Chapter 15

Describe the differences between an inducible operon and a repressible operon?

An inducible operon, such as the lac operon, is turned on when some substance, an inducer, is present. The presence of the inducer (allolactose) induces expression of the operon. A repressible operon, such as the trp operon, is turned off in the presence of a certain substance, a corepressor. The presence of the corepressor (tryptophan) thus represses expression of the operon.

Describe the response that an E. coli cell makes when the internal level of tryptophan becomes too high?

E. coli have several genes that all help synthesize tryptophan and these genes are organized within the trp operon, under the control of a single regulatory region. The trp operon by default is on, so the genes are expressed as proteins, which catalyze tryptophan synthesis. When levels of tryptophan are high enough that the cell does not need to produce this amino acid, the presence of tryptophan shuts off expression of the trp operon. Tryptophan acts as a corepressor by binding the tryptophan repressor protein, which activates the repressor so it can bind to the operator and block transcription.

For bacteria, what are the main advantages of having genes with similar functions arranged in clusters within the genome? How might some of these advantages be achieved in eukaryotes, where genes are typically not grouped by common function?

For bacteria, an advantage of grouping genes of related function into one transcription unit is that a single on-off switch' can control a whole cluster of functionally related genes. Genes that need to be co-expressed in eukaryotes are often scattered across different chromosomes. However, each of these separate genes may contain a control element that can be bound by a common factor. In this way, activation of one factor can coordinately control the activation of multiple genes spread across the genome.

Protein-phosphorylating enzymes' role in the regulation of gene expression involves _____. a) protein activation b) translation c) protein degradation d) regulating the transport of mRNA to the cytoplasm e) RNA processing

a) protein activation Proteins are often activated by phosphorylation.

Enzyme complexes that break down protein are called _____. a) lipases b) ubiquitins c) amylase d) proteasomes e) nucleases

d) proteasomes Proteasomes are enzyme complexes that break down proteins.

True or false? Regulatory and basal transcription factors regulate transcription by binding to the promoter.

False Basal transcription factors do indeed bind to the promoter, but regulatory transcription factors bind to promoter-proximal elements and enhancers.

True or false? One possible way to alter chromatin structure such that genes could be transcribed would be to make histone proteins more positively charged.

False The positive charge on histone proteins allows them to interact tightly with negatively charged DNA, thus inhibiting transcription. To disrupt this interaction, the histone proteins would have to be made more negatively charged.

True or false? The mechanism by which glucose inhibits expression of the lac structural genes is known as catabolite stimulation, whereas the mechanism by which lactose stimulates expression of the lac structural genes is known as allosteric regulation.

False The process by which lactose binds to the lac repressor and inactivates it by causing it to change shape is known as allosteric regulation. However, the process by which glucose causes cAMP levels in the cell to drop, thereby preventing CAP from stimulating expression of the lac structural genes, is known as catabolite repression.

Why do transcription factors often bind to the major groove of the DNA double helix?

Transcription factors (TFs) must be able to bind to specific DNA sequences in order to activate expression of certain genes. The DNA sugar-phosphate background is uniform across the genome and thus cannot support sequence-specific binding, although it can support non-specific binding. In order to recognize the different bases of DNA, a TF must bind within the major or minor groove where the edges of the chemical bases are exposed. The major groove has a greater diversity of binding sites for transcription factors to bind in comparison to the minor groove and thus serves as a common place for TFs to bind.

Which of the following events in transcription initiation likely occurs last? a) RNA polymerase binds to the promoter of the gene. b) Regulatory transcription factors bind to enhancers. c) Basal transcription factors form a basal transcription complex. c) TBP is recruited to the promoter.

a) RNA polymerase binds to the promoter of the gene. RNA polymerase is recruited only when other transcription factors, including TBP, are assembled at the promoter.

Regulatory proteins bind to _____. a) the operator b) the lactose-utilization genes c) the regulatory gene d) RNA polymerase e) transcription factors

a) the operator Transcription is inhibited when a regulatory protein binds to the lac operon operator.

Under which of the following conditions will the trp operon be actively expressed? (select all) a) when trp is absent b) when the trp repressor is bound to the trp operator c) in a cell with a trp operator that has been mutated and cannot bind to trp repressor

a) when trp is absent c) in a cell with a trp operator that has been mutated and cannot bind to trp repressor

What is allosteric regulation? a) In allosteric regulation, a gene is turned off by a repressor protein. b) In allosteric regulation, a small molecule binds to a large protein and causes it to change its shape and activity. c) In allosteric regulation, genes are expressed constitutively. d) In allosteric regulation, a gene is turned on by an activator protein.

b) In allosteric regulation, a small molecule binds to a large protein and causes it to change its shape and activity. Allosteric regulation is an important mechanism for changing enzyme activity, as well as for changing the function of some gene repressors and activators.

Under which conditions are the lac structural genes expressed most efficiently? a) High glucose, high lactose b) No glucose, high lactose c) No glucose, no lactose d) High glucose, no lactose

b) No glucose, high lactose When glucose is absent and lactose levels are high, the lac structural genes are expressed the most efficiently. Without glucose, cAMP is produced and CAP can stimulate transcription of the structural genes. In the presence of lactose, the repressor does not bind to the operator and therefore does not block transcription.

What molecule binds to promoters in bacteria and transcribes the coding regions of the genes? a) DNA polymerase b) RNA polymerase c) DNA ligase d) A nucleotide

b) RNA polymerase RNA polymerase is the enzyme that binds to promoters and transcribes the coding regions of genes into RNA.

What is the function of the lacZ gene? a) This gene encodes an enzyme, b-galactosidase, that cleaves lactose into two glucose molecules. b) This gene encodes an enzyme, b-galactosidase, which cleaves lactose into glucose and galactose. c) This gene encodes an enzyme, galactoside permease, which transports lactose into the cell. d) This gene encodes the repressor of the lac operon.

b) This gene encodes an enzyme, b-galactosidase, which cleaves lactose into glucose and galactose. The lacZ gene encodes b-galactosidase, a key enzyme in lactose metabolism. When lactose is present in the cell, the cell expresses lacZ and metabolizes lactose.

If the regulation patterns present for the trp and lac operons are conserved for other operons, which of the following general rules would apply? (select all) a) inducible enzymes tend to function in anabolic pathways b) inducible enzymes tend to function in catabolic pathways c) repressible enzymes tend to function in anabolic pathways d) repressible enzymes tend to function in catabolic pathways

b) inducible enzymes tend to function in catabolic pathways c) repressible enzymes tend to function in anabolic pathways

In the presence of a regulatory protein the lac operon is _____. a) transcribed b) not transcribed c) transcribed at a faster than usual rate d) is turned on e) either transcribed or not transcribed

b) not transcribed The regulatory protein of the lac operon is a repressor.

Which of the following regulatory DNA sequences might be located thousands of nucleotides away from the transcription start site of a gene? a) Promoter b) Promoter-proximal element c) Enhancer d) TATA box

c) Enhancer Enhancers can function thousands of nucleotides away from the promoter and transcription start site.

Which of these is NOT a component of the lac operon? a) lactose-utilization genes only b) promoter only c) regulatory gene only d) operator only e) promoter and operator

c) regulatory gene only The regulatory gene, while not a part of the operon, plays a role in regulating the expression of the genes of the operon.

When transcription factors bind to DNA, they tend to bind within the "grooves" of the helix. Why might this be the case? (select all) a) the grooves contain negative and positive charges that can be recognized by the protein b) the protein can wedge itself within the groove and stay attached to the DNA helix c) the grooves contain a richer diversity of binding sites than the DNA backbone

c) the grooves contain a richer diversity of binding sites than the DNA backbone

Which of the following is true regarding the pathway that synthesizes tryptophan in bacterial cells? (select all) a) high levels of tryptophan lead to higher activity of tryptophan-synthesizing enzymes b) high levels of tryptophan lead to increased expression of tryptophan-synthesizing enzymes c) tryptophan negatively regulates the rate at which more tryptophan is synthesized d) tryptophan levels will fluctuate dramatically in the cell as a result of these regulatory mechanisms

c) tryptophan negatively regulates the rate at which more tryptophan is synthesized

_____ bind(s) to DNA enhancer regions. a) RNA polymerase b) Promoters c) Introns d) Activators e) Exons

d) Activators Activators are a type of transcription factor that bind to enhancer regions.

Which of the following regulatory elements is not composed of DNA sequences? a) Silencers b) Promoter-proximal elements c) Enhancers d) Activators

d) Activators Activators are proteins that are involved in transcription initiation.

Which of the following enzymes converts ATP to cAMP? a) Galactoside permease b) b-galactosidase c) ATP synthase d) Adenylyl cyclase

d) Adenylyl cyclase Adenylyl cyclase converts ATP to cAMP, which helps CAP bind and facilitates binding of RNA polymerase to the lac promoter.

Which of the following statements best defines the term operon? a) An operon is a region of DNA that consists of a single gene regulated by more than one promoter. b) An operon is a region of RNA that consists of the coding regions of more than one gene. c) An operon is a region of DNA that codes for sugar-metabolizing enzymes. d) An operon is a region of DNA that codes for a series of functionally related genes under the control of the same promoter.

d) An operon is a region of DNA that codes for a series of functionally related genes under the control of the same promoter. This arrangement of genes is common in bacteria. For example, genes involved in lactose metabolism are clustered in the lac operon of E. coli, and genes involved in tryptophan metabolism are in the trp operon.

The operon model of the regulation of gene expression in bacteria was proposed by _____. a) Watson and Crick b) Franklin c) Darwin d) Jacob and Monod e) Mendel

d) Jacob and Monod In 1961 Jacob and Monod proposed the operon model of gene regulation

Which of the following terms describes the DNA-protein complexes that look like beads on a string? a) Chromatin b) Histones c) 30-nanometer fiber d) Nucleosome

d) Nucleosome The "beads on a string" appearance of nucleosomes comes from the wrapping of DNA around a core of eight histone proteins.

What happens to the expression of the lacI gene if lactose is not available in the cell? a) The lacI gene turns off. b) The lacI gene increases its rate of transcription. c) The lacI gene turns on. d) There is no change—the lacI gene is constitutively expressed.

d) There is no change—the lacI gene is constitutively expressed. The lacI gene is expressed regardless of the presence of lactose. Only the structural genes of the lac operon are affected by the presence or absence of lactose.

The nuclear membrane's role in the regulation of gene expression involves _____. a) protein activation b) translation c) protein degradation d) regulating the transport of mRNA to the cytoplasm e) RNA processing

d) regulating the transport of mRNA to the cytoplasm This is the role of the nuclear membrane in the regulation of gene expression.

What is the function of a spliceosome? a) protein activation b) translation c) protein degradation d) regulating the transport of mRNA to the cytoplasm e) RNA processing

e) RNA processing Spliceosomes are involved in RNA processing.

The _____ __ __ _______ are arranged sequentially after the promoter.

genes of an operon

An _______ is a specific small molecule that binds to a bacterial regulatory protein and changes its shape so that it cannot bind to an operator, thus switching an operon on.

inducer

Regulatory proteins bind to the _______ to control the expression of the operon.

operator

An ________ is a stretch of DNA consisting of an operator, a promoter, and genes for a related set of proteins, usually making up an entire metabolic pathway.

operon

A _______ is a specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

promoter

A __________ _____ codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes.

regulatory gene

A ________ is a protein that inhibits gene transcription. In prokaryotes, this protein binds to the DNA in or near the promoter.

repressor