L4 Gene Regulation Flashcards
example of prokaryotes
bacteria and archaea
examples of eukaryotics
plants, animals, fungi
where is the main site of control for most genes in pro and eukaryotes?
transcription
in eukaryotes - post transcriptional and posttranslational modifications are also involve in gene regulation
in bacteria, when do transcription and translation occur?
simultaneously - geared for speed -
DNA is just free floating in cytoplasm
how are genes regulated in prokaryotes?
- transcription*** mainly used
- mRNA processing
- translation
the amount of what dictates protein synthesis in bacteria?
mRNA - short half life - the amount of transcription taking place dictates how much protein is produced
what are constitutive genes?
house keeping genes low level happens continuously always on essential metabolic functions
what are regulated genes?
only expressed under certain conditions
can be turned on and off
what are the 2 main types of regulatory proteins in bacteria?
- negative regulation
- positive regulation
*genes can use both types of regulation
what is negative regulation?
repressors bind to operator = will prevent RNA polymerase initiation of transcription
what is an operator?
DNA element which is found upstream of a gene
what is positive regulation?
activators bind to operator = allow RNA polymerase to initiate transcription
what has a rapid response to the presence or absence of lactose?
lac operon
glucose is the preferred energy source of bacteria, but they can also use lactose!
when lactose is absent, lac genes are ____
repressed - repressor protein binds to the operator and blocks transcription
when lactose is present, the enzymes responsible for lactose metabolism are ___
induced - lac operon is induced
repressor proteins undergoes a conformational change and can’t bind the operator DNA
RNA polymerase is not blocked = transcription
define positive control
lactose is present AND glucose is absent
what are the components of the lac operon?
proteins coded - structural genes = polycistronic
- lac Z
- lac Y
- lac A
control regions
- lac O
- lac P
regulatory proteins
-Lac I
what does lac Z do?
beta-galatosidase - breaks 1-4 glycosidic link in lactose dissacharide
what does lac Y do?
lactose permease - helps lactose move around cell
what does Lac A do?
transacetylase - unknown function - maybe detox of beta galactosides
what does Lac O do?
operator - main “switch” - binds repressor protein
what does Lac P do?
promoter - binds RNA polymerase
what does Lac I do?
lac repressor - turns structural genes off
define negative control:repression?
transcription occurs only when the repressor FAILS to bind to the operator region
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
when glucose is present is the lac operon expresseD?
NO - positive regulation by glucose
what is the role of cAMP?
hunger signal that allows the expression of genes that break down other sugar including lactose
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
when are cAMP levels increased?
in the absence of glucose, presence of lactose
results in cAMP-CAP = transcription
what is the role of glucose?
inhibit adenyl cyclase = decrease in cAMP
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
what happens if the bacteria produces unneeded proteins?
slows the rate of bacterial cell division
what protein makes up a sizeable fraction in bacteria?
beta galatosidase
E coli and other bacterias are often in competitive environments so…they need to be good at what?
growing quickly and monopolizing resources
what does ‘ mean
mutations in genes that results in non-functional proteins - cannot perform function!
what happens if Lac I’ is present?
non-functional repressor - transcription always ON! because its unable to bind to operator to shut it off
what happens if LacI s is present?
repressor is unable to bind to allolactose and will not dissociate from operator - system always OFF
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
is the trp operon an example of negative or positive regulation?
negative
-operator is blocked by repressor protein when trp is around = no transcription
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
what modulates gene expression?
DNA binding proteins = TF
what are the 2 types of regulatory sequences?
regulated and basal cis element factors
what are DNA sequences required for basal transcription?
promoter regions
what do basal TF bind to?
TATA box – binding of RNA polymerase II
what regulates gene expression in repsonse to hormones and chemicals?
enhancers and response regions
what are the basal cis TF in eukaryotic promoters?
TATA box
CAAT box
GC box
what are the two kinds of TFs?
basal and enhancer TFs
what does basal transcription require?
RNA pol II
TFs - 2A, B, D, E, F, H
TF 2D has TATA binding protein
what do enhancer TF need?
bind to specific DNA sequences (cis elements) to activate or repress transcription
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
what are cis regulatory elements
DNA binding sites
i.e. TF binding sites, enhancer binding sites
what are trans regulatory elements
TFs or enahcner binding PROTEINS
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
where is there competition?
for enhancer sequence binding between activator and repressor proteins
repressor protiens reduce transcription levels through ___
competition
what occurs during quenching
the activator cannot bind to enhancer sequence
repressor proteins can bind to and block the DNA binding domain fo an _____
activator protein
what occurs during blocking
repressor proteins block the activation domain of a TF
repressor proteins can bind to and block the activation domain of an activator protein adn prevent it from interacting with the _____
basal transcription machinery
different genes possess ____ cis regulatory sequences
similar
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
- embryonic development
- tissue specific expression
- response to external stimuli
what are the hypoxia response elements?
HIF 1 alpha
HIF 1 beta
under normal conditions, HIF1a is degraded in the cytoplasm by
oxygen dependent prolyl hydroxylase domain (PHD) and factor inhibiting HIF1 (FIH) hydroxylases
when are PHD and FIH inactive
under hypoxic conditions
what occurs with the HIFs during hypoxia
alpha binds to beta = inducing binding to DNA of target genes carrying a hypoxia-response element (HRE)
HRE allow coordination gene expression in response to ?
anoxia
what type of TF is glucocorticoid receptor
zinc finger
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
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
what is the myc/max system role?
regulatory mechanism for switching between gene activation or repression
when does gene activation occurs wrt myc/max
when both myc/max are made in cells
what does Max prefer as a partner
myc
myc/max are always ___ dimers
hetero (if possible)
when does gene repession (non proliferating cells) result wrt myc/max
when only the max polypeptide is made in the cell
there are ___ dimers when there is no myc
homo= inhibit the transcription of genes
describe the myc?
transactivation domain
cannot form homodimers or bind DNA
describe max?
can form homodimers and bind dan
has no transactivation domain
what is the only heterodimer that can bind DNA and transactivate it
myc-max
overexpression of ___ occurs in many tumors
myc
overepxression of myc disrupts the equilibrium between
activation and repression of genes
what mutations are a cause of hereditary pheochromocytoma
max
what acts as a candidate therapeutic target in the treatment of metastatic pheochromocytoma
myc
how is iron storage regulated
by regulation of mRNA and translation or stability
what is an iron storage protein
ferritin
when does ferritin mRNA translation is blocking allowing free iron
in low iron
when is ferritin protein made and excess iron is stored
in high iron
what is an iron transport protein
transferrin
when is transferrin mRNA more stabilized to allow translation of more transferrin
in low iron
when is transferrin mRNA degraded to reduce protein level
in high iron
what happens without an iron storage mechanism
free iron can facilitate the formation of ROS
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
what are IREs recognized by
trans-acting proteins known as iron regulatory proteins that control mRNA translation rate and stability
there is competition between IRPs and what
40S ribosome for binding to mRNA
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
low iron requires increase in free iron
transferrin receptor expression —
ferritin expression –
on
off
high iron requires the prevention of accumulation of toxic levels of free iron
transferrin receptor expression—
ferritin expression –
off
on
what is RNAi
RNA interface
what does RNAi include
miRNA and siRNA
what processes long pre-mRNAs to mature miRNAs hairpin structures
Drosha
what processes the miRNA hairpin structures to single stranded RNA and initiates the formation of the RNA-induced silencing complex (RISC)
Dicer
microRNAs regulate gene epxression by binding to sequence elements in hte ___
3’ UTR
in cancer tumors what happens to genes that encode miRNas
amplified - their DNA sequence is duplicated
what play an essential role in heart development
miRNA
you can force a cell to make what using recombinant tech
siRNA
slience CCR5 gene in HIV
Bcl-2 in cancer
