Chapter 14-Regulation of bacterial cellular processes

positive control of an inducible gene

*Activator + inducer the activator protein is only able to bind DNA and activates transcription when it interacts with inducer if the activator protein does not interact with the inducer, transcription will not happen

positive control of a repressible gene

*Activator + inhibitor the activator binds DNA and promotes transcription unless the inhibitor is present. when the inhibitor is present the activator undergoes a conformational change that prevents it from binding DNA; this inhibits transcription

Which two of the following are encoded by the lac operon?

3 structural genes, lacI

Which two of the following are characteristics of the lac repressor protein?

4 identical subunits (tetramer) -Each monomer has a helix-turn-helix domain

LuxR

A DNA binding transcriptional activator on luxCDABE operon that encodes bioluminescence proteins - needs high concentrations of autoinducer

Two-component signal transduction system

A message relay system composed of a sensor kinase protein and a response regulator protein that regulates gene expression in response to external stimuli -ex: EnvZ/OmpR system

If transcription and translation were not coupled in bacteria, what type of regulation would be affected?

Attenuation

positive transcriptional control

Control of transcription by an activator protein. When the activator is bound to the activator-binding site, the level of transcription increases.

restriction modification system (innate)

DNA destruction system; only effective against double-stranded DNA viruses -microbes produce methylase enzymes that modify nitrogenous bases in short DNA strands -restriction endonucleases (REs): hydrolyze phosphodiester bonds of DNA that has not been methylated ---which allows the microbe to protect it's own DNA by adding methyl groups ---if unmethylated DNA enters the cytoplasm, they are destroyed by restriction endonucleases

Which three of the following are characteristics of the attenuator terminator loop?

Immediately followed by a poly-U region Formed by the pairing of regions 3 and 4 Similar to factor-independent transcription terminators

negative transcriptional control

Inhibition of transcription by a repressor protein. When bound to the repressor-binding site, transcription is inhibited.

In the sporulation initiation pathway of Bacillus subtilis, ____ acts as a sensor kinase Senses nutrient starvation Autophosphorylates a specific histidine residue

KinA

Transcription of the trp operon is controlled by which two of the following mechanisms?

Premature termination through attenuation Repressor protein inhibits initiation

Which four of the following are characteristics of the attenuator antiterminator loop?

Prevents the generation of the pause loop Formed by the pairing of regions 2 and 3 Prevents the generation of the terminator loop Located in the leader region

Which two of the following are mechanisms that can control transcription of the trp operon by way of the attenuator region?

Ribosome stalls in region 1 due to low tryptophan levels - antiterminator loop forms Ribosome translates at normal rate due to adequate tryptophan levels - pause and terminator loops are formed

Which two of the following are characteristics of the attenuator pause loop?

Slows down RNA polymerase; Formed by the pairing of regions 1 and 2

attenutation

Termination of transcription elongation before RNA polymerase enters the first structural gene of an operon -transcription is terminated in the leader

HAI-1

V. harveyi autoinducer -homoserine lactone -synthesized by LuxM gene

structural gene

a gene that codes for nonregulatory polypeptides ( such as an enzyme, protein, or RNA) rather than serving as a regulator

repressible genes

a gene that is regulated by a corepressor or inhibitor, which are small effector molecules that cause transcription to decrease -in anabolic/biosynthetic pathways -makes repressible enzymes that are not present if the end product of the pathway is available

___ protein is a DNA-binding protein that promotes transcription initiation.

activator

inducible genes

express inducible enzyme; gene expression is turned on by the presence of some substance. Regulate catabolic pathways. -enzyme levels rise in the presence of an inducer (small effector molecule)

constitutive genes

expressed continuously by the cell

DNA-bound activator proteins promote transcription initiation by

facilitating RNA polymerase binding

sensor kinase

protein that spans the plasma membrane and internal part of the cytoplasm so that it can detect outside changes and communicate them inside

response regulator

receives a signal from the sensor kinase and undergoes a conformational change so it can interact with other molecules by: -forming homodimers that bind to DNA and activate or repress transcription initiation -interact with enzymes and proteins in the global network

The trp operon of E. coli is regulated by attenuation. If tryptophan levels are high in the cell, ___

regions 3 & 4 of the mRNA will base pair and transcription terminates

methyleterase CheB

removes methyl groups from MCP

CRISPR/Cas system (adaptive immunity)

used to recognize future viral attacks -found in 50% of bacterial and 90% of archaeal genomes stage 1 function- adaptation: after viral infection, viral genome pieces are added at the end of the genome close to the cas genes stage 2: expression: CRISPR region is transcribed to make a large RNA with all repeats and spacers and cas proteins mature it into crRNAs (each consisting of 1 repeat and 1 spacer) ---crRNA associate with viral DNA or mRNA which leads to destruction stage 3: interference: crRNA prevents viral multiplication -constitutively transcribed at lower levels quorum sensing signals CRISPR/cas expression

Following the partitioning of the mother cell and the forespore, the first sigma factor to be found in the forespore is ____.

σF

In E.coli regulatory pathways, which molecule functions to ensure that glucose is used as the preferred carbon and energy source?

CAP

Which statement best describes the result of CAP binding to the CAP recognition site?

CAP bends the DNA within two helical turns

when glucose is present but not lactose

CAP is inactive because cAMP does not bind, lac repressor binds to the operator and inhibits transcription

cells run (counterclockwise) when attractants bind MCPs and ___ is inactive

CheA

Which type of motion results from the interaction of activated CheY with flagellar motor protein?

Clockwise rotation (tumble)

The two types of response regulators in two-component signal transduction systems are

DNA-binding proteins Proteins that control enzymes

housekeeping genes

a gene that is transcribed continually because housekeeping enzymes are needed at all times and in all cells

In the absence of lactose, the lac repressor is __________.

active and can bind to the operator

Which of the following is the inducer of the lac operon?

allacotose

A repressor protein synthesized in its inactive form is referred to as a(n)

aporepressor; activated by a corepressor

Transcription of the trp operon is regulated at the level of initiation by the trp repressor, and at the level of elongation by a process called

attenutation

for the lac operon, transcription levels are highest when lactose is _____ and glucose is ____

available, NOT

The lac repressor protein inhibits transcription by ____.

bending DNA in the promoter region

activator proteins

bind to the activator binding site (upstream from the promoter) and makes the promoter a better target for RNA polymerase or interacts with RNA polymerase's alpha and beta subunits to facilitate binding

repressor proteins

bind to the operator (downstream of promoter) and block RNA polymerase from binding

An active repressor protein _________.

binds to the DNA molecule and prevents transcription

when neither lactose nor glucose are present

cAMP binds to CAP and activates it, activated CAP binds to the CAP operon binding site, the lac repressor binds to the operator site and transcription is blocked

Types of second messengers

cAMP, ppGpp, pppGpp, GMP, c-di-AMP, cGMP, ATP, ppTpp

When in a complex with ________, the CAP protein binds to the CAP site and ________ the expression of the lac operon.

cAMP; switches on

The global control of operons encoding enzymes for the catabolism of carbohydrates that must be modified prior to entering glycolysis is referred to as

catabolite repression

The positive regulatory system called ____ prevents the expression of genes encoding proteins necessary for the utilization of sugars other than glucose when adequate supplies of glucose are present.

catabolite repression

MCP (methyl-accepting chemotaxis proteins)

chemoreceptors that bind to 2 component signal transduction system that control flagellar rotation; in the plasma membrane, with parts exposed on each side

CAI-2

cholerae autoinducer -product of CqsA enzyme (made by vibrios genus)

lac repressor protein

inhibits transcription when lactose is absent (negative control) -binds to O1 operator site and either 03 or 02 to make a DNA loop transcription happens when an inducer (allolactose) binds to the lac repressor

Negative transcriptional control of inducible genes (i.e., turned "off" until turned "on")

lac operon

AHL is synthesized by the enzyme AHL synthase, encoded by the gene

luxI

CheR and CheB

measure methylation of MCPs at different times to remember attractant concentration

Cellular DNA is _____; viral DNA is not.

methylated

The "modification" component of a restriction-modification system involves _____ in DNA.

methylation of nitrogenous bases

The lac operon is considered a _____ control system because it is considered to be turned off until lactose is present.

negative

The trp operon is a ____ control system because it is turned off by a repressor protein when not needed.

negative

sigma F and sigma B

only found in forespore

sigma E and sigma K

only found in mother cell

Bacterial repressor proteins bind to a DNA sequence called the

operator

factors that control sporulation

phosphorelay posttranslational modification of proteins, transcription initiation regulatory proteins, and alternate sigma factors

CheY

response regulator

SpoOA

response regulator protein -controls sporulation initiationf Activates genes required for sporulation Bacillus subtilis Is phosphorylated by SpoOB Alters the expression of about 500 genes-"master regulator"

CheA

sensor kinase

Sigma factor σF is encoded by the gene

sigF

transcriptional regulatory proteins

small DNA binding proteins that form dimers and bind to palindromes (short, inverted sequences of bases in DNA) -DNA binding protein portion (small portion of this protein) interacts with the palindrome -large portion of the protein interacts with effectors

The ___response is observed in many bacteria that are starved for amino acids.

stringent

Environmental signals like oxygen levels or light are detected by sensory domains on diguanylate cyclase enzymes, and these enzymes act to _____.

synthesize c-di-GMP

trans-encoded sRNA

synthesized at other sites that don't encode their mRNA target but they still have complementary regions; accompanied by their Hfq chaperone

cis-encoded sRNA

synthesized from the sense strand of the gene that creates the mRNA target

adenyl cyclase enzyme

synthesizes cAMP from ATP when glucose is unavailable

when lactose and glucose are both present

the inducer allolactose will bind to and inactivate the lac repressor protein, cAMP will not bind to CAP (inactive) so transcription is inhibited because CAP can't bind to the CAP site on the operon

mycotoxins

toxins produced by fungi; contaminate food, crops, water

When is adenyl cyclase active?

Little or no glucose is available

inducers

Small effector molecules whose presence increases the level of specific enzymes

Aporepressors are activated by the binding of a(n)

corepressor

When E. coli is grown on medium containing glucose and lactose, a two phase pattern called ____ growth is seen as the glucose is preferentially metabolized.

diauxic

regulated genes

encodes enzymes that are only needed at certain times -ex: B-galactosidase enzyme (catalyzes the hydrolysis of lactose to glucose and galactose)

In the early steps of sporulation, sigma factors σF and σE are primarily involved in controlling genes necessary for the process of ____.

engulfment

AI-2

fluoroborate: small molecule that contains a boron atom -made by LuxS gene -both gram +/-

Regulatory systems that simultaneously control the expression of multiple operons or pathways are referred to as ________.

global regulatory systems; ex CAP

riboswitches

regulatory sequences in 5' untranslated mRNA leader that act as switches regulating protein synthesis in response to environmental conditions -small effector molecules binds to the mRNA to stop transcription -can fold into different patterns based upon the binding of an effector molecule to the mRNA. -This type of regulation is used by Gram-positive bacteria to regulate amino acid-related genes.

The nucleotide sequence that encodes the leader sequence of the trp operon is ____.

trpL

The stringent response is regulated by the second messenger _____.

guanosine tetraphosphate and pentaphosphate (ppGpp)

The "restriction" component of a restriction-modification system involves _____ in DNA.

hydrolysis of the phosphodiester bond

The mechanism to synthesize cAMP when glucose is absent involves the system for _____.

phosphorylating glucose as it enters the cell

alarmones

ppGpp/pppGpp; respond to nutritional stress

CAP (catabolite activator protein)

regulates the lac operon in response to the presence or absence of glucose; works alongside with the lac repressor

when lactose is present but not glucose

the inducer allolactose will bind to and inactivate the lac repressor protein, then cAMP will bind to CAP to activate it and transcription will procede

As a general rule, Gram-negative bacteria use riboswitches to regulate the ____ of mRNA, and Gram-positive bacteria use riboswitches to regulate ____ termination.

translation, transcription

The intracellular level of cAMP depends on the state of a protein that functions in the phosphoenolpyruvate:sugar phosphotransferase system (PTS).

true

True or false: The ara operon is an example of both a positive and negative control system.

true

as internal AHL concentration increases, AHL activates LuxR which increases LuxI gene transcription whose products help bioluminescence

true

In E. coli, the production of proteins called ___ are controlled by the EnvZ/OmpR two-component signal transduction system.

porins

negative control of a repressible gene

*Repressor + corepressor (usually a product of the biosynthetic pathway like an amino acid) in the absence of a corepressor, the aporepressor (inactive repressor) is unable to bind DNA and transcription will occur. when the corepressor interacts with the repressor, the repressor is able to attach to DNA and transcription is blocked. -ex: trp operon

negative control of an inducible gene

the repressor protein is active/binds to promoter and prevents transcription when the substrate of the pathway is unavailable -inducible genes encode for enzymes in catabolic pathways the repressor protein is inactivated by the inducer and transcription will happen ex: lac operon