Regulation Ch 14, 15 Connect Assignment
True or false: Gene expression is always the same.
False
True or false: Gene regulation is constant.
False
Constitutive genes ______.
Multiple choice question.
are regulated by glucose levels.
respond to amino acid levels in the cell.
respond to lactose levels in the cell.
are unregulated.
are unregulated.
Constitutive genes encode proteins the cell needs ______.
Multiple choice question.
all the time
occasionally
to make amino acids
when certain nutrients are in the environment
all the time
True or false: A benefit of gene regulation is that encoded proteins will not be produced when they are not needed.
True
The phenomenon in which the level of gene expression can vary under different conditions is gene ____.
regulation
Control of gene expression leads to the production of specific proteins to assist bacterial cells in responses to environmental stressors, preparation for cell division, and ______.
Multiple choice question.
metabolism
transport of nutrients
pathogenicity
chemotaxis
metabolism
Unregulated genes have ______
Multiple choice question.
constant levels of expression.
constant or variable levels of expression depending on the gene.
variable levels of expression.
constant levels of expression.
Reason:
The level of transcription for unregulated genes is unchanged over time, neither inhibited or enhanced.
In bacteria, the most common way to regulate gene expression is by influencing ______.
Multiple choice question.
the rate of transcription initiation
the rate of translation initiation
the frequency of cell division
the rate of transcription elongation
the rate of transcription initiation
Unregulated genes are also called ____ genes.
constitutive
Transcription regulation by an activator protein is considered to be ______ control.
positive
Reason:
Transcription regulation by a repressor protein is termed negative control.
What type of genes encode proteins the bacterial cell needs all the time?
Repressor genes
Constitutive genes
Activator genes
Riboswitches
Constitutive genes
Reason:
Activator gene products are needed only at certain times to initiate transcription of specific genes.
A regulatory protein that increases the rate of transcription is a(n) ____.
activator
A benefit of gene regulation is that encoded proteins are not made when they are not needed. This ______.
makes it difficult for the cell to respond to changing environments
keeps gene expression constant
ensures that all proteins are produced all the time
prevents the cell from wasting energy
prevents the cell from wasting energy
How does an effector molecule influence gene expression?
Multiple choice question.
The effector molecule binds to DNA and affects the ability of RNA polymerase to initiate transcription.
The effector molecule causes the mRNA to form a stem/loop structure that blocks the ribosome.
The effector molecule binds to the mRNA and affects the ability of the ribosome to initiate translation.
The effector molecule binds to a regulatory protein and affects its ability to bind DNA.
The effector molecule binds to a regulatory protein and affects its ability to bind DNA.
Reason:
Effector molecules can bind to proteins called activators which then stimulate transcription.
Select all that apply
Genetic control of the production of specific proteins at specific times would occur in which of the following situations?
Multiple select question.
When bacterial cells are getting ready to divide
When a bacterial cell encounters a toxin in the environment
When bacteria are subject to heat stress
Producing enzymes to metabolize specific sugars when those sugars are found in the environment
Producing the proteins needed to assemble ribosomes
When bacterial cells are getting ready to divide
When bacteria are subject to heat stress
Producing enzymes to metabolize specific sugars when those sugars are found in the environment
True or false: The rate of transcription initiation rarely influences overall gene expression.
False
Reason:
The most common way that bacteria regulate gene expression is by influencing the rate of transcription initiation.
An inducer is a small effector molecule that causes transcription to ______.
Multiple choice question.
decrease
remain constant
increase
increase
A protein such as a repressor that inhibits transcription is exerting ____ control of transcription.
negative
A corepressor is a small molecule that binds to a(n) ____ protein, thereby causing the protein to bind to the DNA, while an inhibitor binds to a(n) ____ protein and prevents it from binding to the DNA.
Blank 1: repressor
Blank 2: activator
A regulatory protein that binds to DNA and inhibits transcription is a(n) ____.
repressor
Monod and Jacob studied ____ metabolism in E. coli.
lactose
True or false: Effector molecules influence gene expression by binding to DNA.
False
Reason:
An effector molecule exerts its effects by binding to a repressor or activator.
An operon is a group of two or more genes under the transcriptional control of ______.
a single promoter
two or more promoters
different polymerases
a single promoter
Control of gene expression leads to the production of specific proteins to assist bacterial cells in responses to environmental stressors, preparation for cell division, and ______.
pathogenicity
metabolism
transport of nutrients
chemotaxis
metabolism
An operon encodes a ____ mRNA, an RNA that contains the sequences of two or more genes.
polycistronic
An inducer could bind to a(n) ______ and prevent it from binding to the DNA, or it could bind to a(n) ______ and cause it to bind to the DNA.
Multiple choice question.
repressor; activator
activator; polymerase
repressor; ribosome
activator; repressor
repressor; activator
In an operon, the ______ signals the beginning of transcription.
Multiple choice question.
promoter
origin
terminator
ribosome binding site
promoter
How do a corepressor and an inhibitor differ?
Multiple choice question.
A corepressor binds directly to the DNA, while an inhibitor binds to the activator protein and prevents it from binding to DNA.
A corepressor binds to a repressor protein, while an inhibitor binds to an activator protein.
A corepressor binds to a repressor protein, thereby causing the protein to bind to the DNA, and an inhibitor binds directly to DNA.
An inhibitor binds to a repressor protein, while a corepressor binds to an activator protein.
A corepressor binds to a repressor protein, while an inhibitor binds to an activator protein.
Reason:
A corepressor binds to a repressor, causing the activated repressor to bind to DNA.
Reason:
An inhibitor is a protein that binds to another protein, preventing its binding to DNA.
Select all that apply
Select all of the following that are protein-encoding genes in the lac operon.
Multiple select question.
lacO
lacY
lacA
lacX
lacZ
lacY
lacA
lacZ
Reason:
The lacO gene is the operator site. The three protein-encoding genes are lacZ, lacY, and lacA.
Monod and Jacob studied lactose metabolism in ____.
Blank 1: Escherichia, E., or E
Blank 2: coli
A(n) ____ is a group of two or more genes under the transcriptional control of a single promoter.
operon
The enzyme beta-galactosidase cleaves the sugar lactose into ____ and ____.
glucose; galactose
A polycistronic mRNA contains the sequence(s) ______.
Multiple choice question.
for several genes and control regions
for only one gene
for genes from different operons
of two or more genes
of two or more genes
Reason:
Polycistronic mRNA has a single promoter that regulates expression of two or more genes.
The product of the lacY gene is required for ______.
Multiple choice question.
the transport of lactose into the bacterial cell
converting a small amount of lactose into allolactose
cleaving lactose into glucose and galactose
covalently modifying lactose and lactose analogs
the transport of lactose into the bacterial cell
Reason:
Cleavage of lactose is catalyzed by the product of the lacZ gene.
The operon is flanked by a(n) ____ that signals the beginning of transcription and a(n) ____ that signals the end of transcription.
promoter; terminator
The lacA gene encodes the enzyme ____.
galactoside transacetylase
The three protein-encoding genes in the lac operon are ____, ____, and ____.
Blank 1: lacZ or Z
Blank 2: lacY or Y
Blank 3: lacA or A
Which protein binds to which site?
Catabolite activator protein
Repressor
RNA polymerase
Operator
Promoter
CAP site
- Catabolite activator protein CAP site
- Repressor Operator
- RNA polymerase Promoter
The ______ gene encodes a repressor protein.
Multiple choice question.
lacZ
lacP
lacI
lacA
lacO
lacI
The enzyme β-galactosidase is encoded by which gene?
Multiple choice question.
LacZ
LacA
LacY
LacO
LacZ
Fill in the blank question.
When the lac repressor binds to the lac ____ site, RNA polymerase cannot transcribe the lacZ, lacY or lacA genes.
Blank 1: operator, nucleotides, or O
The lacY gene encodes lactose ____, a membrane protein.
permease
Allolactose is a small effector molecule that binds to the lac repressor and ______.
Multiple choice question.
increases the affinity of repressor for CAP
facilitates repressor binding to DNA
prevents repressor from binding to DNA
prevents repressor from binding to RNA polymerase
prevents repressor from binding to DNA
Reason:
Allolcatose is an inducer, which when present, binds to the repressor and prevents it from binding to the operator.
The lacA gene encodes galactoside transacetylase, an enzyme that covalently modifies ______.
Multiple choice question.
lactose
beta-galactosidase
CAP
lactose permease
lactose
Reason:
Beta-galactosidase is the product of the lacZ gene and is not modified by the transacetylase.
Reason:
Lactose permease is the product of the lacY gene and is not modified by the transacetylase.
The CAP site and the operator site are ______ that function in gene regulation.
Multiple choice question.
regulatory RNAs
short DNA segments
disaccharides
large proteins
short DNA segments
The Lac repressor protein binds to the operator and ______.
Multiple choice question.
prevents translation
aids RNA polymerase
blocks transcription
stops transport of lactose
blocks transcription
Reason:
The operator is a region in the DNA of the lac operon.
When four molecules of allolactose are bound to the lac repressor, the lac operon is induced, and RNA polymerase ______.
Multiple choice question.
binds to operator
is blocked from transcribing any genes
transcribes the operon
transcribes more slowly
transcribes the operon
When the lac repressor is bound to the operator, RNA polymerase ______ the lacZ, lacY, or lacA genes.
Multiple choice question.
transcribes one of
increases transcription of
cannot transcribe
cannot transcribe
A conformational change that prevents the lac repressor from binding to the lac operator occurs when ____ binds to the lac repressor.
Blank 1: allolactose, lactose, or inducer
The small effector molecule ____ prevents the lac repressor from binding to the operator site.
allolactose/inducer
The lacA gene encodes the enzyme ____ ____.
galactoside transacetylase
When four molecules of allolactose are bound to lac repressor, and repressor can no longer bind to operator, and RNA polymerase is free to transcribe the operon, the operon has been ____.
induced
The binding of the allolactose inducer to the lac repressor occurs at a(n) ______ site.
Multiple choice question.
allosteric
operator
active
allosteric
Reason:
The operator is a DNA sequence to which the lac repressor binds.
The binding of ______ to the lac repressor promotes a conformational change that prevents the repressor from binding to the lac operator.
Multiple choice question.
Lac permease
lactose
allolactose
β-galactosidase
allolactose
Monod, Jacob, and Pardee studied an E. coli strain with a lacI - mutation in which the lac operon was expressed ______.
Multiple choice question.
only when there were very high levels of lactose
only in the presence of glucose
even in the absence of lactose
even in the absence of lactose
Reason:
Expression in the presence of high levels of lactose is associated with the I+ genotype.
How will transcription of the lac operon be affected by a mutation in the lacI gene that results in an inability to synthesize any repressor protein or produces a repressor protein that is unable to bind to the operator?
Multiple choice question.
The operon will only be repressed in the absence of lactose.
The operon cannot be repressed.
The operon will always be repressed.
The operon will only be repressed in the presence of glucose.
The operon cannot be repressed.
When bound to operator, the lac repressor ______.
Multiple choice question.
prevents all transcription of the genes encoding the lac enzymes
allows synthesis of β-galactosidase, but not of lac permease
allows transcription of the lacZ gene but not of the lacA gene
allows very small amounts of the lac enzymes to be made
allows very small amounts of the lac enzymes to be made
Reason:
In reality the repressor does not completely inhibit transcription, so very small amounts of the operon products are made.
The CAP site and the operator site are ______ that function in gene regulation.
allolactose
As levels of allolactose increase within an E. coli cell, allolactose binds to the lac ____, promoting a conformational change that prevents binding to the ____ site on the DNA.
repressor; operator
Allolactose molecules bind to regulatory sites on the lac repressor protein called ____ sites that differ from the region of the repressor that binds the operator.
allosteric
Jacob, Monod, and Pardee isolated bacteria with mutations that resulted in the constitutive expression of the ____ operon even in the absence of lactose.
lac
LacI S mutations would result in a lac operon that is ______.
Multiple choice question.
only repressed in the presence of glucose
always repressed
only repressed in the absence of lactose
never repressed
always repressed
True or false: The lac repressor does not completely inhibit transcription of the lacZ, lacY, and lacA genes.
True
Reason:
Due to the reversible nature of its binding to the operator, the lac repressor allows low levels of transcription of the lac operon.
What happens when levels of allolactose rise inside an E. coli cell?
Multiple choice question.
Allolactose binds to the lac repressor and prevents it from binding to the operator.
Allolactose binds to the operator and blocks transcription of lacZ, lacY, and lacA genes.
Transciption of the lac operon begins but is terminated prematurely.
Allolactose binds to and activates the lac repressor, which binds to the operator region.
Allolactose binds to the lac repressor and prevents it from binding to the operator.
A strain of bacteria containing F' factor genes is called a ____, or a partial diploid.
merozygote
β-galactosidase activity can be detected using the lactose analog β-____ because β-glalactosidase cleaves it to a product with a yellow color. (Use an abbreviation.)
ONPG
Monod, Jacob, and Pardee studied an E. coli strain with a lacI - mutation in which the lac operon was expressed ______.
Multiple choice question.
even in the absence of lactose
only in the presence of glucose
only when there were very high levels of lactose
even in the absence of lactose
Reason:
Expression in the presence of high levels of lactose is associated with the I+ genotype.
A DNA segment that must be adjacent to the gene(s) it regulates is a ____-____ element.
cis-acting
Why is a merozygote better at complementing a mutation in a trans-acting factor than in a cis-acting element?
Multiple choice question.
A cis-acting element must be adjacent to the gene it is regulating.
A trans-acting factor must be adjacent to the gene it is regulating.
A cis-acting element makes a diffusible product.
A cis-acting element must be adjacent to the gene it is regulating.
What is the name for a strain of bacteria containing an F' factor?
Multiple choice question.
Merozygote
Diploid
Mutant
Heterodimer
Merozygote
The somewhat imprecise term that describes how transcriptional regulation is influenced by glucose is
catabolite repression
β-ONPG can be used to detect levels of β-galactosidase, because β-galactosidase cleaves β-ONPG into a substance with a ______ color.
Multiple choice question.
black
blue
green
yellow
yellow
What type of regulatory element does not need to be adjacent to the gene(s) it is regulating?
Multiple choice question.
Trans-acting factor
Cis-acting factor
Trans-acting factor
The sequential use of sugars by a bacterial cell is called
diauxic growth
LacI S mutations would result in a lac operon that is ______.
Multiple choice question.
only repressed in the absence of lactose
never repressed
always repressed
only repressed in the presence of glucose
always repressed
Cyclic-AMP is a small effector molecule produced by the enzyme
adenylyl cyclase
Would using a merozygote better indicate regulation of a gene by a trans-acting factor or a cis-acting element?
Multiple choice question.
A trans-acting factor
Neither
Both
A cis-acting element
A trans-acting factor
Reason:
A mutation in a cis-acting element is not affected by the introduction of another cis-acting element with normal function into the cell.
Reason:
A mutation in a cis-acting element is not affected by the introduction of another cis-acting element with normal function into the cell.
In catabolite repression, transcription is influenced by the presence of _____.
Multiple choice question.
fructose
glucose
lactose
galactose
glucose
Reason:
Catabolite repression is an additional mechanism for regulating the lac operon that does not involve lactose.
The transport of glucose into a bacterial cell causes the intracellular level of cyclic-AMP to fall because the enzyme ____ ____ is inhibited.
adenylyl cyclase
When only lactose is present in bacterial cells, levels of the effector molecules ____ and ____ are high.
Blank 1: allolactose
Blank 2: cAMP or cyclic AMP
Many bacterial species use sugars sequentially. This is called ______. Multiple choice question. catabolite repression bacterial conjugation cis-regulation
diauxic growth
Select all that apply.
When both lactose and glucose are absent ______.
Multiple select question.
CAP does not bind to DNA
lac repressor is bound to the operator
lac operon transcription rate is very low
lac operon transcription rate is very high
CAP is bound to the DNA
lac repressor does not bind to the operator
lac repressor is bound to the operator
lac operon transcription rate is very low
CAP is bound to the DNA
The small effector molecule produced by the enzyme adenylyl cyclase is ______.
Multiple choice question.
cAMP
β-galactosidase
ATP
allolactose
cAMP
It has been shown that the lac operon has three ____ sites to which the lac repressor can bind.
operator
The transport of ______ into a cell causes a _______ in the concentration of cyclic-AMP by inhibiting adenylate cyclase.
Multiple choice question.
lactose; decrease
tryptophan; increase
allolactose; increase
glucose; decrease
glucose; decrease
When only ______ is present, allolactose and cAMP levels are high.
Multiple choice question.
lactose
glucose
galactose
tryptophan
lactose
Reason:
Allolactose levels will be low if only glucose is present.
Why is the transcription rate of the lac operon low when both glucose and lactose are absent?
Multiple choice question.
CAP protein cannot bind to the DNA to enhance transcription.
Lac repressor blocks transcription by binding to the operator region.
CAP protein blocks transcription by binding to a region near the promoter.
CAP protein blocks transcription by binding to the operator region.
Lac repressor blocks transcription by binding to the operator region.
In attenuation, transcription ______.
Multiple choice question.
proceeds half-way through the operon
continues to the transcription stop site
never starts
is stopped prematurely
is stopped prematurely
Studies indicate that the lac operon has ______ operator site(s) for the lac repressor.
Multiple choice question.
dozens of
a single
three
two
three
Reason:
While mutational analysis first identified a single site, two additional sites were later detected.
Select all that apply
Select the genes in the trp operon.
Multiple select question.
trpY
trpC
trpZ
trpD
trpB
trpA
trpE
trpC
trpD
trpB
trpA
trpE
When tryptophan levels are low, the transcription of the trp operon will occur at a ______ rate because ______.
Multiple choice question.
high; the trp repressor cannot bind to the operator site.
high; attenuation increases the rate.
low; tryptophan activates the repressor.
low; the trp repressor binds to the operator to inhibit transcription.
low; attenuation decreases the rate.
high; the trp repressor cannot bind to the operator site.
When both lactose and glucose are absent, concentrations of cAMP are ______.
Multiple choice question.
either high or low depending on other factors
high
low
high
Reason:
When both lactose and glucose are absent, concentrations of cAMP are high. However, the transcription rate is low due to the binding of the lac repressor.
Reason:
When glucose is present, cAMP levels are low.
During attenuation, transcription begins, ______.
Multiple choice question.
and continues beyond the operon
but it is terminated before the entire mRNA is made
but then a repressor protein binds to the operator
but translation stops after the eighth codon
but it is terminated before the entire mRNA is made
The trp operon is regulated by a repressor protein and by ____ in which transcription is stopped prematurely.
attenuation
In the trpL mRNA, ____ stem-loops are possible.
three
The genes in the trp operon encode ______.
Multiple choice question.
enzymes used to metabolize tryptophan in the environment
only the subunits of the trp repressor protein
regulatory proteins only
enzymes used in tryptophan biosynthesis
enzymes used in tryptophan biosynthesis
Reason:
The proteins encoded by the trp operon are used to produce the amino acid tryptophan.
In the trpL gene, which stem-loop together with the U-rich attenuator sequence acts as an intrinsic terminator?
Multiple choice question.
1-4
1-2
3-4
2-3
3-4
Select all that apply
In an E. coli cell, when tryptophan levels are low ______.
Multiple select question.
trp repressor binds to the operator site
attenuation will occur
trpE, trpD, trpC, trpB, and trp A genes will be transcribed
products of the trpE, trpD, trpC, trpB, and trp A genes will not be made
trp repressor cannot bind to the operator site
trpE, trpD, trpC, trpB, and trp A genes will be transcribed
trp repressor cannot bind to the operator site
Why does transcription of the trp operon continue when tryptophan levels are low?
Multiple choice question.
The ribosome pauses in region 2, causing the 3-4 stem-loop to form.
The ribosome continues through the trpL mRNA, causing the 3-4 stem-loop to form.
The ribosome pauses in region 1, preventing the 3-4 stem-loop from forming.
The ribosome continues through the trpL mRNA, preventing the 3-4 stem-loop from forming.
The ribosome pauses in region 1, preventing the 3-4 stem-loop from forming.
Reason:
The ribosome stops at the Trp codons in the trpL mRNA because it is waiting for charged tRNATrp, which is in short supply due to the low level of tryptophan.
Transcription begins but terminates before the entire mRNA is made during
attenuation
When attenuation occurs, the mRNA from the trp operon is made as a short piece that terminates shortly past the _____ gene.
Multiple choice question.
trpL
trpE
trpD
trpA
trpL
Can a particular segment of mRNA from the trp operon participate in the formation of more than one stem loop at the same time?
Multiple choice question.
No
Yes
Maybe, it depends on the level of tryptophan.
No
Reason:
If Region 3 is paired with Region 2, its bases are not available to pair with Region 4.
In the trpL sequence, the 3-4 stem-loop together with the U-rich attenuator sequence acts as a(n)
intrinsic terminator
When the tryptophan level in the cell is ______, the ribosome pauses in region one of the trpL mRNA, causing region 2 to to bind to region 3 and transcription to continue.
Multiple choice question.
high
low
low
In the trp operon, the attenuator DNA ______.
Multiple choice question.
binds CAP
encodes an enzyme
increases the rate of transcription
does not encode an enzyme
does not encode an enzyme
Reason:
Attenuator DNA does not encode any of the enzymes required for tryptophan biosynthesis.
The mRNA made from the ______ gene contains codons for 14 amino acids that form the trp leader peptide.
Multiple choice question.
trpC
trpB
trpA
trpL
trpL
The mRNA from the trpL genes has four regions that are complementary to each other and cause the mRNA to form
stem-loops
During attenuation, intrinsic termination of the trpL gene transcript occurs due to a U-rich region combined with a stem-loop structure formed between ______.
Multiple choice question.
region 1 and region 3
region 1 and region 2
region 3 and region 4
region 2 and region 3
region 3 and region 4
Anabolic enzymes are usually encoded by ______ operons, and ______ operons usually encode catabolic enzymes.
Multiple choice question.
inducible; repressible
repressible; inducible
repressible; inducible
The mRNA made form the trpL gene contains codons for 14 amino acids that form ______.
Multiple choice question.
anthranilate synthase
the trp repressor protein
chorismate synthase
the trp leader peptide
the trp leader peptide
Reason:
The repressor is encoded by the trpR gene.
Posttranslational regulation refers to ______.
Multiple choice question.
regulation of transcription termination
regulation of translation of mRNAs
control of transcription initiation
control of proteins already in the cell
control of proteins already in the cell
The mRNA made from the trpL gene has four regions that can ______.
Multiple choice question.
form a CAP site
form stem-loops
bind repressor protein
contain a translation stop site
form stem-loops
A translational repressor recognizes sequences within ______ and ______ translation.
Multiple choice question.
mRNA; inhibits
DNA; inhibits
rRNA; inhibits
mRNA; increases
tRNA; increases
mRNA; inhibits
In the attenuation process, formation of the 3-4 stem loop from the trpL gene transcript in combination with a U-rich region results in ____ termination, also known as ____-independent termination.
Blank 1: intrinsic
Blank 2: rho, ρ, or P
Inducible operons usually encode ______ enzymes, and repressible operons usually encode ______ enzymes.
Multiple choice question.
catabolic; anabolic
anabolic; catabolic
catabolic; anabolic
A translational repressor protein may bind to the mRNA and ______.
Multiple choice question.
cause the ribosome to bind too tightly to the Shine-Delgarno sequence
cause the RNA polymerase to release the DNA
cause the mRNA to be terminated prematurely
stabilize a secondary structure that prevents translation
stabilize a secondary structure that prevents translation
Reason:
Translational regulatory proteins recognize and bind sequences within the mRNA, and then inhibit translation.
What do you call an RNA strand that is complementary to an mRNA molecule?
Multiple choice question.
Messenger RNA
Small nuclear RNA
Ribosomal RNA
Antisense RNA
Antisense RNA
The term ____ regulation refers to control of proteins already present in the cell.
posttranslational
A regulatory protein that inhibits translation is called a
translational repressor
In feedback inhibition, the final product in a metabolic pathway ______.
Multiple choice question.
causes increased production of enzymes that act early in the pathway
prevents translation of its own mRNA
causes the formation of a stem-loop structure in the mRNA that prevents translation
inhibits an enzyme that acts early in the pathway
inhibits an enzyme that acts early in the pathway
A translational repressor protein binds to ______.
Multiple choice question.
the operator sequence of the DNA
an enzyme in an amino acid biosynthetic pathway
an uncharged tRNA
mRNA near the start codon
mRNA near the start codon
Reason:
The operator sequence helps to regulate transcription, not translation.
In postranslational regulation, the final product of a metabolic pathway may bind to the ____ site of an enzyme and inhibit its catalytic ability.
allosteric
Antisense RNA is an RNA strand that is ____ to an mRNA molecule.
complementary
Posttranslational regulation refers to ______.
Multiple choice question.
regulation of translation of mRNAs
control of transcription initiation
control of proteins already in the cell
regulation of transcription termination
control of proteins already in the cell
The conversion of a riboswitch form one conformation to another is due to ______.
Multiple choice question.
the covalent modification of the final product
a corepressor
the presence of CAP
the binding of a small molecule
the binding of a small molecule
When the product of a gene produced in a metabolic pathway inhibits an enzyme that acts early on in the pathway it is called
feedback inhibition
An enzyme may contain two sites: a catalytic site, and a regulatory or ____ site.
allosteric
In the thi operon, when levels of TPP are low, the 5' end of the mRNA forms an ____ stem-loop structure that allows transcription to continue.
antiterminator
The TPP riboswitch in E. coli controls ____, whereas the TPP riboswitch in B. subtilis controls ____.
translation; transcription
When TPP levels are low, the mRNA of the E. coli thiMD operon forms a stem-loop structure that ______.
Multiple choice question.
keeps the Shine-Dalgarno sequence hidden from the ribosome
makes the Shine-Dalgarno sequence available to the ribosome
causes premature termination of transcription
causes premature termination of translation
makes the Shine-Dalgarno sequence available to the ribosome
Reason:
The folding produces an anti-sequestor that makes the Shine-Dalgarno sequence accessible to the ribosome.
An RNA molecule that can exist in two different secondary conformations and thereby affect gene regulation is known as a(n)
riboswitch
Gene regulation means that ______.
Multiple choice question.
only certain genes are included in the genome of a species
gene expression can be controlled so that genes can be expressed at high or low levels
gene expression is controlled so that all genes in a genome are expressed at the same level
gene expression can be controlled so that genes can be expressed at high or low levels
In feedback inhibition, the final product in a metabolic pathway ______.
Multiple choice question.
causes the formation of a stem-loop structure in the mRNA that prevents translation
prevents translation of its own mRNA
causes increased production of enzymes that act early in the pathway
inhibits an enzyme that acts early in the pathway
inhibits an enzyme that acts early in the pathway
Reason:
Inhibition refers to reduced production of enzymes.
In the thi operon, when levels of TPP are low, the mRNA folds into a stem-loop structure that ______.
Multiple choice question.
prevents the ribosome form binding to the start codon
causes attenuation
prevents formation of the terminator stem-loop
causes premature termination of transcription
prevents formation of the terminator stem-loop
Reason:
When TPP levels are low, the antiterminator forms.
Select all that apply
Select examples of how gene regulation benefits eukaryotic organisms.
Multiple select question.
The ability to respond to changes in nutrient availability
The ability to remove deleterious genes
The ability to respond to environmental stresses
The ability to respond to changes in nutrient availability
The ability to respond to environmental stresses
Riboswitches can regulate ______.
Multiple choice question.
transcription or translation
translation only
posttranslational modification
transcription only
transcription or translation
In the E. coli thiMD operon, the 5' end of the mRNA folds into a structure with a stem-loop called the ____-____ ____ that keeps the Shine-Dalgarno sequence accessible to the ribosome.
Shine-Dalgarno antisequestor
The phenomenon where the level of gene expression is controlled so that genes can be expressed at high or low levels is called gene
regulation
Human nerve cells and muscle cells look quite different from each other due to differences in ______.
Multiple choice question.
gene regulation
cell cycle
DNA content
gene regulation
If gene regulation acts to prevent translation, what molecule will not be produced?
Multiple choice question.
Protein
DNA
mRNA
pre-mRNA
Protein
Reason:
mRNA will not be produced if transcription or processing has been prevented.
The ability of humans to develop tans to protect their skin cells from UV rays by inducing genes that provide protection against UV radiation is an example of gene
regulation
A ____ ____ is a protein that influences the ability of RNA polymerase to transcribe a given gene.
transcription factor
Proteins that regulate the rate of transcription of target genes are called ____ transcription factors.
regulatory
Select all that apply
Plants and animals require a greater level of gene regulation than single-celled eukaryotes because of ______.
Multiple select question.
presence of multiple organelles
different developmental stages
different tissue types
multicellularity
more complex cell structure
different developmental stages
different tissue types
multicellularity
more complex cell structure
Select all that apply
Select the steps at which gene regulation can occur.
Multiple select question.
RNA processing
Translation
Transcription
Posttranslational modification
DNA replication
RNA processing
Translation
Transcription
Posttranslational modification
Select all that apply
DNA sequences in eukaryotes that can be bound by regulatory transcription factors, which then affect the ability of RNA polymerase to transcribe a particular gene are called ______.
Multiple select question.
regulatory sequences
operator sequences
regulatory elements
control elements
core promoters
regulatory sequences
regulatory elements
control elements
Reason:
Operator sequences are found in prokaryotic cells.
Reason:
Cis-acting elements in the vicinity of the core promoter are recognized.
Select all that apply
Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by ______.
Multiple select question.
preventing DNA replication
regulating the unwinding of the double-stranded DNA at the promoter sequence
controlling the switch from the initiation to the elongation stage of transcription
regulating the binding of the transcriptional complex to the core promoter
regulating RNA processing
controlling the switch from the initiation to the elongation stage of transcription
regulating the binding of the transcriptional complex to the core promoter
A regulatory transcription factor that enhances the rate of transcription is called a(n)
activator
General transcription factors are required for the binding of ____ ____ to the core promoter and its progression to the elongation stage.
RNA polymerase
Repressors bind to ______.
Multiple choice question.
enhancers
silencers
activators
silencers
Human nerve cells and muscle cells look quite different from each other due to differences in ______.
Multiple choice question.
gene regulation
cell cycle
DNA content
gene regulation
The phenomenon in which the combination of many factors determines the expression of a given gene is known as
combinatorial control
DNA sequences that are analogous to the operator sites found near bacterial promoters are called ____ elements or ____ sequences.
control; regulatory
Transcription factor proteins contain regions called ____ that have specific functions.
domains
Activators bind to ______.
Multiple choice question.
RNA
enhancers
repressors
silencers
enhancers
What is a motif?
Multiple choice question.
The DNA sequence that is bound by a repressor protein
A domain that is dimerized
A domain that has a very similar structure in many different proteins
The DNA sequence that is bound by an enhancer
A domain that has a very similar structure in many different proteins
Regulatory transcription factors that prevent transcription from occurring are called
repressors
In helix-____-helix and helix-____-helix motifs, an α-helix recognizes a base sequence in the major groove of the DNA.
Blank 1: turn
Blank 2: loop
Most eukaryotic genes are regulated by ______ factor(s).
Multiple choice question.
one
zero
many
many
The α-helix is often found in transcription factors because it is the ______.
Multiple choice question.
proper width to bind into the major groove of the DNA double helix
proper width to bind into the minor groove of the DNA double helix
only motif that can bind DNA at regulatory elements
only motif that can bind DNA
proper width to bind into the major groove of the DNA double helix
True or false: A transcription factor can have multiple domains.
True
Reason:
Each domain in a protein has a specific function, and a protein can have more than one different domain.
Similarly to an α-helix, a ____ finger motif can also recognize the ____ groove of DNA.
zinc; major
A domain that has a very similar structure in many different proteins is called a(n)
motif
The dimerization of two different proteins leads to a
heterodimer
General transcription factors are required for the binding of ____ ____ to the core promoter and its progression to the elongation stage.
RNA polymerase
The binding of a regulatory transcription factor to a(n) ____ can stimulate transcription 10- to 1000-fold, which is called ____ regulation.
enhancer; up
In helix-turn-helix and helix-loop-helix motifs ____ ____ side chains of the α-helix form ____ bonds with nucleotide bases.
Blank 1: amino
Blank 2: acid or acids
Blank 3: hydrogen or H
Regulatory elements that inhibit transcription are called silencers and their effect on transcription is called ______ regulation.
Multiple choice question.
up
down
down
A domain called an α-____ is often found in transcription factors because it is the proper width to fit into the ____ groove of the DNA double helix.
helix; major
A regulatory element that functions in the forward or reverse direction is said to be
bidirectional
Select all that apply
Select the elements that compose a zinc finger motif.
Multiple select question.
Two β-sheet structures
Two zinc metal ions
A zinc metal ion
Two α-helices
One β-sheet structure
One α-helix
Two β-sheet structures
A zinc metal ion
One α-helix
The dimerization of two identical proteins results in a
homodimer
True or false: Regulatory elements must be located within 200 base pairs upstream from the core promoter.
False
Reason:
Regulatory elements are often located within 200 bp upstream from the core promoter, but can also be quite distant, even 100,000 bp away.
An enhancer is a DNA element that can be bound to a regulatory transcription factor, which leads to ______.
Multiple choice question.
transcriptional repression
up regulation
down regulation
DNA replication
up regulation
Activator proteins might help ____ bind to the ____ box.
TFIID; TATA
You are studying a transcription factor that binds to DNA near a gene of interest. You discover that once the transcription factor binds, transcription of your gene of interest becomes undetectable. This is an example of ______.
Multiple choice question.
a mediator
down regulation
an activator
up regulation
down regulation
The function of TFIID is to ______.
Multiple choice question.
bind to an enhancer to increase transcription from the core promoter
prevent the binding of RNA polymerase II to the core promoter
bind to the TATA box and recruit RNA polymerase II to the core promoter
bind to the core promoter and recruit RNA polymerase II to the TATA box
bind to the TATA box and recruit RNA polymerase II to the core promoter
You are studying a bidirectional enhancer with the sequence 5'-CCTA-3'. Regulatory transcription factors that bind this sequence should also bind ______.
Multiple choice question.
5'-GGAT-3'
3'-ATCC-5'
3'-TAGG-5'
3'-ATCC-5'
Reason:
Bidirectional enhancers function in the forward or reverse direction. Notice 3'-ATCC-5' is the reverse of 5'-CCTA-3'.
Activator proteins often increase transcription through an interaction with ______.
Multiple choice question.
coactivators
RNA polymerase
repressors
RNA
coactivators
Relative to the promoter for a gene of interest, regulatory elements are located ______.
Multiple choice question.
at various distances
more than 100,000 bp away
on top of the promoter
within 200 bp
at various distances
Reason:
There is striking variation in the location of regulatory elements. They are often about 200 bp upstream from the promoter, but may be as far as 100,000 bp away.
What kind of protein is expected to enhance the ability of TFIID to initiate transcription?
Multiple choice question.
Repressor proteins
Mediator
Activator proteins
Activator proteins
The transactivation domain of coactivators promotes the activation of RNA polymerase, often by interacting with ______.
Multiple choice question.
general transcription factors
DNA
origin of replication
repressors
general transcription factors
TFIID binds to the ____ box and helps recruit RNA polymerase II to the core ____.
TATA; promoter
The function of TFIID is inhibited by ____, which prevent the binding of TFIID to the ____ box.
repressors; TATA
A regulatory element that functions in the forward or reverse direction is said to be
bidirectional
The protein complex that mediates the interaction between RNA polymerase II and regulatory transcription factors is called
mediator
A protein that increases the rate of transcription but does not directly bind to the DNA is called a
coactivator
Activator proteins stimulate the ability of ____ to phosphorylate the carboxyl-terminus of RNA polymerase II, which facilitates the switch between transcriptional initiation and elongation.
mediator
True or false: Regulatory elements must be located within 200 base pairs upstream from the core promoter.
False
Reason:
Regulatory elements are often located within 200 bp upstream from the core promoter, but can also be quite distant, even 100,000 bp away.
Select all that apply
The function of regulatory transcription factors must be modulated to ensure that genes are turned on ______.
Multiple select question.
all the time
at the proper time
in the correct cell type
in growing cells only
under the appropriate environmental conditions
at the proper time
in the correct cell type
under the appropriate environmental conditions
Coactivators usually contain a ____ domain that promotes the activation of RNA polymerase.
transactivation
Select all that apply
Repressors inhibit TFIID by ______.
Multiple select question.
inhibiting the function of mediator
preventing the binding of TFIID to the TATA box
changing nucleosome organization near the promoter region
inhibiting the ability of TFIID to recruit RNA polymerase II to the core promoter
preventing the binding of TFIID to the TATA box
inhibiting the ability of TFIID to recruit RNA polymerase II to the core promoter
What type of regulatory transcription factor utilizes the strategy depicted in the picture?
Multiple choice question.
HSP90
CREB protein
Steroid receptor
Steroid receptor
Mediator phosphorylates the ____-terminus of RNA polymerase II, stimulating progression to the ____ stage of transcription.
Blank 1: C, carboxy, or carboxyl
Blank 2: elongation
Steroid hormones are synthesized by ____ glands and secreted into the bloodstream, ultimately affecting the transcription or expression of genes in target cells.
endocrine
Activator proteins stimulate mediator to make what modification on RNA polymerase II?
Multiple choice question.
Phosphorylation
Methylation
Acetylation
Phosphorylation
Reason:
Methylation is associated with inactivation of gene regions.
Click and drag on elements in order
Place the steps in glucocorticoid hormone and receptor action in order from first to last.
The glucocorticoid hormone diffuses through the plasma membrane.
Two glucocorticoid receptors form a homodimer and travel through a nuclear pore into the nucleus.
HSP90 is released from the glucocorticoid receptor.
The glucocorticoid hormone binds to glucocorticoid receptors.
1. The glucocorticoid hormone diffuses through the plasma
membrane.
2. The glucocorticoid hormone binds to the
glucocorticoid receptors.
3. HSP90 is released from the glucocorticoid receptor.
4. Two glucocorticoid receptors form a homodimer and travel through a nuclear pore into the nucleus.
True or false: The function of regulatory transcription factors is modulated.
True
Reason:
Regulatory transcription factor function is modulated to ensure genes are turned on at the right time, in the correct cell type, and under appropriate environmental conditions.
A glucocorticoid response element functions as a(n) ______.
Multiple choice question.
enhancer
terminator
repressor
silencer
enhancer
The CREB protein is a regulatory transcription factor that is activated following an increase in ______.
Multiple choice question.
steroid hormones
cAMP
RNA
glucocorticoid hormones
cAMP
Regulatory transcription factors that respond to steroid hormones are called
steroid receptors
Steroid hormones bind regulatory transcription factors called steroid receptors in order to ______.
Multiple choice question.
be secreted into the bloodstream
make a covalent modification
affect gene transcription
affect gene transcription
Reason:
Before a hormone can be secreted it must be transcribed and translated.
The cAMP response element (CRE) contains ______ of a consensus sequence bound by the CREB protein, which has ______.
Multiple choice question.
one copy; one subunit.
two copies; two identical subunits.
one copy; two identical subunits.
two copies; two different subunits.
two copies; two identical subunits.
Following the binding of a hormone, two glucocorticoid ____ form a dimer and travel to the ____.
receptors; nucleus
The binding of a glucocorticoid receptor homodimer to a glucocorticoid response element ____ the transcription of the nearby gene.
activates or increases
Select all that apply
Select the factors that are involved in activation of the CREB protein.
Multiple select question.
Protein kinase A
G protein
cAMP
Mediator
Adenylyl cyclase
Protein kinase A
G protein
cAMP
Adenylyl cyclase
The cAMP ____ element-binding protein (____ protein) is a regulatory transcription factor that is activated in response to signaling molecules that increase cytoplasmic cAMP.
response; CREB
If chromatin is in a ____ conformation, transcription may be difficult or impossible.
closed
When chromatin is accessible to transcription factors and RNA polymerase, it is referred to as being in the ______ conformation.
Multiple choice question.
transcriptional
closed
open
open
The CREB protein binds to DNA at a sequence called the cAMP
response element
The placement of ____ at or near promoters often plays a key role in whether a gene is active or inactive.
nucleosomes
Click and drag on elements in order
Place the steps leading to the activation of the CREB protein in order from first to last. putting the first step at the top.
Protein kinase A travels to the nucleus and phosphorylates the CREB protein.
cAMP binds to protein kinase A.
Adenylyl cyclase catalyzes the synthesis of cAMP.
A G protein is activated, that subsequently activates adenylyl cyclase.
An extracellular signaling molecule binds to a plasma membrane receptor.
The CREB protein binds to CBP, and RNA polymerase is activated.
1. An extracellular signaling molecule binds to a plasma membrane receptor.
2. A G protein is activated, that subsequently activates adenylyl cyclase.
3. Adenylyl cyclase catalyzes the synthesis of cAMP.
4. cAMP binds to protein kinase A.
5. Protein kinase A travels to the nucleus and phosphorylates the CREB protein.
6. The CREB protein binds to CBP, and RNA polymerase is activated.
If chromatin is in a closed conformation, nucleosome position and histone composition ______.
Multiple choice question.
make it easier for the DNA to become single stranded during transcription
make it difficult for transcription factors to gain access to and bind their target sequences in the promoter DNA
make it difficult for the DNA to become single stranded during transcription
enhance the ability of transcription factors to gain access to and bind their target sequences in the promoter DNA
make it difficult for transcription factors to gain access to and bind their target sequences in the promoter DNA
ATP-____ ____ remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes.
dependent chromatin
Transcription can occur more easily when chromatin is in a(n) ______ conformation.
Multiple choice question.
closed
open
open
Reason:
Chromatin in an open conformation is more easily accessible to transcription factors and RNA polymerase.
A change in chromatin confirmation from closed to open often involves the movement of ______.
Multiple choice question.
helicases
nucleosomes
genes
promoters
nucleosomes
The SWI/SNF-family, the ISWI-family, the INO80-family, and the Mi-2 family are families of ______.
Multiple choice question.
chromatin-remodeling complexes
RNA polymerases
general transcription factors
regulatory transcription factors
chromatin-remodeling complexes
The ATPase subunit of chromatin-remodeling complexes is called DNA
translocase
What effect can ATP-dependent chromatin remodeling have on transcription?
Multiple choice question.
Repression only
Activation only
Neither activation nor repression
Both activation and repression
Both activation and repression
Most histone genes encode standard histone proteins, but some have accumulated mutations that change the amino acid sequence of the histone proteins. These proteins are called histone
variants
When chromatin is accessible to transcription factors and RNA polymerase, it is referred to as being in the ______ conformation.
Multiple choice question.
closed
open
transcriptional
open
Generally, ____ histones are incorporated into nucleosomes during S phase of the cell cycle. Later, histone ____ are added by chromatin-remodeling complexes.
standard; variants
The placement of ____ at or near promoters often plays a key role in whether a gene is active or inactive.
nucleosomes
Which histone variant favors gene activation when incorporated into a chromosomal region where a particular gene is found?
Multiple choice question.
H2A.Bbd
cenH3
MacroH2A
H10
H2A.X
H2A.Bbd
Reason:
MacroH2A is found in inactivated chromatin and plays a role in chromatin compaction.
Reason:
H2A.X plays a role in DNA repair.
ATP-dependent chromatin remodeling is carried out by a protein complex that recognizes ____ and uses ____ to alter their configuration.
nucleosomes; ATP
Core ____ proteins contain a globular domain and a flexible amino-terminal tail. DNA wraps around the globular domains, and the amino-terminal tails protrude from the chromatin.
histone
Which reaction is catalyzed by the DNA translocase enzyme found in all chromatin-remodeling complexes?
Multiple choice question.
histone methylation
DNA methylation
ATP hydrolysis
histone acetylation
ATP hydrolysis
Select all that apply
Select the histones for which variants have been identified.
Multiple select question.
H3
H1
H2A
H4
H2B
H3
H1
H2A
H2B
What is the purpose of histone variants?
Multiple choice question.
To change nucleosome positioning
To stop transcription
They are mutant proteins with no special function.
To create functionally specialized regions of chromatin
To create functionally specialized regions of chromatin
Reason:
Only some variants promote an open conformation of chromatin.
Which histone variant is abundant on the inactivated X chromosome in female mammals?
Multiple choice question.
cenH3
H2A.X
MacroH2A
spH2B
MacroH2A
Reason:
H2A.X is found in nucleosomes surrounding the transcriptional start sites of promoters on many chromosomes.
Select all that apply
Select the common types of covalent modifications made to the amino-terminal tails of histones.
Multiple select question.
Ubiquitination
Acetylation
Methylation
Phosphorylation
Acetylation
Methylation
Phosphorylation
Positively charged ____ within core histone proteins can be acetylated by histone ____.
lysines; acetyltransferases
The pattern of covalent modifications to histone tails provides binding sites for proteins that affect the degree of transcription. Certain patterns can either ____ or ____ transcription.
Blank 1: promote, activate, enhance, increase, or induce
Blank 2: inhibit, repress, silence, or decrease
According to the histone code hypothesis, different patterns of covalent modifications to the amino-terminal tails of histones can _____ the degree of transcription of genes in the region.
Multiple choice question.
increase only
neither increase or decrease
decrease only
either increase or decrease
either increase or decrease
What affect does acetylation have on lysines in core histone protein tails?
Multiple choice question.
Eliminates the negative charge on lysine, disrupting the electrostatic attraction between the histone and the positively charged DNA backbone
Makes an additional positive charge on lysine, causing the DNA to bind more strongly to the histone
Eliminates the positive charge on lysine, disrupting the electrostatic attraction between the histone and the negatively charged DNA backbone
Makes an additional negative charge on lysine, causing the DNA and the histone to repel one another
Eliminates the positive charge on lysine, disrupting the electrostatic attraction between the histone and the negatively charged DNA backbone
Reason:
The lysine side chain has a positive charge.
____ can change in location along a DNA molecule, by replacement of a standard histone with a histone variant, and through covalent modifications on histone tails.
Nucleosomes
According to the ____ ____ hypothesis, the pattern of ____ modification acts like a language or code in specifying alterations in chromatin structure.
histone code; histone
Select all that apply
Mapping the locations of nucleosomes in the genomes allows for the determination of ______.
Multiple select question.
where nucleosomes are located
whether genes will be active or not
where DNA mutations occur
where histone variants are found
where covalent modifications of histones occur
where nucleosomes are located
where histone variants are found
where covalent modifications of histones occur
Select all that apply
The pattern of covalent modifications of amino acids on the amino-termini of histones can ______.
Multiple select question.
edit the sequence of RNA produced from the histone-associated DNA
attract chromatin remodeling complexes that alter nucleosome positions to promote transcription
interfere with proteins involved in DNA replication
attract proteins that inhibit transcription
attract chromatin remodeling complexes that alter nucleosome positions to promote transcription
attract proteins that inhibit transcription
Select all that apply
Select the procedures that are used in chromatin immunoprecipitation sequencing (ChIP-Seq).
Multiple select question.
PCR
DNA sequencing
Protein gel electrophoresis
Immunoprecipitation
DNA gel electrophoresis
PCR
DNA sequencing
Immunoprecipitation
DNA gel electrophoresis
Which histone variant is abundant on the inactivated X chromosome in female mammals?
Multiple choice question.
cenH3
H2A.X
MacroH2A
spH2B
MacroH2A
Reason:
H2A.X is found in nucleosomes surrounding the transcriptional start sites of promoters on many chromosomes.
True or false: The ChIP-Seq method is used on species whose entire genome has been sequenced already.
True
Reason:
The ChIP-Seq method is used on species whose genome has already been sequenced because scientists use computers to analyze where in the genome the sequenced fragments of DNA from ChIP-Seq are located.
Select all that apply
Select ways that nucleosomes can change.
Multiple select question.
Change in histones to variants with specialized roles
Change in location
Covalent modifications to the carboxyl-terminal tails of histones
Covalent modifications to the amino-terminal tails of histones
Change from DNA to RNA within nucleosomes
Change in histones to variants with specialized roles
Change in location
Covalent modifications to the amino-terminal tails of histones
The mapping of ____ allows researchers to understand their location, to understand where ____ variants are found, and to learn where covalent modifications of histones occur.
nucleosomes; histone
The core promoter of active genes is found in a(n) ____-free ____, which is a segment of DNA that is missing histones.
nucleosome; region
Click and drag on elements in order
Order the steps in chromatin immunoprecipitation sequencing (ChIP-Seq) from first to last, putting the first step at the top.
The remaining DNA is subjected to gel electrophoresis. Fragments of 150 bp are saved.
Heavy beads attached to antibodies that recognize specific histones are added the nucleosome mixture.
Living cells are treated with formaldehyde, broken open, and treated with micrococcal nuclease.
The mixture is centrifuged to separate the immunoprecipitated material, crosslinks are reversed, and proteases partially digest core histones.
Linkers are added to the DNA, then they are PCR amplified and subjected to DNA sequencing. DNA sequences are analyzed.
1. Living cells are treated with formaldehyde, broken open, and treated with micrococcal nuclease.
2. Heavy beads attached to antibodies that recognize specific histones are added the nucleosome mixture.
3. The mixture is centrifuged to separate the immunoprecipitated material, crosslinks are reversed, and proteases partially digest core histones.
4. The remaining DNA is subject to gel electrophoresis. Fragments of 150 bp are saved.
5. Linkers are added to the DNA, then they are PCR amplified and subjected to DNA sequencing, DNA sequences are analyzed.
Scientists use computer software to match sequences obtained from ChIP-____ to sequences on a genome map. In this way they can determine the positions of ____ in relation to genes of interest.
Seq; nucleosomes
A gene you are studying has an NFR flanked by a -1 and +1 nucleosome. Its transcriptional start site is located at the boundary between the NFR and the +1 nucleosome. This gene is likely found in ______.
Multiple choice question.
bacteria
mice
yeast
humans
yeast
Reason:
In animals, the transcriptional start site is located about 60 bp upstream, into the NFR region.
Select all that apply
Mapping the locations of nucleosomes in the genomes allows for the determination of ______.
Multiple select question.
where nucleosomes are located
where covalent modifications of histones occur
whether genes will be active or not
where histone variants are found
where DNA mutations occur
where nucleosomes are located
where covalent modifications of histones occur
where histone variants are found
What is the size of the nucleosome-free region found at the core promoter of active genes?
Multiple choice question.
15 bp
150 bp
1,500 bp
15,000 bp
150 bp
Nucleosomes containing the histone variant ____, which are usually found at the +1 nucleosome, are thought to be more easily removed from the DNA than those containing the standard histone ____.
Blank 1: H2A.Z, H2AZ, or H2A Z
Blank 2: H2A or h2a
Select all that apply
Select the procedures that are used in chromatin immunoprecipitation sequencing (ChIP-Seq).
Multiple select question.
PCR
DNA gel electrophoresis
Immunoprecipitation
Protein gel electrophoresis
DNA sequencing
PCR
DNA gel electrophoresis
Immunoprecipitation
DNA sequencing
Select all that apply
Enzymes that carry out what functions travel along with RNA polymerase II?
Multiple select question.
H4 methylation
Histone acetylation
H2B ubiquitination
H3 methylation
H2A phosphorylation
Histone acetylation
H2B ubiquitination
H3 methylation
At the end of many eukaryotic genes, a well-positioned nucleosome is followed by an NFR. This arrangement may be important for ______.
Multiple choice question.
transcriptional termination
transcriptional initiation
transcriptional repression
transcriptional termination
The mapping of ____ allows researchers to understand their location, to understand where ____ variants are found, and to learn where covalent modifications of histones occur.
nucleosomes; histone
Histone variant H3.3 is often found in the ______ regions of genes but is less common in ______ genes.
Multiple choice question.
silent; non-transcribed
transcribed; silent
silent; transcribed
non-transcribed; silent
transcribed; silent
Click and drag on elements in order
Place these steps in a simplified model for transcriptional activation of a eukaryotic gene in order from first to last, putting the first step at the top.
Recruitment of a chromatin-remodeling complex and a histone-modifying enzyme
Binding of an activator to an enhancer in the NFR
Recruitment of general transcription factors and RNA Pol II to the core promoter, allowing the formation of a preinitiation complex
Eviction or destabilization of histone octamers, allowing RNA pol II to pass, and elongation to occur
1. Binding of an activator to an enhancer in the NFR
2.
Recruitment of a chromatin-remodeling complex and a histone-modifying
enzyme
3. Recruitment of general transcription factors and RNA
Pol II to the core promoter, allowing the formation of a preinitiation
complex
4. Eviction or destabilization of histone octamers,
allowing RNA pol II to pass, and elongation to occur
Select the organism with the highest amount of DNA methylation.
Multiple choice question.
Yeast
Vertebrates
Drosophila
Vertebrates
What DNA sequence is methylated?
Multiple choice question.
5'-CG-3'
5'-CA-3'
5'-AC-3'
5'-GC-3'
5'-CG-3'
Histone ____ are proteins that bind histones and aid in the assembly of histone octamers.
chaperones
A histone variant found in the transcribed regions of genes is ______.
Multiple choice question.
H3.3
H10
MacroH2A
H2A.X
cenH3
H3.3
DNA methylation is the ____ attachment of methyl groups to DNA.
covalent
Methylation of the cytosine in both strands is called ____ methylation, and methylation of only one strand is called ____.
full; hemimethylation
Select all that apply
Enzymes that carry out what functions travel along with RNA polymerase II?
Multiple select question.
H2B ubiquitination
H2A phosphorylation
H3 methylation
Histone acetylation
H4 methylation
H2B ubiquitination
H3 methylation
Histone acetylation
What is the name for stretches of DNA of 1000-2000 bp in length containing a high number of CpG sites that are found near gene promoters?
Multiple choice question.
transcription factors
start codons
CpG islands
stop codons
CpG islands
Histone variant H3.3 is often found in the ______ regions of genes but is less common in ______ genes.
Multiple choice question.
silent; non-transcribed
transcribed; silent
silent; transcribed
non-transcribed; silent
transcribed; silent
Genes that code for proteins that are required in most cells of a multicellular organism are called ______.
Multiple choice question.
CpG islands
tissue-specific genes
promoter genes
housekeeping genes
housekeeping genes
Genes that are highly regulated and may be expressed only in certain cell types are called ____-____ genes.
tissue-specific
In general ____ CpG islands correlate with active genes, and ____ CpG islands correlate with suppressed genes.
unmethylated; methylated
Select all that apply
Select the ways methylation can affect transcription.
Multiple select question.
The methylation of CpG islands may prevent or enhance the binding of regulatory transcription factors to the promoter region.
Methyl-CpG binding proteins recruit other proteins that enhance transcription.
RNA polymerase movement is hindered by CpG methylation.
Methyl-CpG binding proteins recruit other proteins that inhibit transcription.
The methylation of CpG islands may prevent or enhance the binding of regulatory transcription factors to the promoter region.
Methyl-CpG binding proteins recruit other proteins that inhibit transcription.
In order to inhibit transcription, a methyl-CpG-binding protein would bind to a methylated CpG island and recruit which of the following enzymes to modify the histones in the region?
Multiple choice question.
histone deacetylase
histone acetyltransferase
histone phosphorylase
DNA methyltransferase
histone deacetylase
The cytosines in CpG islands near housekeeping genes are
unmethylated
If fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be ____. If the same sequence of nonmethylated DNA is introduced into a cell, it will be ____ in daughter cells.
Blank 1: methylated or fully methylated
Blank 2: nonmethylated, unmethylated, or non methylated
CpG islands near the promoters of tissue-specific genes are often ______.
Multiple choice question.
unmethylated
methylated
hemimethylated
phosphorylated
methylated
Reason:
Expression of tissue-specific genes are highly regulated and may be silenced by methylation of CpG islands.
The methylation of DNA that was previously unmethylated is called ____ ____ methylation.
de novo
Proteins called ____-CpG-____ proteins bind methylated sequences and recruit other proteins to the region to ____ transcription.
Blank 1: methyl or methylated
Blank 2: binding
Blank 3: inhibit, repress, stop, suppress, minimize, reduce, or block
A process called ____ methylation seems to be the primary mechanism by which DNA in vertebrate and plant cells are methylated.
maintenance
When a methyl-CpG-binding protein associates with a methylated CpG island, it recruits an enzyme called histone ____ to modify histone proteins which makes it more difficult to remove nucleosomes from the DNA.
deacetylase
Genes that code for proteins that are required in most cells of a multicellular organism are called ______.
Multiple choice question.
promoter genes
housekeeping genes
CpG islands
tissue-specific genes
housekeeping genes
When a fully methylated DNA segment of DNA is replicated, the newly made daughter strand contains ____ cytosines. This DNA is said to be ____.
Blank 1: unmethylated
Blank 2: hemimethylated
True or false: The methylation state of DNA is inherited during cell division.
True
Reason:
DNA methylation patterns are retained following DNA replication and into future daughter cells.
In genomic ____, specific genes are ____ during oogenesis or spermatogenesis, but not both.
imprinting; methylated
Which of the following represents de novo methylation?
Multiple choice question.
The methylation of DNA that was previously unmethylated
The methylation of DNA that was previously methylated
The methylation of any DNA, regardless of previous methylation status
The methylation of DNA that was previously unmethylated
Select the most common process regarding methylation.
Multiple choice question.
Demethylation
Maintenance methylation
De novo methylation
Maintenance methylation
Reason:
De novo methylation and demethylation occur infrequently and are highly regulated events.
A protein called ____ usually cleaves DNA at sites where regulatory transcription factors bind, but does not usually cleave DNA that is wrapped around ____.
Blank 1: DNaseI, DNasel, or DNase1
Blank 2: histones or histone
When fully methylated DNA is replicated, it is initially hemimethylated. The hemimethylated DNA is recognized by DNA methyltransferase, which makes it fully methylated. This process is called ______ methylation.
Multiple choice question.
replication
maintenance
de novo
maintenance
The ENCODE Project mapped more than 4 ____ regulatory regions where ____ specifically interact with the DNA.
Blank 1: million
Blank 2: proteins or protein
In genomic imprinting, following fertilization, if a gene is methylated only during spermatogenesis, ______.
Multiple choice question.
the alleles from the father and mother will both be methylated in the somatic cells of the offspring
neither the maternal or paternal alleles will be methylated in the somatic cells of the offspring
the allele from the father will be methylated in the somatic cells of the offspring, but the allele from the mother will be unmethylated
the allele from the father will be methylated in the somatic cells of the offspring, but the allele from the mother will be unmethylated
Select all that apply
Select the strategies used by ENCODE investigators to identify functional elements in the human genome.
Multiple select question.
Identify sites of histone modification.
Identify sites where DNAseI can cleave the DNA.
Isolate and sequence RNA molecules transcribed by the human genome.
Identify DNA mutations.
Map DNA methylation sites.
Identify sites where DNA is phosphorylated.
Identify DNA binding sites for transcription factors.
Identify sites of histone modification.
Identify sites where DNAseI can cleave the DNA.
Isolate and sequence RNA molecules transcribed by the human genome.
Map DNA methylation sites.
Identify DNA binding sites for transcription factors.
In order to regulate the translation of both ferritin and transferrin receptor mRNAs, the iron regulatory protein (IRP) binds to the _____ of the mRNAs.
Multiple choice question.
terminator region
coding sequence
iron response element
promoter region
iron response element
True or false: The majority of the human genome is junk DNA with no function.
False
Reason:
Scientists once thought that the human genome is mostly non-functional DNA; however, they have recently discovered that more than 80% of the human genome is linked to a biological function.
Binding of IRP to the iron response element (IRE) 3'-UTR ______.
Multiple choice question.
stabilizes the ferritin mRNA
induces degradation of the ferritin mRNA
induces degradation of the transferrin receptor mRNA
stabilizes the transferrin receptor mRNA
stabilizes the transferrin receptor mRNA
Reason:
Binding of IRP to the iron response element (IRE) 3'-UTR stabilizes the transferrin mRNA by blocking the action of endonucleases that degrade RNA.
Which of the following represents de novo methylation?
Multiple choice question.
The methylation of DNA that was previously methylated
The methylation of any DNA, regardless of previous methylation status
The methylation of DNA that was previously unmethylated
The methylation of DNA that was previously unmethylated
A sequence found in both ferritin and transferrin receptor mRNAs that is recognized by an RNA-binding protein is called the ______.
Multiple choice question.
iron regulatory protein site
iron response element
iron regulatory element
iron response element
When iron levels in the cytosol rise, iron binds to an iron response protein (IRP) so that it dissociates from the mRNA for transferrin receptor. The mRNA is then ______.
Multiple choice question.
translated at a low rate
degraded
translated at a high rate
degraded
When iron levels are abundant in the cytosol, iron binds to the ____, enabling the translation of ____ mRNA.
IRP; ferritin
Which statement accurately describes the location of iron response elements (IREs) in mRNAs for ferritin and transferrin receptor?
Multiple choice question.
The IRE is in the 5'-UTR of both mRNAs.
The IRE is in the 3'-UTR end of ferritin mRNA but in the 5'-UTR of transferrin receptor mRNA.
The IRE is in the 5'-UTR end of ferritin mRNA but in the 3'-UTR of transferrin receptor mRNA.
The IRE is in the 3'-UTR of both mRNAs.
The IRE is in the 5'-UTR end of ferritin mRNA but in the 3'-UTR of transferrin receptor mRNA.
When cytosolic iron levels are very low, binding of an iron response protein (IRP) to the iron regulatory element (IRE) of transferrin receptor mRNA ______.
Multiple choice question.
prevents degradation of the mRNA
prevents the binding of the mRNA to the ribosome
causes the mRNA to be digested by an endonuclease
prevents degradation of the mRNA
Binding of IRP to the iron response element (IRE) 3'-UTR ______.
Multiple choice question.
induces degradation of the transferrin receptor mRNA
induces degradation of the ferritin mRNA
stabilizes the transferrin receptor mRNA
stabilizes the ferritin mRNA
stabilizes the transferrin receptor mRNA
Reason:
Binding of IRP to the iron response element (IRE) 3'-UTR stabilizes the transferrin mRNA by blocking the action of endonucleases that degrade RNA.
Iron response elements (IREs) can be found in the 5'-UTR of ____ mRNA and in the 3'-UTR of ____ ____ mRNA.
Blank 1: ferritin, ferritin-encoding, or ferritin encoding
Blank 2: transferrin
Blank 3: receptor
Which statement accurately describes the location of iron response elements (IREs) in mRNAs for ferritin and transferrin receptor?
Multiple choice question.
The IRE is in the 3'-UTR of both mRNAs.
The IRE is in the 5'-UTR end of ferritin mRNA but in the 3'-UTR of transferrin receptor mRNA.
The IRE is in the 3'-UTR end of ferritin mRNA but in the 5'-UTR of transferrin receptor mRNA.
The IRE is in the 5'-UTR of both mRNAs.
The IRE is in the 5'-UTR end of ferritin mRNA but in the 3'-UTR of transferrin receptor mRNA.