Ch 16

cis acting

A DNA segment that must be adjacent to the gene(s) it regulates is a __________-_________ element.

allolactose

A conformational change that prevents the repressor from binding to the lac operator occurs when ___________ binds to the lac repressor.

repressor activator

A corepressor is a small molecule that binds to a __________ protein, thereby causing the protein to bind to the DNA, while an inhibitor binds to an ___________ protein and prevents it from binding to the DNA.

operator site.

A loss-of-function mutation in a gene encoding a repressor protein has the same effect as a mutation in the lacY gene operator site. promoter sequence. lacZ gene

repressor

A regulatory protein that binds to DNA and inhibits transcription is a(n) ________.

activator

A regulatory protein that increases the rate of transcription is a(n) ___________.

prevents the repressor from binding to DNA.

Allolactose is a small effector molecule that binds to the lac repressor and increases the affinity of the repressor for CAP. facilitates the repressor binding to DNA. prevents the repressor from binding to DNA. prevents the repressor from binding to RNA polymerase.

repressor; activator

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. activator; polymerase activator; repressor repressor; ribosome repressor; activator

increase.

An inducer is a small effector molecule that causes transcription to decrease. increase. remain constant

b. the combination of several factors determines the expression of any given gene

Combinatorial control refers to the phenomenon that a. transcription factors always combine with each other when regulating genes b. the combination of several factors determines the expression of any given gene c. small effector molecules and regulatory transcription factors are found in many different combinations d. genes and regulatory transcription factors must combine with each other during gene regulation

A knot-like structure would prevent proteins such as TFIID and RNA polymerase from binding to the gene and would thereby inhibit transcription of the gene.

Describe how the compaction of nucleosomes into a knot-like structure could silence gene expression

histone modifications may directly affect the interaction between histones and the DNA, or they may affect the binding of other proteins to the chromatin

Describe two different ways that histone modifications may alter chromatin structure

but it is terminated before the entire mRNA is made.

During attenuation, transcription begins, but translation stops after the eighth codon. but then a repressor protein binds to the operator. but it is terminated before the entire mRNA is made. and continues beyond the operon.

a particular enzyme appears within a cell only after the cell has been exposed to the substrate for that enzyme.

Enzyme adaptation refers to the observation that enzymes are always present in cells regardless of whether a substrate is present or absent. a particular enzyme appears within a cell only after the cell has been exposed to the substrate for that enzyme. an enzyme must be present in a cell prior to the cell being exposed to the substrate for that enzyme. a particular substrate appears within a cell only after the cell has been exposed to the enzyme for that substrate.

The glucocorticoid receptor binds specifically next to genes that have an adjacent GRE.

Explain why the glucocorticoid receptor binds specifically next to the core promoter of certain genes, but not next to the core promoter of most genes.

A corepressor binds to a repressor protein, while an inhibitor binds to an activator protein.

How do a corepressor and an inhibitor differ? 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. An inhibitor binds to a repressor protein, while a corepressor 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.

nucleosome eviction may allow certain proteins access to bind to particular sites in the DNA

How might nucleosome eviction affect transcription

catabolic; anabolic

Inducible operons usually encode ______ enzymes, and repressible operons usually encode ______ enzymes. anabolic; catabolic catabolic; anabolic

F' factor

Monod, Jacob, and Pardee learned about the lac operon using bacterial strains called merozygotes. Since lacI encodes a diffusible protein, in a merozygote, the gene on ________ __________the could supply the mutant cell with functional repressor protein.

control of proteins already in the cell.

Posttranslational regulation refers to regulation of translation of mRNAs. control of transcription initiation. control of proteins already in the cell. regulation of transcription termination.

lacZ, lacY, lacA

Select all of the following that are protein-encoding genes in the lac operon. lacZ lacX lacO lacA lacY

trpA trpE trpB trpD trpC

Select the genes in the trp operon. trpA trpE trpB trpD trpY trpZ trpC

three

Studies indicate that the lac operon has ______ operator site(s) for the lac repressor. a single three dozens of two

blocks transcription.

The Lac repressor protein binds to the operator and blocks transcription. stops transport of lactose. prevents translation. aids RNA polymerase.

lacI

The ______ gene encodes a repressor protein. lacP lacO lacI lacA lacZ

glucose and galactose

The enzyme beta-galactosidase cleaves the sugar lactose into __________ and __________.

LacZ

The enzyme β-galactosidase is encoded by which gene? LacA LacZ LacO LacY

enzymes used in tryptophan biosynthesis.

The genes in the trp operon encode enzymes used in tryptophan biosynthesis. regulatory proteins only. enzymes used to metabolize tryptophan in the environment. only the subunits of the trp repressor protein.

allolactose

The intracellular concentration of the inducer _____________ remains high as long as lactose is available in the environment.

the trp leader peptide.

The mRNA made form the trpL gene contains codons for 14 amino acids that form chorismate synthase. anthranilate synthase. the trp leader peptide. the trp repressor protein.

regulation

The phenomenon in which the level of gene expression can vary under different conditions is gene __________.

concentration

The probability that allolactose will bind to the lac repressor depends on the allolactose ________ in the bacterial cell.

b. de novo methylation

The process in which completely unmethylated DNA becomes methylated is called a. maintenance methylation b. de novo methylation c. primary methylation d. demethylation

allolactose

The small effector molecule _________ prevents the lac repressor from binding to the operator site.

catabolite repression

The somewhat imprecise term that describes how transcriptional regulation is influenced by glucose is ___________ ___________

attenuation

Transcription begins but terminates before the entire mRNA is made during ___________.

constitutive

Unregulated genes are also called ___________ genes.

constant levels of expression.

Unregulated genes have ______ variable levels of expression. constant or variable levels of expression depending on the gene. constant levels of expression.

Both result in constitutive expression of the lac operon.

What effect would either a loss-of-function mutation in the lacI gene or a mutation in operator that prevents repressor binding have? Both result in no expression of the lac operon under any circumstance. Both result in constitutive expression of the lac operon. The two mutations would result in completely different phenotypes.

Merozygote

What is the name for a strain of bacteria containing an F' factor? Diploid Heterodimer Mutant Merozygote

A cis-acting element must be adjacent to the gene it is regulating.

Why is a merozygote better at complementing a mutation in a trans-acting factor than in a cis-acting element? A cis-acting element makes a diffusible product. 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.

An NFR is needed at the core promoter so that transcription factors can recognize enhancers and the preinitiation complex can form

Why is an NFR needed at the core promoter for transcription to occur

A trans-acting factor

Would using a merozygote better indicate regulation of a gene by a trans-acting factor or a cis-acting element? Both A cis-acting element A trans-acting factor Neither

b.5'-TGAC-3' 3'-ACTG-5'

a bidirectional enhancer has the following sequence 5'-GTCA-3' 3'-CAGT-5' which of the following sequence would also be a functional enhancer? a. 5'-ACTG-3' 3'-TGAC-5' b.5'-TGAC-3' 3'-ACTG-5' c. 3'-GTCA-5' 5'-CAGT-3' d. 3'-TGAC-5' 5'-ACTG-3'

d. do all of the above

a chromatin-remodeling complex may a. change the locations of nucleosomes b. evict nucleosomes from DNA c. replace standard histones with histone variants d. do all of the above

d. be both a and b

epigenetic changes may a. be programmed during development b. be caused by environmental changes c. involve changes in the DNA sequence of a gene d. be both a and b

in part (a), DNA methylation blocks and activator protein from binding to the DNA. This prevents transcriptional activation.

explain why the events shown in part (a) inhibit transcription

d. Xist is expressed only on Xi, and Tsix is expressed only on Xi

for XCI to occur, where are the Xist and Tsix genes expressed a. Xist is expressed only on Xa, and Tsix is expressed only on Xi b. Xist is expressed only on Xi, and Tsix is expressed only on Xa c. Xist is expressed only on Xa, and Tsix is expressed only on Xa d. Xist is expressed only on Xi, and Tsix is expressed only on Xi

d. all of the above are possible ways for methylation to affect transcription

how can methylation affect transcription a. it may prevent the binding of regulatory transcription factors b. it may enhance the binding of regulatory transcription factors. c. it may promote the binding of methyl-CpG-binding proteins, which inhibit transcription d. all of the above are possible ways for methylation to affect transcription

if TFIID cannot bind to the TATA box, RNA polymerase will not be recruited to the core promoter, and therefore transcription will not begin.

if a repressor prevents TFIID from binding to the TATA box, why does this inhibit transcription?

operator

t has been shown that the lac operon has three___________ sites to which the lac repressor can bind.

d. all of the above

transcriptional activation of eukaryotic genes involves which of the following events a. changes in nucleosome locations b. changes in histone composition within nucleosomes c. histone modifications d. all of the above

contains the sequences of two or more genes.

A polycistronic mRNA contains the sequences for several genes and control regions. contains the sequences for genes from different operons. contains the sequence for only one gene. contains the sequences of two or more genes.

polycistronic

An operon encodes a __________ mRNA, an RNA that contains the sequences of two or more genes.

a single promoter.

An operon is a group of two or more genes under the transcriptional control of two or more promoters. different polymerases. a single promoter.

repressible; inducible

Anabolic enzymes are usually encoded by ______ operons, and ______ operons usually encode catabolic enzymes. inducible; repressible repressible; inducible

are unregulated.

Constitutive genes are unregulated. respond to amino acid levels in the cell. are regulated by glucose levels. respond to lactose levels in the cell.

c. de novo methylation occurs in sperm and maintenance methylation occurs in somatic cells of offspring

For the Igf2 gene, where do de novo methylation and maintenance methylation occur a. de novo methylation occurs in sperm, and maintenance methylation occurs in egg cells d. de novo methylation occurs in egg cells, and maintenance methylation occurs in sperm cells. c. de novo methylation occurs in sperm and maintenance methylation occurs in somatic cells of offspring d. de novo methylation occurs in egg cells, and maintenance methylation occurs in somatic cells of offspring

the mutation would cause the overproduction of ferritin, because ferritin synthesis would occur even if iron levels were low

If a mutation prevented IRP from binding to the IRE in the ferritin mRNA, how would the mutation affect the regulation of ferritin synthesis? Do you think there would be too much or too little ferritin?

promoter

In an operon, the ______ signals the beginning of transcription. origin promoter terminator ribosome binding site

is stopped prematurely.

In attenuation, transcription is stopped prematurely. continues to the transcription stop site. proceeds half-way through the operon. never starts.

the rate of transcription initiation.

In bacteria, the most common way to regulate gene expression is by influencing the rate of transcription elongation. the rate of translation initiation. the frequency of cell division. the rate of transcription initiation.

glucose

In catabolite repression, transcription is influenced by the presence of glucose. lactose. fructose. galactose.

d. any of the above

Regulatory transcription factors can be modulated by a. the binding of small effector molecules b. protein-protein interventions c. covalent modifications d. any of the above

allolactose

The binding of ______ to the lac repressor promotes a conformational change that prevents the repressor from binding to the lac operator. β-galactosidase Lac permease allolactose lactose

a. inhibition of translation of the ferritin mRNA

The binding of iron regulatory protein (IRP) to the iron response element (IRE) in the 5'-untranslated region of the ferritin mRNA results in a. inhibition of translation of the ferritin mRNA b. stimulation of translation of the ferritin mRNA c. degradation of fthe ferritin mRNA d. both a and c

depleted from the environment.

The binding of the lac repressor to the operator shuts down transcription from the lac operon when lactose is plentiful in the environment. depleted from the environment. present in or absent from the environment.

trpL

The mRNA made from the ______ gene contains codons for 14 amino acids that form the trp leader peptide. trpA trpC trpB trpL

glucose; decrease

The transport of ______ into a cell causes a _______ in the concentration of cyclic-AMP by inhibiting adenylate cyclase. tryptophan; increase allolactose; increase glucose; decrease lactose; decrease

adenyl cyclase

The transport of glucose into a bacterial cell causes the intracellular level of cyclic-AMP to fall because the enzyme _____________ _________ is inhibited.

attenuation

The trp operon is regulated by a repressor protein and by ___________ in which transcription is stopped prematurely.

False

True or false: Gene expression is always the same. True False

False Gene expression can vary under different conditions.

True or false: Gene regulation is constant. True False

Trans-acting factor

What type of regulation does not need to be adjacent to the gene(s) it is regulating? Trans-acting factor Cis-acting factor

a. a greater level of DNA methylation and a decrease in the expression of the Agouti gene.

When mice carrying the A^vy allele exhibit a darker coat, this phenotype is thought to be caused by dietary factors that result in a. a greater level of DNA methylation and a decrease in the expression of the Agouti gene. b. a lower level of DNA methylation and a decrease in the expression of the Agouti gene c. a greater level of DNA methylation and the over expression of the Agouti gene d. a lower level of DNA methylation and the overexpression of the Agouti gene

a. influences chromatin structure

according to the histone code hypothesis, the pattern of histone modifications acts like a language that a. influences chromatin structure b. promotes transcriptional termination c. inhibits the elongation of RNA polymerase d. does all of the above

c. both a and b

an epigenetic modification to a specific gene may initially be established by a. a transcription factor b. a non-coding RNA c. both a and b d. none of the above

at the level of DNA sequences, queen and worker bees are not different from each other. However, differences in gene expression due to epigenetics can explain the morphological differences between the two types of female bees.

are queen and worker bees genetically different from each other?

histone eviction or displacement is needed for elongation to occur because RNA polymerase cannot transcribe through nucleosomes. It needs to unwind the DNA for transcription to take place.

explain why histone eviction or displacement is needed for the elongation phase of transcription to occur

The choice occurs only during embryonic development

in X-chromosome inactivation, when is the choice made as to which X chromosome is inactivated? Does this choice occur in embryonic cells, in adult somatic cells, or both?

De novo methylation occurs on unmethylated DNA, whereas maintenance methylation occurs on hemimethylated DNA

what is the difference between de novo methylation and maintenance methylation

inhibits an enzyme that acts early in the pathway.

In feedback inhibition, the final product in a metabolic pathway 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.

trpL

The mRNA made from the ______ gene contains codons for 14 amino acids that form the trp leader peptide. trpB trpL trpC trpA

diffusible protein.

The normal lacI gene on the F' factor could rescue the lacI-mutants because the product of the lacI gene encodes a phospholipid. membrane protein. diffusible protein. cis-acting protein.

adaptation

The observation that a particular enzyme appears within a cell only after a cell has been exposed to the enzyme's substrate is called enzyme ___________

promoter terminator

The operon is flanked by a _______ that signals the beginning of transcription and a _________ that signals the end of transcription.

posttranslational

The term ____________ regulation refers to control of proteins already present in the cell.

lacZ, lacY, lacA

The three protein-encoding genes in the lac operon are _________, _________, and ________.

False The most common way that bacteria regulate gene expression is by influencing the rate of transcription initiation.

True or false: The rate of transcription initiation rarely influences overall gene expression. True False

is terminated before transcription of the genes required for tryptophan biosynthesis.

When attenuation occurs, the mRNA is transcribed to include the genes required for tryptophan biosynthesis. is terminated before transcription of the genes required for tryptophan biosynthesis. is transcribed past the attenuator sequence.

When an activator interacts with mediator, it causes mediator to phosphorylate CTD, which causes RNA polymerase to proceed to the elongation phase of transcription.

when an activator protein interacts with mediator, how does this affect the function of RNA polymerase

f. all of the above can have an epigenetic effect on gene expression

which of the following are examples of molecular changes that can have an epigenetic effect on gene expression? a. chromatin remodeling b. covalent histone modification c. localization of histone variants d. DNA methylation e. feedback loops f. all of the above can have an epigenetic effect on gene expression

b. the core promoter is found in a nucleosome-free region

which of the following characteristics is typical of a eukaryotic gene that can be transcribed a. the core promoter is wrapped around a nucleosome b. the core promoter is found in a nucleosome-free region c. the terminator is wrapped around a nucleosome d. none of the above characteristics is typical of a eukaryotic gene

merozygote

A strain of bacteria containing F' factor genes is called a ________, or a partial diploid.

mRNA near the start codon.

A translational repressor protein binds to mRNA near the start codon. an enzyme in an amino acid biosynthetic pathway. an uncharged tRNA. the operator sequence of the DNA.

stabilize a secondary structure that prevents translation.

A translational repressor protein may bind to the mRNA and cause the mRNA to be terminated prematurely. stabilize a secondary structure that prevents translation. cause the ribosome to bind too tightly to the Shine-Delgarno sequence. cause the RNA polymerase to release the DNA.

operon

A(n) _________ is a group of two or more genes under the transcriptional control of a single promoter.

trpL

When attenuation occurs, the mRNA from the trp operon is made as a short piece that terminates shortly past the _____ gene. trpE trpD trpL trpA

the intracellular concentration of allolactose falls.

When lactose is depleted from the environment, the intracellular concentration of allolactose falls. the intracellular concentration of allolactose rises. the affinity of the repressor for DNA decreases. the affinity of allolactose for the repressor increases.

b. the attachment of ubiquitin to histone proteins

which of the following mechanisms may be involved when PRC1 complexes silence gene expression? a. the compaction of nucleosomes b. the attachment of ubiquitin to histone proteins c. the direct inhibition of transcription factors, such as TFIID d. any of the above may be involved in silencing of gene expression by PRC1 complexes