BIOL 1951 Quiz 7
1) regulatory elements 2) TATA box 3) Transcriptional start site
3 common factors common among most promoters for eukaryotic protein-encoding genes
1) Transcription (how much mRNA made) 2) Translation (ability of mRNA to be translated into a protein) 3) Post-translation (protein is controlled after it is synthesized)
3 different levels of gene regulation in bacteria
lacZ, lacY, lacA
3 genes in the Lac Operon
1) RNA Polymerase II 2) General transcription factors (GTFs) 3) Mediator
3 types of proteins that play a role in initiating transcription at the core promoter (TATA box + trascriptional start site)
1) change locations of nucleosomes 2) evict histone octamers from DNA - creating gaps where nucleosomes are not found 3) replace standard histone proteins with histone variants (slightly different AA sequence)
3 ways that ATP-dependent chromatin remodeling complexes change chromatin sturcture
1) Transcription (most common) 2) RNA Modification 3) Translation 4) Post translation
4 levels of gene regulation in eukaryotic cells
1) Influence interactions bt DNA and histones 2) Provide binding sites that are recognized by other proteins
Affects of covalent modifications on histone protein tails
inducible operon
An operon under positive control. It is usually "off" but can be turned "on" via an inducer. Ex = the lac operon
regulatory sequence
Binding site for proteins that influence transcription (regulatory transcription factors)
allolactose
Inducer of the lac operon; structurally similar to lactose; generated by b-galactosidase
DNA methylation
The addition of methyl groups (—CH3) to cytosine bases of DNA after DNA synthesis
1) Conserves energy 2) ensures that genes are expressed in the appropriate cell types and at the correct stage of development
Why is gene regulation necessary?
cis-acting elements
a DNA segment that must be adjacent to to the gene(s) that it regulates
iron regulatory protein (IRP)
a translational regulatory protein that recognizes iron response elements that are found in specific mRNAs. It may inhibit translation or stabilize the mRNA.
lacZ gene
protein encoding gene in the lac operon that encodes B-galactosidase
small effector molecules
with regard to transcription,refers to a molecule that exerts its effects by binding to a regulatory transcription factor,causing a conformational change in the protein.
repressible operon (trp operon)
-repressor is initially inactive -corepressor (tryptophan) binds to the repressor and makes it active
TATA box
A promoter DNA sequence crucial in forming the transcription initiation complex.
polycistronic mRNA
A single molecule of messenger RNA that encodes more than 1 protein that results from a group of genes transcribed as a single unit
cyclic AMP (cAMP)
A small effector molecule formed from ATP that controls CAP
DNA methyltransferase
An enzyme that catalyzes the methylation of DNA by attaching methyl groups to DNA bases (cytosine)
regulatory elements
DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences
Catabolite repression of the lac operon
E. coli prefers to use glucose(catabolite) as its carbon source so it represses the lac operon because its is a waster of energy to make product and then use glucose instead
F' factor
F factors that carry genes that were originally found within the bacterial chromosome
DNA methylation
Modification of DNA structure from DNA methyltransferase that typically inhibits the transcription of eukaryotic genes
chromatin
Substance found in eukaryotic chromosomes that consists of DNA tightly coiled around histones
operator
a DNA sequence in bacteria that is recognized by activator and repressor proteins that regulate the level of gene transcription
transcription factor II D (TFIID)
a GTF that binds to the TATA box that can be repressed or enhanced by the binding of silencers or enhancers
merozygote
a bacterial cell that contains an F' factor
lac operon
a gene system whose operator gene and three structural genes control lactose metabolism in E. coli
CpG islands
a group of CG sequences that may be clustered near a promoter region of a gene. The methylation of the cytosine bases usually inhibits transcription.
basal transcription
a low level of transcription resulting from just the core promoter and no TATA box
lac repressor
a protein that binds to the operator site of the lac operon and inhibits transcription of lacA, lacX, and lacY
CAP site (in lac operon)
a regulatory sequence recognized by an activator
operon
a set of 2 or more genes in bacteria that are under the transcriptional control of a single promoter
Nucleosome-free region (NFR)
a site in the chromatin in which the DNA is not wrapped around histone proteins to form nucleosomes wherein the core promoter is found in active genes
gene regulation
ability of an organism to control the expression on their genes
genome, proteomes
all differentiated cells have the same ____ but different _____
cis-effect
an effect on gene expression due to genetic sequences that are within the same chromosome and often are immediately adjacent to the gene of interest
trans-effect
an effect on gene expression that occurs even though two DNA segments are not physically adjacent to each other. Trans-effects are mediated through by genes that encode regulatory proteins.
galactoside transacetylase
an enzyme that covalently modifies lactose and lactose analogs by attaching an acetyl group (COCH3) to prevent toxic build-up of these proteins in the cytoplasm
histone acetyltransferase
an enzyme that loosens the compaction of chromatin by attaching acetyl groups to histone proteins. Aids in transcription
allolactose
an inducer that binds to the lac repressor to cause a conformational change that prevents the lac repressor from binding to the operator site
open conformation of chromatin
chromatin that can be transcribed into mRNA because it is accessible to GTFs and RNA polymerase II
closed conformation of chromatin
chromatin that cannot be transcribed into mRNA
preinitiation complex
cluster of transcription factors (GTFs) and other proteins that recruit RNA polymerase II at the TATA box
combinational control
combination of many factors determines the expression of any given gene
ATP-dependent chromatin remodeling complexes
complex of proteins that alter chromatin structure by using energy from ATP hydrolysis. This altering of chromatin structure can incr or prevent transcription of DNA into mRNA
cAMP + CAP
complex that binds to CAP site near the lac promoter and causes the DNA to bend in a way that enhances the ability of RNA polymerase to bind to the promoter (positive control)
Mediator
composed of many proteins that bind together to form an elliptically shped complex that partially wraps itself around RNA polymerase II and GTFs to 'mediate' the interactions between the preinitiation complex and regulatory transcription factors
1) genes in eukaryotes almost always regulated individually,not in operons 2) more complexity in eukaryotic gene regulation 3) eukaryotic genes = controlled by many factors (combinational control)
differences between gene regulation in eukaryotes and bacteria
lactose high, glucose high
environmental condition that an E. Coli bacterium might experience with regard to glucose and lactose wherein CAP does not bind to CAP site; inhibits transcription. Bacterium uses glucose
lactose high, glucose low
environmental condition that an E. Coli bacterium might experience with regard to glucose and lactose wherein binding of RNA polymerase to promoter is enhanced by CAP binding. Transcription rate is high.
lactose low, glucose high or low (doesnt matter)
environmental condition that an E. Coli bacterium might experience with regard to glucose and lactose wherein the lac repressor prevents transcription of the lac operon
lactose permease
enzyme in bacterium E. Coli that functions to transport lactose into a cell. Very little of this enzyme is produced if lactose is not available in the environment.
β-Galactosidase
enzyme that catalyzes the breakdown of lactose as well as converts a small amount of lactose into allolactose, a structurally similar sugar
lacI gene
gene adjacent to the lac operon that encodes the lac repressor
transcription
in bacteria, gene regulation most often occurs at the level of ____
catabolite repression
key function of CAP
lacI-
mutant lacI strain that inhibits synthesis of a functional lac repressor and prevents the lac repressor from inhibiting transcription
trp operon
operon in e. coli that encodes enzymes that are required to make the amino acid tryptophan
gene expression
process by which a gene produces its product and the product carries out its function
lacP
promoter of the lac operon that's involved in the transcription of 3 protein-encoding genes
histone code hypothesis
proposes that specific combinations of modifications help determine chromatin configuration and influence transcription
lacA
protein encoding gene in the lac operon that encodes galactoside transacetylase
lacY
protein encoding gene in the lac operon that encodes lactose permease
regulatory transcription factors
proteins that bind to regulatory sequences in the DNA in the vicinity of a promoter and affect the rate of transcription of one or more nearby genes.
methyl-CpG-binding proteins
proteins that change chromatin structure by binding to methylated sequences and recruiting other transcription inhibiting proteins
coactivators
proteins that increase the rate of transcription but do not directly bind to the DNA itself, instead bind to activators and can stimulate the function of the mediator
core promoter
refers to the TATA box and the transcriptional start site of a eukaryotic structural gene
alternative splicing
regulated process during gene expression that results in a single gene coding for multiple proteins at different stages of development, different cell types, an/or in response to a change in environmental conditions
Enhancers
regulatory elements that increase the rate of transcription
silencers
regulatory elements that prevent transcription of a given gene
repressors
regulatory transcription factors that bind to the DNA and decrease the rate of transcription (negative control)
activators
regulatory transcription factors that bind to the DNA and increase the rate of transcription (positive control)
inducer
small effector molecule that causes transcription to increase
catabolite activator protein (CAP)
the activator protein for the lac operon- positively controls this operon
histone variants that promote transcription
the nucleosome free region is often flanked by...
cell differentiation
the process by which a cell becomes specialized into particular types (muscle cells, neurons, etc)
repressible
the trp operon is an example of a _____ operon because it is regulated by a repressor protein that's encoded by the trpR gene
repressible operon
transcription is usually on, but can be inhibited (repressed) when a specific small effector molecule binds to a regulatory protein (example tryptophan)
positive control
transcriptional regulation by activator proteins
negative control
transcriptional regulation by repressor proteins
domains
two functional regions on repressors and activators that respond to small effector molecules
1) Repressors 2) activators
types of regulatory transcription factors
allows bacterium to coordinately regulate a group of genes that encode proteins whose functions are used in a common pathway
what is the advantage of having an operon?
allolactose
whether or not the lac repressor bids to the lac operator depends on...