MbioS 404 Exam 3

In periods of nutrient deprivation, E. coli initiate a stress response that involves the coordinated regulation of gene expression.(1) Which E. coli regulatory RNA represses translation of mRNAs transcribed from the rpoS gene?(2) Which E. coli regulatory RNA represses transcription by binding to the σ70 subunit of RNA polymerase?

(1) OxyS; (2) 6S RNA When E. coli enter the stationary phase (stop dividing because of nutrient depletion), 6S RNA molecules accumulate and bind to σ70 subunits, which, in turn, down-regulates transcription of σ70 promoters. At the same time, a different σ subunit, σS, becomes produced in response to the stress. The rposS gene, which encodes σS, is regulated by at least three sRNAs. Two of them, DsrA and RprA, stimulate translation of mRNAS transcribed off rpoS, while the third, OxyS, represses translation of this gene. Through inhibition of σ70 subunits by 6S RNAs combined with the sRNA-stimulated production of σS subunits, the appropriate genes are expressed to help E. coli survive the stationary phase.

Which concepts of gene expression "noise" best describes a situation in which a population of cells shows:(1) variation in gene expression among copies of the same gene within the same cell at a particular time;(2) variation in expression of the same gene among different cells in the population; and(3) variation in expression of a gene in the same cell over time.

(1) intrinsic noise; (2) extrinsic noise; (3) extrinsic noise

Outline the general steps of differential gene expression induced by concentration-dependent morphogens.

1 - A cell or cells synthesize and release the morphogen or signaling molecule. 2 - The distribution of morphogen establishes an extracellular concentration gradient. 3 - The morphogen binds receptors on the surface of other cells. The percent occupancy of morphogen decreases as the distance increases between the source cell and the receptor cell. 4 - Through a signaling pathway, activated receptor leads to an increase in expression of a transcriptional regulator that controls expression of many genes.

Rank the steps whereby miRNAs are generated and act to silence gene expression in order from first to last.

1 - RNA polymerase transcribes the pri-miRNA in the nucleus that forms a stem-loop. 2 - Drosha cleaves the pri-miRNA at two sites to create a 65-70-nucleotide-long pre-miRNA. 3 - Dicer cleaves the loop from the pre-miRNA to a 22-nucleotide-long double-stranded RNA. 4 - The double-stranded RNA is denatured to become the single-stranded guide RNA that can be incorporated into the RNA-induced silencing complex (RISC). The guide RNA brings RISC to the target mRNA. 5 - RISC can repress gene expression through Slicer by clearing the target mRNA or non-Slicer-dependent mechanisms.

In the scheme of feeding bacteria to worms to induce an RNAi response in worms, explain the purpose of the following components: lac promoter incorporated into the genome of E. coli, T7 gene incorporated into the genome of E. coli, and T7 promoter on the plasmid introduced into E. coli.

1 - T7 gene incorporated into the genome of E. coli encodes the single-subunit RNA polymerase from the bacteriophage. 2 - Lac promoter incorporated into the genome of E. coli allows for inducible expression of the T7 RNA polymerase by the normal transcription machinery in the cell. 3 - T7 promoter on the plasmid introduced into E. coli is placed in front of the DNA encoding the shRNA. The T7 RNA polymerase recognizes and transcribes from this promoter.

Which of these is responsible for initiating a signal transduction pathway?

A This is a signal molecule. The attachment of a signal molecule to a plasma membrane receptor initiates a signal transduction pathway.

What type of regulatory circuit controls Bacillus subtilis cells switching between the swimming and chaining states?

A double-negative loop involving SinR and SlrR proteins controls the swimming or chaining state of B. subtilis.

Similar to the domain swapping experiments discussed in Chapter 19, you create either truncated versions or hybrid versions of proteins containing domains from the eukaryotic activator Gal4 and/or the bacterial repressor LexA. The ability of these altered proteins to activate transcription is assayed using a reporter construct engineered by placing either the LexA or Gal4 DNA-binding site upstream of the lacZ gene. Which scenario leads to expression of the lacZ gene in S. cerevisiae?

A hybrid protein containing the LexA DNA-binding domain fused to the Gal4-activating domain is tested using a reporter that contains the LexA-binding site upstream of lacZ. The LexA DNA-binding domain will bind to the LexA-binding site upstream of lacZ. The fusion with the Gal4-activating domain will initiate transcription of the lacZ promoter.

Which of the following mutations could lead to constitutive expression of the genes of the lac operon?

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

Explain what is meant by the term "AND gate" in terms of regulation.

A regulatory circuit that follows the logic of an "AND gate" requires that two input conditions are met for output rather than operating as a simple on and off switch.

Consider the predominant types of alternative splicing events that occur in mammals. Which of the following choices represent mRNA molecules that could be produced from the primary RNA transcript by alternative RNA splicing? (In each choice, the yellow part on the left represents the 5' cap, and the yellow part on the right represents the poly-A tail.) (A)B(C)D(E)F(G)I

ACGI ACEI ACEGI

Which of the following enzymes converts ATP to cAMP?

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

A protein kinase activating many other protein kinases is an example of _____.

Amplification By activating many other molecules the initial signal is amplified.

Which of the following statements best defines the term operon?

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.

Which of these is a membrane receptor?

B This is a receptor molecule.

Compare and contrast the DNA sequence elements involved in regulating transcription in bacterial cells and eukaryotic cells.

Bacterial and eukaryotic cells - include DNA-binding sites for regulatory proteins like repressors or activators include promoter sequences within the DNA upstream of the coding sequence of a gene Bacterial cells - the regulatory elements are mostly located close to the gene they regulate genes are typically controlled by one activator and/or one repressor protein Eukaryotic cells - the regulatory elements may be located at great distances from the gene they regulate genes are typically controlled by multiple activator and repressor proteins

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. 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.

Which statements about the regulation of transcription initiation in these genes are true?

Both the fantasin gene and the imaginin gene will be transcribed at high levels when activators specific for control elements A, B, C, D, and E are present in the cell. The fantasin gene will be transcribed at a high level when activators specific for control elements A, B, and C are present in the cell. Control elements C, D, and E are distal control elements for the imaginin gene. Only certain genes are transcribed in a eukaryotic cell at any particular time. The regulation of transcription initiation depends on the interaction of specific transcription factors with specific control elements in enhancers. In the imaginary eukaryotic cell used as an example here, the enhancers for the fantasin gene and imaginin gene are unique because they contain different sets of control elements (A, B, and C for the fantasin gene; C, D, and E for the imaginin gene). Each gene will be transcribed at a high level when activators specific for all of the control elements in its enhancer are present in the cell.

What role does a transcription factor play in a signal transduction pathway?

By binding to DNA it triggers the transcription of a specific gene. This is the function of a transcription factor.

How long do cells persist in the swimming or chaining states?

Cells persist in one state for several generations but stochastically switch states.

The regulation of gene expression in individual cells coordinates the development of multicellular organisms, ensuring that tissues and organs form in their characteristic places. Researchers can study how multicellular organisms develop their spatial organization by examining normal and mutant forms of organisms, such as the fruit fly, Drosophila. Which of the following statements about pattern formation are true? Cells receive molecular signals that communicate their position in relation to other cells. Pattern formation begins in adult animals. Differential gene expression affects the developmental process in animals. The process of pattern formation involves segmentation of the body but does not involve the development of segment-specific body parts. Homeotic genes code for transcription factors that control the development of segment-specific body parts. Homeotic genes establish major body axes. Positional information controls pattern formation.

Cells receive molecular signals that communicate their position in relation to other cells. Differential gene expression affects the developmental process in animals. Homeotic genes code for transcription factors that control the development of segment-specific body parts. Positional information controls pattern formation. Pattern formation is the development of a multicellular organism's spatial organization, including the arrangement of tissues and organs. Cells receive molecular signals, collectively called positional information, that inform the cells about their location in relation to other cells and to the body axes. Positional information regulates pattern formation. Homeotic genes are regulatory genes that work after the body axes have been established. Homeotic genes identify particular body segments in an individual, eventually leading to the formation of segment-specific body structures in the correct locations on the body.

You discover a novel DNA-binding protein. What would be the best technique to define the identity of the specific DNA sequence to which this protein can bind?

ChIP-Seq assay ChIP-Seq is an improvement over the general ChIP (chromatin immunoprecipitation) assay. In ChIP-Seq, the DNA fragment bound by the novel DNA-binding protein is liberated and directly sequenced using next-generation sequencing methods. This allows one to know the precise identity of the DNA sequence to which the protein of interest is bound.

Which of these acts as a second messenger?

D

Which statements about the modification of chromatin structure in eukaryotes are true? DNA is not transcribed when chromatin is packaged tightly in a condensed form. Acetylation of histone tails is a reversible process. Methylation of histone tails in chromatin can promote condensation of the chromatin. *Deacetylation of histone tails in chromatin loosens the association between nucleosomes and DNA.* Some forms of chromatin modification can be passed on to future generations of cells. Acetylation of histone tails in chromatin allows access to DNA for transcription.

DNA is not transcribed when chromatin is packaged tightly in a condensed form. Acetylation of histone tails is a reversible process. Methylation of histone tails in chromatin can promote condensation of the chromatin. Some forms of chromatin modification can be passed on to future generations of cells. Acetylation of histone tails in chromatin allows access to DNA for transcription. One of the mechanisms by which eukaryotes regulate gene expression is through modifications to chromatin structure. When chromatin is condensed, DNA is not accessible for transcription. Acetylation of histone tails reduces the attraction between neighboring nucleosomes, causing chromatin to assume a looser structure and allowing access to the DNA for transcription. If the histone tails undergo deacetylation, chromatin can recondense, once again making DNA inaccessible for transcription. Recent evidence suggests that methylation of histone tails can promote either the condensation or the decondensation of chromatin, depending on where the methyl groups are located on the histones. Thus, methylation can either inactivate or activate transcription, and demethylation can reverse the effect of methylation. Changes in chromatin structure may be passed on to future generations of cells in a type of inheritance called epigenetic inheritance.

Define differential gene expression in the context of development.

Differential gene expression is the synthesis of a protein or non-coding RNA in a subset of embryonic cells.

Which of the following statements about the development of an early Drosophila embryo is NOT true? Dorsal protein activates rhomboid expression only in the ventral neurogenic ectoderm region. rhomboid and sog both have enhancers containing binding sites for Snail protein but twist does not. Dorsal protein activates sog expression only in the ventral and lateral neurogenic ectoderm regions. Dorsal protein activates Twist expression in the ventral neurogenic ectoderm regions of the embryo.

Dorsal protein activates Twist expression in the ventral neurogenic ectoderm regions of the embryo. In the early developing Drosophila embryo, a concentration gradient of the morphogen Dorsal protein is established with the highest concentration in the ventral region and lowest in the dorsal region of the embryo. One of the gene targets of Dorsal is twist, which has two low-affinity Dorsal-binding sites that can be occupied only by peak levels of the Dorsal gradient. This means that twist is only expressed in the ventralmost 18 cells, which will form the mesoderm of the embryo. twist cannot be expressed in what will become neurogenic ectoderm regions because the concentration of Dorsal protein is too low.

T or F? Attenuator systems such as the one described for regulation of tryptophan synthesis would be just as likely to occur in eukaryotes as in prokaryotes.

False Correct. Regulation by attenuation requires that translation of a given transcript can begin before transcription is completed. This is not possible in eukaryotes, as the two processes are spatially separated by the nuclear membrane.

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.

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.

T or F? Maternal effect genes are transcribed in the egg after fertilization.

False. Correct. Maternal effect genes are transcribed during oogenesis (in the mother). The mRNA is translated in the embryo after fertilization.

Which of the following is NOT true about the genetic circuits referred to as feed-forward loops?

Feed-forward loops are oscillating gene circuits. Evolution has favored two different feed-forward motifs. In the first motif, called a coherent feed-forward loop, two transcriptional activators each directly stimulate transcription of a third "target" gene. Because one of the activators is also responsible for directly stimulating the production of the second activator protein, a strong sustained signal is output. Thus, this type of genetic circuit cannot be confused with an oscillatory circuit. In the second motif, which is called an incoherent feed-forward loop, the three genes involved code for one activator protein, a repressor protein, and a target protein. The activator directly stimulates the target and the repressor genes, which results in switching the target gene ON. However, after a short time, enough repressor is made to turn the target OFF. Thus, an incoherent feed-forward loop is termed a pulse generator. An oscillatory regulatory circuit differs from an incoherent feed-forward loop by showing true oscillatory behavior as a result of two genes being produced out of phase with each other—as one product starts to accumulate the other product starts to fall, and so on.

The presence of a DNA template (e.g., a product from PCR), general transcription factors, and RNA polymerase II allows for the initiation of transcription in vitro. Explain why the initiation of transcription is not possible with only general transcription factors and RNA polymerase II using the genomic DNA as a template.

Genomic DNA is wrapped in nucleosomes, while template DNA from PCR is not. For remodeling or removing nucleosomes additional proteins are required.

A set of known mutations in the BX-C genes in Drosophila results in the development of wings on a body segment that would not ordinarily have wings. This is an example of mutation in which class of developmental genes?

Homeotic genes Correct. Homeotic genes specify segment identity with respect to the body part that will develop at metamorphosis.

Hox genes are a complex of homeotic genes that are expressed in a particular pattern along the anterior-posterior axis of many animals, including mice, birds, humans, and fruit flies (Drosophila). The image below shows the arrangement of Hox genes on a fruit fly chromosome and the corresponding expression of Hox genes in different body segments of a fruit fly embryo.

Hox genes code for transcription factors that are involved in the production of segment-specific structures. The Hox genes of homeotic mutant fruit flies contain mutations resulting in abnormal pattern formation. This often results in the formation of structures in the wrong location on the body—for example, legs where antennae are produced in wild-type (normal) fruit flies.

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

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. If repressor level is too low, the cells might induce the lytic cycle without the bacteriophage being ready for release.

What is allosteric regulation?

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.

What is the function of the PAZ domains in Dicer and Argonaute proteins?

In both proteins, the PAZ domains recognize and bind the 3′ end of a double-stranded RNA molecule. After the Microprocessor complex processes a pri-miRNA transcript to produce a pre-miRNA with a two-nucleotide overhang on its 3′ end, a second RNA-cleaving enzyme called Dicer further cleaves the double-stranded pre-miRNA. Dicer's PAZ domain binds the 3′ overhang of the pre-miRNA. This allows Dicer to precisely position the two RNase subunits at its opposite end and make cuts in the right location of each strand of the pre-miRNAs. This action generates an ~22-bp miRNA that will eventually become single-stranded and supply the RISC complex with its guide RNA strand. In the RISC complex, the guide RNA strand is arranged such that its 3′ end is bound by the PAZ domain of Argonaute. Once positioned within Argonaute, the guide RNA is available for binding to a complementary (target) mRNA molecule followed by cleavage of the target in the catalytic site of Argonaute.

Consider the experiment in which the expression of two copies of the same gene are measured using the green fluorescent protein reporter for the first copy of the gene and red fluorescent protein reporter for the second copy of the gene in E. coli cells. Provide an example of intrinsic versus extrinsic noise observed for this system.

Intrinsic noise: At a given time, cells are not all yellow (equally expressing the green and red reporter from each gene copy). Instead, some cells are red, some are green, and some are yellow. Within a given cell, the relative expression of each copy of the gene varies. Extrinsic noise: When tracking the gene expression of a specific cell over time, the gene expression of both genes varies synchronously over time.

Which of the following statements is true regarding cooperative binding? 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.

It decreases the concentration of protein required to fill adjacent protein binding sites 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 a cell dedicates resources to the production of enzymes involved in lactose metabolism only when lactose is available in the environment. Correct. The cell expends energy to produce the proteins necessary for lactose metabolism only when lactose is present.

Match the mechanism for transcriptional repression in prokaryotes with an example of a protein that uses the mechanism.

Lac repressor - A repressor binds a site that overlaps with the promoter to block RNA polymerase binding. MerR protein - A protein binds the promoter and holds the DNA in a conformation that prevents initiation of transcription. 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.

Recall the use of combinatorial control in regulation of the S. cerevisiae mating type specific gene expression. Describe how Mcm1 serves to repress and activate transcription of target genes in haploid MAT α cells.

Mcm1 is a site-specific DNA-binding transcription factor that forms repressor or activator complexes. A dimer of α2 binds cooperatively with Mcm1 upstream of a-specific genes to repress Mcm1 is a site-specific DNA-binding transcription factor that forms repressor or activator complexes. A dimer of α2 binds cooperatively with Mcm1 upstream of a-specific genes to repress the transcription of those genes in haploid alpha cells. At the same time, Mcm1 binds cooperatively with α1 upstream of alpha-specific genes to activate transcription of those genes in haploid α cells. the transcription of those genes in haploid alpha cells. At the same time, Mcm1 binds cooperatively with α1 upstream of alpha-specific genes to activate Mcm1 is a site-specific DNA-binding transcription factor that forms repressor or activator complexes. A dimer of α2 binds cooperatively with Mcm1 upstream of a-specific genes to repress the transcription of those genes in haploid alpha cells. At the same time, Mcm1 binds cooperatively with α1 upstream of alpha-specific genes to activate transcription of those genes in haploid α cells. transcription of those genes in haploid α cells.

Explain why a regulatory circuit under negative autoregulation is described as robust.

Negative autoregulation allows the output of the regulatory circuit to be insensitive to a parameter causing noise while maintaining homeostasis.

Under which conditions are the lac structural genes expressed most efficiently?

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.

Which regulatory circuit represents the expression of a regulatory protein that if turned on quickly, will be maintained at a constant level?

Node and flat arrow Negative autoregulation

How are nodes and edges depicted?

Nodes depicted with a dot. An edge would have → for positive regulation and ⊣ symbol for negative regulation.

What do nodes and edges represent in regulatory circuits?

Nodes represent genes with a dot, whereas edges represent the regulation of one gene by the product of another gene with a line.

Which of the following proteins combine to form the Microprocessor complex used to produce active miRNA?

Pasha (or DGCR8) and Drosha The Microprocessor complex consists of an RNA-cleaving enzyme called Drosha and an essential specificity subunit called Pasha (DGCR8 in some organisms). This complex processes the primary miRNA (pri-miRNA) transcript producing a pre-miRNA product. The cleavage event occurs in the nucleus.

In circadian rhythm regulation in flies and mammals, which event occurs next in the cell after enough Per (Period) protein has accumulated to shut off its own synthesis?

Per proteins become degraded in the cell. Two transcriptional activators, Clock and Cycle, stimulate the transcription of the per gene. This results in production of Per protein, which is an autorepressor and therefore shuts off its own transcription when enough of the protein has accumulated. Because Per protein is proteolytically unstable, it soon breaks down allowing Clock and Cycle proteins to re-activate the transcription of the per gene. This periodicity is the mechanism behind the natural clock or "circadian rhythm" found in flies and mammals.

_____ catalyzes the production of _____, which then opens an ion channel that releases _____ into the cell's cytoplasm.

Phospholipase C ... IP3 .... Ca2+ Phospholipase C cleaves IP3 from a membrane protein, and IP3 then binds to a calcium channel on the ER.

What molecule binds to promoters in bacteria and transcribes the coding regions of the genes?

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

Describe an experiment that showed that the 3′ UTR of bicoid and oskar mRNAs is required for proper localization in the Drosophila oocyte.

Researchers engineered an mRNA that had the 3' UTR of oskar mRNA replaced with the 3' UTR from bicoid mRNA. They observed oskar mRNA localization in the anterior pole as normally observed for bicoid mRNA normally. This is enough to induce pole cell formation at the wrong locations.

Which of the following statements about riboswitches is true?

Riboswitches control gene expression through changes in RNA secondary structure. Riboswitches are cis-acting regulatory elements that regulate either transcription termination or translation initiation. These RNA sequence elements, which are usually located in the 5′-untranslated region (upstream) of the genes they are regulating, control gene expression in response to changes in the concentration of a small-molecule ligand usually produced by the gene under their regulation. Riboswitches accomplish this via changes in their secondary structure, which in turn is determined by whether or not its ligand is bound to its aptamer. When the aptamer is not bound to its ligand, transcription or translation is switched "on." When the aptamer is bound to its ligand, the secondary structure of the expression platform is altered in a manner that results in transcription or translation being switched "off."

Name the relevant mRNA or protein used in the strategy.

SpoIIR σE σF pro-σE

Which of the following are signaling proteins that stimulate the proteolytic processing of intracellular proteins important for transcription activation?

SpoIIR and Delta In the bacterium Bacillus subtilis, spore formation begins when a forespore cell produces a signaling protein called SpoIIR. SpoIIR then travels to the septum separating the forespore cell from the mother cell where it triggers the proteolytic activation of an inactive form of σE called "pro-σE" found in the mother cell. The activated σE subunits then help initiate transcription of specific genes in the mother cell. In the early development of insects, a neuroblast (precursor cell to a neuron) secretes signaling molecules called Delta. These secreted molecules bind to Notch receptors on the surfaces of neighboring cells in the neurogenic ectoderm. Upon activation, the intracellular domain of Notch is cleaved by intracellular proteases. Cleavage produces a molecular subunit called NotchIC, which then travels to the nucleus where it associates with a DNA-binding protein called Su(H). The NotchIC-Su(H) complex activates genes that encode transcriptional repressors that prevent the cell from becoming a neuron. This developmental mechanism prevents cells in physical contact with a neuroblast from developing into neurons themselves and instead they become skin cells.

Describe the relationship between noise and stochasticity.

Stochasticity means that a system is subject to some degree of randomness. This randomness in regulation of gene expression produces noise or variation in gene expression under apparently identical conditions.

Describe the key features of piwi-interacting RNAs (piRNA) found in eukaryotes.

The 24-34-nucleotide-long piRNAs typically are expressed in the germline to protect organisms against transposons. piRNAs do not require processing by Dicer because they result from processing a longer single-stranded RNA rather than a double-stranded precursor. These single-stranded RNAs are transcribed from piRNA clusters that consist of various segments of transposon sequence.

Which of the following occurs as a result of an abundance of tryptophan in E. coli?

The 5 trp genes (TrpA - TrpE) are not transcribed. Correct. When trp is abundant, the genes involved in tryptophan synthesis are negatively regulated at the level of transcription.

Which of the following statements concerning the localization of Ash1 mRNAs in the yeast Saccharomyces cerevisiae is true?

The daughter cell cannot change its mating type. A mother cell and its daughter cell can show different mating types. Although both mother and daughter cells might initially, for example, exhibit the "a" mating type, only the mother is capable of switching to the "α" mating type. The mother is able to switch mating types because the HO gene, which controls switching, can be activated in the mother because of the absence of Ash1 repressor protein, whereas HO in the daughter is repressed by Ash1. Ash1 mRNAs transcribed in the nucleus of the mother cell before budding become localized in the daughter cell during the budding process because of cytoskeletal-mediated transport of Ash1 mRNAs from mother cell to daughter cell.

How does the source and generation of miRNAs differ from those of siRNAs?

The genome encodes pri-miRNAs that form a secondary structure (stem-loop) after being transcribed. pri-miRNAs are processed by Drosha to cleave the lower stem from the upper stem, and these pre-miRNAs can then be further processed by Dicer to liberate mature miRNAs. siRNAs arise from double-stranded RNAs that form when two complementary RNAs base-pair. After processing by Dicer, they look similar to the processed miRNAs and inhibit gene expression in a similar manner.

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 form tetramers. - can still bind DNA and form dimers

Which of the following features of the trp operon is likely least essential to the process of attenuation? Trp codons near the beginning of the leader sequence Transcription and translation of the leader sequence occur simultaneously. The ability of sequences within the leader mRNA to pair with one another The order of the structural genes, E, D, C, B, A

The order of the structural genes, E, D, C, B, A Correct. Because each gene encodes an enzyme involved in the trp synthetic pathway, the order in which the genes occur is likely not important in terms of the attenuation process.

The regulation of a novel operon in E. coli involves two operators that sandwich a promoter and three structural genes. RNA polymerase transcribes the structural genes from the promoter, and a specific repressor represses transcription from that promoter. In the presence of the relevant signal, the repressor binding to DNA is disrupted and repression is alleviated. To study the mechanism of repression, researchers created a reporter containing the promoter but replaced the operators with lac operator sites. Wild-type lac repressor was able to repress expression from this construct in the cell. In vitro, researchers visualized protein-DNA complexes in electron micrographs using the reporter construct after incubation with either wild-type Lac repressor or a mutant of the Lac repressor that binds to the operator sites, dimerizes, but fails to tetramerize. The scored data of their observations are given in the table below. In addition, it was shown that the mutant Lac repressor was not able to repress expression from the reporter construct in vivo, although it was able to repress the endogenous lac operon. Given the data in the table, propose a model for repression stating how the data supports your model. What other information would you want to know about the novel repression protein to support this model?

The researchers observed that the wild-type Lac repressor could bind DNA in a way that caused formation of a loop and could repress the reporter. They did not observe the loop structure in the presence of the mutant Lac repressor that could bind DNA but could not repress the reporter. The mutant Lac repressor could still bind to DNA in tandem (i.e., to both sites). Thus, the model would be that the novel repressor probably does not repress its operon binding to a site overlapping the promoter but rather forms a loop that inhibits transcription. You would want to show that the novel repressor can indeed form loops when bound to DNA.

What property of ComK binding to the promoter for comK allows this regulatory circuit to be a bistable switch?

The response in the positive autoregulation is highly sensitive to slight changes in ComK protein levels, and therefore the output is not linear when threshold is met. The switch is said to be at a "knife edge" between the ON and OFF states.

What happens to the expression of the lacI gene if lactose is not available in the cell?

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. 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.

T or F? The placement of the operator sequence between the promotor and the structural genes is critical to the proper function of the lac operon.

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

Which of the following statements about the function of regulatory RNAs in X-chromosome inactivation is NOT true?

Xist RNAs produced by one X-chromosome can initiate inactivation of genes located on the other X-chromosome (they are trans-acting regulators). The regulatory RNA that initiates X-chromosome inactivation is called Xist. This RNA is transcribed from the Xic gene found on the X- chromosome. It is believed that Xist RNAs produced by one X-chromosome are can only coat genes on that same X-chromosome. The reason why Xist is only cis-acting is not yet clear.

Which of the following is an accurate description of synteny?

a block of genes linked together on the same chromosome that is conserved between distantly related animals Comparative genome analysis has revealed that distantly related animals share conserved blocks of linked genes (show a high degree of synteny). Even organisms that have not had a common ancestor for hundreds of millions of years can exhibit some synteny.

Which type of switch is characterized by a rapid response time?

a negative autoregulatory switch Negative autoregulation has been selected repeatedly in evolution. One important benefit of this type of switch is that it permits a rapid response time: a strong promoter enables the cell to quickly generate new regulatory proteins, but, as their concentration begins to exceed normal limits, these repressors shut down their own transcription.

Which of the following protein domains would be most likely to recognize and bind to acetylated lysine residues on nucleosomes?

bromodomains Acelylation creates specific binding sites for bromodomain-containing proteins. A component of TFIID contains a bromodomain that allows it to bind with more efficiency to acetylated nucleosomes than to unacetylated nucleosomes. Thus, a gene bearing acetylated nucleosomes at its promoter will be more likely to recruit transcriptional machinery than one with unacetylated nucleosomes.

Which strategy for differential gene expression do Bacillus subtilis cells use when the forespore influences gene expression in the mother cell?

cell-to-cell contact

Which of these acts as a second messenger?

cyclic AMP Cyclic AMP can act as second messengers.

Calcium ions that act as second messengers are stored in _____.

endoplasmic reticula The ER stores calcium ions.

In which of the following pre-mRNA sequence elements can pre-miRNAs be coded?

exons, introns, and noncoding regions Pre-miRNAs can be found any part of a pre-mRNA transcript, meaning exons, introns, or noncoding regions.

A eukaryotic gene is most likely to be transcribed if it is located where?

in a euchromatic region of the genome Euchromatin is less packed than heterochromatin and is usually associated with active transcription.

In prokaryotes, when can basal level (constitutive) expression of a gene occur?

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 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.

Which of the following can regulate gene expression during development, but does NOT represent a pathway of cell-to-cell signal transduction or establishment of an extracellular gradient?

mRNA localization Three strategies have evolved for instructing cells to express specific genes during development: cell-to-cell contact, signaling through the diffusion of a secreted signaling molecule (morphogen), and localization of maternal mRNAs in an egg (either before or after fertilization). Only the third listed process—mRNA localization—does not represent a pathway of cell-to-cell signal transduction or establishment of an extracellular gradient for regulating gene expression. Localization of mRNAs allows cells to distribute critical regulatory molecules asymmetrically to specific parts of a cell, typically via transport along elements of the cytoskeleton.

Which of the following is a shared characteristic of miRNAs and siRNAs?

miRNAs and siRNAs are both processed in the cytoplasm by the protein Dicer. Dicer processes pre-miRNAs in the cytoplasm to produce the mature miRNA used in the RISC complex. Similarly, Dicer processes long double-stranded RNA molecules into short siRNAs that are subsequently used in RISC or RITS complexes.

Given the following mutants and conditions, predict the expression of the of the lacZ gene (no expression, basal level of expression, or activated level of expression). 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 the absence of glucose, absence of lactose. Mutant 2: In the presence of glucose, presence of lactose. Mutant 2: In the presence of glucose, absence of lactose. Mutant 2: In the absence of glucose, presence of lactose. basal level of expression - Mutant 1: In the presence of glucose, absence of lactose. Mutant 1: In the presence of glucose, presence of lactose. activated level of expression - Mutant 1: In the absence of glucose, presence of lactose. Mutant 1: In the absence of glucose, absence of lactose.

What general pattern of transcription did researchers observe for the synthetically made three-node circuit involving the genes for bacterial repressors λCI, LacI, and TetR?

oscillatory To better understand the design principles that govern regulatory networks, researchers have constructed simple genetic circuits that share some characteristics with those found in natural systems. One artificial circuit called the "repressilator" was created in E. coli. This three-node circuit linked three bacterial repressors (λCI, LacI, and TetR) into a circular network with each gene repressing another gene: λCI repressed the gene for LacI, LacI repressed the gene for TetR, and TetR repressed the gene for λCI. Researchers found that the repressilator exhibited a striking oscillatory pattern of transcription with a periodicity of about 2 hours.

Which of the following mechanisms illustrates a form of transcriptional repression that is unique to eukaryotes?

repressors recruiting enzymes to modify groups on histones to compact chromatin Bacterial DNA is not wrapped around nucleosomes. Eukaryotes use this mechanism of repression often. An example of this mechanism is seen in the recruitment of deacetylases that remove acetyl groups from histones, resulting in tighter winding of the DNA around the histone core.

Players in a signal transduction pathway can be classified into the following categories: signal, receptor, relay molecule, and output. Classify each component of the STAT pathway pictured in the Figure as signal, receptor, relay molecule, and output. You can use a term more than once.

signal - cytokine receptor - cytokine receptor relay molecule - JAK, STAT output - Transcriptional expression of specific genes

A signal transduction pathway is initiated when a _____ binds to a receptor.

signal molecule The binding of a signal molecule to a receptor initiates a signal transduction pathway.

In Drosophila development, the effects of BICOID protein vary along the axis of the embryo. This is because _______.

there is an anterior to posterior gradient in BICOID protein concentration in the embryo Correct. After fertilization, BICOID mRNA is translated and a concentration gradient of BICOID protein forms along the anterior-posterior axis of the embryo.

In the language of systems biology, which of the following sets of terms accurately describes the regulatory circuit of the lactose operon?

three nodes, three edges, an AND gate The lactose operon circuit consists of three nodes: the gene encoding CAP (an activator), the gene encoding LacI (a repressor), and the lactose operon (the target). These three nodes are linked together by three edges (lines that give direction and sign of interaction) and an "AND gate." Transcription of the lactose operon is only permitted when the CAP activator (bound by its ligand cAMP) is present AND the Lac repressor is inactivated by lactose.

Which of the following is the major goal of systems biology?

to understand the underlying design principles governing complex molecular processes Traditionally, molecular biology has largely consisted of a mechanistic approach towards making discoveries, such as identifying all the individual molecules involved in a signaling pathway. In contrast, the emerging field of systems biology relies on a more holistic approach in an effort to discover the underlying design principles that govern molecular processes. This type of approach necessitates the integration of a variety of disciplines including molecular and cellular biology, mathematics, engineering, physics, and computer science.

In this animation, which of the following, when activated by a signal transduction pathway, moved from the cytoplasm to the nucleus of a cell? To view the animation, click here. Then click on the image to start the animation.

transcription factor Activated transcription factors trigger transcription.

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

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.