CHAPTER 18

MerR protein

A protein binds the promoter and holds the DNA in a conformation that prevents initiation of transcription.

Under which conditions are the lac structural genes expressed most efficiently? No glucose, high lactose No glucose, no lactose High glucose, high lactose High glucose, no lactose

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.

The _____ is/are arranged sequentially after the promoter.

genes of an operon

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

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.

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

repressor

Regulatory proteins bind to _____. the operator the lactose-utilization genes the regulatory gene RNA polymerase transcription factors

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

*****Which one of the following statements is false regarding the role of λ repressor in the regulation of phage transcription? λ repressor cooperatively binds DNA. λ repressor bound to DNA excludes RNA polymerase. λ repressor lacks an activation domain. λ repressor recruits RNA polymerase to the promoter.

λ repressor lacks an activation domain. Although we call it a repressor, λ is able to activate transcription. As an activator, λ repressor works like CAP—it recruits RNA polymerase to the promoter. This is accomplished via interactions between the activation domain in the repressor's amino-terminus and RNA polymerase.

Explain why it is to the advantage of bacteriophage lambda to tightly regulate the level of lambda repressor made in lysogenic E. coli cells.

1. If repressor level is too high, induction would be inefficient, as more repressor would need to be inactivated before repressor vacates OR1 and OR2 and lytic growth is induced. 2. If repressor level is too low, the cells might induce the lytic cycle without the bacteriophage being ready for release.

Which of the following mutations could lead to constitutive expression of the genes of the lac operon? A mutation in the operator sequence A mutation in the lac-Z gene A super repressor mutation A mutation in the lac-Y gene

A mutation in the operator sequence Such a mutation could prevent binding of the repressor, allowing expression under all conditions.

Gal repressor and the P4 protein

A repressor binds DNA at a site near the promoter and prevents transcription by binding RNA polymerase and keeping RNA polymerase in the closed complex or prevent RNA polymerase escape from the promoter

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

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

Provide 3 examples of allosteric regulation provided in this chapter.

Allolactose binds THE LAC REPRESSOR in a region separate from its DNA binding domain. Once bound, allolactose causes the Lac repressor to change shape and release from the DNA, stopping repression. Similarly, allosteric effectors exist to regulate the araBAD and gal operons. In the presence of low glucose levels, cAMP binds CAP to induce a change it shape that allows it to bind the DNA for activation. Through allostery, NtrC and MerR activate transcription of the glnA and merT genes, respectively.

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

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.

AraC and CAP both regulate transcription of the araBAD operon. Which statement best describes the role of these two proteins in the presence of arabinose and the absence of glucose? Both AraC and CAP are inducers of transcription. AraC is a repressor of transcription, while CAP is an inducer of transcription. AraC is an inducer of transcription, while CAP is a repressor of transcription. Both AraC and CAP are repressors of transcription.

Both AraC and CAP are inducers of transcription. When arabinose is present, AraC binds that sugar and adopts a conformation that allows it to bind as a dimer near the promoter of the araBAD operon. AraC binding helps to recruit RNA polymerase to the promoter. CAP helps facilitate RNA polymerase binding when it is able to bind to the nearby CAP site. CAP adopts a conformation that binds DNA only when it is complexed with cAMP. cAMP levels are high enough to bind CAP only when glucose levels are low. Both proteins function to positively activate transcription when bound, and thus are both considered inducers of transcription.

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 asallosteric regulation. True False

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 preventingCAP from stimulating expression of the lac structural genes, is known as catabolite repression.

Which statements about viruses are true? Select the four statements that are true. HIV contains two identical strands of DNA. HIV contains reverse transcriptase. Some viruses contain DNA and RNA. A retrovirus contains RNA. Enveloped viruses bud from the host cell. The capsid enters the host cell if the virus is enveloped. All RNA-containing viruses are retroviruses.

HIV contains reverse transcriptase. A retrovirus contains RNA. Enveloped viruses bud from the host cell. The capsid enters the host cell if the virus is enveloped. Viruses are classified into two major groups: nonenveloped and enveloped. Nonenveloped viruses (a) typically exit the host cell by bursting through the plasma membrane. Enveloped viruses (b) generally escape from the host cell by budding. Because of this, the viral envelope is often derived from the host cell's plasma membrane. Viruses contain either single-stranded DNA, double-stranded DNA, single-stranded RNA, or double-stranded RNA. Human immunodeficiency virus (HIV) is a retrovirus that contains two copies of its RNA genome and two copies of reverse transcriptase. The HIV viral envelope facilitates binding to a white blood cell. After HIV enters the cell, the reverse transcriptase synthesizes viral DNA from viral RNA.

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

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.

*****Which of the following statements is true regarding cooperative binding? It decreases the affinity of a protein for its correct binding site on DNA. It is observed only in DNA-binding proteins. It decreases the concentration of protein required to fill adjacent protein binding sites on DNA. It increases the concentration of protein required to fill adjacent protein binding sites on DNA.

It decreases the affinity of a protein for its correct binding site on DNA. In cooperative binding, binding of a first protein to DNA increases the affinity of a second protein because the second interacts not only with DNA but with the first protein as well. As a result of this increased affinity, a lower concentration of protein is required to fill adjacent binding sites.

Which of the following best describes the biological role of the lac operon? It ensures that bacterial cells produce lactose only when no other food sources are available. It prevents other sugars from being metabolized until all available lactose has been used. It ensures that a cell dedicates resources to the production of enzymes involved in lactose metabolism only when lactose is available in the environment. It ensures that a cell produces enzymes involved in lactose metabolism in a constitutive manner.

It ensures that a cell dedicates resources to the production of enzymes involved in lactose metabolism only when lactose is available in the environment. The cell expends energy to produce the proteins necessary for lactose metabolism only when lactose is present.

The operon model of the regulation of gene expression in bacteria was proposed by _____. Watson and Crick Franklin Darwin Jacob and Monod Mendel

Jacob and Monod

Classify each phrase as applying to the lytic cycle, the lysogenic cycle, or both types of reproductive cycles of phages.

Lytic cycle: The cell is lysed (broken open) new phages are assembled from viral DNA and proteins Lysogenic cycle: The viral DNA integrates into the chromosome of the host cell The cell repreoduces normally both cycles: viral genes are replicated Bacteriophages, which contain double-stranded DNA, can reproduce by two alternative mechanisms: the lytic cycle and the lysogenic cycle. In the lytic cycle, virus parts are made, new viruses are assembled, and the cell is lysed, releasing the newly assembled viruses. In the lysogenic cycle, the viral DNA incorporates into the bacterial DNA and is passed on to daughter bacterial cells when the infected bacteria reproduce normally. Occasionally, an infected bacterium in the lysogenic cycle can enter the lytic cycle, in which viral particles are produced and the cell is eventually ruptured.

A(n) ____ 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

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

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

Describe how alternative sigma factors play a role in the regulation of transcription in prokaryotes.

RNA polymerase carrying sigma70 recognizes most promoters in E. coli. But sigma70 can be replaced by alternative sigma factors in a proportion of RNA polymerases in a cell, or under special circumstances. Thus, by increasing the level of sigma32 during heat shock, sigma32 replaces sigma70 and directs polymerase to alternative promoters that control trancription of heat shock genes. Similarly, sigma54 directs the transcription of genes encoding proteins involved in nitrogen metabolism. Another set of alternative sigma factors regulate transcription in sporulation in B. subtilis cells.

Given a loss-of-function mutation in the tetramerization domain of the l repressor and using the figure below, predict the specific functional effect of the mutation on the lambda repressor. The lambda repressor would no longer be able to bind DNA. The lambda repressor would no longer be able to form tetramers. The lambda repressor would no longer be able to form dimers. All of the above.

The lambda repressor would no longer be able to form tetramers.

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

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.

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

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.

The placement of the operator sequence between the promotor and the structural genes is critical to the proper function of the lac operon. True False

True When the repressor binds to the operator, RNA polymerase cannot transcribe the structural genes.

Sort the items according to whether they may be found only in free virus particles, only in uninfected host cells, or in both viruses and host cells.

Virus only: capsid envelope with glycoproteins capsomere (core protein_ Host cells only: ribosome Both: DNA RNA protein Viruses are infectious particles that contain genetic material (either DNA or RNA) surrounded by a capsid (protein shell). Some viruses also have a membranous envelope that contains glycoproteins.

Describe the mechanism of negative autoregulation by lambda repressor. When the concentration of lambda repressor is too low, lambda repressor prevents translation of itself by binding OR3. This inhibits RNA polymerase from binding at PRM. When the concentration of lambda repressor is too high, lambda repressor prevents transcription of itself by binding OR3. This inhibits RNA polymerase from binding at PRM. When the concentration of lambda repressor is too low, lambda repressor prevents transcription of itself by binding PRM. This inhibits RNA polymerase from binding at OR3. When the concentration of lambda repressor is too high, lambda repressor prevents translation of itself by binding PRM. This inhibits RNA polymerase from binding at OR3.

When the concentration of lambda repressor is too high, lambda repressor prevents transcription of itself by binding OR3. This inhibits RNA polymerase from binding at PRM.

Lac repressor

a repressor binds a site that overlaps with the promoter to block RNA polymerase binding

*****You create an E. coli mutant that has a two bp deletion between the -10 and -35 elements of the merT promoter. In the absence of mercury, which of the following outcomes do you expect? constitutive expression of merT expression of merT, but only in the presence of the activator MerR expression of merT, but only in the presence of the activator MerR no expression of merT

constitutive expression of merT With the two bp deletion, the -10 and -35 elements are optimally separated and aligned on the DNA helix for σ70 to efficiently recognize and bind the merT promoter. Constitutive transcription can occur in the absence of MerR and mercury.

****In prokaryotes, when can basal level (constitutive) expression of a gene occur? in the absence of activator and repressor binding only when an activator binds only if the expression of the gene is regulated by a repressor when an activator and repressor bind

in the absence of activator and repressor binding In the absence of activator and repressor binding, RNA polymerase will sometimes weakly bind the promoter and spontaneously transition into an open complex in which the DNA at the start site of transcription is unwound. This will initiate a low level of constitutive transcription producing the basal level of transcription.

Under which set of conditions does the lac operon in E. coli produce high levels of lacZ, lacY, and lacA transcripts? in the presence of lactose and absence of glucose in the absence of lactose and presence of glucose in the presence of both lactose and glucose in the absence of both lactose and glucose

in the presence of lactose and absence of glucose In the presence of lactose, the Lac repressor is not bound to the operator, so the promoter is available for RNA polymerase binding. In the absence of glucose, cAMP levels are high, so the CAP activator is supplied with the effector it needs in order to bind to the CAP site and specifically recruit RNA polymerase to the promoter. Specific recruitment increases the strength of DNA binding by RNA polymerase. Transcription of the lac operon is thus activated, producing higher levels of lacZ, lacY, and lacA transcripts than might occur in the absence of activation.

A _____ 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

Mutant 1: A mutant of E. coli that has a mutation in the operator of the lac operon that prevents the repressor from binding. Mutant 2: A mutant of E. coli that has a mutation in the promoter of the lac operon (for the lacZ, lacY, and lacA genes) that prevents RNA polymerase from binding.

no expression: Mutant 2 in all conditions basal expression: Mutant 1 in presence of glucose and presence of lactose Mutant 1 in presence of glucose, absence of lactose activated level of expression: Mutant 1 in absence of glucose and presence of lactose. Mutant 1 in absence of glucose and absence of lactose.

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

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

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

operator

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