Chapter 7

The major site of protein binding in DNA is the major groove. Why is this a good site for binding?

• The major groove has lower frequencies of inverted repeats; this lower frequency of inverted repeats makes binding easier.

• Because the minor groove is wider, it is more accessible to binding proteins.

• The major groove has a more heavily methylated base composition, which aids in the binding of proteins.

• Because the major groove is wider, it is more accessible to binding proteins.

Because the major groove is wider, it is more accessible to binding proteins.

Regulation by induction and repression are called negative control because __.

• Translation proceeds in the absence of the repressor protein.

• Transcription proceeds in the presence of the repressor protein.

• Translation proceeds in the presence of the repressor protein.

• Transcription proceeds in the absence of the repressor protein. The organism wants transcription to occur only when the substrate (the activator protein) of the gene product is present.

Transcription proceeds in the absence of the repressor protein. The organism wants transcription to occur only when the substrate (the activator protein) of the gene product is present.

Short regions at the beginning and end of gene sequences are not translated into proteins.

• True

• False

True

One way that regulation is often studied is by examining the effects of mutations. For example, mutations within the parts of the lac operon have been well studied. Which of these mutants would be considered a constitutive mutant?

• a mutation that disables the promoter for the operon

• a mutation that disables the repressor

• a mutation in the gene for beta-galactosidase

• a mutation in the gene for beta-galactosidase permease

a mutation that disables the repressor

Which type of regulator(s) specifically binds to operator regions of DNA?

• repressors

• repressors and corepressors

• activators and inducers

• activators

repressors

Some proteins that bind to DNA block transcription, whereas other proteins activate transcription.

• True

• False

True

Which of the following is an example of negative control using an inducible system?

• The lac operon in E. coli is turned off unless lactose is present. A repressor binds to the operator and prevents RNA polymerase from binding to the promoter. When allolactose (closely related to lactose) is present, it binds to the repressor and prevents the repressor from binding. In this way, the presence of lactose allows the operon to be turned on to express the genes need to use lactose.

• Glucose inhibits the synthesis of cyclic AMP and stimulates cyclic AMP transport out of the cell. The lower cyclic AMP levels prevent CRP from binding DNA, and RNA polymerase cannot bind to the promoters of operons subject to catabolite repression.

• The trp operon in E. coli is turned on by default. When there are sufficient amounts of tryptophan, a repressor can bind to the operator to turn off the operon. Additionally, when there are sufficient amounts of tryptophan, attenuation occurs and the operon is turned off.

• The maltose operons in E. coli are turned off by default. When maltose is present, it binds to the maltose activator protein. The maltose activator protein can then bind to the activator binding site to allow the genes of the operons to be expressed. (There are multiple operons affected by the maltose activator protein).

The lac operon in E. coli is turned off unless lactose is present. A repressor binds to the operator and prevents RNA polymerase from binding to the promoter. When allolactose (closely related to lactose) is present, it binds to the repressor and prevents the repressor from binding. In this way, the presence of lactose allows the operon to be turned on to express the genes need to use lactose.

The lac operon is an example of __ control in which the presence of an __ is required for transcription to occur.

• negative / inducer

• positive / inducer

• negative / activator

• positive / activator

negative / inducer

__ pathways typically rely on __ proteins to inhibit mRNA synthesis.

• Catabolic; activator

• Anabolic; repressor

• Catabolic; repressor

• Anabolic; activator

Anabolic; repressor

Which statement best explains why positively controlled genes have weak promoters and need an activator protein to help the RNA polymerase bind?

• The organism only wants translation to stop when the substrate (the activator protein) of the gene product is present.

• The organism only wants translation to occur when the substrate (the activator protein) of the gene product is present.

• The organism wants transcription to stop when the substrate (the activator protein) of the gene product is present.

• The organism wants transcription to occur only when the substrate (the activator protein) of the gene product is present.

The organism wants transcription to occur only when the substrate (the activator protein) of the gene product is present.

Enzyme repression typically affects catabolic pathways.

• True

• False

False

The function of a kinase is

• response regulation.

• phosphorylation.

• methylation.

• glycosylation.

phosphorylation

Bacteria can regulate gene expression due to changes in the environment. How are these changes communicated to the cell?

• A sensor kinase on the cell membrane recognizes the change and transfers the information to a response regulator in the cytoplasm.

• A sensor kinase in the cytoplasm recognizes a change and transfers the information to a response regulator on the cell membrane.

• A response regulator on the cell membrane recognizes the change and transfers the information to a sensory kinase in the cytoplasm.

• A sensor kinase of the cell membrane recognizes the change and transfers the information to the repressor or inducer molecule, which then binds to DNA.

A sensor kinase on the cell membrane recognizes the change and transfers the information to a response regulator in the cytoplasm.

Quorum sensing is a regulatory system that requires a certain cell density to work effectively. Each of the following activities utilizes quorum sensing EXCEPT

• Staphylococcus aureus infection.

• light emission by Aliivibrio fischeri.

• transition of Candida albicans from budding yeast to elongated filaments.

• flagella synthesis in Proteus vulgaris.

flagella synthesis in Proteus vulgaris.

A bacterium that either partially or fully catabolizes an acyl-homoserine lactone will likely disrupt

• endospore formation.

• attenuation.

• chemotaxis.

• quorum sensing.

quorum sensing.

Quorum sensing relies upon a large cell population which then turns on transcription.

• True

• False

True

Which of the following examples describes a type of catabolite repression?

• A mutation in the promoter of the lac operon prevents the expression of the genes needed for the bacterium to utilize lactose.

• The presence of abundant tryptophan inhibits the trp operon.

• Allolactose binds to a repressor, preventing it from binding to the operator of the lac operon.

• When glucose is present, the lac operon is inhibited.

When glucose is present, the lac operon is inhibited.

Cyclic AMP is synthesized from ATP by an enzyme called __ which is involved in __.

• adenylate cyclase / transcriptional activation

• cAMP receptor protein (CRP) synthase / transcriptional activation

• adenylate cyclase / catabolite repression

• cAMP receptor protein (CRP) synthase / catabolite repression

adenylate cyclase / catabolite repression

In negative control of transcription by the lac operon, how does the presence of an inducer affect transcription?

• The inducer prevents the repressor from binding to the operator.

• The inducer causes the repressor to bind to the operator.

• The inducer binds to the operator.

• The inducer does not bind to the operator.

The inducer prevents the repressor from binding to the operator.

A mutation in the gene encoding the lactose repressor (Lacl) that prevents lactose from binding to the Lacl protein would result in

• constant expression of the lac operon in the absence of lactose.

• constant repression of the lac operon in the presence of lactose.

• constant repression of the lac operon in the absence of lactose.

• constant expression of the lac operon in the presence of lactose.

constant repression of the lac operon in the presence of lactose.

The synthesis of β-galactosidase is regulated by __.

• induction

• induction and catabolite repression

• repression

• catabolite repression

induction and catabolite repression

The preferential use of glucose over other available carbon substrates for growth is mechanistically explained by catabolite repression.

• True

• False

True

Cyclic AMP (cAMP) is involved in the global regulation of catabolic pathways in Escherichia coli, including the lac operon. A high activity of the enzyme adenylate cyclase, which makes cAMP, is suggestive of catabolite repression.

• True

• False

False

All of the following are functions of heat shock proteins in bacteria EXCEPT

• responding to exposure to high levels of ethanol.

• stimulation of binary fission.

• prevention of inappropriate protein subunit aggregation.

• degradation of denatured proteins.

stimulation of binary fission

The most frequent way in which small regulatory RNA molecules exert their effects is by

• signal transduction.

• binding to a repressor and repressing enzyme transcription.

• base pairing with other RNA molecules that have regions of complementary sequence.

• acting as an inducer that then binds to an activator protein to allow transcription to proceed.

base pairing with other RNA molecules that have regions of complementary sequence.

How would you design an sRNA to bind to a sequence?

• take the complementary sequence of 200 continuous nucleotides

• take the complementary sequence of six continuous nucleotides

• select six continuous nucleotides from the sequence

• select 200 continuous nucleotides from the sequence

take the complementary sequence of 200 continuous nucleotides

Attenuation is a type of regulation that can control

• allosteric enzyme activity.

• transcriptional activity exclusively.

• translational activity exclusively.

• both transcriptional and translational activity.

transcriptional activity exclusively.

Which regulatory mechanism does NOT depend on a conformational change in protein/enzyme structure to change activity?

• attenuation

• negative control

• catabolite repression

• feedback inhibition

attenuation

Which of the following is a characteristic of an isoenzyme?

• More than one enzyme is regulated by the same mechanism.

• More than one gene makes the same enzyme.

• Multiple binding sites on the same enzyme enable multiple regulation mechanisms.

• The same reaction can be catalyzed by multiple enzyme variants.

The same reaction can be catalyzed by multiple enzyme variants.

Regulation of enzyme activity occurs

• at the start of translation.

• posttranslationally.

• at any point on the enzymatic production pathway.

• at the start of transcription.

posttranslationally.