What are constitutive genes/housekeeping genes?

Genes that encode these enzymes of basic cellular functions that are regularly transcribed and translated to provide a constant supply of active enzymes.

What does it mean to say genes are regulated?

They are expressed only when needed.

Why must genes be regulated?

To conserve energy and cellular materials.

What genes are present all of the time?

Housekeeping or constitutive genes.

What processes have their genes commonly regulated in bacteria?

-Initiation of transcription -Initiation of translation -Transcription elongation

What molecules help increase the level of specific enzymes?

Inducers.

Enzymes whose level is increased by the presence of small effector molecules are encoded by what?

Inducible genes

What is the most common enzyme in biosynthetic pathways?

Repressible enzymes

What is transcriptional control?

Control of mRNA synthesis.

What is translational control?

Control of protein synthesis.

What is protein activity control?

Control of postransitional modification.

What is an example of an inducer enzyme?

Beta-galactosidase

What are the genes that encode enzymes whose expression levels decrease in presence of pathway end products?

Repressible

What pathways contain inducible enzymes?

Catabolic pathways.

What are transcription factors?

Proteins that regulate gene expression at the level of RNA polymerase binding to the promoter.

What do the domains of transcription factors do?

-interact with an effector molecule -binds to DNA at the promoter region

What is allosteric control?

An effector binding in one domain changing the conformation of another domain.

What domain do transcriptional regulatory proteins?

Helix-turn-helix (HTH)

What is in the HTH domain?

Two alpha-helices separated by a beta-turn.

How do HTH domains recognize specific DNA sequences in the promoter regions?

The HTH places its recognition helix in the major groove to contact the bases.

What is domain for proteins?

A portion of a protein with a specific function.

What is negative transcriptional control?

The binding of a repressor protein to DNA inhibits transcription initiation.

What is a repressor protein?

A DNA-binding protein that inhibits transcription initiation by binding to an operator.

Where is one helix located from the HTH domain?

On the major groove of DNA.

What is positive transcriptional control?

Binding of an activator protein to DNA promotes transcription initiation.

What are activator proteins?

Proteins that promote transcription initiation by binding to DNA.

What is an operator?

A DNA sequence that bacterial repressor proteins bind to.

What is an activator?

A DNA binding protein that promotes transcription initiation.

How are genes arranged in terms of functionally in bacteria?

They line up together on the chromosome.

What is an operon?

A unit that comprises the structural genes that encode enzymes in a single pathway and the upstream regulatory that controls their expression.

How do repressor proteins inhibit the initiation of transcription?

-blocking the binding of RNA polymerase -preventing the movement of RNA polymerase

What system is a lac operon?

Negative control system.

When does the lac operon turn on?

-Lactose is present -There is a lack of carbon and energy sources

How many structural genes are in a lac operon?

3

What do structural genes in bacteria produce?

Polycistronic mRNA

What are the components of a bacterial operon?

-promoter -structural genes -operator

What does lac operon in E. coli control?

Negative transcriptional control of inducible genes

What does lacZ encode?

Beta-galactosidase

What does lacY encode?

lactose permease

What does lacA encode?

beta-galactoside tranacetylase

What are the subunits lac repressor protein is made up of?

4 identical subunits

How does the lac repressor protein inhibit transcription?

-Bends DNA in the promoter region. -Binds to the O1 and another lac operator site.

How is lactose transporter into the E. coli cell?

By the enzyme lactose permease.

What operator site must lac repressor bind to ensure transcription inhibition?

O1

What does beta-galactosidase convert lactose into?

allolactose

What is the inducer of the lac operon?

allolactose

How does lactose enable the activity of the lac operon?

Lactose converts into allolactose. Allolactose binds to the lac repressor This prevents the repressor from blocking the promoter.

What proteins are regulators of lac operon expression?

-lac repressor -catabolite activator protein

What is the catabolite activator protein (CAP)?

A regulatory network that allows E. coli to use glucose over all other carbon/energy sources.

How does the inducer binding affect the repressor?

-Changes the repressor shape -Forces the repressor to lose its ability to bind to the operator sites.

What do the trp operon's genes do?

Encode enzymes needed for tryptophan biosynthesis

When is the trp operon active?

When there is a small presence of tryptophan (trp).

What regulates the trp operon?

trp repressor (TrpR)

What regulates the transcription initiation of the trp operon?

-TrpR -Attenuation

What is attenuation?

The process of regulating trp operon on the level of initiation of TrpR and level of elongation.

Transcription proceeds through what during attenuation?

Transcript leader

What determines the ability for bacteria to terminate transcription?

-Folding pattern of mRNA leader sequence -Coupling of transcription and translation

What is unique about the trp operon leader?

It encodes a small peptide called the leader peptide.

What is the extent of the trp operon leader reach>

The transcription start site to the start codon of the first structural gene.

What makes up the attenuator pause loop?

Pairing of regions 1 and 2

What does the attenuator pause loop do?

It slows down RNA polymerase

What makes up the attenuator terminator loop?

Pairing by regions 3 and 4

What follows the attenuator terminator loop?

Poly-U region

What is the attenuator terminator loop similar to?

The intrinsic transcription terminators.

What does the attenuator antiterminator loop do?

-Prevents the formation of the terminator loop -Prevents the formation of the pause loop

What is the attenuator antiterminator loop made up of?

Pairing regions 2 and 3.

How does the attenuator antiterminator loop form in the transcript with little tRNA-Trp is present?

The ribosome stalls but RNA polymerase keeps moving along the transcript.

What is the order of events in the regulation of trp operon of E. coli when charged tRNA-Trp is ABUNDANT in the cell?

1. RNA polymerase initiates transcription at the promoter 2. A ribosome initiates translation of the leader peptide gene 3. The leader peptide is synthesized efficiently 4. The terminator loop forms in the transcript 5. RNA polymerase falls off the template 6. Translation terminates at the UGA stop codon.

What is the order of events in the regulation of trp operon of E. coli when the charged tRNA-Trp is LOW in the cell?

1. RNA polymerase initiates transcription at the promoter 2. A ribosome initiates translation of the leader peptide 3. The ribosome stalls, in need of charged tRNA-Trp. 4. The antiterminator loop forms in the transcript 5. RNA polymerase transcribes the structural genes of the trp operon

What determines whether or not the trp operon genes should be transcribed?

Process of attenuation measuring the speed with which ribosome translates the leader peptide.

Which regulator process of trp operon has the most negative effect on transcription?

Repression/repressor genes.

What are riboswitches?

Genetic regulatory features that can fold into different patterns based upon the binding of an effector molecule to the mRNA.

What causes transcription termination in attenuation?

A fast-moving ribosome in the leader peptide.

The more negative effect a regulatory process has on termination, the more _____.

fold decreases

What determines the pattern of folding for riboswitches?

Direct binding of an effector molecule to mRNA.

What does the folding pattern of transcriptional riboswitches?

Transcriptional terminator

What determines the configuration of the leader region of mRNA?

Effector binding to the mRNA.

What level do riboswitches usually block translation?

Initiation

Translational riboswitches inhibit _____ binding at the Shine-Dalgarno sequence.

ribosomal

What is the name of RNA molecules that are not mRNA, tRNA, or rRNA?

small RNA/noncoding RNA

When does alternate configuration result in expression of the operon?

When the effector is not present in the cell.

Where are trans-encoded sRNA synthesized from?

Genes at sites distinct from their target.

Where are cis-encoded sRNA synthesized from?

The non-template strand of their target

Where are the effector-binding from the riboswitches?

At the 5' end of mRNA.

What are sRNAs?

Small RNAs

What are of the 2 main types of mRNA-targetting sRNAs?

Cis-acting and trans-acting sRNAs

Cis-acting small RNAs control the expression of what?

One gene

How does mRNA-targetting sRNA regulater gene expression?

-Interferes with ribosome binding -Interferes with mRNA moving through the ribosome

What are antisense RNAs?

Sequences of RNA that are complementary to a mRNA sequence and can either silence or promote mRNA translation.

What does trans-acting sRNAs control?

Multiple genes

What is a global regulatory protein?

A protein that activates or represses multiple operons or genes.

What do two component signal transduction systems link to?

Environmental conditions outside the cell and gene expression.

What is a regulon?

A collection of genes and operons under the control of a single global regulatory protein.

Where is the sensor kinase in the diderm bacterium located?

In the plasma membrane, with its sensor portion in the periplasm.

What are the two components of the signal transduction system?

Sensor kinase and response regulator

What happens in response to osmotic change in the complex genetic regulation?

Phosphorylated OmpR activates expression of: -small RNAs -Certain structural genes

What does EnvZ detect?

Osmolarity in the periplasm

What are phosphorelay signal transduction systems?

Signaling pathways in which two proteins or more participate in the transfer of phosphoryl groups.

What kind of protein is a sensor kinase?

A transmembrane protein.

What are the steps for signal transduction?

1. Sensor kinase detects a change in the environmental conditions 2. Kinase phosphorylates itseld 3.Kinase transfer phosphate group to its response regulator 4. Response regulator has conformational change 5. Regulator binds to DNA to alter gene expression

What does the response to osmolarity use in E coli?

-two component signal transduction -small RNAs

What does OmpR do after receiving a signal from EnvZ?

its DNA binding domain changes shape

Where does signal transduction systems transfer phosphoryl groups to?

From one protein to another

What can immediately change the expression of many bacterial genes?

Producing alternate versions to sigma factors.

Each sigma factor has its own set of what?

Promoter consensus sequences

What do sigma factors do?

Direct RNA polymerase to the specific promoter sequence of particular genes.

What will produced sigma factor 32?

High temperature stress

What are secondary messengers?

Small molecules produced inside of cells in response to an external signaling event

What are examples of second messengers?

-ppGpp -cAMP -cyclic dimeric GMP

What is catabolite repression?

Inhibition of the synthesis of multiple catabolic enzymes by a preferred carbon and energy source e.g. glucose.

What is the role of catabolite activator protein?

Activates specific operons when glucose is not available

What binds to catabolite activator protein to cause form changes?

cAMP/ cyclic AMP

What kind of system is catabolite repression?

A positive regulatory system.

What happens after CAP binds to the recognition site?

CAP binds DNA through HTH motif

What does adenyl cyclase enzyme convert ATP into?

cAMP and inorganic PP

What is inversely proportional to the activity of adenyl cyclase?

Glucose levels

When is adenyl cyclase active?

In conditions of little to no glucose

What causes bacterial cells to give out a stringent response?

Nutritional stress

What happens during a bacterial stringent response?

-increased transcription of amino acid synthesis genes -decreased synthesis of tRNA and rRNA

What is wasteful for cells to produce during a bacterial stringent response?

-Ribosomal proteins -tRNAs

What enzyme produces ppGpp when uncharged tRNAs enter the ribosomal A site?

ReIA

What does phosphodiesterase do?

catalyzes the degradation c-di-GMP

What 2 enzymatic activites determine the level of c-di-GMP in a cell?

1. Diguanylate cyclase 2. phosphodiesterase

What are the cellular effects of ppGpp production?

-promoter open complexes are destabilized -DNA primase in inhibited -translation factors are inhibited

What is found in the cytoplasmic domains of membrane sensors?

-Diguanylate cyclase (DGCs) -Phosphodiesterases (PDE)

What is the order of events for pseudomones motile to sessile transition?

1. Pseudomonas flagellum hits a solid object 2. A membrane sensor activates its DGC domain 3. c-do-GMP concentration rises in the cell 4. Genes encoding adhesins are activated 5. The cells adheres to the surface of the substrate.

What prevents lactose import when high glucose levels are present?

Dephosphorylation enzyme IIA

Quorum sensing can control production of what?

Light/bioluminescence

What does the luxl gene produce when AHL binds to it?

LuxR

What are the order of events of quorum sensing response for vibrio harveyi?

1. Autoinducing signals are at low levels in the environment 2. Sensor kinases autophosphorylate 3. Phosphate grops are transferred to LuxU and LuxO 4. Trans-acting small RNAs synthesize and bind to luxR mRNA 5. Lux operon is not expressed

What is the default position of an inducer gene?

Off

What is the default position of a repressible gene?

On

What is a modulon?

An operon network under control of a common global regulatory protein but individual operons are controlled separately by their own regulators.

What is diauxic growth?

Biphasic growth response in which microorganisms, when exposed to 2 nutrients, uses one for growth and then have to alter their metabolism first before consuming the other.

What regulation is catabolic repression?

Positive regulation.

What are microRNAs

Base pair with mRNA to make it double-stranded.

What happens when RNA becomes double stranded?

It's enzymatically destroyed; prevents production of proteins.

What do methylating nucleotides do?

Turn genes off temporarily

What are the types of mutations?

-Base substitution -Silent -Missense -Nonsense -Frameshift -Neutral -Conditional

What are silent mutations?

One that doesn't change an organism proteins or phenotype even though the DNA base sequence has been changed.

What are missense mutations?

A single base substitution in DNA that changes a codon for 1 amino acid into a codon of another.

What are nonsense mutations?

One that converts a sense codon to a nonsense/stop codon.

What are neutral mutations?

A missense mutation that does not affect the function of the protein. So, the same type of amino acid has been swapped with one another.

What are frameshift mutations?

Arises from losing or gaining a base or DNA segment leading to a change in the codon reading frame. This causes amino acids in the proteins to be changed as well.

What are conditional mutations?

Mutations with phenotypes that are expressed only under certain environmental parameters.

What are chemical mutagens?

Chemicals that disrupt the DNA structure.

What are induced mutations?

Mutations caused by agents that directly damage DNA.

What are base analogues?

Incorporated into a growing polynucleotide chain during replication to exhibit base-pairing properties different from the bases they replace, causing mutation.

What are intercalating agents?

Planar molecules that insert in-between stacked bases of the helix to distort the structure.

What are DNA-modifying agents?

Changes a base to cause a mis pair mutation.

What causes thymine dimers?

UV radiation.

What do ionizing radiation cause?

Formation of ions that can oxidize nucleotides and break deoxyribose-phosphate backbone.

What is the Ames test?

A biological assay to detect mutation potential in chemical compounds. It uses bacteria to test this out.