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 tRNA^Trp, 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.