chapter sixteen: control of gene expression

What percentage of the total mRNA produced as primary transcript exits the nucleus? a) 5% b) 100% c) 50%

5%

Some activators interact directly with RNA polymerase II while others require the assistance of a ______.

coactivator

The production of a functional miRNA begins in the nucleus and ends in the ______ of the cell.

cytoplasm

The structure of chromatin can be modified by altering either the DNA or the ______ attached to DNA.

histones

In eukaryotes, gene regulation is geared toward maintaining which of the following? a) The function of the nucleus b) Homeostasis c) Constant levels of all necessary enzyme throughout the life of a cell d) Constant levels of oxygen

homeostasis

High levels of DNA methylation correlate with which of the following? a) Areas of significant mutations b) Inactive genes c) Active genes d) Allele-specific gene expression seen in genomic imprinting

inactive genes allele-specific gene expression seen in genomic imprinting

Which of the following are modifications that have been documented during RNA editing? a) Insertion of uracil residues b) Chemical modification of bases that change their base-pairing properties c) Replacement of uracil residues with thymine residues d) Excision of several codons from the mRNA

insertion of uracil residues chemical modification of bases that change their base-pairing properties

Select the statements that are true about ubiquitin. a) It is a modified amino acid found in all eukaryotic cells. b) It can exist as an isolated molecule. c) It can be in the form of longer chains attached to other proteins. d) It is made of 76 amino acids. e) When attached to other proteins, It marks them for export out of the cell.

it can exist as an isolated molecule it can be in the form of longer chains attached to other proteins it is made of 76 amino acids

In the absence of tryptophan, which of the following describes the trp repressor? a) It can bind its operator. b) It cannot bind its operator.

it cannot bind its operator

The short half-life of mRNAs for regulatory proteins is crucial for which reason? a) Those proteins need to be present in very low amounts to function properly. b) It enables the cell to change the levels of those proteins very rapidly. c) Many viral mRNAs are similar to the mRNA of regulatory genes in cells.

it enables the cell to change the levels of those proteins very rapidly

The lac repressor binds to what site within the lac operon? a) lacZ b) lacO c) lacA d) lacl e) lacP

lacO

Which of the following is not part of the lac operon? a) lacO b) lacZ c) lacA d) lacl e) lacP

lacl

miRNAs were first discovered in a group of organisms called ______.

nematodes

Which of the following are considered parts of the lac operon? a) Regulatory regions of the operon (promoter and operator) b) Repressor gene (lacI) c) Enhancer gene located downstream from the operon d) The gene encoding the CAP protein e) Genes required for utilization of lactose

regulatory regions of the operon (promoter and operator) repressor gene (lacI) genes required for utilization of lactose

Large complexes of proteins that include enzymes that can modify histones, DNA and chromatin structure itself are known as chromatin-______ complexes.

remodeling

When the lac repressor is bound to the operator region of DNA which of the following enzymes is prevented from binding to the promoter region? a) RNA polymerase b) Catalase c) DNA polymerase d) Helicase

rna polymerase

The binding of the corepressor to the trp repressor results in what? a) The enzymes that synthesize tryptophan become more active. b) The repressor cannot bind to the operator, so transcription is turned on. c) The repressor binds to the operator and prevents transcription. d) The enzymes that synthesize tryptophan are inhibited.

the repressor binds to the operator and prevents transcription

If lacI were mutated, what effect would this have on lactose metabolism? a) One of the enzymes that are involved in lactose metabolism would not be able to carry out its reaction, and lactose would not be metabolized b) The cell would not be able to recognize the presence of lactose, and the lac operon would be under expressed c) RNA polymerase would not properly bind to the promoter, and the lac operon would be under expressed d) The repressor protein would not function properly, and the lac operon would be over expressed

the repressor protein would not function properly, and the lac operon would be over expressed

If lacO were mutated, what effect would this have on lactose metabolism? a) The repressor would not properly bind to the operator, and the lac operon would be over expressed b) The repressor would not properly bind to the operator, and the lac operon would be under expressed c) RNA polymerase would not properly bind to the promoter, and the lac operon would be under expressed d) The repressor protein would not function properly, and the lac operon would be over expressed

the repressor would not properly bind to the operator, and the lac operon would be over expressed

miRNAs were discovered during studies of the lin-4 gene in C. elegans; this gene encodes for which of the following? a) Two small RNAs (22 and 61 nucleotides, respectively) b) A small RNA (61 nucleotides) and a small polypeptide (22 amino acids) c) A short polypeptide (22 amino acids) d) Two short poplypeptides (22 and 61 amino acids, respectively)

two small rnas (22 and 61 nucleotides, respectively)

Chromatin can be altered in a number of ways, such as histone modification and DNA methylation. When are such alterations considered to be epigenetic (choose all that apply)? a) When they only affect one chromosome (paternal or maternal) b) When they are inherited through cell division c) When they lead to inactivation of DNA d) When they persist in the absence of the initiation stimulus

when they are inherited through cell division when they persist in the absence of the initiation stimulus

The ______ of histones tends to loosen the coiling of DNA, making it more accessible for transcription.

acetylation

In some cells, DNA combines with proteins to form a substance called ______.

chromatin

The trp operon consists of ______ genes that encode tryptophan biosynthesis enzymes. a) one b) two c) three d) four e) five

five

DNA ______ was the first modification of chromosome structure shown to act epigenetically.

methylation

Repressors are proteins that bind to regulatory sites on DNA called ______. These prevent transcription.

operators

An ______ is a cluster of genes that are part of a single transcription unit that is under the control of a single promoter.

operon

Match the structural gene in the lac operon with the enzyme it produces: lacY a) B-galactosidase b) permease c) transacetylase

permease

Match the structural gene in the lac operon with the enzyme it produces: lacA a) B-galactosidase b) permease c) transacetylase

transacetylase

In both prokaryotes and eukaryotes, gene regulation most commonly occurs at the level of ______ initiation.

transcription

True or False. Gene regulation allows bacteria to survive in changing environments.

true

Which organism has the simplest transcription regulation? a) A plant, such as A. thaliana b) A bacterium, such as E. coli c) A nematode, such as C. elegans d) A mammal, such as H. sapiens

a bacterium, such as e. coli

What is an operon? a) A cluster of genes controlled by a single promoter b) A transcription factor that binds to DNA to control the expression of a cluster of genes c) A region of DNA that is responsible for regulation of transcription of a cluster of genes d) A small molecule that binds to a transcription factor to regulate its activity

a cluster of genes controlled by a single promoter

Your boss at a pharmaceutical company has asked you to design a drug that can recognize the DNA sequence of a specific gene and increase transcription. What molecule is most likely to be able to do this? a) A protein with a helix-turn-helix motif that can bind in the major groove of DNA b) A protein with a leucine zipper motif that can bind in the minor groove of DNA c) A small RNA that can bind along the promoter sequence of the gene d) A helicase that can unwind the DNA and bind along the bases e) An RNA with a zinc finger motif that can bind along the bases of DNA

a protein with a helix-turn-helix motif that can bind in the major groove of dna

An ______ is a regulatory protein that acts to increase the rate of transcription above the basal rate.

activator

The lac repressor is inactivated by binding to which of the following? a) Lactose b) Betagalactosidase c) Transcription factors d) Glucose e) Allolactose

allolactose

A class of chromatin-remodeling complexes that function as molecular motors that modify DNA and histones are dependent on what molecule? a) ADP b) ATP c) GDP d) GTP

atp

The coding region of a gene is located ______ from its promoter.

downstream

The miRNA in the nucleus is cleaved by a nuclease called ______ that trims the miRNA to just a stem-and-loop structure which is now called ______.

drosha; pre-mirna

The repressor of the lac operon binds to the region called the ______.

operator

The correct order of gene expression control mechanisms in eukaryotes is a) translation, transcription, nuclear export, post-transcriptional modifications, post-translational modifications. b) transcription initiation, transcription elongation, transcription termination, post-transcriptional processing, nuclear export. c) replication, transcription, nuclear export, translation, protein degradation. d) origin of replication, transcription initiation, elongation, termination, post-transcriptional processing, nuclear export, protein synthesis, protein degradation.

transcription initiation, transcription elongation, transcription termination, post-transcriptional processing, nuclear export

MicroRNAs and short-interfering RNAs regulate gene expression at what level? a) Transcription b) Post-translational regulation of protein function c) Translation d) RNA processing

translation

If a protein in the coactivator complex does not function properly, what would be a consequence? a) RNA polymerase will not bind to the template DNA b) RNA will not bind to the template at the promoter, but instead at an improper location on the template DNA c) Activators will not be able to properly affect the rate of transcription d) RNA polymerase will not be able to leave the promoter to begin transcription of the gene e) All of these would occur

activators will not be able to properly affect the rate of transcription

Match the structural gene in the lac operon with the enzyme it produces: lacZ a) B-galactosidase b) permease c) transacetylase

b-galactosidase

Intracellular receptors usually contain binding sites for a) signaling molecules only. b) DNA only. c) both DNA and signaling molecules. d) either DNA or signaling molecules. e) neither DNA nor signaling molecules.

both dna and signaling molecules

How can proteins interact with DNA and recognize DNA sequences without unwinding the DNA double helix? a) By reading the histone code b) By interacting with the minor groove of the double helix c) By interacting with the major groove of the double helix d) By reading the pattern of methylation in DNA e) By interacting with histone proteins

by interacting with the major groove of the double helix

Addition of ubiquitin marks proteins for which of the following? a) Degradation b) Import into the nucleus c) Transmembrane channels d) Export out of the cell

degradation

Enhancers can act at a distance from the gene being transcribed because ______ can form loops.

dna

The best description of how regulatory proteins recognize and bind to the correct sequences without unwinding the DNA double helix is a) DNA-binding domains can recognize the chemical groups that protrude from the base-pairs into the major groove. b) DNA-binding domains can recognize the chemical groups that protrude from the base-pairs into the minor groove. c) DNA-binding domains can recognize the chemical groups that protrude from the sugar-phosphate backbone into the major groove. d) DNA-binding domains can recognize the chemical groups that protrude from the sugar-phosphate backbone into the minor groove. e) Regulatory proteins have DNA-binding domains that are inserted into the major groove and can recognize the shape of each nitrogenous base.

dna-binding domains can recognize the chemical groups that protrude from the base-pairs into the major groove

Almost 2000 miRNAs have been identified in various organisms including humans and ______, the fruit fly.

drosophila

Chemical modification of bases in the RNA to change their base-pairing properties (deamination of cytosine to uracil and deamination of adenine to inosine) are examples of RNA ______.

editing

Intracellular receptors may be found a) in the cytoplasm only. b) in the nucleus only. c) either in the cytoplasm or the nucleus. d) either in the cytoplasm or on the cell membrane. e) either in the nucleus or on the cell membrane.

either in the cytoplasm or the nucleus

Which of the following describes the control of the initiation of transcription? a) Always positive b) Always negative c) Either positive or negative

either positive or negative

Each specific transcription factor binds to a segment of DNA called an ______.

enhancer

Gene regulation allows bacteria to survive in response to ______ changes, such as the availability of specific nutrients.

environmental

Eukaryotic promoters are binding sites for ______ transcription factors.

general

Some corepressors that alter chromatin structure have been shown to act as which of the following? a) Histone methylases b) Histone deacetylases c) Histone acetylases d) Histone demethylases

histone deacetylases

All of the following are examples of post-transcriptional regulation in eukaryotes, except which of the following? a) Histone modification b) Alternative splicing c) RNA interference d) RNA editing

histone modification

What is a major disadvantage to a bacterial cell of having an operon? a) The cell must transcribe multiple proteins at one time. b) If there is a mutation in a regulatory region, none of the proteins will be synthesized. c) If there is a mutation in one of the structural genes, none of the proteins will be functional. d) The cell is unable to regulate the transcription of the genes in the operon. e) The cell must use alternative splicing to separate the different mRNAs.

if there is a mutation in a regulatory region, none of the proteins will be synthesized

When observing the reactions within eukaryotic transcription you find there is a greater energy expenditure and several more enzymes and transcription factors than within prokaryotic transcription. The best explanation for this is that a) eukaryotes have more genes than prokaryotes. b) prokaryotic genomes are smaller than eukaryotic genomes. c) in eukaryotes, DNA is complexed with chromatin and transcription elements can be located far away from the transcription start site. d) prokaryotes do no have a true nucleus and therefore require less energy to transcribe genes. e) eukaryotes are just bigger organisms and therefore require more genes than smaller organisms.

in eukaryotes, dna is complexed with chromatin and transcription elements can be located far away from the transcription start site

Formation of the transcription initiation complex begins when general transcription factors bind to a segment of DNA called the ______.

promoter

The formation of nucleosomes may block the binding of transcription factors and RNA polymerase II to the ______.

promoter

Proteins marked with ubiquitin enter the ______ at one end and exit the other side as amino acids or polypeptide fragments.

proteasome

Repressors are which type of molecules? a) Carbohydrates b) Nucleic acids c) Phospholipids d) Proteins e) Lipids

proteins

General transcription factors, along with TAFs, recruit ______ and position it at the start of the protein-coding sequence.

rna polymerase II

The process whereby different transcripts are made from a single gene is called alternative ______.

splicing

Which of the following describes the regulation of the lac and trp operons in bacteria? a) The lac and trp operons are positively controlled by a repressor protein. b) Only the lac operon is negatively controlled by a repressor protein. c) Only the trp operon is negatively controlled by a repressor protein. d) The lac and trp operons are negatively controlled by a repressor protein.

the lac and trp operons are negatively controlled by a repressor protein

RNA polymerase II, together with all of the general and specific transcription factors and associated mediators and co-activators, form the eukaryotic ______ complex.

transcription

In all cells, gene regulation most commonly happens at which level? a) mRNA maturation b) Transcription termination c) Translation initiation d) Transcription initiation

transcription initiation

Select ways in which the initiation of translation can be regulated. a) tRNAs can be targeted for degradation b) Translation factors can be modified. c) Translation repressor proteins can block translation initiation. d) Ribosome degrading proteins can prevent ribosomes from assembling.

translation factors can be modified translation repressor proteins can block translation initiation

In some cases, the initiation of translation is regulated when ______ ______ proteins bind to the beginning of an mRNA so that the mRNA cannot attach to the ribosome.

translation repressor

True or False. Small RNAs likely evolved to protect the genome.

true

What is the order of the lac genes following the operator? a) A, Y, Z b) Y, A, Z c) Z, Y, A d) Z, A, Y

z, y, a

Chromatin undergoes an ______ alteration when the alteration persists in the absence of a stimulus and is passed to daughter cells during cell division.

epigenetic

True or False. Typically, once a protein is synthesized in a healthy cell, it will perform its function indefinitely because the cell environment is highly controlled.

false. proteins lose their function over time

Proteins called ______ transcription factors can initiate transcription only at the basal rate.

general

Transcription factors that are necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase II to a promoter are called which of the following? a) Nonspecific transcription factors b) General transcription factors c) Specific transcription factors

general transcription factors

Which of the following is a mechanism by which glucose represses the expression of the lac operon? a) Glucose binds directly to the DNA and prevents the binding of RNA polymerase. b) Glucose inhibits the production of cAMP, thereby preventing the activation of the lac operon. c) Glucose binds to the lac operon and enhances its ability to block expression of the lac operon. d) Glucose binds to CAP, which enables it to prevent transcription of the lac operon.

glucose inhibits the production of camp, thereby preventing the activation of the lac operon

Chromatin that contains highly condensed DNA which is not being expressed is called ______.

heterochromatin

Coactivators can affect the structure of chromatin by acting as which of the following? a) Histone deacetylases b) HIstone proteases c) HIstone acetylases d) Histone methylases

histone acetylases

You and a group of scientists are mapping out gene regulation in a new species. Based on what is currently known about control of gene expression, what type of regulation is likely to be most important for most genes in this species? a) Degradation of mRNA b) Splicing of mRNA c) The passage of mRNA through the nuclear membrane d) Initiation of transcription e) Initiation of translation f) Posttranslational modification of proteins

initiation of transcription

How does the cell recognize that lactose needs to be metabolized? a) Lactose directly activates the transcription of the lac operon b) Lactose stimulates a transcription factor that activates transcription of the lac operon c) Lactose is converted into allolactose, which inhibits the lac repressor d) Lactose is converted into beta-galactosidase, which inhibits the lac repressor e) Lactose stimulates the production of cAMP, which activates kinases that activate transcription of the lac operon

lactose is converted into allolactose, which inhibits the lac repressor

Proteins can recognize specific base pair sequences in DNA without unwinding the double helix by interacting with the ______ ______ of the helix.

major groove

The ______ of histones is correlated with tighter coiling of the DNA and inactive regions of chromatin.

methylation

Which of the following RNA molecules act in post-transcriptional gene regulation? a) RISC b) tRNA c) miRNA d) siRNA e) rRNA

mirna sirna

Which of the following cell signaling molecules crosses the cell membrane the easiest? a) Molecules that are small and lipid-insoluble b) Molecules that are small and lipid-soluble c) Molecules that are small and water-soluble d) Molecules that are large and water-soluble e) Molecules that are large and lipid-insoluble

molecules that are small and lipid-soluble

The short half-life of ______ transcripts for regulatory proteins is crucial as it enables the cell to change the levels of those proteins very quickly.

mrna

Transcription regulation in eukaryotes is how complex as compared to transcriptional regulation in prokaryotes? a) About as b) Much less c) Much more

much more

The lowest level of chromatin structure consists of DNA wrapped twice around a group of histones to form a ______.

nucleosome

Proteins that have a ubiquitin chain attached to them are called ______ proteins.

polyubiquitinated

Which of the following statements most accurately describes the function of the proteasome? a) Proteins marked with ubiquitin enter one end of the proteasome and exit the other end as amino acids or peptide fragments. b) Unmarked proteins enter one end of the proteasome and exit the other end ubiquinated. c) Proteins marked with ubiqutin enter the proteasome and exit in a vesicle which merges with a lysosome. d) Proteins marked with ubiquitin enter one end of the proteasome and then exit through the same end as amino acids.

proteins marked with ubiquitin enter one end of the proteasome and exit the other end as amino acids or peptide fragments

The term polyubiquitinated protein refers to which of the following? a) Several polypeptides linked to a single ubiquitin molecule b) Proteins which have many single molecules of ubiquitin attached to many of the amino acid residues c) Proteins which have a ubiquitin chain attached to them d) Several polypeptides linked though a chain of ubiquitins

proteins which have a ubiquitin chain attached to them

Which of the following is a difference between regulatory proteins with leucine zipper and helix-turn-helix DNA binding motifs? a) Proteins with leucine zippers employ beta sheets, while proteins with helix-turn-helix motifs employ alpha helices. b) Proteins with leucine zippers bind DNA with several leucines, while proteins with helix-turn-helix motifs employ a recognition helix. c) Proteins with leucine zippers have two different recognition helices, while proteins with helix-turn-helix motifs are made of two identical units.

proteins with leucine zippers have two different recognition helices, while proteins with helix-turn-helix motifs are made of two identical units

Which type of eukaryotic transcription factors can increase the level of transcription in certain cells in response to signals? a) Specific transcription factors b) General transcription factors c) Signaling transcription factors d) Response transcription factors

specific transcription factors

In the following list, choose all that are components of the eukaryotic transcription complex. a) Specific transcription factors b) Histones c) General transcription factors d) RNA polymerase II e) mRNA transcript f) Mediators and co-activators

specific transcription factors general transcription factors rna polymerase II mediators and co-activators

Choose all ways in which glucose represses the utilization of lactose in glucose repression. a) Glucose binds to the repressor instead of allolactose. b) The presence of glucose leads to low level of cAMP. c) Glucose directly binds to the operator affecting how strongly RNA polymerase binds to the promoter. d) The presence of glucose inhibits the transport of lactose in the cell (inducer exclusion).

the presence of glucose leads to low level of camp the presence of glucose inhibits the transport of lactose in the cell (inducer exclusion)

An operon is derepressed when which of the following occurs? a) The repressor and corepressor are bound to the operator b) The repressor alone cannot bind to the operator c) An inducer is bound to the repressor d) The repressor alone is bound to the operator

the repressor alone cannot bind to the operator

The inhibitor of an intracellular signal receptor is defective, such that even when stimulated by a signal molecule, the inhibitor stays bound to the receptor. What effect will this have on the signaling pathway? a) The signal molecule will not enter the cell b) The signal molecule will bind to and activate the receptor, but the receptor will not be able to enter the nucleus c) The signal molecule will bind to the receptor, but it will not be able to activate it. d) The signaling pathway will be unaffected

the signal molecule will bind to the receptor, but it will not be able to activate it

What is the function of a promoter in eukaryotic cells? a) They are binding sites for general transcription factors which recruit RNA polymerase in order to initiate transcription. b) They are directly recognized by RNA polymerase II. c) They are binding sites for specific transcription factors which recruit RNA polymerase in order to initiate transcription.

they are binding sites for general transcription factors which recruit rna polymerase in order to initiate transcription

Which of the following is a major difference between different DNA-binding motifs? a) They employ different mechanisms to position and stabilize a recognition alpha helix in the major groove of DNA. b) They differ in the type of structure that directly interacts with DNA bases - some employ an alpha helix, some, a beta sheet and some metal ions. c) They interact with different parts of DNA - some interact with the major groove, others with the minor groove.

they employ different mechanisms to position and stabilize a recognition alpha helix in the major groove of dna