3/18 regulation continued Flashcards
when do we need to stop the trp operon?
when there are high levels or trptophan
is the trp operon anabolic or catabolic
it is anabolic, it makes trptophan
what are the two types of mechanisms for regulation of the trp operon?
the repression with a repressor protein and the formation of attenuating stem loops in the leader regions
what is the leader region
it is a sequence in the trp operon that contains an attenuator sequence
does the leader region encode for a polypeptide
no it does not
when the ribosome does not jump on to the DNA before transcription begins in the trp operon, what will occur?
the early terminator stem loop will form and attenuate the RNA polymerase
when there are high levels of trptophan, how is the trp operon affected?
high levels of trptophan correspond to high amounts of charged tRNAs. the ribosome will be able to move through the trp codons quickly and cause the formation of an early terminator which will attenuate transcription
when there are low levels of trptophan, how is the trp operon affected
low levels of trptophan correspond to low amounts of charged tRNAs. The ribosome will stall on the trp codons and cause the formation of an alternative loops that will allow transcription to continue
operons in catabolic processes will be
inducible (turned on)
in catabolic procsses, what typically acts as an inducer?
the substance to be broken down typically acts as the inducer
ex) allolactose
operons involved in anabolic processes are
repressible (shut off)
in anabolic processes, what acts as the inhibitor/corepressor
the product of the operon acts as the inhibitor/corepressor
ex) trptophan
provide an example of post-transcriptional regulation
anti-sense RNA
what is anti-sense RNA
it is a complementary strand of RNA that exists in the opposite direction of the sense strand and it will block translation by forming a double stranded RNA
how does translational regulation occur most commonly?
initiation of translation will be inhibited by regulatory proteins not allowing the ribosome to bind
what is direct translational regulation
the translational repressor binds next to the ribosome binding site or the start codon and this blocks the ribosome form binding
what is indirect translational regulation?
the regulatory protein will bind outside of the ribosome binding site or start codon and will stabilize a secondary mRNA structure that will prevent initiation
what is a riboswitch
it is an RNA that exists in two secondary conformations
what are the two conformations formed by a riboswitch?
an active conformation and an inactive one that inhibits gene expression
do riboswitches have anything to do with ribosomes?
no, they only refer to RNA
how do riboswitches work?
small molecules will bind to the RNA and cause a conformational change usually through a feedback mechanism
how does bacillus subtilis use a riboswitch
it utilizes riboswitches to trigger attenuation and stop transcription
For bacillus subtilis, how do low concentrations of TPP affect the riboswitch?
an anti terminator stem loop will form and transcription can continue
for bacillus subtilis, how do high concentrations of TPP affect the riboswitch?
TPP binds to the RNA and causes a conformation change where a terminator stem-loop will form and transcription will be attenuated
when do riboswitches occur in E-coli?
they occur in translation
for E. coli, how is the riboswitch affected when TPP concentrations are high
TPP acts as a feedback and will cause a stem-loop that blocks the ribosome binding site, ultimately inhibiting translation.
what is feedback inhibition?
it is a form of post-translational regulation where the final product in the enzymatic pathway will inhibit earlier enzymes to stop the process
in feedback inhibition, how does the product interact with the initial enzyme
it binds allosterically with the enzyme at high concentrations and will change its conformation, ultimately turning it off
what do low affinity binding sites depend on?
they depend on the concentration of the effector molecule. high concentrations result in better binding while low concentrations result in an unbound state
in addition to feedback inhibition, what is the other form of postranslational regulation?
covalent modification of proteins to alter their structure and function
what are three types of post translational covalent modifications that are reversible and alter the proteins function?
phosphorylation, acetylation, methylation
why is gene regulation essential in eukaryotes?
genes need to be expressed at certain developmental periods and there are differences in cell types that may require different gene regulations
what are the types of gene regulation in prokaryotes and eukaryotes
transcription, post-transcription, translation, post translation
what are general transcription factors
proteins that are required for basal level transcription
what transcription factors affect constitutive genes?
only general transcription factors, not regulatory
where are general transcription factors always located?
next to the gene
what are regulatory/specific transcription factors
they regulate the rate of transcription
where are STFs located?
they are trans acting so they come from anywhere in cell, they can also act from far away
what do regulatory transcription factors recognize?
they recognize cis regulatory elements located near the core promoter
what do activator transcription factors bind to?
enhancer DNA binding elements to increase transcription
what do repressor TFs bind to?
silencer DNA elements
are activators and repressors always present in eukaryotes?
no, it depends when the cell needs them but they are not always present
what is combinatorial control
ieukaryotic genes are regulated by a combination of factors
why are nucleosomes relevant in eukaryotic gene regulation
the levels of compaction can affect transcription but this can be altered by regulatory proteins
what are epigenetic modifications
they are reversible changes in gene expression that do not alter the DNA (chromatin structure)
what is up regulation
it increases transcription by the binding of a TF to an enhancer
what is down regulation
it decreases transcription due to the binding of a repressor to a silencer
what does it mean for a DNA regulatory element to be bidirectional
they can regulate promoters that are up or downstream of the element
response elements for specific transcription factors can be located:
anywhere and very far from the promoter
True or false: regulatory transcription factors will directly interact with the core promoter
false, they can but not always
how do TFs directly interact with the core promoter
they can directly interact with TFIID or through coactivators
how does indirect transcription regulation occur?
through a mediator, the repressors will inhibit mediators while activators will stimulate them
what are the three ways regulatory transcription factors are regulated
1) effector molecule binding
2) protein-protein interactions
3) covalent interactions
how do effector molecules regulate TFs
they allosterically bind and induce conformational changes that enable their function
what is a protein-protein interaction
it is a form of TF regulation, where two TFs of the same type (homo) or different (hetero) form dimers that enable them to access the major grooves of the DNA
how does post translational modification of a TF enable transcription?
covalent modifications like phosphorylation can activate them into their roles
for hormones like glucocorticord and gonadoticoids, how are they regulated?
by combinatorial factors
true or false, transcription factors can only interact with one specific regulatory element and regualate one gene
false, they can spread throughout the genome and interact with multiple different genes as long as they have the same recognition sequence
true or false, trasncription factors only interact with one promoter or gene
false, they will coordinately regulate multiple genes and promoters
eukaryotic DNA response elements can be found upstream or downstream from a gene and will influence the gene expression of more than one gene which is similar to bacterial operons but they do so by regulating more than one promoter rather than a single promoter in operons
true
what is epigenetic modification/ ATP-dependent chromatin remodeling
they are dynamic changes to chromatin structure that change their gene expression
what is the closed conformation? open?
closed is when the chromatin are highly condensed and inactive in transcription. The open is when the chromatin are looser and can be actively transcribed
why using ATP, how can chromatin be altered?
the structure of nucleosomes cana be changed to make DNA more accesible
what are the four forms of ATP-dependent chromatin remodeling
- Change in relative positions of a few nucleosomes
2> change in overall spacing
3.) eviction or histone removal
4) replacement of a histone variant
is translational regulation found in eukaryotes
yes
