Ch. 16 Control of Gene Expression in Bacteria

Attenuation results when which regions of the 5′ UTR region pair? 1 and 3 2 and 3 2 and 4 3 and 4

3 and 4

Lactose, a major carbohydrate found in milk, consists of two _-____ sugars linked together. The lac operon regulates _____ metabolism. In the lac operon, the operator _____ the promoter and the 5′ end of the first structural gene.

6-carbon; lactose; overlaps

What is a constitutive gene?

A gene that is not regulated and is expressed continually

operon

A group of bacterial structural genes that are transcribed together, along with their promoter and additional sequences that control their transcription. promoter + additional sequences that control transcription (operator) + structural genes

The trp Operon of E. coli

A negative repressible operon Five structural genes trpE, trpD, trpC, trpB, and trpA—five enzymes together convert chorismate to tryptophan controls the biosynthesis of the amino acid tryptophan

partial-diploid

Bacterial cell that possesses two copies of some genes, one on the bacterial chromosome and the other on an extra piece of DNA (usually a plasmid); also called a merozygote.

operator

DNA sequence in an operon to which a regulator protein binds; this binding affects the rate of transcription of the structural genes.

regulatory elements

DNA sequence that affects the transcription of other DNA sequences to which it is physically linked. DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

regulatory genes

DNA sequence that encodes a protein or RNA molecule that interacts with other DNA sequences and affects transcription or translation of those sequences. encoding products that interact with other sequences and affect the transcription and translation of these sequences

structural genes

DNA sequence that encodes a protein that functions in metabolism or biosynthesis or that has a structural role in the cell. encoding proteins

constitutive expression

Describes a gene that is expressed continually without regulation. continuously expressed under normal cellular conditions

Attenuation in the trp Operon of E. coli

Four regions of the long 5′ UTR (leader) region of trpE mRNA When tryptophan is high, region 1 binds to region 2, which leads to the binding of region 3 and region 4, terminating transcription prematurely. Four regions of the long 5′ UTR (leader) region of trpE mRNA When tryptophan is low, region 2 binds to region 3, which prevents the binding of region 3 and region 4, and transcription continues

domain

Functional part of a protein ~ 60-90 amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA

regulator gene

Gene associated with an operon in bacterial cells that encodes a protein or RNA molecule that functions in controlling the transcription of other genes. DNA sequence-encoding products that affect the operon function but are not part of the operon

Genes and Regulatory elements

In bacteria, gene regulation maintains internal flexibility, turning genes on and off in response to environmental changes. In multicellular eukaryotic organisms, gene regulation also brings about cell differentiation.

In the trp operon, what happens to the trp repressor in the absence of tryptophan? It binds to the operator and represses transcription. It cannot bind to the operator, and transcription takes place. It binds to the regulator gene and represses transcription. It cannot bind to the regulator gene, and transcription takes place.

It binds to the regulator gene and represses transcription.

What is the effect of high levels of glucose on the lac operon? Transcription is stimulated. Little transcription takes place. Transcription is not affected. Transcription may be stimulated or inhibited, depending on the levels of lactose.

Little transcription takes place.

gene regulation

Mechanisms and systems that control the expression of genes.

3′, 5′-cyclic adenosine monophosphate (cAMP)

Modified nucleotide that functions in catabolite repression. Low levels of glucose stimulate high levels of cAMP; cAMP then attaches to CAP, which binds to the promoters of certain operons and stimulates transcription. The concentration of cAMP is inversely proportional to the level of available glucose.

Inducible operons

Operon in which transcription is normally off (not taking place); something must happen to induce transcription, or turn it on. Transcription is usually off and needs to be turned on.

repressible operons

Operon in which transcription is normally on (taking place); something must happen to repress transcription, or turn it off. Transcription is normally on and needs to be turned off.

antiterminator

Protein or DNA sequence that prevents the termination of transcription.

regulator protein

Protein produced by a regulator gene that binds to another DNA sequence and controls the transcription of other genes.

allosteric proteins

Protein that changes its conformation upon binding to another molecule.

catabolite activator protein (CAP)

Protein that functions in catabolite repression. When bound with cAMP, CAP binds to the promoters of certain operons and stimulates transcription.

Attenuation of the trp operon involves

RNA secondary structure formation, untranslated regions of RNA, high tryptophan levels, and 5' UTR. The 5' UTR contains four regions with complementarities, which allow the 5' UTR to fold into two different secondary structures, and one of these secondary structures causes attenuation.

attenuator

Secondary structure that forms in the 5′ untranslated region of some operons and causes the premature termination of transcription.

What is the difference between a structural gene and a regulator gene? Structural genes are transcribed into mRNA, but regulator genes are not. Structural genes have complex structures; regulator genes have simple structure. Structural genes encode proteins that function in the structure of the cell; regulator genes carry out metabolic reactions. Structural genes encode proteins; regulator genes control the transcription of structural genes.

Structural genes encode proteins; regulator genes control the transcription of structural genes.

negative repressible operons

The control at the operator site is negative. But such transcription is usually on and needs to be turned off, so the transcription is repressible.

negative inducible operons

The control at the operator site is negative. Molecule binding is to the operator, inhibiting transcription. Such operons are usually off and need to be turned on, so the transcription is inducible.

coordinate induction

The simultaneous synthesis of several proteins stimulated by a specific molecule, the inducer.

When a structural gene is under negative inducible control, what would be the result of a mutation that eliminates the regulatory protein?

The structural gene will be constitutively expressed due to the lack of an active repressor. The regulatory protein functions as an active repressor.

In the absence of tryptophan, what happens in the trp operon when the ribosome stalls at the tryptophan codons?

Transcription continues and moves ahead of translation. The stalling of translation allows for transcription to continue through regions 2, 3, and 4.

Why is transcription a particularly important level of gene regulation in both bacteria and eukaryotes?

Transcription is the first step in the process of information transfer from DNA to protein. For cellular efficiency, gene expression is often regulated early in the process of protein production.

Characteristics of lac operon mutations

Type Location Cis/Trans Effect Structural-gene mutations lacZ, lacY Affect only lacZ or lacY Alter amino acid sequence of protein encoded by gene in which mutation occurs Regulator-gene mutations lacI Trans Affect transcription of structural genes Operator mutations lacO Cis Affect transcription of structural genes Promoter mutations lacP Cis Affect transcription of structural gene

attenuation

Type of gene regulation in some bacterial operons in which transcription begins at the transcription start site but terminates prematurely, before the RNA polymerase even reaches the structural genes. affects the continuation of transcription, not its initiation. This action terminates the transcription before it reaches the structural genes.

If regions 2 and 3 of the 5' UTR trp operon base pair to form a hairpin, will the structural genes be transcribed?

Yes, this hairpin does not prevent transcription. Transcription continues if regions 2 + 3 form a hairpin.

Regulator-gene mutations

acI− leads to constitutive transcription of three structural genes. lacI+ is dominant over lacI− and is trans acting. A single copy of lacI+ brings about normal regulation of lac operon. lacI+lacZ−/lacI−lacZ+ produce fully functional β-galactosidase.

Structural gene mutations

affect the structure of the enzymes but not the regulations of their synthesis lacZ+lacY−/lacZ−lacY+ produces fully functional β-galactosidase and permease.

How do amino acids in DNA-binding proteins interact with DNA? by forming covalent bonds with DNA base by forming hydrogen bonds with DNA base by forming covalent bonds with sugars

by forming hydrogen bonds with DNA base

In the presence of allolactose, the lac repressor binds to the operator. binds to the promoter. cannot bind to the operator. binds to the regulator gene.

cannot bind to the operator.

In the presence of allolactose, the lac repressor

cannot bind to the operator. Allolactose binds to the repressor and causes the repressor to be released from the operator.

A bacterial cell is grown in the presence of both glucose and lactose. Over time, a researcher measures the amount of glucose and lactose that have been used by the cells. She finds that glucose levels are reduced, but lactose levels have remained constant. She proposes that these bacterial cells are exhibiting

catabolite repression

Antisense RNA

complementary to targeted partial sequence of mRNA Small RNA molecule that base pairs with a complementary DNA or RNA sequence and affects its functioning.

Ribozymes, when bound by small regulatory molecules, can induce the cleavage and _____ of mRNA.

degradation

partial diploid

full bacterial chromosome + an extra piece of DNA on F plasmid

What secondary structure forms in the 5' UTR of the trp operon when tryptophan levels are high?

hairpin between regions 3 and 4 High levels of tryptophan covers region 2 and leads to a hairpin structure between 3 and 4.

When tryptophan levels are _____, regions _____ of the 5' UTR pair, followed by a string of uracil nucleotides.

high; 3 and 4 When tryptophan is high, regions 3 and 4 pair and leads to attenuation.

In a negative repressible operon, the regulator protein is synthesized as an active activator. inactive activator. active repressor. inactive repressor.

inactive repressor.

Bacterial enhancers

increase the rate of transcription at genes that are distant from the enhancer

negative control

inhibit gene expression Transcriptional control in which a regulatory protein is a repressor, binding to DNA and inhibiting transcription.

Operator mutations

lacOc: C = constitutive lacOc is dominant over lacO+, which is cis acting. lacI+lacO+Z−/lacI+lacOclacZ+ produce fully functional β-galactosidase constitutively.

Riboswitches are RNA sequences in ____ that affect gene expression.

mRNA

Ribozymes

mRNA molecules with catalytic activity

Riboswitches

molecules influence the formation of secondary structures in mRNA Regulatory sequence in an RNA molecule. When an inducer molecule binds to the riboswitch, this changes the configuration of the RNA molecule and alters the expression of the RNA, usually by affecting the termination of transcription or by affecting translation.

DNA-binding proteins can be grouped into several types on the basis of their structures, or _____.

motifs

An _____ is a single transcriptional unit that includes a series of structural genes, a promoter, and an operator.

operon

The _____ diploid lacI + lacZ −/lacI − lacZ + produces β-galactosidase only in the presence of lactose because the lacI gene is trans dominant.

partial

The partial diploid lacIs lacZ+ / lacI+ lacZ+ fails to produce β-galactosidase in the _____ and _____ of lactose because the lacIs gene encodes a super-repressor.

presence; absence

The catabolite activator protein (CAP) binds to the _____ of the lac operon and stimulates transcription. The binding of the cAMP-CAP complex to DNA produces a _____ _____ in DNA that activates transcription.

promoter; sharp bend

Antisense RNA can ____ translation.

regulate

Two different _____ structures can be formed by the 5′ UTR of the mRNA transcript of the trp operon.

secondary

positive control

stimulate gene expression Transcriptional control in which a regulatory protein is an activator, stimulating transcription. In positive transcriptional control, the regulatory protein involved is an activator. It binds to DNA (usually at a site other than the operator) and stimulates transcription.

Mutations in which of these lac operon genes or regions are trans in their effect on the regulation of the operon?

the lacI gene A mutation in the lacI gene would affect the regulator protein the lac repressor, which is diffusible and acts in trans.

Attenuation depends on the fact that, in prokaryotes, transcription and _____ are coupled.

translation (occur at the same time)

motif

within the binding domain, a simple structure that fits into the major groove of the DNA Distinctive types of DNA-binding proteins based on the motif

Common DNA-binding motifs

Motif Location Characteristics Binding Site in DNA Helix-turn-helix Bacterial regulatory proteins; related motifs in eukaryotic proteins Two alpha helices Major groove Zinc finger Eukaryotic regulatory and other proteins Loop of amino acids with zinc at base Major groove Steroid receptor Eukaryotic proteins Two perpendicular alpha helices with zinc surrounded by four cysteines Major groove and DNA backbone Leucine zipper Eukaryotic transcription factors Helix of leucine and a basic arm; two leucines interdigitate Two adjacent major grooves Helix-loop-helix Eukaryotic proteins Two alpha helices separated by a loop of amino acids Major groove Homeodomain Eukaryotic regulatory proteins Three alpha helices Major groove

corepressor

Substance that inhibits transcription in a repressible system of gene regulation; usually a small molecule that binds to a repressor protein and alters it so that the repressor is able to bind to DNA and inhibit transcription. a small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription

inducer

Substance that stimulates transcription in an inducible system of gene regulation; usually a small molecule that binds to a repressor protein and alters that repressor so that it can no longer bind to DNA and inhibit transcription. small molecule that turns on the transcription

catabolite repression

System of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose. using glucose when available and repressing the metabolite of other sugars This is a positive control mechanism. The positive effect is activated by catabolite activator protein (CAP). cAMP binds to CAP; together CAP-cAMP complex binds to a site slightly upstream from the lac gene promoter.

A plasmid carries a copy of the lac operator region (lacO), but no other part of the lac operon (the lac repressor can bind to single operator regions). This plasmid is placed in an E. coli cell which has a normal copy of the lac operon in its chromosome. When this strain is grown, the number of plasmids reaches about 40 copies per bacterial cell. What is the expected phenotype of such a strain in the absence of glucose?

The lac operon will be turned on even in the absence of lactose. Almost all the lac repressor molecules will be bound to operators carried by copies of the plasmid and not bound to the lac operator, so the presence of lactose is not needed for the lac operon to be expressed.

In E. coli, under conditions of high extracellular osmolarity, which of these occur? The micF gene produces an antisense RNA that binds to the mRNA of the ompF gene and blocks its translation. The micF gene produces a corepressor that combines with the ompF gene product to produce an active repressor that prevents transcription of the ompF gene. The micF gene produces a protein repression that prevents the transcription of the ompF gene. The micF gene produces an activator protein that stimulates the transcription of the ompF gene by binding the promoter region.

The micF gene produces an antisense RNA that binds to the mRNA of the ompF gene and blocks its translation. The micF gene makes an antisense RNA that is complementary to the ompF mRNA.

A mutation in the 5' UTR of the trp operon reduces the ability for region 2 to pair with region 3. What would be the effect of this mutation on the trp operon when tryptophan levels are high?

The mutation would have no effect on the trp operon. When tryptophan levels are high, regions 2 and 3 never pair, so this mutation would have no effect. Transcription would be terminated.

Mutations in lacO are ______ and cis acting.

constitutive

Which of these E. coli strains with the lac genotypes will synthesize β-galactosidase in the absence of lactose? lacIs lacP- lacO+ lacZ- lacY+/lacI+ lacP+ lacO+ lacZ+ lacY+ lacI+ lacP+ lacO+ lacZ+ lacY+ lacI- lacP- lacO+ lacZ+ lacY+ lacI- lacP+ lacO+ lacZ+ lacY-

lacI- lacP+ lacO+ lacZ+ lacY- Here, the lac repressor gene is mutated and nonfunctional; constitutive expression would occur if the rest of the operon is wild type. Therefore, no induction is required to activate transcription.

Gene expression can be controlled at _____ level(s).

multiple

Some mutations in the trp 5' UTR region increase termination by the attenuator. An example of a mutation that may have this effect is a

mutation that disrupts the antiterminator structure, a deletion in region 2 that prevents it from pairing with region 3. The antiterminator structure occurs when regions 2 and 3 pair, preventing transcription termination. This can only occur when the ribosome stalls at the UGG codons, which encode tryptophan, in region 1.

A mutant strain of E. coli produces β-galactosidase in the presence and in the absence of lactose. The mutation in this operon lies in the

operator. This is where the lac repressor binds to prevent RNA polymerase from binding. If the lac repressor cannot bind, then RNA polymerase will always be able to bind and stimulate transcription.

Genes encoding proteins with related functions that are all under the control of a single promoter are called a(n)

operon

Whether the ______ termination of transcription (attenuation) takes place in the trp operon depends on the cellular level of tryptophan.

premature

Synchronization of translation and transcription is due to a site in what region in regards to the trp operon?

region 1 The presence of stop codons regarding tryptophan in region 1 allows for translation to halt while transcription is moving ahead. Once the RNA takes an alternative configuration, the ribosome translation can catch up to the process of transcription.