Exam 2 pt2 Flashcards
constitutive genes
- unregulated
- constant levels of expressionn
- code proteins that are needed for survival
benefit of gene regulation is that
saving energy from only making proteins when they are needed
gene regulation is important to processes like
- metabolism
- response to stress
- cell division
regulation can happen during
transcription or translation or posttranslation
attenuation
gene regulation during transcription where it is stoped right after beginning bc of protein binding
translational repressor proteins can
bind to the mRNA and prevent translation from starting
riboswitches can
produce an mRNA conformation that prevents translation from starting
antisense RNA can
bind to mRNA and prevent translation from starting
post translational modification examples
2
- feedback inhibition
- covalent modifications
3 examples of translation regulation of gene expression
- translational repressor mproteins
- riboswitches
- antisense RNA
most common way of gene regulation
influencing rate of transcription (RNA synthesis)
repressors bind to DNA and
inhibit transcription
activators bind to _ and
DNA and increase transcription
negative control
transcriptional regulation by repressor proteins
positive control
regulation by activator proteins
small effector molecules bind to
regulatory proteins, not DNA
inducers
bind to and effect
- small regulatory molecule
- bind to activators and increase binding to DNA
- bind to repressors and decrease binding of DNA
- increase transcription
corepressors
bind to and effect
- bind to repressors and cause DNA binding
- decrease transcription
inhibitors
bind to and effect
- bind to activators and prevent DNA binding
- decrease transcription
repressible genes are regulated by
- corepressors
- inhibitors
inducers cause a _ in _ to prevent binding
conformational change in repressor proteins to prevent binding
corepressors cause a _ in _ to increase binding
conformational change in repressor proteins to increase binding
decrease transcription
corepressors cause a _ in _ to increase binding
conformational change in repressor proteins to increase binding
decrease transcription
enzyme adaptation
when an enzyme appears in the cell only after the cell is exposed to the enzyme substrate
operon is a
regulatory unit that consists of protein encoding genes under control of one promoter
polycistronic mRNA contains _ and is encoded by _
contains coding sequence for two or more protein genes and is encoded under control of operon
the lac operon consists of DNA regulatory elements…
list and what each binds
- promoter (binds RNA polymerase)
- operator (binds lac repressor protein)
- CAP site (binds CAP)
lac operon has protein encoding genes for…
list
- lac Z (beta galactogase)
- lacY (permease)
- lacA (transacetylase)
lacZ encodes _ , which _ function
- encodes beta galactosidase
- ^ cleaves lactose to allolactose
lacY encodes _ which _ function
- encodes lactose permease
- ^ required for transport of lactose
lacA encodes _ which _ function
- encodes galactoside transacetylase
- ^ covalently modifies lactose and analogs
- prevents toxic buildup of lactose
What are the two conditions for the efficient utilization of lactose?
lactose is present
What is LacI? Is lacI included in the lac operon?
No, it is not included in the lac operon. LacI has its own promoter, is constantly expressed at low levels (10 proteins per cell) and encodes the lac repressor. Negatively regulates the lac operon.
Where does the lac repressor bind? How does this prevent transcription?
Lac operator. RNA polymerase cannot access the promoter when the repressor is bound.
Where does CAP bind? What is CAP’s coactivator?
It binds to CAP site. cAMP is an inducer that allows LacI to bond. Binding of CAP is necessary for transcription to occur.
allolactose binds to _ and _
lac repressor and prevents the repressor from binding to DNA
operon is on
when there is no lactose in enviroments,
there is no allolactose so the repressor is binded and the lac operon is off
when lactose is present
beta galactosidase makes allolactose, which binds the repressor and prevents it from binding to DNA, which turns on lac operon
the lacI gene encodes _ and is _
lac repressor and is always on
the lacI- mutation
eliminates the function of the lac repressor
in the merozygote, in the absence of lactose
what does indicate
- both lac operons are repressed by >1%
- this inndicates that the repressor on the F factor can repress both operons
in the presence of lactose, in the merozygote
- both lac operons are induced
- lac operon activity is 220%
trans effect
genetic regulation between genes that are not physically next to each other
* mediated by genes that encode regalatory proteins
the lac repressor is a cis or trans effect
trans
cis effect
- DNA sequence must be next to the gene it regulates
- mediated by sequences that bind regulatory proteins
the lac operator is a cis or trans element
cis
a mutation in a trans element is _ by the introduction of a second normal gene
complemented
* the normal copy fixes the problem
a mutation in a cis acting element is _ by the introduction of another normal gene
- is not affected
- normal copy of the gene does not fix the problem since its not right next to the mutated copy
a mutated gene with a normal gene, an enzyme that has double expression in the presence of lactose but no expression without lactase is what type of effect
trans effect
the lac operon regulation by an activator is called
catabolite repression
when exposed to both lactose and glucose, e coli
uses the glucose first and lactose is catabolitely repressed
* lac operon not expressed until glucose is depleted
diauxic growth
sequential use of two sugars by a bacteria
the small effector molecule in catabolite repression of lac operon is
cAMP
in the lac operon, cAMP binds to
catabolite activator protein (CAP)
the cAMP-CAP complex is an example of transcritoinal regulation that is _ and under _ control
inducible and under positive control
the cAMP-CAP complex binds _ and _
binds CAP site and increases transcription
why does transcription of lac operon decrease in presence of glucose
- Glucose inhibits adenylyl cyclase
- cAMP levels go down
- cAMP-CAP complex cannot bind to CAP site
- transcription rate decreases
when there is no lactose or glucose but high cAMP, transcription is _
and why
low
* repressor bound bc no allolactose
* cAMP-CAP bound but repressor downstream
order of CAP site, promoter and operator on lac
- CAP site
- Promoter
- Operator (binds repressor)
lactose and glucose present, transcription is _
medium low
* no cAMP so no CAP binding
* but no repressor bound since allolactose present
glucose present but no lactose, transcription is
and why
transcription is very low
* no CAP binding bc glucose
* repressor bound bc no allolactose
the lac operon has _ operator sites for the lac repressor
3
where are the operator sites for the lac operon
- O1 next to the promoter
- O2 downstream of lacZ coding genes
- O3 slightly upstream of promoter
the lac repressor must always have binding at operator _ and should _ for good repression
always binding at operator 1 and should have two repressors for good repression
why is binding of lac repressors to two sites required
so that the lac repressors can use its domains to bind both the operator sites and form a loop that inhibits transcription
lac repressor structure and why important
lac repressor is a tetramer that uses 2 domains each to bind different operator sites to form a loop that inhibits transcription
RNA exists _ and _ is due to the binding of a small molecule
RNA exists in 2 secondary conformations (active and inhibitory) and conversion is due to binding
the active form of thiamin is
thiamin pyrophosphate (TPP)
thiamin genes is found in
thi operon
is TPP is _ transcription is _
- low, transcription completed
- high, terminantor stem loop forms and attenuation
TPP causes a
conformational change from antiterminator stem loop to a terminator stem loop
causes transcription to end at U rich seq
thiMD operon controls
translation of TPP
low TPP means _ binds to mRNA and _
low TTP means ribsome binds and mRNA is translated
high TPP means _ binds to mRNA and _
TPP binds to mRNA and a stem loop forms that prevents translation of mRNA
when there is _ TPP, the _ in not accessible
high TPP, shine-dalgarno sequence not accessible
translation inhibited
at different stages of development, there is variation
in gene expression in cell types
transcription factors are proteins that
influence the ability of RNA polymerase to transcribe
general transcription factors are
required for the bidning of RNA polymerase to the core promotor and progressing to elongation phase
regulatory transcription factors function to
regulate the rate of transcription of genes by influencing the ability of RNA polymerase to begin transcription
regulatory transcription factors recognize _ that are located _
recognize cis elements located near the promoter
regulatory transcription factors vs effector molecules
regulatory TF bind to DNA while effectors molecules bind to a regulatory TF
regulatory protein that increases transcription is a _ and binds to _ sequence
activator, enhancer sequence
regulatory protein that decreases transcription is a _ and binds to _ sequence
repressor, silencer sequence
common factors contributing to combinatorial control
- one or more activators
- one or more repressors
- activators & repressors modulated by: effector proteins, protein interactions, covalent modifications
- regulator proteins may alter nucleosomes near the promoter
- DNA methylation
- formation of hetrochromatin
transcription factor proteins have regions called _ that have functions like
domains
* DNA binding
* binding siite for effector molecules
* dimerization
motif
domain parts that have similar structures between proteins
4 types of motifs
- helix turn helix
- helix loop helix
- zinc finger motif
- leurcine finger motif
many response elements are _
orientation independent or bidirectional
regulation via TFIID
described
- activator/coactivator complex recruits TFIID to the core promoter: transcription is enhanced
- repressor protein inhibits the binding of TFIID to the core promoter: transcription is silenced
transcriptional activation via mediator
described
- activator protein interacts with mediator
- phosphorylates the carboxyl domain of RNA polymerase
- general transcriptional factors are released
- RNA pol proceeds to elongation phase
transcriptional repression via mediator
- repressor protein interaction prevents the phsophorylation of RNA polymerase
- it cannot proceed to elongation
activators & repressors modulated by:
- effector proteins
- protein interactions
- covalent modifications
glucocorticoids influence
- nutrient metabolism in cells
- glucose utilization, fat, protein breakdown
glucocorticoids influence
- nutrient metabolism in cells
- glucose utilization, fat, protein breakdown
gonadocorticoids include
- estrogen and testosterone
GRE function as
enhancers
creb protein responses to
cAMP
chromotin closed conformation
- Chromatin is very tightly packed
- Transcription may be difficult or impossible
chromatin open conformation features
- Chromatin is accessible to transcription factors
- Transcription can take place
ATP-dependent chromatin remodeling
- Energy of ATP hydrolysis is used to drive changes in the locations and/or composition of nucleosomes
- Makes the DNA more or less amenable to transcription
Chromatin remodeling complexes change chromatin structure in one of 3 ways:
- Change in the position of nucleosomes
- Eviction of histone octamers
- Change in the composition of nucleosomes
histone variants
mutations in histones
Histone variants are
incorporated into a subset of nucleosomes to create specialized chromatin
changes in composition of histone variants can
regulate gene transcription
enzymes that modify the tails of histones affect the level of transcription
2 ways
- may influence interactions between DNA and proteins
- occur in patterns, histone code
histone code
- The pattern of modifications provide binding sites for proteins that promote alterations in chromatin structure
- These proteins bind to histones based on the code and affect transcription
p
phosphate
ac
acetyle group
m
methyl group
acetylation of _ eliminates _ and causes the DNA _
Acetylation of* positively charged lysines* eliminates the positive charge and causes the DNA to less tightly bound
acetylation of lysines _ transcription
increases transcriptions
ChIP Seq is used to
map the locations of specific nucleosomes within a genome
ChIP sequencing allows determinations of
- Where nucleosomes are located
- Where histone variants are found
- Where covalent modifications of histones occur
_ is combined with ChIP Seq and performed in species where _
Chromatin immunoprecipitation is combined with ChIP Seq and performed in species where the entire genome has been sequenced
A nucleosome-free region (NFR) is found…
at the beginning and end of many (most) eukaryotic genes.
DNA methylation is…
the covalent attachment of methyl groups
DNA methylation is carried out by
DNA methyltransferase
DNA methylation usually _ transcription
inhibits
In housekeeping genes, the CpG islands are _
unmethylated
Methylation inhibits…
the binding of an activator protein
Methyl-CpG-binding protein recruits…
other proteins that change the chromatin to a closed conformation.
maintenance methylation
Pattern of one copy of the gene being methylated and the other not is maintained in the resulting offspring
De novo methylation is an _ and _
infrequent and highly regulated event
To be epigenetic, molecular changes must
be passed from cell to cell
Genes or chromosomes can be targeted for epigenetic regulation in two ways:
- Via transcription factors
- Via noncoding RNA
Cis-epigenetic changes are maintained
maintained at a specific site
a cis-epigenetic change may affect…genes
only one copy of gene but not the other copy
Trans-epigenetic changes are maintained
by diffusible factors, such as transcription factors
a trans-epigenetic change affects…genes
both copies of a gene
Cis- and trans-epigenetic mechanisms can be distinguished from each other by…
describe/define
cell fusion experiments
* One cell has gene B modified to be transcriptionally active; same gene in another cell is inactive
Fuse cells: if a cis mechanism is involved _ will be modified.
only gene B that was originally modified
Fuse cells: If trans mechanism, _ modified
both copies of the gene will be
Euchromatin
4 things
- not stained during interpahse
- loop domains loose
- transcriptionally active
- central position in nucleus
hetrochromatin
4 thin
- stained during interphase
- compact
- inhibit gene expression
- localized periphery of nucleus
roles of heterochromatin formation
- silencing viral genes
- prevention of TE movement
- gene silencing
Constitutive heterochromatin –
regions that are heterochromatic at the same location in all cell types
Facultative heterochromatin –
heterochromatin that varies in its location among different cell types
facultative hertrochromatin allow for
silencing of genes in cell specfic manner
facultative heterochromatin formation is _ and depends on _
reversible and depends on stage of develeopment or cell type
DNA methylation in facultative heterochrom
methylation at CpG islands in gene regulatory regions
reader domains
specific proteins bind to posttranslational modifications at these domains
reader domains
specific proteins bind to posttranslational modifications at these domains
Recruiter domains
recruit other proteins, such as chromatin remodelers or chromatin-modifying enzymes
Eraser domains
remove PTMs
writer domains
addition of PTMs
heterochromatin with higher order structure features
- Has closer, more stable contacts of nucleosomes with each other
- Forms closer loop domains
- Binds to the nuclear lamina
Closer, more stable contacts of nucleosomes with each other
process
- H3K9me3 recognized by HP1
- HP1 bridges nucleosomes; makes them more compact
Lamina-associated domains (LADS)
- Organize chromosomes into chromatin territories
- May be involved in gene repression
HP1 binding to H3K9me3 modifications on AA tails causes
tighter compaction, no access to DNA
H3K9me3
Histone 3 Lys at 9th position methylated 3x
Initial formation of facultative and constitutive chromatin occurs in 3 phases:
describe each
- Nucleation – short chromosomal site bound by chromatin-modifying enzymes and chromatin-remodeling complexes
- Spreading – adjacent euchromatin is turned into heterochromatin
- Barrier – in interphase chromosomes, spreading stops when it reaches a barrier
Mechanisms to Maintain Epigenetic Marks
- maintainance DNA methylation
- histone modifications
- DNA polymerases recruit chromatin modifying complexes
- higher order structure self maintains
ICF can be due to
Can be due to a mutation in a DNA methyltransferase gene
roberts syndrome caused by
mutations in a gene for acetyltransferase
genomic imprinting occurs at two sites:
- the imprinting control region (ICR)
- differentially methylated region (DMR)
genomic imprinting, methylation _ binding of _ so lgf2 gene is _
methulation prevents binding of CTCF and lgf2 gene is enhanced
genomic imprinting, methylation _ binding of _ so lgf2 gene is _
methulation prevents binding of CTCF and lgf2 gene is enhanced
The Xic encodes , _ which are _
Xist and Tsix, which are transcribed in opposite directions
prior to X chromosome inactivation, _ is expressed in both chromosomes
Tsix
mechanism of X chromosome inactivation
- Tsix active in both bc pluripotency factors
- CTCF bind to Xic, X chromosomes link and pass potency and CTCFs to one X that will stay active
- on inactive X, Xist with bind to Xic
- Xist RNA bind to each other in both directions
- continues until spread along chromosome
- Xist pull in and compact and barr body the inactive X
Trx Group incolved in
gene activation in differentiation
Pc group involved in
gene repression during differenciation
PcG two types
PRC2 and PRC1
how genes are silenced by Pc group
PRC2 binds to response element and trimythelates K27 on H3
* PRC1 compact chromosome
* PRC1 may modify H2A by attach Uq tags
* PRC1 may use direct inhibition
3 options
how genes are silenced by Pc group
PRC2 binds to response element and trimythelates K27 on H3
* PRC1 compact chromosome
* PRC1 may modify H2A by attach Uq tags
* PRC1 may use direct inhibition
3 options
_ inhibits the Agouti gene
DNA methylation
the more methylated CpG islands, the _ the coat color
darker
Vernalization
certain species of plants must be exposed to the cold before they can undergo flowering
cold activates Vin3 and COLDAIR….
which activate VRN1 & 2
which activate PRC2
which inhibitsFLC
which disinhibits budding
so flowering happens
cold activates Vin3 and COLDAIR….
which activate VRN1 & 2
which activate PRC2
which inhibitsFLC
which disinhibits budding
so flowering happens
