Deck 12: Control of Gene Expression

Question 1

A promoter that affects only genes that are on the same piece of DNA is referred to as a _____-acting promoter.

A)cis
B)trans
C)positive
D)negative
E)None of the answers is correct.

Answer 1

A

Question 2

Which of the following generally get transcribed constitutively?

A)Regulatory gene
B)Structural gene
C)Operator element
D)Promoter element
E)Operon

Answer 2

B

Question 3

Which of the following types of eukaryotic gene regulation is at the level of DNA?

A)Alternation of chromatin structure
B)mRNA processing
C)RNA interference
D)mRNA stability
E)Post-translational modification

Answer 3

A

Question 4

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

A)The structural gene will be constitutively expressed due to the lack of negative inducible control.
B)The transcription of the structural gene will not be affected, as a repressor is not required.
C)The mutation will lead to activation of an activator upon the lack of a repressor protein, which will allow the transcription to continue.
D)As the transcription will require a repressor protein, the transcription will be turned off.
E)More cAMP will be produced in a cell to compensate for the lack of a repressor protein.

Question 5

An operon is controlled by a repressor.When the repressor binds to a small molecule, it binds to DNA near the operon.The operon is constitutively expressed if a mutation prevents the repressor from binding to the small molecule.The type of control illustrated is:

A)negative inducible.
B)negative repressible.
C)positive inducible.
D)positive repressible.
E)catabolite repression.

Question 6

An example of a gene product encoded by a regulatory gene is:

A)beta-galactosidase enzyme.
B)allolactose.
C)repressor protein.
D)an operator.
E)a terminator.

Question 7

In the absence of tryptophan, what happens to the genes within the trp operon?

A)The regulator without tryptophan-binding prevents the genes from being transcribed.
B)The regulator falls off the operator and structural genes get transcribed.
C)Lack of tryptophan increases the level of cAMP, which leads to activation of CAP protein and gene expression.
D)The active repressor binds to the operator and genes do not get transcribed.
E)The active activator binds to the operator and transcription of structural genes takes place.

Question 8

What is the function of allolactose in regulation of the lac operon?

A)Inducer
B)Repressor
C)Activator
D)Promoter
E)Regulatory protein

Question 9

Which of the following statements about gene regulation concerning operon is INCORRECT?

A)A repressible gene is controlled by a regulatory protein that inhibits transcription.
B)For a gene under negative repressible control, a small molecule is required to prevent the gene's repressor from binding to DNA.
C)For a gene under positive repressible control, the normal state is transcription of a gene, stimulated by a transcriptional activator.
D)A regulator gene has its own promoter and is transcribed into an independent mRNA.
E)Presence of operon where genes of related functions are clustered is common in bacteria, but not in eukaryotes.

Question 10

All of the following are points of gene regulation EXCEPT for:

A)alteration of chromatin structures.
B)transcription.
C)mRNA processing.
D)mRNA stability.
E)point mutation in the ORF.

Question 11

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

A)The structural gene would to be constitutively expressed due to the lack of inducible control.
B)The transcription of a structural gene will not be affected, as an activator is not required.
C)The mutation will lead to activation of a repressor upon the lack of an activator protein, which will block transcription.
D)As the transcription will require an activator protein, the transcription will be turned off.
E)More cAMP will be produced in a cell to compensate for the lack of an activator protein.

Question 12

The _____ is a type of regulator protein that binds to a region of DNA in the promoter of a gene called the operator and prevents transcription from taking place.

A)inducer
B)repressor
C)activator
D)inactivator
E)terminator

Question 13

Which of the following statements about regulation of gene expression is CORRECT?

A)An inducible gene is transcribed when a specific substance is absent.
B)A gene is any DNA sequence that is transcribed into an mRNA molecule only.
C)All genes are transcribed at all times as long as they have a functional promoter.
D)The regulation of gene expression is the same in both eukaryotes and prokaryotes.
E)The regulation of gene expression is critical for the control of life processes in all organisms.

Question 14

What is the function of cAMP in regulation of the lac operon?

A)It activates a repressor protein.
B)It activates an activator protein.
C)It inactivates a repressor protein.
D)It inactivates an activator protein.
E)It activates both a repressor protein and an activator protein.

Question 15

E.coli lac operon control by CAP is:

A)negative inducible.
B)negative repressible.
C)positive inducible.
D)positive repressible.
E)both negative inducible and negative repressible.

Question 16

An operon is controlled by a repressor.When the repressor binds to a small molecule, it is released from binding to DNA near the operon.The operon is never expressed if a mutation prevents the repressor from binding to the small molecule.The type of control illustrated is:

A)negative inducible.
B)negative repressible.
C)positive inducible.
D)positive repressible.

Question 17

What would happen to the lac operon in the absence of allolactose?

A)The structural genes within the lac operon will be constitutively transcribed.
B)The activator protein will be bound to the operator, which will turn on the structural gene behind it.
C)The repressor regulator protein binds to the operator and prevents the transcription of the structural gene.
D)The catabolite activator protein becomes inactivated and no transcription occurs.
E)The cAMP level rises in the absence of allolactose, which in turn inactivates the transcription.

Question 18

It is possible for a repressor to negatively regulate the expression of an operon because:

A)the repressor induces the expression of the inducer by binding to the promoter that comes before the inducer gene.
B)one of the structural genes expressed in the operon negatively regulates the repressor.
C)the repressor-binding site overlaps the promoter site of the operon, allowing it to physically block the binding of RNA polymerase.
D)the repressor-binding site on the DNA overlaps with the translation start site, hence preventing the transcription.
E)the repressor physically blocks where the activator should be binding on the operator region.

Question 19

E.coli lac operon control by lacI is:

A)negative inducible.
B)negative repressible.
C)positive inducible.
D)positive repressible.
E)None of the above answers is correct.

Question 20

When binding of the inducer to the repressor causes a conformational change, which then prevents the repressor from binding to DNA, the repressor is called a(n)_____ protein.

A)coactivator
B)allosteric
C)structural
D)operating
E)responsive

Question 21

Where would the lac repressor be bound in a (nonmutant)E.coli cell that is growing in low glucose and high lactose? (I = lac repressor gene; Z, Y, A = lac operon structural genes; P = lac promoter; O = lac operator)

A)P
B)O
C)P and O
D)I, P, O
E)The repressor would not be bound.

Question 22

In Arabidopsis, FLD (a deacetylase enzyme)stimulates flowering.Which of the following is TRUE?

A)FLD deacetylates histones that bind to regions of FLC gene and stimulates its transcription.
B)FLD deacetylates histones surrounding FLD gene, causing suppression of FLD transcription.
C)FLD deacetylates histones that bind to FLC gene, causing repression of FLC transcription.
D)FLD causes repression of FLC translation.

Question 23

Alternative splicing is known to be important in the regulation of the:

A)production of heat-shock elements.
B)Drosophila sexual development.
C)lac operon in E.coli.
D)trp operon.
E)None of the answers is correct.

Question 24

Which parts of the DNA region shown in the diagram encode proteins? (I = lac repressor gene; Z, Y, A = lac operon structural genes; P = lac promoter; O = lac operator)

A)P
B)I, P, O
C)P, O, Z, Y, A
D)I, Z, Y, A
E)I, P, O, Z, Y, A

Question 25

A mutant E.coli strain, grown under conditions that normally induce the lac operon, produces high amounts of $\beta$ -galactosidase.What is a possible genotype of the cells?

A)lacI⁺ lacP⁺ lacO⁺ lacZ^- lacY⁺ lacA⁺
B)lacI⁺ lacP⁺ lacO^c lacZ⁺ lacY⁺ lacA⁺
C)lacI^- lacP⁺ lacO⁺ lacZ^- lacY⁺ lacA⁺
D)lacI⁺ lacP^- lacO⁺ lacZ⁺ lacY⁺ lacA⁺
E)lacI^- lacP^- lacO⁺ lacZ^- lacY⁺ lacA^-

Question 26

A mutant E.coli strain, grown under conditions that normally induce the lac operon, does not produce $\beta$ -galactosidase.What is a possible genotype of the cells?

A)lacI⁺ lacP⁺ lacO⁺ lacZ⁺ lacY^- lacA⁺
B)lacI⁺ lacP⁺ lacO^c lacZ⁺ lacY⁺ lacA⁺
C)lacl⁺ lacP⁺ lacO⁺ lacZ⁺ lacY⁺ lacA⁺
D)lacI⁺ lacP^- lacO⁺ lacZ⁺ lacY⁺ lacA⁺
E)lacI^_ lacP⁺ lacO^-lacZ⁺ lacY⁺ lacA^-

Question 27

Which of the following statements about histone and gene expression is CORRECT?

A)In a general sense, highly condensed DNA bound with histone proteins represses gene expression.
B)Acetylation involves the addition of acetyl groups to histone proteins, and it usually results in repression of transcription.
C)Addition of methyl groups to the tails of histone proteins always results in activation of transcription.
D)Histone code is referring to the modification that takes place on the globular domain of the octomeric histone core.
E)All statements above are correct.

Question 28

Which of the following statements about regulation of the eukaryotic gene expression is INCORRECT?

A)The presence of a nuclear membrane separating transcription and translation in eukaryotes led to the evolution of additional mechanisms of gene regulation.
B)In eukaryotes, most structural genes are found within operons.
C)Eukaryotic mRNAs are generally more stable than prokaryotic mRNAs.
D)The rate of degradation of mRNAs is important in regulation in eukaryotes.
E)Post-translational regulation of histones is unique to the eukaryotes.

Question 29

mRNAs are degraded by enzymes called:

A)DNAse I.
B)ribozymes.
C)heat-shock proteins.
D)silencers.
E)ribonucleases.

Question 30

A boundary element is also known as a(n):

A)insulator.
B)repressor.
C)enhancer.
D)coactivator.
E)mediator.

Question 31

If there are mutations that inactivate lacP and lacI, which of the following is true? (I = lac repressor gene; Z, Y, A = lac operon structural genes; P = lac promoter; O = lac operator)

A)These are mutations that are, respectively, cis- and trans-acting on lac operon expression.
B)These are mutations that are, respectively, trans- and cis-acting on lac operon expression.
C)These will affect the expression of I only.
D)These will affect the expression of only Z, Y, and A.
E)These mutations will have no effect.

Question 32

RITS consists of:

A)siRNAs and proteins.
B)miRNAs and proteins.
C)RISCs and mRNAs.
D)methyl groups and histone proteins.
E)DNA, histone proteins, and mRNAs.

Question 33

Degradation of a eukaryotic mRNA is generally initiated by:

A)cleavage of the 5' end.
B)random cleavages throughout the mRNA strand.
C)shortening of poly(A)tail.
D)lengthening of poly(A)tail.
E)removal of the 5' cap.

Question 34

In which part of the mRNA does degradation generally begin?

A)At the 5'end with the removal of the poly(A)tail
B)At the 5'end with the removal of the methyl cap
C)At the 3'end with the removal of the poly(A)tail
D)At the 3'end with the removal of the methyl cap
E)Removal from either end is equally likely.

Question 35

Insulators can block the effects of enhancers only when they lie:

A)between an enhancer and a promoter.
B)upstream of a promoter.
C)adjacent to a promoter.
D)within the structural genes.
E)within a consensus sequence.

Question 36

Which of the following process is also known as RNA silencing and post-transcriptional gene silencing?

A)Protein degradation
B)RNA splicing
C)Transcriptional repression
D)RNA interference
E)None of the answers is correct.

Question 37

Which of the following statements about response elements is INCORRECT?

A)A single eukaryotic gene is regulated by only one unique response element.
B)Response elements are composed of specific consensus sequences that are unique from one another.
C)Different genes can possess a common regulatory element upstream of their start site.
D)Multiple response elements allow the same gene to be activated by different stimuli.
E)Response elements allow complex biochemical responses in eukaryotic cells.

Question 38

Which of the following terms is LEAST relevant to the assembly of basal transcription apparatus for transcription?

A)Core promoter
B)General transcription factors
C)TATA box
D)RNA polymerase
E)Enhancer

Question 39

Although operons are not common in eukaryotes, eukaryotic genes may be activated by the same stimulus.Which of the following DNA regulatory sequences makes this coordinated gene expression possible?

A)Core promoter
B)Enhancer element
C)Response element
D)Boundary element
E)Silencer element

Question 40

A eukaryotic DNA sequence that affects transcription at distant promoters is called a(n):

A)insulator.
B)silencer.
C)mediator.
D)enhancer.
E)repressor.

Question 41

Which of the mechanisms involving siRNA- and miRNA-based gene regulation is INCORRECT?

A)Cleavage of mRNA
B)Inhibition of translation
C)Post-translational modification
D)Degradation of mRNA
E)Transcriptional silencing

Question 42

Why is it that the presence of lactose positively affects transcription of the lac genes while tryptophan negatively affects transcription of the trp genes?

Question 43

Which of the following is NOT true of DNA methylation?

A)It is associated with transcription repression.
B)It occurs on cytosines adjacent to guanines.
C)Cytosines on both strands are usually methylated.
D)It is carried out by DNA methyltransferases.
E)Methylation is permanent and cannot be reversed.

Question 44

If the lacY gene is turned off when lactose is absent, how do the first molecules of lactose enter the cell to induce transcription of the all three lac operon genes?

Question 45

How is foreign DNA transferred into Arabidopsis?

A)Electroporation
B)Ti plasmid
C)Biolistics
D)Dissection
E)Nuclear injection

Question 46

Which of the following is NOT an example of epigenetics?

A)Independent assortment of alleles
B)Genomic imprinting
C)Creation of iPSCs
D)Paramutation
E)X inactivation

Question 47

Which of the following is NOT a defining feature of paramutation?

A)The expression pattern is transmitted to future generations.
B)The altered allele is able to convert other alleles.
C)There are no DNA sequence differences between alleles.
D)Mutation of coding sequences generates new alleles.
E)These are all defining features of paramutation.

Question 48

How is the epigenetic trait induced by vinclozolin transmitted to offspring?

A)DNA methylation is increased in sperm of treated males, and this methylation pattern is inherited by offspring.
B)Treated males are more successful at mating, so more offspring inherit the trait.
C)Females exposed to the drug produce fewer eggs, and the resulting offspring exhibit this same phenotype.
D)Treated females have increased DNA methylation in neuronal cells, which alters their mating behaviors.

Question 49

What is the consequence of methylation of DNA sequence called CpG islands?

A)Active transcription
B)Transcription repression
C)Recruitment of chromosome remodeling complex
D)Transcriptional stalling
E)Insulator sequence formation

Question 50

Which of the following statements about CpG islands is CORRECT?

A)CpG islands are commonly found at the 3'UTR regions.
B)The CpG island methylation is universal across both prokaryotes and eukaryotes.
C)Methylated CpG islands is associated with gene repression.
D)Transcriptionally active DNA has higher frequency of methylated CpG.
E)An association exists between DNA methylation at the CpG island and acetylation of histone via recruitment of acetylases.

Question 51

How would you expect DNA methylation to alter gene expression?

A)Extremely increase expression
B)Moderately increase expression
C)No change in expression
D)Measurably decrease expression
E)Either increase or decrease expression

Question 52

What characteristic of DNA allows methylation patterns to be maintained through replication and cell division?

A)Semiconservative replication
B)Recombination and repair
C)The absence of uracil
D)Topoisomerases
E)Deoxyribonucleotide synthesis

Question 53

What type of enzyme would MOST likely promote increased gene expression?

A)DNA methyltransferase
B)DNA demethylase
C)DNA polymerase
D)DNA ligase
E)DNase

Question 54

When siRNAs are present, the rate of mRNA degradation _____ and the rate of protein production _____.

A)increases; increases
B)increases; decreases
C)decreases; decreases
D)decreases; increases
E)stays constant; decreases

Question 55

Describe one similarity and one difference in how the Trp and Lac repressor proteins function.

Question 56

What is the difference between a transcription regulation system that uses induction and a system that uses repression?

Question 57

After translation, eukaryotic proteins can be modified by:

A)acetylation.
B)the addition of phosphate groups.
C)the removal of amino acids.
D)the addition of methyl groups.
E)All of the answers are correct.

Question 58

Which one of these is NOT an advantage of using Arabidopsis thaliana as a model organism?

A)It is small in size.
B)It has prolific reproduction.
C)It is a weed.
D)It has a small genome.
E)It has features in common with other flowering plants.

Question 59

How do epigenetic marks compare in monozygotic twins?

A)They are similar early in life but are increasingly dissimilar with age.
B)They are different at birth, but a similar environment during childhood causes them to become more similar with time.
C)They stay the same throughout their lives because monozygotic twins are genetically identical.
D)DNA methylation patterns are similar, but histone acetylation patterns are very different.

Question 60

siRNAs and miRNAs are produced by the:

A)cleavage of RISCs by endonucleases.
B)cleavage of functional mRNA within the cytoplasm.
C)cleavage of pre-mRNA in the nucleus.
D)cutting and processing of double-stranded RNA by Dicer enzymes.
E)cutting and processing of double-stranded RNA by Slicer enzymes.

Question 61

Eukaryotic genes can be introduced into bacteria by recombinant DNA techniques.If the introduced gene encodes a protein that is also found in bacteria-for example, a universally used glycolysis enzyme-expression of the eukaryotic gene may produce a protein that functions in the bacterial cell.
The mouse gene for a glycolysis enzyme is introduced into an E.coli cell that has a mutant gene for the bacterial version of the same enzyme.Even though the mouse enzyme should function in the bacterial cell and restore the cell's ability to perform glycolysis, it does not.
Provide two possible reasons why this experiment does not work and propose a solution to overcome one of the problems you suggest.

Question 62

An E.coli strain of chromosomal genotype lacI^- lacP⁺ lacO⁺ lacZ⁺ lacY⁺ constitutively expresses the genes of the lac operon.The strain is converted to wild-type lac operon regulation by the addition of an extra piece of DNA.What gene or genes are contained on this extra DNA that explain this conversion to wild type? Include an explanation of cis- or trans-acting factors and how they work.

Question 63

In the experiments described in the text, Jacob and Monad deciphered that the lacI⁺ gene product can function in trans and regulate the lac operon either on the plasmid or on the chromosome.What genotype of the partial diploid bacterial strain was key to their experiments, leading them to such a conclusion? Explain why this strain helped them to reach that conclusion.

Question 64

Aside from the case of lacO^c, where the operator is unable to bind to the repressor protein, briefly describe another mutant that could have caused constitutive expression of lac operon.

Question 65

What are three ways in which gene regulation is accomplished by modifying the structure of chromatin?

Question 66

You isolated two mutations linked to the lac operon, which you designate Lac1^- and Lac2, that cause constitutive expression of the operon.You construct strains carrying a lac operon with a mutant lacY gene on an F'.You test both $\beta$ -galactosidase activity and Lac permease activity in the strains you constructed using the artificial inducer IPTG. Are Lac1^- and Lac2^- dominant or recessive? Do they act in cis or in trans? Indicate how you can determine both of these properties for each mutation.What type of lac mutations best fit the properties of Lac1^- and of Lac2^-?

Question 67

What would be the advantage of regulating gene expression at many levels rather than simply regulating at one level (such as at the start of transcription)?

Question 68

The bacterium, Bacillus subtilis, can grow on minimal media with a variety of sugars as its carbon source.One such sugar is mannose, metabolized by the products of the man operon.Expression of the operon is controlled by a regulatory protein encoded in a separate gene, manR.Depending on conditions, the regulatory protein may bind at one of two sites in the operon, as follows:
(i)When mannose is absent from the cell, the regulatory protein is in a conformation called R1.R1 can bind specifically at an operator site manO.Binding of R1 at manO reduces transcription of the operon four-fold from a basal level of 20 units.
(ii)When mannose is present in the cell, it binds to the regulatory protein, causing it to undergo an allosteric transition from conformation R1 to a new conformation, called R2.R2 cannot bind at manO.However, R2 can bind specifically at a different site called the initiator, manI.Binding of R2 at manI increases transcription of the operon two-fold from the basal level.
Mutations, m1-m3, which affect expression of this operon, were identified.Each mutation affects only a single component of the operon.Levels of operon activity were measured in haploids.They were also measured in partial diploids with an F' carrying the wild-type alleles of all genes and regulatory elements described above. For each mutation, describe which component is affected.In addition, explain the observed activity in the haploid and partial diploid in each case.

Question 69

In both prokaryotes and eukaryotes, groups of genes can be regulated simultaneously (coordinately expressed).However, each group accomplishes this task differently.Explain how coordinate expression differs in prokaryotes compared with eukaryotes.

Question 70

Explain why glucose-dependent catabolite repression in E.coli is important and how it is possible to achieve this repression without influencing glucose metabolism.

Question 71

What is the connection among DNA methylation, histone deacetylation, and gene regulation in eukaryotes?

Question 72

The dotted line in the following graph shows levels of glucose in a culture of wild-type E.coli grown in medium that initially contains both glucose and lactose.The solid line shows levels of transcription of the lac operon.Describe what is happening to the culture and the lac operon, referring to the lac repressor, allolactose, cAMP, and CAP (catabolite activator protein).

Question 73

In the nematode roundworm, Caenorhabditis elegans, the LIN-14 protein controls the timing of certain cell divisions during development.LIN-14 protein levels are normally high in early development but decrease in the later stages.In a lin-4 mutant, the level of LIN-14 protein stays high throughout development, changing the pattern of cell divisions in the animal and producing defects in the shape of the animal.The lin-4 gene encodes a microRNA that binds to a sequence in the 3'UTR of the lin-14 mRNA.
a.How does the lin-4 microRNA likely regulate LIN-14 protein levels? Explain why the lin-4 mutant has high levels of LIN-14 throughout development.
b.Mutations in the 3' UTR of lin-14 have been identified that alter the sequence to which lin-4 normally binds.What effect would these mutations be expected to have on the expression of LIN-14 protein in the animal?

Question 74

Histone methylation can have many different effects on gene expression.In some cases, histone methylation is associated with activation of transcription, whereas in other cases it can trigger the formation of heterochromatin and a decrease in transcription.If histone methylation has been detected in the region of gene X in yeast, describe an experiment that could distinguish whether the methylation is important to activate or repress transcription of gene X.

Question 75

Explain how the poly(A)-binding protein that binds to the poly(A)tails located in the 3' end of an mRNA can play a key role in an mRNA degradation pathway that proceeds from the 5' end of an mRNA in a 5' $\rightarrow$ 3' direction.

Question 76

Describe the unusual post-transcriptional control of Drosophila sex determination.How does the cascade of events differ between males and females?

Question 77

Define RNA silencing (or interference).Explain how siRNAs arise and how they potentially affect gene expression.How are siRNAs different from the antisense RNA mechanism?

Question 78

What are two distinct functions that transcriptional activator proteins perform in order to regulate gene transcription?

Question 79

Over the past decade, a significant finding in biology has been the identification of miRNAs and siRNAs and their role in regulating the development of many multicellular organisms.Briefly describe the four different ways these small RNAs influence gene expression.

Question 80

Imagine the following scenario: You take the regulatory region of the trp operon (including the promoter, operator, and 5' UTR)and attach it upstream of the structural genes of the lac operon.You then introduce this artificial construct into a mutant in which the lac operon is completely nonfunctional.Indicate the level of $\beta$ -galactosidase activity in each of the following cases and explain why you expect that level of activity:
a.No tryptophan, no lactose
b.High tryptophan, high lactose