Genetics Ch 16

operator site (O1)

- Next to the promoter

•Translational repressors inhibit translation in one of two ways

-1. Binding next to the Shine-Dalgarno sequence and/or the start codon •This will sterically hinder the ribosome from initiating translation • -2. Binding outside the Shine-Dalgarno/start codon region •They stabilize an mRNA secondary structure that prevents initiation

The lac repressor must bind to

-It can bind to O1 and O2 , or to O1 and O3 •But not O2 and O3 -If either O2 or O3 is missing, maximal repression is not achieved

reversible modifications that transiently affect protein function

-Phosphorylation (-PO4) -Acetylation (-COCH3) -Methylation (-CH3)

•irreversible covalent modification to amino acids

-Proteolytic processing -Attachment of prosthetic groups, sugars, or lipids

•The possible hairpin structures are

-Region 1 and region 2 -Region 3 and region 4 -Region 2 and region 3 -If Region 1 binds to region 2, then region 3 can bind to region 4 -If region 1 does not bind to region 2, then region 2 can bind to region 3 and region 4 can not bind to region 3

Jacob and Monod

1950s identified a few rare mutant strains of bacteria with abnormal lactose adaptation due to lacl gene defect -resulted in the constitutive expression of the lac operon even in the absence of lactose -The lacI- mutations mapped very close to the lac operon concluded that the lacl- mutation eliminates the function of the lac repressor -The repressor from the F' factor can diffuse and turn off the lac operon on the bacterial chromosome

•feedback inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway. •The final product in a pathway often can inhibit the an enzyme that acts early in the pathway •Enzyme 1 is an albsteric enzyme, which means it contains two different binding sites -Catalytic site à binds substrate -Regulatory site à binds final product of the pathway When the concentration of the final product becomes high it will bind to enzyme 1, inhibiting enzyme 1

Binding of the lac repressor to two operator sites requires

DNA to form a loop -A loop in the DNA brings the operator sites closer together •This facilitates the binding of the repressor protein

operator site (O2)

Downstream in the lacZ coding region

When both glucose and lactose are absent, the highest rate of transcription occurs?

FALSE

Riboswitches

Folded RNAs that act as switches regulating protein synthesis in response to environmental conditions -RNA can exist in two different confirmations •One confirmation active •One confirmation inactive -Switch from one confirmation to the other relies on a small molecule •control for -Transcription -Translation -RNA stability -Splicing]

the formation of the 3-4 stem-loop causes

RNA pol to terminate transcription at the end of the trpL gene

operator site (O3)

Slightly upstream of the CAP site

•catabolite repression •

System of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose. •This form of genetic regulation involves a small molecule, cyclic AMP (cAMP) -It is produced from ATP via the enzyme adenylyl cyclase cAMP binds an activator protein known as the Catabolite Activator Protein (CAP

-trpL

The first gene in the trp operon •It encodes a short peptide termed the Leader peptide •The RNA can form three different hairpin structures •Which structures form depends on how fast translation of the leader peptide occurs •Leader peptide transcript has several trp codons, how fast it is translated depends on how much trp is in the cell •Which hairpins form controls the transcription of the rest of the operon

lac Operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli allows a bacterium to coordinately regulate a group of genes encoding proteins that are involved in a common process

trpR

a gene that produces a repressor protein •Repression is achieved when the amino acid tryptophan binds to the repressor protein • •Complex then binds to operator region to block transcription

a regulatory protein which increases the rate of transcription.

activator

The lac repressor is inactivated by binding to which of the following?

allolactose

inhibitors

bind to activators and prevent them from binding to DNA activators are repressible

Corepressors

bind to repressors and cause them to bind DNA and inhibit transcription repressors are repressible

The cAMP-CAP complex

binding of cAMP to CAP. binds to CAP site. increases rate of transcription. •is inducible and under positive control -The cAMP-CAP complex binds to the CAP site near the lac promoter and increases transcription • •In the presence of glucose, the enzyme adenylyl cyclase is inhibited -This decreases the levels of cAMP in the cell •Therefore, cAMP is no longer available to bind CAP -Transcription rate decreases

a small effector molecule that causes transcription to increase.

inducer

Which of the following best describes regulation of the lac operon?

inducible, under negative and positive control

The trp operon

is involved in the biosynthesis of the amino acid tryptophan

Which gene is responsible for producing the protein that converts lactose to allolactose?

lacZ

Which of the following is not part of the lac operon?

lacl

A sequence of bases that provides a binding site for a repressor protein

operator

group of two or more genes under the transcriptional control of a single promoter

operon

enzyme adaptatation

particular enzyme appears in the cell only after the cell has been exposed to the enzyme's substrate

A sequence of bases that signals the beginning of transcription

promoter

synthesis of antisense RNA

regulates translation by synthesizing an RNA strand complementary to mRNA

A regulatory protein that binds to the DNA and inhibits transcription

repressor

Osmoregulation

the ability to control the amount of water inside the cell -The protein ompF in E. coli is important in osmoregulation •ompF protein is preferentially produced at low osmolarity -At high osmolarity its synthesis is decreased -The micF transcript is antisense to the ompF transcript •Binds to and inhibits translation of ompF

What is the gene responsible for attenuation in the trp operon?

trpL

Operons involved in catabolism are

typically inducible

Operons involved in anabolism are

typically repressive •The inhibitor or corepressor is the small molecule that is the product of the operon

. Cis-effect or cis-acting element

•A DNA sequence that must be adjacent to the gene(s) it regulates •Mediated by sequences that bind regulatory proteins •Example: The lac operator a mutation in a cis-acting factor is NOT complemented by a second normal gene

inducers

•Bind activators and cause them to bind to DNA •Bind repressors and prevent them from binding to DNA These genes are INDUCIBLE

Unregulated/constitutive gene expression

•Essentially constant levels of expression •Frequently for proteins that are continuously necessary for the survival of the organism

Regulated gene expression

•Expression may be increased or decreased according to the demand for the gene product •Encoded proteins will be produced only when required

Trans-effect

•Genetic regulation that can occur even though DNA segments are not physically adjacent •Mediated by genes that encode regulatory proteins •Example: The action of the lac repressoron the lac operon -A mutation in a trans-acting factor is complemented by the introduction of a second gene with normal function

-High trp

•Region 1 and region 2 form •Region 3 and region 4 also form - acts as a rho independent transcriptional terminator

-Low trp

•Region 2 and region 3 form

•Attenuation

•Short transcript produced that is translated into a short peptide called the leader peptide •Leader peptide has several codons for the amino acid whose biosynthesis is the result of the expression of the operon •If enough of the amino acid is still present in the cell, rest of operon not expressed •occurs in bacteria because of the coupling of transcription and translation • •During attenuation, transcription actually begins but it is terminated before the entire mRNA is made -A segment of DNA, termed the attenuator, is important in facilitating this termination -In the case of the trp operon, transcription terminates shortly past the trpL region -Thus attenuation inhibits the further production of tryptophan

positive transcriptional regulation

•activator - Increase transcription

negative transcriptional regulation

•repressor - Inhibit transcription

Translational Regulation (bacteria)

•translation of mRNA is regulated by the binding of proteins • •A translational regulatory protein recognizes sequences within the mRNA • •In most cases, these proteins act to inhibit translation -These are known as translational repressors