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Questions and Answers
Which of the following best describes the function of regulatory genes?
Which of the following best describes the function of regulatory genes?
- They produce products that interact with other DNA sequences, influencing transcription and translation. (correct)
- They are untranscribed DNA sequences regulating nucleotide sequences.
- They are DNA sequences that are transcribed into functional RNA molecules.
- They directly encode for structural proteins used in cell construction.
How does gene regulation in bacteria primarily contribute to their survival?
How does gene regulation in bacteria primarily contribute to their survival?
- By permanently activating genes necessary for survival.
- By providing internal flexibility, allowing genes to be switched on/off in response to environmental changes. (correct)
- By maintaining a constant internal environment regardless of external conditions.
- By enabling cell differentiation similar to multicellular organisms.
Which statement accurately contrasts positive and negative control in gene regulation?
Which statement accurately contrasts positive and negative control in gene regulation?
- Positive control stimulates gene expression, while negative control inhibits it. (correct)
- Positive control involves constitutive gene expression, whereas negative control requires external signals.
- Positive control relies on repressor proteins exclusively, while negative control uses only activators.
- Positive control inhibits gene expression, while negative control stimulates it.
Why is transcription an important regulatory point in both bacteria and eukaryotes?
Why is transcription an important regulatory point in both bacteria and eukaryotes?
What is the primary function of a motif within a DNA-binding protein?
What is the primary function of a motif within a DNA-binding protein?
How do amino acids in DNA-binding proteins typically interact with DNA?
How do amino acids in DNA-binding proteins typically interact with DNA?
What structural feature is characteristic of a helix-turn-helix motif found in DNA-binding proteins?
What structural feature is characteristic of a helix-turn-helix motif found in DNA-binding proteins?
Within an operon, what is the role of the operator?
Within an operon, what is the role of the operator?
If transcription is normally off and needs to be turned on, what type of operon is this?
If transcription is normally off and needs to be turned on, what type of operon is this?
In a negative inducible operon, what is the function of the inducer?
In a negative inducible operon, what is the function of the inducer?
What occurs in a negative repressible operon when the corepressor is present?
What occurs in a negative repressible operon when the corepressor is present?
What is a key characteristic of positive control in transcriptional regulation?
What is a key characteristic of positive control in transcriptional regulation?
How can the genes lacZ, lacY, and lacA be transcribed in abundance?
How can the genes lacZ, lacY, and lacA be transcribed in abundance?
What is the role of β-galactosidase in lactose metabolism?
What is the role of β-galactosidase in lactose metabolism?
In the lac operon, the operator site overlaps which two regions?
In the lac operon, the operator site overlaps which two regions?
In a bacterial strain with a lacI- mutation, what would be the effect on lac operon expression?
In a bacterial strain with a lacI- mutation, what would be the effect on lac operon expression?
What is the effect of a _lacO_ᶜ mutation (constitutive operator) on the expression of the lac operon?
What is the effect of a _lacO_ᶜ mutation (constitutive operator) on the expression of the lac operon?
What effect does a lacP⁻ (promoter) mutation have on transcription of the lac operon?
What effect does a lacP⁻ (promoter) mutation have on transcription of the lac operon?
How does catabolite repression affect the lac operon when glucose is present?
How does catabolite repression affect the lac operon when glucose is present?
CAMP levels are inversely proportional to the amounts of available:
CAMP levels are inversely proportional to the amounts of available:
In the trp operon, what happens to the trp repressor when tryptophan levels are high?
In the trp operon, what happens to the trp repressor when tryptophan levels are high?
What is the consequence of the binding of region 2 to region 3 in the 5' UTR of the trp operon mRNA when tryptophan levels are low?
What is the consequence of the binding of region 2 to region 3 in the 5' UTR of the trp operon mRNA when tryptophan levels are low?
Attenuation is a regulatory mechanism that affects...
Attenuation is a regulatory mechanism that affects...
When tryptophan levels are high, what is the configuration of the secondary structure formed in the 5' UTR of the trp operon mRNA, leading to attenuation?
When tryptophan levels are high, what is the configuration of the secondary structure formed in the 5' UTR of the trp operon mRNA, leading to attenuation?
What is the function of antisense RNA in controlling gene expression?
What is the function of antisense RNA in controlling gene expression?
How do riboswitches regulate gene expression?
How do riboswitches regulate gene expression?
What function do ribozymes perform in the regulation of gene expression?
What function do ribozymes perform in the regulation of gene expression?
Which of the following best describes the relationship between the concentration of cAMP and glucose in catabolite repression?
Which of the following best describes the relationship between the concentration of cAMP and glucose in catabolite repression?
What is the role of the CAP-cAMP complex in positive control of the lac operon?
What is the role of the CAP-cAMP complex in positive control of the lac operon?
How does the presence of a regulatory protein bound to a riboswitch typically affect gene expression?
How does the presence of a regulatory protein bound to a riboswitch typically affect gene expression?
Which of the following is a common characteristic of both the lac and trp operons?
Which of the following is a common characteristic of both the lac and trp operons?
Which of the following mutations in the lac operon would lead to constitutive expression (i.e., expression even in the absence of lactose)?
Which of the following mutations in the lac operon would lead to constitutive expression (i.e., expression even in the absence of lactose)?
If a bacterial cell has high levels of tryptophan, what regulatory mechanism is activated to control the trp operon?
If a bacterial cell has high levels of tryptophan, what regulatory mechanism is activated to control the trp operon?
How does the presence of allolactose affect the lac repressor protein?
How does the presence of allolactose affect the lac repressor protein?
In terms of its effect on downstream genes in an operon, what is 'cis-acting' referring to?
In terms of its effect on downstream genes in an operon, what is 'cis-acting' referring to?
Compared with wild-type, what phenotype(s) would you expect to observe in a strain with a mutation that inactivates the gene for CAP (catabolite activator protein)?
Compared with wild-type, what phenotype(s) would you expect to observe in a strain with a mutation that inactivates the gene for CAP (catabolite activator protein)?
How will mutating the two tryptophan codons to alanine in the leader peptide region of the trp operon affect regulation?
How will mutating the two tryptophan codons to alanine in the leader peptide region of the trp operon affect regulation?
What distinguishes regulatory elements from structural genes in the context of prokaryotic gene regulation?
What distinguishes regulatory elements from structural genes in the context of prokaryotic gene regulation?
How does gene regulation contribute to cell differentiation in multicellular eukaryotic organisms?
How does gene regulation contribute to cell differentiation in multicellular eukaryotic organisms?
Which of the following best describes the impact of a mutation that disrupts the domain of a DNA-binding protein?
Which of the following best describes the impact of a mutation that disrupts the domain of a DNA-binding protein?
If a mutation occurred in the bacterial regulatory gene that prevents it from being transcribed, what effect would you expect to see on the expression of the structural gene it regulates?
If a mutation occurred in the bacterial regulatory gene that prevents it from being transcribed, what effect would you expect to see on the expression of the structural gene it regulates?
How does the presence of an inducer molecule affect the function of a negative inducible operon?
How does the presence of an inducer molecule affect the function of a negative inducible operon?
What is the role of a corepressor in a negative repressible operon?
What is the role of a corepressor in a negative repressible operon?
In a positive control system, what is the function of an activator protein?
In a positive control system, what is the function of an activator protein?
How does the lack of the lacY gene affect a bacterial cell's ability to metabolize lactose?
How does the lack of the lacY gene affect a bacterial cell's ability to metabolize lactose?
Which of the following events would you expect to observe in a lacI⁻ /lacI⁺ partial diploid strain of bacteria grown in the absence of lactose?
Which of the following events would you expect to observe in a lacI⁻ /lacI⁺ partial diploid strain of bacteria grown in the absence of lactose?
What is the predicted outcome of a bacterial strain carrying a _lacO_ᶜ mutation grown in a lactose-free medium?
What is the predicted outcome of a bacterial strain carrying a _lacO_ᶜ mutation grown in a lactose-free medium?
In a bacterial strain with a lacP⁻ mutation, what effect would this have on transcription of the lac operon?
In a bacterial strain with a lacP⁻ mutation, what effect would this have on transcription of the lac operon?
How does the presence of glucose affect the levels of cAMP in a bacterial cell, and what impact does this have on the lac operon?
How does the presence of glucose affect the levels of cAMP in a bacterial cell, and what impact does this have on the lac operon?
What is the role of the CAP-cAMP complex in the lac operon when lactose is present and glucose is scarce?
What is the role of the CAP-cAMP complex in the lac operon when lactose is present and glucose is scarce?
When tryptophan levels are high in a bacterial cell, how does this affect the trp repressor?
When tryptophan levels are high in a bacterial cell, how does this affect the trp repressor?
In the context of the trp operon, when region 1 is bound to region 2 in the 5' UTR of the mRNA, what does this imply about the levels of tryptophan and the process of transcription?
In the context of the trp operon, when region 1 is bound to region 2 in the 5' UTR of the mRNA, what does this imply about the levels of tryptophan and the process of transcription?
What is the function of the terminator structure formed during attenuation in the trp operon?
What is the function of the terminator structure formed during attenuation in the trp operon?
When tryptophan levels are high, the 3-4 stem-loop structure forms, leading to transcription termination. What is the status of the ribosome?
When tryptophan levels are high, the 3-4 stem-loop structure forms, leading to transcription termination. What is the status of the ribosome?
How does antisense RNA typically function to regulate gene expression?
How does antisense RNA typically function to regulate gene expression?
How do riboswitches typically regulate gene expression in bacteria?
How do riboswitches typically regulate gene expression in bacteria?
What is the primary mechanism by which ribozymes control gene expression?
What is the primary mechanism by which ribozymes control gene expression?
In the lac operon, if glucose levels are high, what is the state of the CAP protein, and how does this affect transcription?
In the lac operon, if glucose levels are high, what is the state of the CAP protein, and how does this affect transcription?
How does a regulatory protein influence gene expression when it binds to a riboswitch?
How does a regulatory protein influence gene expression when it binds to a riboswitch?
What would be the most likely effect if a bacterial gene normally regulated by antisense RNA suffered a mutation that prevented the antisense RNA from binding?
What would be the most likely effect if a bacterial gene normally regulated by antisense RNA suffered a mutation that prevented the antisense RNA from binding?
Which of the following best describes how a mutation in the region of the trp operon affects transcription?
Which of the following best describes how a mutation in the region of the trp operon affects transcription?
If the leader sequence of the trp operon mRNA is altered such that the two tryptophan codons are deleted, what is the likely outcome regarding the operon's regulation?
If the leader sequence of the trp operon mRNA is altered such that the two tryptophan codons are deleted, what is the likely outcome regarding the operon's regulation?
Which of the following mutations would result in the lowest expression of the lac operon when lactose is present and glucose is absent?
Which of the following mutations would result in the lowest expression of the lac operon when lactose is present and glucose is absent?
What effect would you expect from a mutation that disrupts the helix-turn-helix motif in a bacterial regulatory protein?
What effect would you expect from a mutation that disrupts the helix-turn-helix motif in a bacterial regulatory protein?
A bacterial cell carries a mutation that results in a non-functional sigma factor. How will this mutation most directly affect gene expression?
A bacterial cell carries a mutation that results in a non-functional sigma factor. How will this mutation most directly affect gene expression?
In bacteria, if a mutation leads to a loss of function in Rho protein, how would transcription of certain operons be affected?
In bacteria, if a mutation leads to a loss of function in Rho protein, how would transcription of certain operons be affected?
How would you classify bacterial enhancers?
How would you classify bacterial enhancers?
Flashcards
Structural genes
Structural genes
Genes that encode proteins.
Regulatory genes
Regulatory genes
Genes encoding products interacting with sequences, affecting transcription and translation.
Regulatory elements
Regulatory elements
DNA sequences not transcribed, regulating nucleotide sequences.
Constitutive expression
Constitutive expression
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Positive control
Positive control
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Negative control
Negative control
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Domains
Domains
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Motif
Motif
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Operon
Operon
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Regulator gene
Regulator gene
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Inducible operons
Inducible operons
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Repressible operons
Repressible operons
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Negative inducible operons
Negative inducible operons
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Inducer
Inducer
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Negative repressible operons
Negative repressible operons
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Corepressor
Corepressor
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Positive transcriptional control
Positive transcriptional control
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lac operon
lac operon
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Partial diploid
Partial diploid
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Catabolite repression
Catabolite repression
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cAMP
cAMP
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trp Operon of E. coli
trp Operon of E. coli
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Attenuation
Attenuation
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Bacterial enhancers
Bacterial enhancers
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Antisense RNA
Antisense RNA
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Riboswitches
Riboswitches
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Ribozymes
Ribozymes
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Study Notes
Regulation of Gene Expression
- Genes and regulatory elements are critical for gene expression in all organisms.
Genes and Regulatory Elements
- Structural genes encode proteins.
- Regulatory genes encode products affecting transcription and translation.
- Regulatory elements are untranscribed DNA sequences regulating nucleotide sequences.
- Bacteria use gene regulation for internal flexibility, responding to environmental changes.
- Multicellular eukaryotes use gene regulation for cell differentiation.
- Constitutive expression refers to genes continuously expressed under normal conditions.
- Positive control stimulates gene expression.
- Negative control inhibits gene expression.
- A constitutive gene is unregulated and continuously expressed.
Levels of Gene Regulation
- Gene expression can be controlled at multiple levels including DNA structure, transcription, mRNA processing, RNA stability, translation, and post-translational modification.
- Transcription is a key gene regulation level in bacteria and eukaryotes because it's the first step in transferring DNA information to protein and it's efficient to regulate early.
DNA Binding Proteins
- Domains of approximately 60-90 amino acids in DNA-binding proteins are responsible for binding to DNA and forming hydrogen bonds with it.
- A motif represents a simple structure within the binding domain that fits into DNA's major groove.
- Distinct types of DNA-binding proteins exist based on the motif.
- Amino acids in DNA-binding proteins interact with DNA through hydrogen bonds.
- Common DNA-binding motifs include helix-turn-helix (two alpha helices, major groove), zinc finger (loop of amino acids with zinc at base, major groove), steroid receptor (two perpendicular alpha helices with zinc surrounded by cysteines, major groove and DNA backbone), leucine zipper (helix of leucine and basic arm with leucines interdigitated, two adjacent major grooves), helix-loop-helix (two alpha helices separated by loop of amino acids, major groove), and homeodomain (three alpha helices, major groove)
Regulation by Operons
- Transcription in bacterial cells is regulated by operons.
Operon Structure
- An operon includes a promoter, an operator, and structural genes that control transcription.
- A regulator gene's DNA sequence encodes for products that affect the operon's function but are not part of it.
- An operon serves as a single transcriptional unit with structural genes, a promoter, and an operator.
- Structural genes are transcribed into mRNA; regulator genes control structural gene transcription.
Inducible and Repressible Operons
- Inducible operons are typically off, needing to be turned on for transcription.
- Repressible operons are typically on, needing to be turned off.
- Negative inducible operons involve a repressor molecule binding to the operator site, which inhibits transcription and necessitates an inducer to activate it.
- An inducer is a small molecule that initiates transcription.
- Negative repressible operons are usually active, so transcription needs to be repressed by a corepressor.
- A corepressor is a small molecule that binds the repressor, enabling it to bind the operator and halt transcription.
- In positive transcriptional control, a regulatory protein acts as an activator, binding to DNA and stimulating transcription.
- In a negative repressible operon, the regulator protein is synthesized as an inactive repressor.
lac Operon
- The lac operon of E. coli is a negative inducible operon that regulates lactose metabolism through the lacI repressor gene, lacP promoter, and lacO operator, and is induced by allolactose.
- Structural genes of the lac operon include lacZ (β-galactosidases), lacY (permease), and lacA (transacetylase).
- The repression of the lac operon never completely stops transcription.
- The operator overlaps the promoter and the 5' end of the first structural gene in the lac operon.
- In the presence of allolactose, the lac repressor cannot bind to the operator.
lac Operon Mutations
- Partial diploid involves a full bacterial chromosome plus extra DNA on an F plasmid.
- Structural gene mutations affect enzyme structure, not regulation.
- lacZ+lacY-/lacZ-lacY+ produces functional B-galactosidase and permease.
- Regulator-gene mutations (lacI-) lead to constitutive transcription.
- lacI+ is dominant over lacI-, is trans-acting, and allows normal regulation.
- lacI+lacZ-/ lacI-lacZ+ produce functional B-galactosidase.
- Partial diploid lacI+ lacZ-/ lacI-lacZ+ produce B-galactosidase only in presence of lactose because the lacI gene is trans-dominant.
- lacIs lacZ+/lacI+ lacZ+ does not produce B-galactosidase because lacIs encodes a superrepressor.
- Operator mutations (lacOc) are constitutive.
- lacOc is dominant over lacO+ and is cis acting.
- lacI+lacO+Z-/ lacI+lacOclacZ+ produce functional B-galactosidase constitutively.
- Promoter mutations such as lacP- are cis acting and fail to produce functional B-galactosidase.
Catabolite Repression
- Catabolite repression involves the use of glucose repressing the metabolism of other sugars.
- Catabolite repression is a positive control mechanism.
- Catabolite activator protein (CAP) activates the positive effect.
- cAMP binds to CAP, and the CAP-cAMP complex binds to a site upstream from the lac gene promoter.
- The concentration of cAMP is inversely proportional to glucose levels.
- CAP stimulates transcription by binding to the lac operon's promoter
- The binding of cAMP-CAP complex to DNA bends the DNA and activates transcription.
- High levels of glucose result in little transcription taking place
trp Operon
- The trp operon in E. coli is a negative repressible operon with five structural genes.
- The structural genes trpE, trpD, trpC, trpB, and trpA encode enzymes converting chorismate to tryptophan.
- This operon controls tryptophan biosynthesis.
- The trp repressor is normally inactive and cannot bind to the operator.
- In the absence of tryptophan, the trp repressor cannot bind to the operator, so transcription takes place.
Attenuation
- Attenuation affects the continuation of transcription, not its initiation, terminating transcription before reaching structural genes.
- The regions include the attenuator and antiterminator.
- The trp operon has four regions of a long 5' leader region of trpE mRNA sequence
- When tryptophan is high, region 3 pairs with region 4. This structure terminates transcription.
- When tryptophan is low, region 2 pairs with region 3. This structure does not terminate transcription.
RNA Control
- Bacterial enhancers increase transcription rates at distant genes.
- Antisense RNA is complementary to targeted mRNA sequences.
- Riboswitches are molecules influencing mRNA secondary structure formation.
- Ribozymes are mRNA molecules displaying catalytic activity.
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