DNA Regulation and Enzyme Activity
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Questions and Answers

What are regulons characterized by?

  • Sets of genes responding to the same regulatory system (correct)
  • Multiple genes controlled by different regulatory elements
  • Genes that are permanently expressed
  • A single gene responding to multiple signals

Which regulatory protein is involved in the SOS response by cleaving lexA?

  • RNA polymerase
  • repressor protein
  • sigma factor
  • recA (correct)

What does catabolite repression primarily do?

  • Increases the transcription of carbon source operons
  • Enhances the activity of all operons
  • Activates stress response genes
  • Shuts down metabolic pathways when glucose is present (correct)

What role does the sigma factor play in bacterial transcription?

<p>It directs RNA polymerase to specific genes (B)</p> Signup and view all the answers

When is the SOS response typically activated?

<p>In response to serious DNA damage (D)</p> Signup and view all the answers

What is the function of lexA in the SOS response?

<p>To bind and prevent transcription of repair genes when all is well (A)</p> Signup and view all the answers

Which sigma factor is commonly associated with heat response in bacteria?

<p>Sigma-32 (A)</p> Signup and view all the answers

What happens once the damage has been repaired in the SOS response?

<p>lexA can now stop transcription of repair genes (A)</p> Signup and view all the answers

What is the primary function of quorum sensing in microbial communication?

<p>To regulate gene expression according to population density (C)</p> Signup and view all the answers

In the context of quorum sensing, what role do autoinducer molecules play?

<p>They are released by cells and help regulate gene expression (B)</p> Signup and view all the answers

How does the Hawaiian bobtail squid utilize quorum sensing?

<p>To coordinate light emission with symbiotic v. fischeri (A)</p> Signup and view all the answers

What distinguishes the V. fischeri cells when they are in the light organ of the squid?

<p>They exhibit bioluminescence under high population densities (B)</p> Signup and view all the answers

Which of the following is NOT a characteristic of quorum sensing?

<p>Inhibiting gene expression during high densities (D)</p> Signup and view all the answers

What is the primary function of the operator site in DNA with regard to transcription?

<p>It prevents RNA polymerase from transcribing genes. (D)</p> Signup and view all the answers

Which type of enzymes is primarily controlled by repression during negative control?

<p>Biosynthetic enzymes (A)</p> Signup and view all the answers

How does induction affect transcription?

<p>It enables transcription by removing a regulatory protein that blocks RNA polymerase. (B)</p> Signup and view all the answers

What is the role of co-repressor in repression?

<p>To bind to the allosteric site and inhibit transcription. (C)</p> Signup and view all the answers

What mechanism is involved in the positive control of transcription?

<p>An allosteric protein facilitating the binding of RNA polymerase. (B)</p> Signup and view all the answers

What is typically the result when a signal inhibits transcription through repression?

<p>Gene expression is turned off or repressed. (D)</p> Signup and view all the answers

In the context of negative control, what does 'derepression' mean?

<p>Transitioning from inactive to active transcription. (C)</p> Signup and view all the answers

Which of the following describes the role of the allosteric protein in the positive control mechanism?

<p>Activates the transcription process. (A)</p> Signup and view all the answers

What does a high level of glucose detection indicate about its transport?

<p>Transport occurs across a membrane. (D)</p> Signup and view all the answers

What role does tryptophan play in the tryptophan synthesis operon?

<p>It acts as a corepressor binding to the repressor. (C)</p> Signup and view all the answers

In the context of the tryptophan synthesis operon, what is the significance of negative control?

<p>To inhibit synthesis when tryptophan is abundant. (B)</p> Signup and view all the answers

Which mechanism describes how rho-dependent termination occurs in bacterial transcription?

<p>Rho protein displaces RNA pol from the DNA. (B)</p> Signup and view all the answers

What is the key characteristic of rho-independent termination?

<p>It involves an RNA hairpin loop formation. (C)</p> Signup and view all the answers

Which structural genes in the tryptophan operon are necessary for synthesizing tryptophan?

<p>trpE, trpD, trpC, trpB, and trpA. (A)</p> Signup and view all the answers

How does attenuation affect transcription regulation?

<p>It quells the signaling of transcription. (D)</p> Signup and view all the answers

What is the role of RNA polymerase during transcription in bacteria?

<p>It synthesizes mRNA from DNA templates. (A)</p> Signup and view all the answers

What effect does phosphorylated CheY have on flagellar movement?

<p>It interacts with motor proteins and initiates tumbling. (B)</p> Signup and view all the answers

What happens in the absence of attractants in terms of CheA activity?

<p>CheA is phosphorylated, leading to tumbling. (C)</p> Signup and view all the answers

Which protein is responsible for demethylation of MCPs?

<p>CheB (D)</p> Signup and view all the answers

What is the role of MCPs in the adaptation response?

<p>They can be methylated to alter sensitivity to attractants and repellents. (A)</p> Signup and view all the answers

What happens to the sensitivity of MCPs when moving away from a repellent?

<p>Sensitivity increases due to continued methylation by CheR. (A)</p> Signup and view all the answers

How does CheZ contribute to the system after tumbling occurs?

<p>By dephosphorylating CheY and restoring its native state. (C)</p> Signup and view all the answers

What is a feedback loop in the context of MCPs and their adaptation?

<p>It enables the system to reset itself and detect signal concentration changes. (A)</p> Signup and view all the answers

What determines the direction of flagellar rotation in a 'bad' situation?

<p>The phosphorylation state of CheA and CheY. (A)</p> Signup and view all the answers

Which of the following statements about Che proteins is true?

<p>CheR continuously adds methyl groups to regulate sensitivity. (A)</p> Signup and view all the answers

What is the primary function of constitutive genes?

<p>They are required for cell survival and are always turned on. (D)</p> Signup and view all the answers

How do covalent modifications regulate protein activity?

<p>By altering the enzyme's conformations through chemical additions. (B)</p> Signup and view all the answers

What does allosteric regulation involve?

<p>Interactions at a site other than the active site that affect enzyme shape. (D)</p> Signup and view all the answers

Why is energy conservation important in regulating transcription?

<p>It ensures that only essential genes are expressed at all times. (B)</p> Signup and view all the answers

What are inducible genes characterized by?

<p>They are only activated when specific substrates are present. (C)</p> Signup and view all the answers

Which of the following is a key characteristic of the Operon?

<p>It includes a set of structural genes with regulatory elements. (B)</p> Signup and view all the answers

What role do key cellular enzymes play in metabolism?

<p>They are constitutive and essential for maintaining metabolic processes. (B)</p> Signup and view all the answers

What is the impact of changes in environmental conditions on gene regulation?

<p>They necessitate changes in nutrient availability and competition responses. (A)</p> Signup and view all the answers

Which is NOT a method of regulating protein activity?

<p>Gene duplication before transcription. (D)</p> Signup and view all the answers

What is a potential consequence of not turning off certain cellular processes?

<p>Cell death due to resource depletion. (D)</p> Signup and view all the answers

Flashcards

DNA Replication

The process where DNA is copied to produce identical DNA molecules, ensuring that each new cell receives a complete set of genetic instructions.

Transcription

The process where DNA is used as a template to create messenger RNA (mRNA), which carries the genetic code to ribosomes for protein synthesis.

Translation

The process where the genetic information carried by mRNA is used to assemble amino acids into proteins at ribosomes.

Downregulation

The process of turning off unused genes or metabolic pathways to conserve energy and resources.

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Constitutive Genes

Genes that are always expressed, regardless of environmental conditions. They are essential for basic cellular functions.

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Inducible Genes

Genes that are only expressed under specific conditions, like the presence of certain substrates or environmental changes.

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Operon

A multi-gene unit in bacteria that allows for coordinated regulation of multiple genes necessary for a specific metabolic pathway.

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Post-translational Modification

A modification of a protein that occurs after its synthesis, often through the addition of chemical groups. This can alter the protein's structure and function.

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Allosteric Regulation

A type of regulation where a small molecule binds to a protein at a site other than the active site, causing a conformational change that alters the protein's activity.

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Transcriptional Regulation

The control of gene expression, including the initiation and termination of transcription.

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Quorum Sensing

A system used by bacteria to communicate with each other based on population density. It involves releasing and detecting autoinducer molecules, triggering changes in gene expression.

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Autoinducer Molecules

The molecules bacteria release to communicate with each other in quorum sensing. Their concentration increases with population density.

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Regulation of Gene Expression in Quorum Sensing

The process by which the expression of specific genes is controlled in response to changes in the concentration of autoinducer molecules.

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Hawaiian Bobtail Squid Bioluminescence

A symbiotic relationship between a Hawaiian bobtail squid and the bacteria Vibrio fischeri. The bacteria produce light in the squid's light organ to help it camouflage at night.

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Lux System

A model quorum sensing system found in Vibrio fischeri. It controls the production of light by the bacteria.

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Negative control of transcription

A regulatory mechanism that stops or inhibits the transcription of genes.

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Inducer

A molecule that binds to a repressor protein, causing it to change shape and detach from the operator, allowing transcription to proceed.

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Repression

A type of negative control where transcription is inhibited by a signal.

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Repressor protein

A protein that binds to the operator and prevents RNA polymerase from transcribing genes.

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Positive control of transcription

A regulatory mechanism that enhances or allows the transcription of genes.

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Activator protein

A protein that helps RNA polymerase bind to the promoter and initiate transcription.

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Positive control

A type of positive control where an activator protein binds to an upstream region of the gene and promotes transcription.

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Induction

A type of negative control where the repressor is normally bound to the operator, blocking transcription. An inducer molecule binds to the repressor, causing it to detach and allowing transcription to proceed.

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Negative Control

A type of gene regulation where the presence of a specific molecule (the effector) inhibits or represses the transcription of a gene.

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Anabolic Operon (Negative Control)

A type of operon where transcription is repressed in the presence of the end product of the operon, such as the tryptophan synthesis operon.

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Attenuation

A mechanism that controls gene expression by prematurely terminating transcription before the full mRNA molecule is produced.

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Rho protein (rho-dependent termination)

A protein that binds to specific sequences of DNA, called termination sequences, and detaches RNA polymerase from the DNA strand, causing the termination of transcription.

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Rho-independent termination

A mechanism of transcription termination that doesn't require the rho protein. Instead, the RNA transcript forms a hairpin loop structure, causing RNA polymerase to detach from the DNA.

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Structural genes (trp operon)

Genes within the tryptophan operon that code for the enzymes required to synthesize tryptophan (trpE, trpD, trpC, trpB, trpA).

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trpL region (Tryptophan Operon)

A region within the tryptophan operon that contains a sequence of DNA where the ribosome binds to the mRNA transcript to initiate translation.

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What are regulons?

A collection of genes that are regulated by the same system, responding to a common regulatory element (like a sigma factor or regulatory protein).

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What is catabolite repression?

A regulatory mechanism that shuts down genes involved in utilizing various carbon sources when glucose is present. Basically, the cell prioritizes glucose as its primary energy source.

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What is the SOS response?

A multi-gene system that activates DNA repair mechanisms in response to severe DNA damage.

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What is LexA?

A key protein in the SOS response that acts as a repressor, binding to operators of genes involved in DNA repair.

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What is RecA?

A protein that binds to single-stranded DNA, indicating damage, and cleaves LexA, activating DNA repair genes.

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How do sigma factors influence gene expression?

Different sigma factors help RNA polymerase to transcribe different sets of genes.

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What is a repressor protein?

A regulatory protein that binds to a specific DNA sequence, influencing the binding of RNA polymerase and ultimately gene transcription.

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What is sigma 70?

The default sigma factor, responsible for transcribing the majority of genes in the cell.

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What causes bacterial tumbling?

Phosphorylation of CheA triggers a cascade of events that leads to bacterial tumbling, a change in direction.

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How does phosphorylated CheY affect bacterial movement?

CheY, a response regulator protein, binds to bacterial flagella motor proteins, causing a change in the direction of rotation, leading to tumbling.

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What are MCPs and what do they do?

Methyl-accepting chemotaxis proteins (MCPs) are sensory proteins in the bacterial membrane that sense attractants and repellents.

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How does methylation of MCPs affect chemotaxis?

Methylation of MCPs modulates their sensitivity to attractants and repellents, controlling the bacteria's response to chemical gradients.

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What is CheA and what happens when it becomes phosphorylated?

CheA is a sensor kinase that becomes phosphorylated when a repellent is detected.

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What is CheB and what is its role in chemotaxis?

CheB is a phosphatase that removes methyl groups from MCPs, reducing their sensitivity to repellents.

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What is CheZ and how does it affect bacterial movement?

CheZ is a phosphatase that dephosphorylates CheY, reversing the tumbling response and allowing for continued running.

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What is adaptation in chemotaxis?

Adaptation is a process where the sensitivity of MCPs is dynamically adjusted through methylation and demethylation, allowing bacteria to maintain a response to changing environments.

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How do attractants affect the phosphorylation of CheA?

Attractant binding to MCPs decreases the phosphorylation of CheA, reducing tumbling and promoting directed movement towards the attractant.

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How do repellents affect the phosphorylation of CheA?

Repellent binding to MCPs increases the phosphorylation of CheA, increasing tumbling and promoting movement away from the repellent.

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Study Notes

DNA Regulation

  • DNA must be copied to create new cells
  • Transcription converts DNA into working copies for enzymes and structural proteins
  • Not all processes run simultaneously; cell regulation prevents unnecessary functions and cell death

Environmental Conditions

  • Environmental factors like nutrient availability and competition affect gene regulation
  • Cells respond to changes in conditions through specific responses
  • Substrate specificity and metabolism are regulated by environment

Key Cellular Enzymes

  • Constitutive enzymes are always active, preventing cell death
  • Examples include those involved in TCA cycle and ATP synthesis
  • Constitutive genes are housekeeping genes, always expressed

Covalent Modification

  • Enzymes' activity is altered by adding or modifying amino acids
  • Methods include phosphorylation, acetylation, methylation, and glycosylation
  • Conformation changes affect active sites and influence enzyme activity

Allosteric Regulation

  • Small molecules interact with an allosteric site, changing enzyme conformation
  • This might lead to activation (better fit to the substrate) or inhibition (worse fit) of the active site
  • Results from an interaction that is not directly at the active site

Regulating Transcription

  • Energy is conserved through controlling enzyme synthesis to prevent transcription of unnecessary genes
  • The operon, a collection of structural and regulatory elements, controls structural gene expression.

Positive Control

  • A regulatory protein will enhance RNA polymerase binding to the promoter, increasing transcription.
  • RNA polymerase and sigma factor don't bind, activator proteins will help bind

Negative Control

  • Transcription is inhibited by regulatory proteins that block RNA polymerase processes
  • Two types: repression (stopping transcription already in progress) and induction (preventing transcription altogether).

Operon Structure and Control

  • Structural genes are grouped together under one regulatory system.
  • Promoter: DNA sequence where RNA polymerase binds.
  • Operator: DNA sequence where a repressor protein can bind to prevent transcription.

Positive and Negative Control Regulation

  • Positive control uses a regulatory protein to enhance the binding of RNA polymerase to the promoter for increased transcription expression.
  • Negative control utilizes a regulatory protein to prevent RNA polymerase from binding to the promoter, decreasing transcription

Genes and Operons

  • The lac operon regulates lactose metabolism, switching on expression when glucose is depleted.
  • Lactose is better to use than glucose (easier/cheaper) as an energy source
  • Use of lactose expression occurs when glucose is not available, thus transcription occurs to get it in and break it down

Attenuation

  • Transcription can be stopped before termination (transcription is halted before it is completed)
  • Rho-dependent and rho-independent mechanisms are used to end transcription
  • Ribosomes' presence impacts transcription to ensure genes will only be expressed when required

Tryptophan Synthesizing Regulation

  • Genes for tryptophan synthesis are regulated, preventing unnecessary production
  • Attenuation controls tryptophan production based on current levels.

Positive and Negative Control of Transcription

  • Transcription can be either enhanced or suppressed by effector molecules (a chemical/signal) binding to DNA binding proteins.

Quorum Sensing

  • Bacteria communicate with each other through chemical signals, quorum sensing, to coordinate population density-dependent actions.
  • Cells release molecules based on population density to regulate gene expression

Hawaiian Bobtail Squid Bioluminescence

  • Bioluminescence (light production) is regulated to conserve energy
  • N-acyl-homoserine lactone (AHL) regulates it in specific amounts.

No Quorum

  • Lux genes, when they function poorly, do not produce as much light
  • Enzyme (luxI) is present. It produces AHL during the day.
  • The activator protein isn't present thus light is not produced/ made

Chemotaxis

  • Bacteria's response to chemical gradients is chemotaxis.
  • They use chemotaxis proteins to sense chemical gradients to control how they respond to and move toward or away from attractant and repellents

Adaptation

  • Chemotaxis adaptation regulates sensitivity to attractants and repellents based on methylation of certain proteins.
  • Methylation/demethylation changes the sensitivity to attractants/repellents

Two-component regulatory systems

  • The system includes a sensor kinase, which detects stimuli
  • Histidine protein kinases are sensor kinases which add phosphate groups to proteins (phosphate group is a signal)
  • The response regulators regulate transcription based on the signal from the sensory kinase.

Two-Component regulatory systems (additional details)

  • Stimulus outside the cell is detected by sensor proteins (sensor kinase) (HPK)
  • Phosphate group is transferred to the regulator (response) (RR)
  • The regulator controls the gene transcription response to stimulus (short lived response)
  • Re-establishing the original state of the response is crucial for regulating the process
  • Examples include crown gall tumors, and plant bacterial interactions

Other Considerations

  • alternative sigma factors control transcription when the default sigma factor isn't suitable (for instance, in heat, stress, etc.)
  • Regulons are sets of genes coordinately controlled by a single regulatory system for coordinated expression/ action

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Microbiology Topic 8 Regulation PDF

Description

This quiz covers the essential concepts of DNA regulation, including transcription, the influence of environmental conditions on gene expression, and the role of key cellular enzymes. Explore the different mechanisms of enzyme regulation, such as covalent modification and allosteric regulation, to understand cellular function better.

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