prolyl hydroxylase domain (PHD) and factor inhibiting HIF1 (FIH) hydroxylases
64
when are PHD and FIH inactive
under hypoxic conditions
65
what occurs with the HIFs during hypoxia
alpha binds to beta = inducing binding to DNA of target genes carrying a hypoxia-response element (HRE)
66
HRE allow coordination gene expression in response to ?
anoxia
67
what type of TF is glucocorticoid receptor
zinc finger
68
what is the function of the glucocorticoid receptor
up regs the expression of antiinflammatory proteins in nucleus represses the expression of pro-inflammatory proteins in hte cytosol
69
where are HREs found? what is significant about this
promoter and regulatory sequences of many genes | allows for coordinated gene regulation at many sites in genome
70
what is the myc/max system role?
regulatory mechanism for switching between gene activation or repression
71
when does gene activation occurs wrt myc/max
when both myc/max are made in cells
72
what does Max prefer as a partner
myc
73
myc/max are always ___ dimers
hetero (if possible)
74
when does gene repession (non proliferating cells) result wrt myc/max
when only the max polypeptide is made in the cell
75
there are ___ dimers when there is no myc
homo= inhibit the transcription of genes
76
describe the myc?
transactivation domain cannot form homodimers or bind DNA
77
describe max?
can form homodimers and bind dan has no transactivation domain
78
what is the only heterodimer that can bind DNA and transactivate it
myc-max
79
overexpression of ___ occurs in many tumors
myc
80
overepxression of myc disrupts the equilibrium between
activation and repression of genes
81
what mutations are a cause of hereditary pheochromocytoma
max
82
what acts as a candidate therapeutic target in the treatment of metastatic pheochromocytoma
myc
83
how is iron storage regulated
by regulation of mRNA and translation or stability
84
what is an iron storage protein
ferritin
85
when does ferritin mRNA translation is blocking allowing free iron
in low iron
86
when is ferritin protein made and excess iron is stored
in high iron
87
what is an iron transport protein
transferrin
88
when is transferrin mRNA more stabilized to allow translation of more transferrin
in low iron
89
when is transferrin mRNA degraded to reduce protein level
in high iron
90
what happens without an iron storage mechanism
free iron can facilitate the formation of ROS
91
what is the iron responsive element
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
what are IREs recognized by
trans-acting proteins known as iron regulatory proteins that control mRNA translation rate and stability
93
there is competition between IRPs and what
40S ribosome for binding to mRNA
94
binding of what to IRE preventing binding of ribosome
IRP-1 or IRP-2 no protein is produced and iron is not stored and is free for use in the cell
95
low iron requires increase in free iron transferrin receptor expression --- ferritin expression --
on | off
96
high iron requires the prevention of accumulation of toxic levels of free iron transferrin receptor expression--- ferritin expression --
off | on
97
what is RNAi
RNA interface
98
what does RNAi include
miRNA and siRNA
99
what processes long pre-mRNAs to mature miRNAs hairpin structures
Drosha
100
what processes the miRNA hairpin structures to single stranded RNA and initiates the formation of the RNA-induced silencing complex (RISC)
Dicer
101
microRNAs regulate gene epxression by binding to sequence elements in hte ___
3' UTR
102
in cancer tumors what happens to genes that encode miRNas
amplified - their DNA sequence is duplicated
103
what play an essential role in heart development
miRNA
104
you can force a cell to make what using recombinant tech
siRNA slience CCR5 gene in HIV Bcl-2 in cancer

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