#16: Gene regulation in bacteria

What is the primary role of the sigma factor in bacterial transcription?
A) To unwind the DNA helix
B) To recruit RNA polymerase to the promoter
C) To elongate the RNA transcript
D) To terminate transcription

To recruit RNA polymerase to the promoter

In bacterial transcription, what happens immediately after the sigma factor is released from RNA polymerase?
A) Transcription terminates
B) RNA polymerase affinity to the promoter increases
C) RNA polymerase begins the elongation phase
D) DNA replication starts

RNA polymerase begins the elongation phase

Which of the following is NOT a characteristic of bacterial promoters?
A) Typically 20-200 base pairs long
B) Initial binding site for RNA polymerase and transcription factors
C) Require TATA binding protein for recognition
D) Necessary for transcription initiation

Require TATA binding protein for recognition

The ________ factor in bacteria is crucial for increasing the affinity of RNA polymerase to the promoter during transcription initiation

sigma

After transcription initiation in bacteria, the ________ factor is released, which leads to a decrease in RNA polymerase affinity to the promoter and the start of elongation.

sigma

Bacterial promoters are nucleotide sequences that typically range from ________ to ________ base pairs in length.

20; 200

True or False: The TATA binding protein is essential for bacterial RNA polymerase to recognize the promoter.

false

True or False: Once elongation begins, RNA polymerase maintains a high affinity for the promoter sequence.

false

True or False: Sigma factors are essential for transcription initiation in bacteria.

true

In bacterial translation initiation, the small ribosomal subunit binds to which specific sequence on the mRNA?
A) TATA box
B) Kozak sequence
C) Shine-Dalgarno sequence
D) Poly-A tail

Shine-Dalgarno sequence

What is the first amino acid incorporated during bacterial translation initiation?
A) Methionine
B) Formyl-methionine
C) Glycine
D) Alanine

Formyl-methionine

Where does the initiator tRNA carrying N-formyl-methionine bind in the ribosome during initiation?
A) A site
B) P site
C) E site
D) Exit tunnel

P site

Which of the following is NOT required during bacterial translation initiation?
A) Initiation factors
B) Large ribosomal subunit
C) Release factors
D) Small ribosomal subunit

Release factors

In bacteria, the initiator tRNA carries ________, which is a modified form of methionine.

N-formyl-methionine

During initiation, the large ribosomal subunit is recruited after the ________ subunit and initiator tRNA are correctly positioned.

small ribosomal

True or False: In bacteria, the initiator tRNA binds to the A site of the ribosome during translation initiation.

false

True or False: The Shine-Dalgarno sequence is located close to the start codon on bacterial mRNA.

true

True or False: Initiation of bacterial translation does not require any additional proteins besides the ribosomal subunits and tRNA.

false

What term describes a section of DNA that codes for a single protein?
A) Operon
B) Cistron
C) Polycistron
D) Intron

Cistron

What is a key feature of polycistronic mRNA in bacteria?
A) It encodes only one protein per mRNA
B) It contains multiple ribosome-binding sites, each preceding a start codon
C) It is only found in eukaryotes
D) It has a single start codon and ribosome-binding site

It contains multiple ribosome-binding sites, each preceding a start codon

Why do genes within a polycistronic mRNA usually encode proteins involved in the same pathway?
A) To enable simultaneous regulation of the genes
B) To produce unrelated proteins quickly
C) To separate genes physically on the chromosome
D) To inhibit translation efficiency

To enable simultaneous regulation of the genes

A ________ mRNA molecule contains instructions to make several different proteins.

polycistronic

In a polycistronic mRNA, each protein coding region has its own ________ and start codon to allow the ribosome to initiate translation at multiple points.

ribosome-binding site

The genes found on a polycistronic mRNA often encode proteins that participate in the same ________.

metabolic pathway

True or False: A cistron refers to a DNA section that codes for multiple proteins.

false

True or False: Polycistronic mRNAs are common in bacteria but rare in eukaryotes.

true

True or False: In polycistronic mRNA, a single ribosome-binding site is shared by all the proteins encoded.

false

Why is additional gene regulation necessary beyond the basic initiation of transcription?
A) Because all genes naturally turn off after transcription starts
B) To ensure that all genes are expressed at the same levels constantly
C) To fine-tune gene expression so that different genes are expressed at different levels and times
D) Because transcription initiation is the only level of gene regulation

To ensure that all genes are expressed at the same levels constantly

If gene regulation only depended on promoter recognition and transcription initiation, what would be the expected result?
A) Genes would never be expressed
B) Genes would be expressed only under stress
C) All genes would be expressed equally and constantly
D) Genes would be regulated post-transcriptionally

All genes would be expressed equally and constantly

In bacterial negative regulation, what is the default state of gene transcription?
A) Off, until turned on by an activator
B) On, until turned off by a repressor
C) On, until turned off by an inducer
D) Off, until turned on by a repressor

On, until turned off by a repressor

Where does the repressor protein typically bind to inhibit transcription in negative regulation?
A) Downstream of the transcriptional start site
B) At the ribosome binding site
C) Upstream of the transcriptional start site
D) At the 3’ end of the gene

Upstream of the transcriptional start site

Which molecule can remove the repressor protein from DNA, allowing transcription to proceed?
A) Corepressor
B) Aporepressor
C) Inducer
D) Sigma factor

Inducer

In the context of negative regulation, what is the role of an aporepressor?
A) It activates transcription directly
B) It binds DNA and turns transcription on
C) It interacts with a corepressor to block transcription
D) It removes the repressor from DNA

It interacts with a corepressor to block transcription

In negative regulation, a ________ protein binds to DNA upstream of the gene to block RNA polymerase and stop transcription.

repressor

An ________ interacts with a ________ to repress gene transcription in negative regulation.

aporepressor, corepressor

True or False: In negative regulation, gene transcription is off by default until a repressor protein turns it on.

false

In positive regulation, what is the default state of gene transcription?
A) On, until turned off by a repressor
B) Off, until turned on by an activator
C) On, until turned on by a repressor
D) Off, until turned off by an activator

Off, until turned off by an activator

Which of the following best defines transcription factors?
A) RNA molecules that inhibit translation
B) Proteins that control the level of gene expression by turning genes on or off
C) DNA sequences where RNA polymerase binds
D) Lipids that stabilize DNA structure

Proteins that control the level of gene expression by turning genes on or off

A protein that binds DNA to increase the rate of transcription is called a(n):
A) Repressor
B) Activator
C) Corepressor
D) Sigma factor

Activator

Proteins that control gene expression by either increasing or decreasing transcription are called ________.

transcription factors

True or False: Positive regulation requires an activator protein to recruit RNA polymerase to the promoter.

true

What is an operon?
A) A single gene controlled by multiple promoters
B) A group of genes regulated individually
C) A group of genes working in the same pathway controlled by a single promoter and operator
D) A non-coding RNA sequence regulating transcription

A group of genes working in the same pathway controlled by a single promoter and operator

Polycistronic mRNA refers to:
A) mRNA that carries instructions for one protein
B) mRNA that carries instructions for several proteins encoded by an operon
C) A DNA sequence that regulates transcription
D) mRNA that is translated only once

mRNA that carries instructions for several proteins encoded by an operon

In bacteria, genes encoding enzymes that work sequentially in a metabolic pathway are usually:
A) Expressed independently and regulated individually
B) Transcribed together into a polycistronic mRNA and regulated as one unit
C) Transcribed into multiple monocistronic mRNAs
D) Regulated only by positive control

Transcribed together into a polycistronic mRNA and regulated as one unit

An operon consists of adjacent structural genes regulated by a(n) ________ and transcribed into a(n) ________ mRNA.

Answer: operator, polycistronic

In bacterial operons, genes involved in the same metabolic pathway are usually turned ________ or ________ together.

on; off

True or False: Each gene in an operon has its own promoter and is transcribed separately.

false

True or False: Polycistronic mRNA allows multiple proteins to be synthesized from a single mRNA transcript.

true

Which of the following is NOT a component of the lac operon?
A) lacZ
B) lacY
C) lacI
D) lacM

lacM

What is the role of the lacI gene in the lac operon?
A) Encodes the enzyme that breaks down lactose
B) Encodes the permease protein to transport lactose
C) Encodes the repressor protein that regulates the operon
D) Acts as the promoter for transcription initiation

Encodes the repressor protein that regulates the operon

The operator (lacO) in the lac operon functions as:
A) The site where RNA polymerase binds to start transcription
B) The DNA sequence where the repressor protein binds to block transcription
C) A gene encoding lactose-metabolizing enzymes
D) A protein that facilitates lactose transport into the cell

The DNA sequence where the repressor protein binds to block transcription

The structural genes lacZ and lacY encode proteins involved in the ________ and ________ of lactose, respectively.

metabolism, transport

The lac operon’s promoter is called ________, and it is the binding site for ________ during transcription initiation.

lacP; promoter

True or False: The lac operon is an example of negative regulation where the repressor binds to the operator to prevent transcription.

true

What is the function of the lacI gene product in the lac operon?
A) It activates transcription by binding to the promoter
B) It transports lactose into the cell
C) It acts as a repressor that binds to the operator to block transcription
D) It catalyzes the breakdown of lactose

It acts as a repressor that binds to the operator to block transcription

Negative regulation of the lac operon occurs because:
A) The repressor protein binds to the operator to stop transcription
B) An activator protein binds to the promoter to enhance transcription
C) The presence of lactose turns off the operon
D) RNA polymerase is permanently blocked from binding the promoter

The repressor protein binds to the operator to stop transcription

True or False: When the lac repressor is bound to the operator, RNA polymerase cannot initiate transcription of lac mRNA.

true

What role does lactose play in the regulation of the lac operon?
A) It acts as a repressor to block transcription
B) It serves as an inducer that binds to the repressor and changes its shape
C) It directly binds RNA polymerase to start transcription
D) It degrades the lac mRNA after transcription

It serves as an inducer that binds to the repressor and changes its shape

When lactose binds to the lac repressor, what is the immediate effect?
A) The repressor binds more tightly to the operator
B) The repressor changes shape and can no longer bind the operator
C) RNA polymerase is blocked from the promoter
D) The operator sequence is mutated

The repressor changes shape and can no longer bind the operator

The inducer molecule binds to the ____________, causing a conformational change that prevents it from binding to the ____________.

repressor; operator

When the repressor is released from the operator, ____________ can bind to the promoter and initiate transcription of lac genes.

RNA polymerase

True or False: Lactose directly binds to the operator DNA to induce transcription of the lac operon.

false

True or False: The lac repressor has a high affinity for the inducer, which helps regulate the operon efficiently.

true

What happens to lac operon mRNA levels shortly after lactose is added to the bacterial environment?
A) mRNA levels remain unchanged
B) mRNA levels increase quickly
C) mRNA levels decrease gradually
D) mRNA levels permanently increase

mRNA levels increase quickly

Which of the following best describes the change in lac operon expression after lactose removal?
A) The increased mRNA expression continues indefinitely
B) The mRNA expression quickly returns to the baseline level
C) The lac operon is permanently deactivated
D) The repressor gene lacI is deleted

The mRNA expression quickly returns to the baseline level

What is the effect of a mutation in the lacI gene that disrupts the repressor protein?
A) The lac operon is never expressed
B) The lac operon is expressed only in the presence of lactose
C) The lac operon is expressed constitutively (all the time)
D) The lac operon expression is completely shut off

The lac operon is expressed constitutively (all the time)

A lacI mutation that alters the amino acid sequence of the repressor protein primarily affects its:
A) Ability to bind RNA polymerase
B) Ability to bind lactose
C) 3D structure and DNA binding ability
D) Promoter sequence

3D structure and DNA binding ability

Mutations in the __________ gene cause the lac operon to be expressed ____________, regardless of lactose presence.

lacI, constitutively

A lacI mutant strain unable to produce a functional repressor is called a __________ strain.

lac⁻

True or False: In a lacI mutant strain, the repressor protein cannot bind to the operator, so the lac operon is always turned on.

true

What is the effect of a mutation in the lac operator (lacO) sequence?
A) The repressor binds more tightly, shutting off the lac operon permanently
B) The repressor cannot bind, leading to constitutive expression of the lac operon
C) The lac operon is expressed only in the presence of lactose
D) The lac operon is never transcribed

The repressor cannot bind, leading to constitutive expression of the lac operon

A mutation in the operator sequence that prevents repressor binding affects:
A) The structure of the repressor protein
B) The DNA binding site of the repressor
C) The lactose binding site of the repressor
D) The promoter sequence

The DNA binding site of the repressor

Mutations in the __________ sequence prevent the lac repressor from binding, causing the lac operon to be expressed ____________ regardless of lactose presence.

operator (lacO), constitutively

A mutation in the operator region affects gene expression without altering the ___________ of any protein.

coding sequence (not a mutation within the coding region of a protein)

What happens in a lacI super repressor mutation?
A) The repressor cannot bind to the operator, leading to constitutive expression
B) The inducer cannot bind the repressor, so the repressor remains bound to the operator and blocks transcription permanently
C) The repressor binds the inducer normally, allowing normal gene expression in the presence of lactose
D) The lac operon is expressed only when lactose is absent

) The inducer cannot bind the repressor, so the repressor remains bound to the operator and blocks transcription permanently

In the case of a lacI super repressor mutation, what is the expected phenotype?
A) The lac operon is always turned on
B) The lac operon is never expressed, even in the presence of lactose
C) The lac operon expression is normal and inducible by lactose
D) The lac operon expresses only basal levels of enzymes

The lac operon is never expressed, even in the presence of lactose

A lacI super repressor mutation prevents the __________ from binding to the repressor, causing the repressor to remain __________ to the operator and block transcription permanently.

inducer; bound

What did adding a wildtype lacI gene on a plasmid to a lacI⁻ bacterial strain demonstrate?
A) The lac operon regulation is cis-acting and only affects genes on the same DNA molecule
B) The lacI gene product (repressor) is trans-acting and can regulate lac operons on different DNA molecules
C) The plasmid lacI gene cannot restore lac operon regulation in lacI⁻ bacteria
D) The lacI gene on the plasmid produces RNA that blocks transcription

The lacI gene product (repressor) is trans-acting and can regulate lac operons on different DNA molecules

Which of the following best describes a trans-acting factor?
A) A DNA sequence that regulates genes only on the same DNA molecule
B) A protein or RNA molecule that can diffuse and regulate genes on different DNA molecules
C) A mutation that affects only the gene it is located on
D) A plasmid that cannot influence chromosomal gene expression

A protein or RNA molecule that can diffuse and regulate genes on different DNA molecules

In the experiment with partial diploids, the wildtype lacI gene on the plasmid produced a __________ that could bind to the operator on the bacterial chromosome, demonstrating that the lacI gene product is __________-acting.

repressor protein; trans

True or False: The lacI repressor protein produced from a plasmid can regulate the lac operon on the bacterial chromosome.

true

True or False: A trans-acting factor can only regulate the gene located on the DNA molecule that encodes it.

false

Why does adding a wildtype operator on a plasmid fail to restore normal regulation in bacteria with a mutated operator (lacOc) on their chromosome?
A) Because operator sequences act in trans and must be on the same DNA molecule
B) Because operator sequences are cis-acting and only regulate genes on the same DNA molecule where they are located
C) Because plasmids cannot carry functional operators
D) Because the plasmid operator sequence represses the lacI gene

Because operator sequences are cis-acting and only regulate genes on the same DNA molecule where they are located

What does cis-acting mean in the context of gene regulation?
A) A protein or RNA that regulates genes elsewhere in the cell
B) A DNA or RNA element that regulates only the genes on the same DNA or RNA molecule it is part of
C) A mutation that affects multiple DNA molecules
D) A plasmid-encoded gene product that acts throughout the cell

A DNA or RNA element that regulates only the genes on the same DNA or RNA molecule it is part of

A mutation in the operator sequence, such as lacOc, causes __________ expression because the repressor cannot bind. This mutation is __________-acting, affecting only the genes on the same DNA molecule.

constitutive; cis

True or False: The lac operator mutation lacOc can be complemented by a wildtype operator sequence on a plasmid.

false

True or False: The lac operator is a cis-acting element, meaning it regulates only the genes on the DNA molecule where it resides.

true

Which molecule acts as a signaling molecule that increases when glucose is low in bacterial cells?
A) ATP
B) cAMP
C) Lactose
D) cGMP

cAMP

What is the role of the cAMP-CRP complex in lac operon regulation?
A) It represses the lac operon by blocking RNA polymerase binding
B) It increases the affinity of RNA polymerase to the lac promoter, enhancing transcription
C) It degrades glucose to increase lactose availability
D) It binds lactose to activate the operon

It increases the affinity of RNA polymerase to the lac promoter, enhancing transcription

The levels of cAMP in bacterial cells are __________ related to the levels of glucose.

inversely

When glucose levels are low, __________ binds to the __________ protein, forming a complex that increases lac operon expression.

cAMP, cAMP receptor protein (CRP)

True or False: The cAMP-CRP complex allows bacteria to more strongly express lactose-utilization genes when glucose is abundant.

false

True or False: The cAMP-CRP complex functions as a positive regulator by facilitating RNA polymerase binding to the lac operon promoter.

true

Why does the lac operon remain mostly off when glucose is abundant, even if lactose is present?
A) Lactose prevents RNA polymerase from binding
B) High glucose leads to low cAMP levels, reducing activation by CRP
C) Glucose directly binds to the lac operon and represses it
D) The repressor protein is permanently bound to the operator

High glucose leads to low cAMP levels, reducing activation by CRP

Which of the following best explains why bacteria prioritize glucose over lactose?
A) Glucose transport requires less energy than lactose transport
B) Glucose metabolism does not require gene regulation
C) The lac operon cannot be activated in the presence of lactose
D) Lactose inhibits glucose metabolism

Glucose transport requires less energy than lactose transport

When glucose levels are __________, the concentration of cAMP is __________, leading to decreased activation of the lac operon.

high; low

The lac operon is only strongly turned on when glucose is __________ and lactose is __________.

low; present

True or False: The presence of glucose reduces cAMP levels, which decreases the ability of CRP to assist RNA polymerase binding to the lac promoter.

true

What happens to the trp operon when tryptophan is present in the bacterial cell?
A) The repressor cannot bind to the operator, so transcription proceeds
B) Tryptophan binds to the repressor, allowing it to bind the operator and block transcription
C) The trp operon is always active regardless of tryptophan presence
D) RNA polymerase binds more efficiently, increasing transcription

Tryptophan binds to the repressor, allowing it to bind the operator and block transcription

In the trp operon system, the absence of tryptophan causes:
A) The repressor to change shape and bind the operator
B) The repressor to be inactive, so transcription of trp genes proceeds
C) The cell to stop making tryptophan
D) Tryptophan to bind to the operator directly

The repressor to be inactive, so transcription of trp genes proceeds