Genetics Test 4

57) Identify the similarties between an inducible operon and a repressible operon. Check all that apply.

- Both types of regulatory systems use allostery in regulating transcription. - Both types of operons contain multiple genes that share a single promoter and a single operator sequence. - Both types of regulatory systems have promoter and operator regulatory sequences.

34) Are IS and OC mutants cis- or trans-acting? Select the two correct answers.

- OC is a cis-acting mutation because only one molecule of DNA is unable to be repressed due to the mutation. - IS is a trans-acting mutation because the mutation disrupts ligand binding of the repressor to the operator on both copies of the DNA.

54) What are the energetic and evolutionary advantages of regulated gene expression? Select the two correct statements.

- Regulated gene expression allows bacteria to adapt their metabolism to match changes in the environment. - Regulated gene expression prevents synthesis of unnecessary proteins, which might be in competition to the detriment of the organism.

33) How complementation can be used to identify where the mutations have occurred (structural genes versus regulatory regions). Select the two correct answers.

- Trans-acting factors (and complementation) indicate mutations in structural genes. - Cis-acting factors indicate regulatory sequences have been mutated.

65) Why is it more advantageous to the organism to stop translation initiation than to inactivate or destroy the gene product after it is produced? Select the two correct statements.

- Translational regulation prevents the production of proteins that might initiate unnecessary or harmful actions. - Translational regulation is more effective in terms of energy consumption.

8) What are the two active sites or "domains" on a repressor protein? Select the two answers.

- allosteric site - DNA-binding site

72) What parallels can you see between this mechanism and the regulation of transcription of the trp operon in E. coli? Select all that apply.

- both include transcription termination in the 5′5′ UTR - both are regulated by the concentration of the molecule that is synthesized by the enzymes encoded by the operon

100) How many different genes are coordinately regulated by the Gal4 transcriptional activator?

4

93) How is the Gal4 protein inactivated?

By binding to the Gal80 protein

92) At what point during the cell cycle would you expect to observe the decondensation of heterochromatic regions?

S phase

36) 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.

61) How does the binding exert a positive effect?

The CAP-cAMP complex alters the structure of the promoter and allows RNA polymerase to bind to it.

52) How are the expressed genes of an operon usually arranged?

The expressed genes are located one by one after the regulatory region of the operon.

76) If the UGG codons in Region 1 of trpL were changed to AGG codons, what effect would this have on expression of the trp operon?

The operon would be regulated by arginine levels; high levels of arginine would attenuate expression of trp genes.

44) Which of the following regarding riboswitches is correct?

They can regulate bacterial transcription, translation, and mRNA stability.

60) Under what circumstances does the binding occur?

When glucose is not available.

48) In bacteriophage λ, if λ repressor successfully binds OR1 and OR2 within PR, ________ is established.

a lysogenic cycle

88) Gal4 is mutated such that it still binds to the DNA but cannot interact with Gal80. What effect on transcription would you expect to see in the absence of galactose?

activation of transcription

10) Which proteins facilitate RNA polymerase binding at promoters to increase levels of transcription?

activator proteins

77) Which molecules bind regulatory sequences of DNA to encourage positive regulation of transcription?

activator proteins

85) What are the protein-binding sequences that direct enhancers to interact with the intended promoter and that block communication between enhancers and another promoter?

insulator sequences

83) Which of the following would you expect to show the least evolutionary conservation?

intergenic DNA

21) In the presence of glucose, where is the lac repressor bound?

lacO

30) Which of the following can be mutated to result in constitutive expression from the lac operon?

lacO and lacI

20) Which region of the lac operon would you target if you want to disrupt the -10 and -35 consensus sequences?

lacP

19) A bacterium is unable to transport lactose into the cell to be broken down. Which gene is likely mutated in this bacterium?

lacY

18) The enzyme β-galactosidase catalyzes what reaction?

lactose → galactose + glucose

11) Most of the regulation of gene expression in bacteria occurs at the ________.

level of transcription

82) Eukaryotes use these highly specialized enhancer elements, which regulate the transcription of multiple genes packaged in complexes of closely related genes (e.g., β-globin).

locus control regions (LCRs)

55) Is the expression of all bacterial genes subject to regulated expression?

no

86) A transcription factor that binds to a gene first and facilitates binding of other transcription factors is called a(n) ________.

pioneer factor

5) In negative control, what molecule would you expect to find bound to the operator if there is no transcription?

repressor

7) The presence of which combination of molecules could prevent transcription of a repressible operon?

repressor + corepressor

74) The mRNA that is transcribed from the trpL region can alternately fold to form three possible stem-loop structures. Different stem-loop structures have varying effects on transcription. Which stem-loop structure is responsible for terminating transcription?

the 3-4 stem loop

39) In the absence of tryptophan,

the inactive repressor cannot bind trpO, so operon gene transcription occurs.

95) Multicellular organisms generally utilize more complex gene regulation than unicellular organisms via mechanisms that include?

transcriptional repression and epigenetic modification

40) In the trp operon, what gene contains the attenuator region?

trpL

41) Which molecule functions as the corepressor in the trp operon?

tryptophan

31) Which enzyme is the product of the lacZ gene?

β-galactosidase

75) Which of the following mutations would result in higher-than-normal expression of the trp genes in presence of tryptophan? Select all that apply.

- mutations in Region 3 that prevent 3-4 stem loop formation - mutations in Region 1 that prevent 1-2 stem loop formation

1) A mutation occurs in an operon that prevents the transcription factor from binding to its recognition site on the DNA. In which type(s) of gene regulation would this mutation result in constitutive expression of the structural gene? Select all that apply.

- negative inducible - negative repressible

3) In which type(s) of gene regulation does the signal molecule (either a precursor or the final product) cause inactivation of the transcription factor? Select all that apply.

- negative inducible - positive repressible

2) A mutation occurs in an operon that prevents the signal molecule (either a precursor or the final product) from binding to the transcription factor.In which type(s) of gene regulation would this mutation result in constitutive expression of the structural gene? Select all that apply.

- negative repressible - positive repressible

51) Identify the regulatory components you would expect to find in an operon. Select the three correct regulatory components.

- operator - attenuator - promoter

58) Choose the correct mechanism by which lactose gains access to the cell to induce transcription of the genes.

A few molecules of permease are usually present in lac+lac+ bacteria in the absence of lactose because the reversible nature of the repressor protein-operator allows occasional transcription of the lac operon.

29) Which of the following mutations would result in constitutive expression of the lac operon?

A mutation in lacI that prevents the repressor from binding to the operator

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

A mutation in the operator sequence

94) Which of the following may be located tens of kilobases away from the transcriptional start site?

An enhancer sequence

27) Which of the following terms refers to a cluster of genes undergoing coordinated transcriptional regulation by a shared regulatory region?

An operon

63) What is antisense RNA?

Antisense RNA is a single-stranded RNA that is complementary to a portion of a specific mRNA transcript.

73) How could antisense RNARNA be used as an antibiotic? What types of genes would you target using this scheme?

Antisense RNARNAs could be used as antibiotics by designing the RNARNAs to be complementary to bacterial mRNAmRNAs that code for essential proteins

42) How is the Trp repressor protein activated?

By binding tryptophan

62) What role do cAMP and CAP play in transcription of lac operon genes?

CAP and cAMP form a complex that binds the CAP binding site of the lac promoter to carry out positive control of operon gene transcription.

23) Catabolite repression refers to the repression of the lac operon in the presence of which catabolite?

CAP-cAMP complex

59) Identify what binds at this site to produce positive regulation.

CAP-cAMP complex

97) What role do chromatin remodelers play in eukaryotic gene expression?

Chromatin remodeler enzymes can enzymatically change the distribution or composition of nucleosomes (histone octamers)

56) Compare and contrast the difference between regulated gene expression and constitutive gene expression.

Constitutive gene expressions applies to the genes whose expression is always required, whereas regulated gene expression applies to the genes whose expression is required only under certain conditions.

96) Molecular biologists can determine experimentally whether a region of DNA contains closed chromatin or open chromatin by assessing the sensitivity of the region to

DNAse.

53) Why is it essential that bacterial cells be able to regulate the expression of their genes?

Expression of some genes is required only under certain conditions.

38) 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

89) In the GAL gene system, which protein acts as an activator protein through its transcription-initiating effect?

Gal4

90) In the GAL gene system, which protein binds to the activation domain of the activator protein, ultimately blocking transcription in the absence of galactose?

Gal80

26) What is the role of catabolite repression in the lac operon?

Glucose helps to prevent expression of the lac operon genes, a process called "catabolite repression". In the absence of glucose cAMP levels rise, allowing this molecule to bind to the catabolite activator protein (CAP). This complex binds to the lac promoter at the CAP binding site, bending the DNA to allow increased transcription by RNA polymerase.

28) What is the primary function of β-galactosidase?

Hydrolysis of the disaccharide lactose to produce glucose and galactose

32) What is the role of cis-acting and trans-acting factors in transcription? Explain how these factors play a role in the lac operon. Which type of mutations can be complemented by a second gene with normal function? Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

If a factor is ((trans-acting)), genes that are not physically adjacent can be regulated together and are mediated by genes that encode regulatory proteins. The ((lac repressor)) is an example because mutations ((can be)) complemented by a second gene with normal function. If a factor is ((cis-acting)), the DNA sequence must be adjacent to the genes it regulates. The ((lac operator)) is an example because mutations ((cannot be)) complemented by a second normal element.

64) How does antisense RNA affect the translation of a complementary mRNA?

It blocks the translation of a complementary mRNA.

15) 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.

13) What is the primary function of an operator in the regulation of transcription in bacteria?

It is a binding site for a repressor protein.

43) Which of the following is FALSE regarding translational regulation in bacteria?

It is the most predominant mode of controlling gene expression in bacteria.

99) Which protein binds to the silencer sequence and promotes transcriptional silencing in the presence of glucose?

Mig1

50) What is the biological advantage of operons to bacteria?

Operons afford the organism the opportunity to simultaneously regulate transcription of multiple genes, whose products are active in the same process.

4) Which of the following is FALSE regarding regulation of gene expression in bacteria?

Regulated transcription is necessary; constitutive transcription, continuously transcribing genes with no regulatory control, does not occur without mutation.

71) What is a riboswitch?

Riboswitches are regulatory regions in 5′5′ UTR of mRNAmRNAs that regulate transcription or translation in response to the concentration of small molecules in the cell.

25) What is the purpose of the lac operon, and under what circumstances is it activated? Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

The lac operon is responsible for the production of ((three)) polypeptides that permit E. coli to use a specific sugar as ((a carbon source for metabolic energy.)) The lac operon acts as a genetic switch to begin sugar break down, but only if (1) ((lactose)) is present in the cell; and (2) all ((glucose)) has been depleted.

37) Which of the following features of the trp operon is likely least essential to the process of attenuation?

The order of the structural genes, E, D, C, B, A

66) Mutation of consensus sequence in the lac promoter.

Transcription is blocked.

68) Mutation of the lac I gene affecting the allosteric site of the protein.

Transcription is blocked.

70) Mutation of the CAP binding site of the lac promoter.

Transcription is blocked.

67) Mutation of the repressor binding site on the operator sequence.

Transcription is constitutive.

69) Mutation of the lac I gene affecting the DNA-binding site of the protein.

Transcription is constitutive.

9) If a corepressor is inhibited, what effect would you expect to see on transcription in a repressible operon?

Transcription will occur.

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

True

91) In the GAL gene system, ________ are cis-acting regulatory elements, and the ________ protein is a trans-acting regulatory protein.

UAS; Gal4

35) Under which of the following conditions will the lac operon be expressed at the highest level?

When glucose is absent and lactose is present

17) In the lac operon, what acts as the inducer?

allolactose

6) You want to design a repressor protein mutant. Which protein domain is the best target for preventing binding of the corepressor?

allosteric domain

12) Changing conformation at the active site as a result of binding a substance at a different site is known as ________.

allostery

24) When both glucose and lactose are available in the growth medium, the presence of which molecule is capable of inducing basal transcription of the lac operon?

cAMP

49) Which of the following proteins activate and maintains the lysogenic cycle of bacteriophage lambda?

cI (lambda repressor)

78) Which of the following is not involved in control of gene expression in eukaryotes?

change to DNA sequence

45) Which region of the λλ phage genome enables the linear chromosome to circularize when it enters a host cell?

cohesive (cos) site

46) In λ phage, a mutation that inactivates which of the following genes should leave the mutated phage strain capable of establishing lysogeny?

cro

98) Which protein complex directs DNA bending into loops that contact RNA polymerase and transcription factors bound at the core promoter or with protein complexes bound to proximal promoter elements?

enhanceosome

80) You have identified a mutation in a gene that seems to decrease transcription of another gene 2000 bp away from the mutation site. What regulatory sequence, which may be found within another gene, has likely been mutated in this instance?

enhancer sequence

84) Demethylation and acetylation lead to an open chromatin structure and are associated with ________regions of genomes.

euchromatic

81) Prader-Willi syndrome is a genetic disorder involving a partial deletion of chromosome 15q on the paternal chromosome. When both copies of a gene (or chromosome) are functional but only one is expressed, this is an example of _____.

genomic imprinting

22) Catabolite repression refers to the repression of the lac operon in the presence of which catabolite?

glucose

79) Trans-acting regulators of gene expression include?

histone deacetylases

87) Gene regulation in eukaryotes often involves which of the following, which are not also used by prokaryotes?

histone modification

47) What is the process by which a bacterium switches from a lysogenic to the lytic cycle?

induction