BIO Genetics 14, 15, 16

Which of the following is involved in the attenuation mechanism in the regulation of the trp operon?

- A leader region in the mRNA containing codons for Tryptophan - An intrinsic termination signal -coupled transcription-translation

Which of the following is TRUE of positive control when considering the regulation of the lac operon?

- Adenylyl cyclase is inhibited by glucose - If cAMP levels are high the CAP protein will bind to the CAP site in the DNA - CAP protein binding to the CAP site in the DNA stabilizes the RNA polymerase at the promoter

Consider regulation of the lac operon in E.coli. Which of the following is TRUE of the cell in the presence of high levels of glucose and lactose?

- Adenylyl cyclase is not active - The repressor protein is not bound to the operator Chapter: 14 Slides: 78-79

Which of the following is TRUE of alternative sigma factors in E. coli

- Alternative sigma factors bind to promoters with a different -35 sequence element than the main sigma factor (sigma 70). - Alternative sigma factors regulate the expression of genes under specific environmental conditions or stresses.

How are eukaryotic transcription factor regulated?

- Covalent modification - Binding of an effector molecule - Protein interactions Chapter: 15 Slides: 15

Which of the following is TRUE of DNA methylation in eukaryotes?

- DNA methylation occurs at CpG sequences - Methylation typically inhibits transcription by inhibiting initiation of transcription - de novo methylation is a highly regulated process

The inactive X chromosome in a human female somatic cell is called a ____

Barr body

Place each label in the appropriate column to predict whether it will work to increase or decrease transcription

Increase: - Acetylation of histone - recruitment of SWI/SNF complex - decreased methylation of DNA - creation of an NFR Decrease: - removal of core promoter - increased methylation of DNA - increased nucleosome density

Which of the following sequences does a bacterial repressor bind to?

Operator

A protein is covalently modified.

Posttranslation

The product of a metabolic pathway inhibits the first enzyme in a pathway.

Posttranslation

A transcriptional repressor that controls the transcription of gene A is not normally active unless bound by an effector molecule X. In a certain cell, the domain of the repressor that binds X is mutated so that X can no longer be bound. With all other factors being same, what effect do you predict on the transcription of gene A if X is aded to the cell when it is already transcribing gene A?

The transcription of gene A will not be affected

The absence of lactose results in the lac repressor protein ________.

binding to DNA

In _____ inheritance the transmission of the trait may be based not on the allele but on which parent the allele comes from

epigenetic

The modifications made to DNA in epigenetic results in changes in ____ association with the DNA

protein

The trpR gene encodes a ____

repressor

One form of gene expression control found frequently in prokaryotes involves a ____, which occurs when an RNA can exist in two different secondary conformations.

riboswitch

One conformation of the RNA requires a small molecule binding which stabilizes the _____ structure.

secondary

The lac operon consists of three genes: lacZ, lacY and lacA. How many promoters are required to express these three genes?

1

Transcription of the lac operon results in the production of how many different mRNA transcripts?

1

The maltose operon contains three genes: malE, malF, and malG. Transcription of this operon would result in ___ mRNA transcript(s) which encodes ___ stop codon(s).

1:3 Chapter 14 Slides 21-30

Bacteria use riboswitches extensively; about ___ of bacterial genes are regulated this way.

4%

How can antisense RNA inhibit translation?

An antisense RNA binds to a transcript and inhibits translation

Consider the trp operon in E.coli . What would be the result if the U-rich sequence after region 4 was replaced with a G-rich sequence?

Attenuation would not occur when tryptophan levels are adequate Chapter:14 Slides: 63-66

Consider the regulation of the lac operon in E.coli. Which of the following is TRUE when the cell I in the presence of glucose but no lactose?

CAP is not bound to the CAP site in the DNA

The symmetry break that occurs is due to localization of ____ to one X chromosome

CTCFs

T/F: An inducer binds to an activator protein and inhibits transcription

False

T/F: An inhibitor regulates an inducible gene

False

T/F: DNA methylation in eukaryotes, which is associated with transcription inhibition, occurs on A residues at GATC sites

False

T/F: Maintenance methylation of DNA is rare and highly regulated.

False

T/F: The CAP protein is an activator that binds to the operator

False

T/F: The structural proteins encoded by the lac operon are involved in lactose synthesis

False

Place each characteristic in the correct category.

Heterochromatin: - Stained throughout the entire cell cycle - attached to nuclear lamina - inhibits gene expression -more compacted Euchromatin: - Not stained during interphase - Central position in the nucleus - Promotes gene expression - Less compacted

When considering gene regulation in bacteria which of the following is TRUE of inducible genes?

Inducible genes are typically involved in catabolic pathways

How is the lac operon regulated?

It is inducible, under negative and positive control.

Which of the following sets of conditions would result in high levels of gene transcription from the lac operon?

Low glucose, high lactose

A mutation in the lacI gene prevents the LacI protein from binding allolactose. What will the expression level of the operon be in the presence of lactose?

No transcription or a basal (i.e. very low) level of transcription Chapter: 14 Slides: 33-34

Which of the following bonds would mediate the interaction between a regulatory DNA binding protein and the double-stranded DNA?

Non-covalent bonds

What general transcription factor is most often affected by regulatory transcription factors in eukaryotes?

TFIID Chapter: 15 Slides:10

A particular gene has a mutation in its NFR that causes it to bind abnormally tightly to histones. What effect would you expect this mutation has on the expression of this gene?

The expression of the gene would be abnormally low Chapter: 15 Slides: 20

If a cell has a mutation in the lacY gene that produces a non-functional product, how is regulation of the lac operon affected?

The lac operon cannot be induced, because lactose cannot enter the cell.

You identify a CAP protein mutant that is unable to bind cAMP. How will this mutant affect transcription of the lac operon?

The lac operon will never be transcribed at a high rate.

Which of the following is TRUE of an operon that is only regulated by positive control?

The promoter is likely a poor match to the consensus sequence for binding of the sigma factor Chapter: 14 Slides: 16

Which of the following is true regards to enhancer sequences?

They may located either upstream or downstream of the promoter

What is the purpose of the attenuation mechanism for regulating the trp operon?

To sense the amount of tRNAs charged with tryptophan in the cell

A transcription terminator forms in the RNA.

Transcription

If a drug was developed that could inhibit TFIID binding to the core promoter, what would its effect on transcription be?

Transcription that was currently occurring would be finished but there would be no new invitation

Attenuation of the trp operon requires which conditions to be met?

Tryptophan levels must be high, and regions 3 and 4 must pair.

The definition of epigenetic is the study of mechanisms of heritable traits that ____ the result of changes in DNA sequence

are not

The inheritance of traits is sometimes the direct result of specific alleles bring present or absent, but it can also be due to the ability of an allele to be ____

expressed

The trp operon is a repressible operon n regulated by both negative and positive control.

false

The trp repressor is bound to the operator when tryptophan levels are ___

high

Although the Six transcript is produced by both X chromosomes the Xist transcript is only produced from the _____ chromosome.

inactive

Attenuation is similar to rho ___ termination

independent

Which gene is responsible for producing the protein that converts lactose to allolactose?

lacZ

Presence of the xist transcript on the Xi chromosome results in the recruitment of _____

macroH2A

At least some genes are silenced on inactive X chromosome by _____

methylation

In epigenetic, change can be due to ____ of DNA

methylation

Genetic regulatory proteins bind to the DNA.

transcription

In Bacillus subtitles, a riboswitch controls the ____ of the thi operon involved in thiamin pyrophosphate synthesis.

transcription

The trp operon is also regulated by ___ attenuation

transcription

Antisense RNA binds to the mRNA.

translation

Riboswitches can regulate transcription, ____, and RNA stability

translation

Translation of mRNA transcribed from the trp operon can be regulated by formation of a secondary structure within the mRNA. The mRNA that forms this secondary structure is transcribed from which gene in the trp operon?

trpL

T/F: The lacl gene makes a repressor protein

true

Which of the following is TRUE of the lac operon when lactose is present?

- Lactose is converted to allolactose by beta-galactosidase - Allolactose binds to the repressor protein

If a bacterial gene is regulated by both positive and negative control which of the following sites would you find in the DNA?

- Operator site - Activator site

Consider the regulation of the trp operon. Which of the following is TRUE when there is no tryptophan present and coupled transcription-translation is occurring?

- The repressor is not bound to the operator - The ribosome stalls at the Trp-Trp codons in the mRNA molecule

Consider the regulation of the lac operon in E. coli. Which of the following is TRUE when the cell is in the presence of both glucose and lactose?

- The repressor is not bound to the operator in the DNA - CAP is not bound to the CAP site in the DNA

Which of the following is a mechanism for modulating the activity of eukaryotic transcription factors?

- binding of small molecule effectors - formation of homodimers - covalent modification

Which of the following is TRUE of epigenetic changes in gene expression?

-Epigenetic changes can be heritable, meaning these changes can be passed to daughter cells following cell division. -Epigenetic changes may involve changes in chromatin structure

You identify a CAP mutant protein that is constitutively bound to the CAP site. Under which conditions will the lac operon be transcribed at high levels in cells that contain this mutant protein? Check all that apply.

-Lactose is present, glucose is not -Lactose and glucose are both present

Consider a cell in the presence of adequate tryptophan levels. There is enough tryptophan present to keep all of the tRNAtrp charged, but there is no free Tryptophan available in the cell. Describe the regulatory mechanism(s) that control expression of the trp operon under these conditions and indicate whether transcription of the operon will occur

Negative control - there is no free tryptophan to serve as a corepressor so the repressor will NOT be bound to the operator Attenuation - translation of the leader region does NOT stop at the Trp-Trp codons because there is plenty of charged tRNAtrp available. Therefore, regions 3 and 4 pair forming a stem-loop followed by a string of U's which is the intrinsic termination (or rho-independent termination) signal. Transcription - NO! The intrinsic termination signal results in dissociation of RNA polymerase from the DNA and pre-mature termination.

Which of the following would not be considered a reversible posttranslational modification?

Proteolytic processing

Consider regulation of the trp operon in E.coli. Transcription of the leader region has occurred, but there is no translation. Which of the following is TRUE?

Region 1 of the leader region pairs with region 2 and region 3 pairs with region 4

A gene is inducible and under negative control. Which of the following pairs will allow expression of this gene?

Repressor + Inducer Chapter: 14 Slides: 21

An enzyme called phosphodiesterase hydrolyzes cAMP into AMP. Researchers have identified a mutant E. coli strain in which this phosphodiesterase works 10-times faster compared to the enzyme in the wild-type E. coli strain. Explain how this overactive phosphodiesterase would affect diauxic growth in the mutant strain?

This mutant strain would have difficulty inducing the lac operon. Glucose would be metabolized properly, but the shift to metabolizing lactose would be impaired because CAP would be less likely to bind cAMP due to the fact that phosphodiesterase is quickly converting cAMP to AMP. This would prevent CAP from activating transcription of the lac operon.

Repressor proteins bind to an mRNA and prevent ribosome binding.

Translation

Riboswitches produce an RNA conformation that prevents ribosome binding

Translation

Genes controlled by an activator protein typically have a promoter sequence that has a weak affinity for binding sigma factor.

True

In bacteria, small effector molecules control whether or not repressors and activators bind to DNA.

True

Select the functional roles of heterochromatin. Check all that apply

- Gene silencing - Preventing transposition - Preventing viral proliferation

Which of the following is TRUE when there is an excessive amount of tryptophan present in the cell?

Free Tryptophan serves as the corepressor and binds to the repressor protein

T/F: CAP binding causes the DNA to bend facilitating RNA polymerase binding

True

T/F: The presence of a small effector molecule may inhibit transcription

True

T/F: The product of lacl is an allosteric protein that can undergo a conformational change when allolactose binds to it.

True

The selection of which chromosome is inactivated is a ___ process

random

The mRNA from the trpL gene forms stem loops as it is being _____

transcribed