ch 14 and 15 quiz

Describe how genes are flanked by nucleosome free regions (Figure 15.12).

- For genes that can be activated, the transcriptional start site at the core promoter is found in a NFR - NFR may be required for transcription, it is not, by itself, sufficient for gene activation

Describe how regulatory transcription factors interact with TFIID and mediator (Figures 15.4, 15.5).

- activators stimulate TFIID activity and enhance transcription, repressors bind to a silencer and inhibit TFIID activity - repressor + mediator = interaction prevents RNA poly phosphorylation. doesn't proceed to elongation - activator + mediator = interaction phosphorylates carboxyl-terminal of RNA poly and it proceeds to elongation

Describe the action of chromatin remodeling enzymes (Figure 15.9).

- change the locations of nucleosomes - remove histone octamers from the DNA - replace core histones with histone variants

Describe the activation and functions of the CREB protein (Figures 15.7, 15.8).

- extracellular signaling molecule binds to a receptor in the plasma membrane, activating a G protein, which activates adenylyl cyclase, leading to the synthesis of cAMP - cAMP binds to protein kinase A, which activates it. - Protein kinase A travels to the nucleus and phosphorylates the CREB protein - Once phosphorylated, CREB protein acts as a transcriptional activator by promoting the binding of CBP, which is a coactivator

Describe the functions of small effector molecules and how they are named (Figure 14.2).

- inducer causes transcription rate to increase - corepressor binds to a repressor, causing it to bind to DNA - inhibitor binds to an activator stopping it from binding to DNA

Describe the activation and functions of the glucocorticoid receptor (Figures 15.7, 15.8).

- inside the cell, glucocorticoid hormone binds to glucocorticoid receptor, which releases a heat shock protein - exposes a nuclear localization signal (NLS) - Two glucocorticoid receptors form a homodimer and travel to the nucleus, where the dimer binds to a glucocorticoid response element (GRE) next to a gene - binding of the glucocorticoid receptors to the GRE activates the transcription of the adjacent target gene

Explain the action of CAP, and why it is a beneficial form of regulation with regard to the choice between glucose and lactose (Figure 14.8).

- lactose, no glucose (high cAMP) = inactive repressor, high transcription due to cAMP-CAP complex being bound - no lactose, no glucose (high cAMP) = low transcription since repressor is bound - lactose, glucose (low cAMP) = inactive repressor, low transcription since no CAP bound - no lactose, glucose (low cAMP) = low transcription since repressor is bound

Explain how the lac repressor protein works (Figures 14.4, 14.5).

- no [allo]lactose: repressor binds to operator - [allo]lactose present: causes conformational change in repressor so it cant bind to operator

Describe the functions of regulatory proteins and how they are named (Figure 14.2).

- repressor binds to DNA to inhibit transcription - activator binds to DNA and increases rate of transcription - names describe how they affect transcription when they are bound to the DNA (repressor or activator)

Interpret the results of the experiments of Jacob, Monod, and Pardee (Figures 14.6, 14.7).

- the lacI− mutation eliminates the function of lac repressor, which prevents it from repressing the lac operon

According to the histone code hypothesis, the pattern of histone modifications acts like a language that A. influences chromatin structure. B. promotes transcriptional termination. C. inhibits the elongation of RNA polymerase. D. does all of the above.

A

Which of the following combinations will cause the rate of transcription to increase? A. A repressor plus an inducer B. A repressor plus a corepressor C. An activator plus an inhibitor D. None of the above will increase the rate of transcription

A

A bidirectional enhancer has the following sequence: 5′-GTCA-3′ 3′-CAGT-5′ Which of the following sequences would also be a functional enhancer? A. 5′-ACTG-3′ 3′-TGAC-5′ B. 5′-TGAC-3′ 3′-ACTG-5′ C. 3′-GTCA-5′ 5′-CAGT-3′ D. 3′-TGAC-5′ 5′-ACTG-3′

B

A regulatory transcription factor protein typically contains _________ that binds to the ________ of the DNA. A. an α helix, backbone B. an α helix, major groove C. a β sheet, backbone D. a β sheet, major groove

B

Combinatorial control refers to the phenomenon that A. transcription factors always combine with each other when regulating genes. B. the combination of many factors determines the expression of any given gene. C. small effector molecules and regulatory transcription factors are found in many different combinations. D. genes and regulatory transcription factors must combine with each other during gene regulation.

B

On its chromosome, an E. coli cell has the genotype lacI− lacZ+ lacY+ lacA+. It has an F′ factor with the genotype lacI+ lacZ+ lacY+ lacA+. What is the expected level of expression of the lac operon genes (lacZ+ lacY+ lacA+) in the absence of lactose? A. Both lac operons will be expressed. B. Neither lac operon will be expressed. C. Only the chromosomal lac operon will be expressed. D. Only the lac operon on the F′ factor will be expressed

B

What is an operon? A. A site in the DNA where a regulatory protein binds B. A group of genes under the control of a single promoter C. An mRNA that encodes several genes D. All of the above are true of an operon.

B

Which of the following characteristics is typical of a eukaryotic gene that can be transcribed? A. The core promoter is wrapped around a nucleosome. B. The core promoter is found in a nucleosome-free region. C. The terminator is wrapped around a nucleosome. D. None of the above characteristics is typical of a eukaryotic gene

B

he process in which completely unmethylated DNA becomes methylated is called A. maintenance methylation. B. de novo methylation. C. primary methylation. D. demethylation.

B

Describe how the binding of the lac repressor results in a loop in the DNA (Figure 14.10).

Because the two sites are far apart, a loop must form in the DNA - Each repressor dimer binds to one operator site, so the repressor tetramer brings the two operator sites together - causes the formation of a DNA loop in the intervening region - sequences recognized by σ factor of RNA polymerase - loop also contains the binding site for the cAMP-CAP complex

A repressor is a __________ that _________ transcription. A. small effector molecule, inhibits B. small effector molecule, enhances C. regulatory protein, inhibits D. regulatory protein, enhances

C

A chromatin-remodeling complex may A. change the locations of nucleosomes. B. evict histones from DNA. C. replace standard histones with histone variants. D. do all of the above.

D

How can methylation affect transcription? A. It may prevent the binding of regulatory transcription factors. B. It may enhance the binding of regulatory transcription factors. C. It may promote the binding of methyl-CpG-binding proteins, which inhibit transcription, to a methylated sequence. D. All of the above are possible ways for methylation to affect transcription.

D

How does exposing an E. coli cell to glucose affect the regulation of the lac operon via CAP? A. cAMP binds to CAP and transcription is increased. B. cAMP binds to CAP and transcription is decreased. C. cAMP does not bind to CAP and transcription is increased. D. cAMP does not bind to CAP and transcription is decreased

D

Regulatory transcription factors can be modulated by A. the binding of small effector molecules. B. protein-protein interactions. C. covalent modifications. D. any of the above

D

The binding of _______ to lac repressor causes lac repressor to _______ to the operator site, thereby _______ transcription. A. glucose, bind, inhibiting B. allolactose, bind, inhibiting C. glucose, not bind, increasing D. allolactose, not bind, increasing

D

Transcriptional activation of eukaryotic genes involves which of the following events? A. Changes in nucleosome locations B. Changes in histone composition within nucleosomes C. Histone modifications D. All of the above

D

Explain the concept of gene regulation, and where it may occur in the gene expression pathway (Figure 14.1).

Gene regulation is the phenomenon in which the level of gene expression can vary under different conditions - can occur in transcription, translation, or post-translation

Explain how activators and repressors bind to enhancers and silencers to modulate gene expression (Figure 15.2).

a regulatory transcription factor can act as either an activator to increase the rate of transcription or a repressor to decrease the rate of transcription

Explain how DNA methylation affects gene expression and how it is heritable (see Figures 15.14, 15.15, 15.16).

gene expression: - methylation of CpG islands may silence gene expression or compact chromatin - methylation may also influence binding of transcription factors heritable: - specific genes methylated in gametes via de novo methylation - maintenance methylation- pattern of 1 methylated gene copy and the other isn't

Describe what a histone variant is, and why they are functionally important (Table 15.1, but don't memorize the variants).

histone variant = histone proteins whose amino acid sequences are slightly different from those of the standard histones. They often play specialized roles in chromatin structure and function

Outline the organization of the lac operon left to right (Figure 14.3).

i promoter, lacI, CAP site, lac promoter, lacO, lacZ, lacY, lacA, lac terminator

Compare and contrast the effects of loss-of-function mutations in lacI versus lacO (Table 14.1).

look !

Explain how the lac operon makes a bacterial cell more efficient in the utilization of lactose (Figure 14.3).

look !

Describe how nucleosomes are displaced when a gene is transcriptionally activated (Figure 15.13).

nucleosomes are removed as activator protein recruits histone modifying enzyme and chromatin remodeling complex

Outline how eukaryotic genes may be regulated at many points along the gene expression pathway (Figure 15.1).

occurs during transcription, RNA processing, translation, posttranslational modifications

Describe the concept of combinatorial control.

phenomenon widely observed in eukaryotes in which the combination of many factors determines the expression of any given gene

Provide examples of covalent histone modifications (Figure 15.10)

phosphorylation, acetylation, methylation

explain the concept of the histone code.

the pattern of histone modification acts much like a language or code in specifying alterations in chromatin structure

Interpret the results of experiments which showed that the lac operon actually has three operator sites (Figure 14.9).

when all three operator sites are present, the repression of the lac operon is 1300-fold