chapter 14 prokaryotic gene regulation

conditions, constitutive, constant, necessary, required

• regulation of expression introduction

  • the term gene regulation means that the level of gene expression can vary under different ….

  • genes that unregulated are termed ….

    • they have essentially … levels of expression

    • frequently, these genes encode proteins that are continuously ….. fort the survival of the organism

  • the benefit of regulating genes is that encoded proteins will be produced only when …..

metabolism, environmental stress, cell division, any, points, disease

• gene regulation is important for cellular processes:

  • 1) …

  • 2) response to … …

  • 3) … ….

• regulation can occur at … of the … on the pathway to gene expression

• aberrant regulation can lead to ….

lac, trp

• specific examples of transcriptional regulation in prokaryotes:

  • …. operon

  • …. operon

initiation, increased, decreased, regulatory, repressors, dna, inhibit, negative, activators, dna, increase, positive, 2, small effector, dna, small effector, regulatory, not

• transcriptional regulation

  • the most common way to regulate gene expression in bacteria is by influencing the … of transcription

    • the rate of rna synthesis can be … or …

  • transcriptional regulation involves the actions of 2 main types of … proteins

    • …. → bind to …. and … transcription (.. control)

    • … → bind to … and increase …. (… control)

  • regulatory proteins have … binding sites

    • one for a … … molecule

    • the other for …

  • … …. molecules affect transcription regulation by binding to … proteins but …. to dna directly

small effector, increase, activators, cause, repressors, prevent, inducible

• inducible genes: activator proteins, inducer molecules

  • inducers are … … molecules that … transcription rates

    • they can function in 2 ways:

      • bind …. and … them to bind to dna

      • bind …. and …. them from binding to dna

    • genes that are regulated in this manner are termed ……

activator, inducer, activator, dna, transcription

• inducible genes: activator proteins, inducer molecules

  • this … protein cannot bind to the dna unless an …. is present

  • when the inducer is bound to the activator protein, this enables the … protein to bind to the … and activate ….

absense, repressor, transcription, presence, conformational, inhibits, repressor, dna, proceeds

• inducible genes: repressor proteins, inducer molecules

  • in the … of the inducer, this …. protein blocks …

  • the … of the inducer causes a …. change that … the ability of the … protein to bind to the …

  • transcription ….

small effector, repressors, inhibit, activators, prevent, repressible

• repressible genes: repressor/copressor proteins, inhibitor molecules

  • corepressors are … … molecules that bind to … in order to …. transcription

    • inhibitors bind to .. and … them from binding to dna

    • genes that are regulated in this manner are termed …..

absence, repressor, not, occur, corepressor, repressor, conformational, repressor, bind, inhibit

• repressible genes: repressor/corepressor proteins, inhibitor molecules

  • in the … of a corepressor, this …. protein will …. bind to the dna

  • therefore, transcription can …

  • when the …. is bound to the … protein, a … change occurs that allows the … to … to the dna and …. transcription

contiguous, bacterial, single mrna, common

• bacterial operons

  • operon: a group of … genes in a … chromosome that are transcribed into a … … to perform a …. function

regulatory, structural, one promoter, polycistronic mrna, coding, structural, bacterium, regulate, proteins, common, promoter, terminator, structural, operator

• the lac operon

  • an operon is a … unit consisting of a few … genes under the control of … …

    • an operon encodes a …. … that contains the …. sequence for 2 or more … genes

    • this allows a … to coordinately regulate a group of genes that encode proteins with a …. functional goal

  • an operon contains several important dna sequences

    • ….

    • …

    • …. genes

    • ……..

glucose, lactose, not, lactose, cell, beta, galactosidase, glucose, galactose, high, beta, galactosidase, present, inducer, allolactose

• lac operon big picture

  • e. coli prefers to metabolize …. to …

  • if glucose is … present:

    • … is transported into the …., where the enzyme ..-… cleaves it to produce … and …

  • …. levels of ..-…. only when lactose is ..

  • lactose is an …

    • ….. = modified form of lactose

substrate, lactose, high, sugar

• enzyme adaptation

  • a particular enzyme appears in the cell only after the cell has been exposed to the enzyme’s ….

  • enzymes for … metabolism are only present at … concentrations when it is needed as a …. source

beta, galactosidase side, small, allolactose, small molecule

• allolactose

  • …-… …. reaction

    • a …. amount of lactose is converted to …

  • functions as a .. .. effector

lactose, z, beta, gal, cleaves, y, lactose permease, transport, a, galactoside transacetylase, modifies

• components of lac operon

  • purpose: to metabolize …

  • structural genes:

    • lac … = …-… (… lactose

    • lac…. = … … (required for lactose … into the cell)

    • lac … = … … (covalently … lactose)

lacI promoter, polymerase, lacI gene, repressor, cap, catabolite activator protein, lacP, promoter, polymerase, laco, operator, lac repressor protein

• components of the lac operon

  • regulatory proteins:

    • … …. - … binds

    • … … - encodes the ….

    • … site - where the .. .. … binds

    • ….: lac … - where the … binds

    • …: …. - where the .. .. .. binds

not, operon, promoter, i, constitutively, low, lac repressor protein, tetramer, small, repress

• components of the lac operon:

  • the lacI gene

    • …. considered part of the lac operon

    • has its own …, the … promoter

    • … expressed at fairly … levels

    • encodes the .. .. …

      • functions as a …

      • only a … amount of protein is needed to repress the lac operon

transcriptionally, lac repressor protein, inducible, negative, allolactose, lac repressor, inactivates, activator, catabolite activator protein, cAMP, low glucose

• the lac operon is regulated by a repressor protein

  • the lac operon can be … regulated

    • 1) by the .. .. ..

      • an …, … control mechanism

      • the inducer is …., which binds to the .. .. and … it

    • 2) by an … protein

      • .. … .. (CAP)

      • requires … and .. …

allolactose, inducer, lac repressor, repression, absence, repressor, tightly, operator, inhibiting, polymerase, transcribe, operon

• no lactose in the environment = no … = no … present

• lac operon is inhibited by the .. .. protein = …

• picture:

  • in the … of the inducer allolactose, the .. protein is … bound to the .. site, thereby … the ability of rna … to … the ….

allolactose, inducer present, inactivated, induced, structural, expression, allolactose, repressor, conformation, repressor, prevents, operator, polymerase, operon

• lactose in the environment = … = … .. = repressor ….

• lac operon is … and … genes are made = … of lac operon

• picture:

  • when … is available, it binds to the …

  • this alters the .. of the … protein, which … it from binding to the … site

  • therefore, rna … can transcribe the ….

small, allolactose, beta, galactosidase, repressor, fall, operator, proteins, uptake, metabolism, lactose, depleted, decrease, released, repressor, operator, degraded, not, small

• the cycle of lac operon induction and repression - never totally shuts off

  • 1) when lactose becomes available, a … amount of it is taken up and converted to … by …-…

    • the allolactose binds to the … causing it to … off the .. site

  • 2) lac operon … are synthesized

    • this promotes the efficient … and …. of …

  • 3) the lactose is …

    • allolactose levels ….

    • allolactose is .. from the …, allowing it to bind to the … site

  • 4) most proteins involved with lactose utilization are …

• repressor does … completely inhibit transcription, so a very … amount of the lac operon proteins are made

laci, laci-, constitutive, lac operon, absence, lac operon

• discovering that the lacI gene encodes a repressor gene

  • in the 1950s, jacob, monod, pardee identified a few rare mutant strains of bacteria with abnormal lactose metabolism

  • 1 type of mutant involved a defect in the … gene

    • it was designated …

    • it resulted in the … expression of the … … even in the … of …

    • the … mutations mapped very close to the … …

z, import, not, y, not, i, beta, galactoside, z, galactoside permease, y, constitutively

• lac operon mutants isolated in screen

  • lac .. mutant - cell could .. lactose but .. cleave it

  • lac .. mutant - cell could … import lactose

  • lac … mutant - cell makes ..-… (lac …) and .. … (lac …)

    • …. expressed

catabolite repression, lactose, glucose, glucose, catabolite repression, lactose, depleted, alleviated, expressed, 2, bacterium, diauxic growth

• the lac operon is also regulated by an activator protein

  • the lac operon can also be transcriptionally regulated by … …

  • when exposed to both … and ..

    • e. coli uses … first, and … … prevents the use of …

    • when glucose is …., catabolite repression is … and the lac operon is ..

  • the sequential use of … sugars by a … is termed … ….

cyclic amp, atp, adenylyl cyclase, activator, catabolite activator protein, glucose, intracellular, camp, drop, adenylyl cyclase, cap, not, high glucose

• the lac operon is also regulated by an activator protein

  • this form of regulation involves a small molecule, … … (cAMP)

    • cAMP is produced from … via the enzyme … …

    • cAMP binds an … protein known as .. … … (CAP)

    • the transport of … into the cell causes … concentrations of … to … due to inhibition of .. …, therefore the … activator is … stimulated under conditions of .. ..

cap, promoter, increases, glucose, lactose, low, default, low, cap, repressor,

• cAMP-CAP regulation

  • the cAMP-CAP complex binds to the …. site near the lac … and … transcription

  • picture:

    • ….., no … (… cAMP)

      • … setting

      • transcription is very … due to the lack of …. binding and by the binding of the ….

lactose, glucose, high, high, polymerase, promoter, cap

• cAMP-CAP regulation

  • picture:

    • …., no … (… cAMP)

    • .. rate of transcription

    • binding of rna … to … is enhanced by …. binding

no, high, low, repressor

• cAMP-CAP regulation

  • picture

    • …. lactose or glucose (… cAMP)

    • transcription is very … due to the binding of the …

lactose, glucose, low, cap

• cAMP-CAP regulation

  • picture:

    • … and … (… cAMP)

    • transcription rate is very … due to the lack of … binding

3, promoter, downstream, downstream, z coding, upstream, promoter, 2, repression, 2, 3, maximal, not

• the lac operon has … operator sites for the lac repressor

  • in all, …. operator sites have been discovered

    • O1 → next to the …. (slightly …)

    • O2 → … in the lac… … region

    • O3 → slightly … of the ….

  • then the lac repressor must bind to … of the 3 operators to cause …

    • it can bind to O1 and O2, or to O1 and O3

      • but not O… and O….

    • if either O2 or O3 is missing, … repression is … achieved

2, loop, operator, closer, repressor, o1, one

• binding of the lac repressor to … operator sites requires that the dna form a …

• a loop in the dna brings the … sites closer together

  • this facilitates the binding of the … protein

• the loop inhibits rna polymerase movement past …

• each repressor dimer binds to … operator site

negatively, repressor, tryptophan

• the trp operon - another example of an operon that is … regulated by a …

  • required to produce … (if not provided in the environment)

tryptophan, trpe, trpd, trpc, trpb, trpa, biosynthesis, trpr, trpl, operon, repressor, short peptide, leader, attenuation

• regulation of the trp operon

  • the trp operon is involved in the biosynthesis of the amino acid ….

    • the genes …., …, …, … and .. encode enzymes involved in tryptophan …

    • the genes … and … are involved in regulation of the trp …

      • trpR → encodes the trp … protein

      • trpL → encodes a .. .. called the … peptide

        • functions in …

bound repressor, expression, low, not, repressor, operator, polymerase, transcribe, trpe, trpd, trpc, trpb, trpa, enzymes

• no tryptophan = no .. .. = …

• picture:

  • when trytophan levels are …, trytophan does … bind to the trp … protein, which prevents the repressor protein from binding to the … site

  • under these conditions, rna … can … the operon, which leads to the expression of the …, …, …, .. and .. genes

  • these genes encode … involved in tryptophan biosynthesis

corepressor, repressor, operator, repression, high, corepressor, repressor, tryptophan, trp repressor, operator, inhibit, 2, conformation, active, operator, blocks

• high tryptophan levels = …. tryptophan binds …. = repressor binds to … = …

• when tryptophan levels are …, tryptophan acts as a … that binds to the trp … protein

• the ..-… … complex then binds to the … site to inhibit transcription

• picture:

  • … tryptophan molecules bind, which causes a … change

  • corepressor-repressor form … complex

  • corepressor-repressor binds to … and …. transcription

attenutation, rna, attenuator, terminated, begins, attenuator

• another mechanism of trp operon is …

  • when this happens, the … is transcribed only to the … sequence, and their transcription is …

  • transcription …. but stops at the … sequence

bacteria, coupled, begins, mrna, attenuator, shortly, trpl, tryptophan, downstream, operator, trpl, short, leader, 14, 2, sense, protein synthesis

• attenuation can occur in … because transcription and translation are …. ; translation can begin while transcription is occurring

• during attenuation, transcription actually … but it is terminated before the entire … is made

  • a segment of dna, called the …, is important in facilitating this termination

  • in the case of the trp operon, transcription terminates … past the … region

  • attenuation inhibits further production of …

• the segment of trp operon immediately … from the …. site plays a critical role in attenuation

  • the first gene in the trp operon is ….

    • it encodes a … peptide termed the … peptide

      • that peptide contains codons for … amino acids including … trp codons

      • allows the cell to … whether or not it has enough tryptophan for … …

1, 3, 2, 4, 3

• trpL mrna has 4 different complementary regions that can adopt different hairpin structures

  • region 2 is complementary to regions … and …

  • region 3 is complementary to regions … and …

    • therefore, … stem loops structures are possible

U, intrinsic, p, independent, pol, transcriptional

• trpL mrna has 4 different complementary regions that can adopt different hairpin structures

  • the 3-4 stem loop is followed by a sequence of … which acts as an … (…-…) terminator

  • formation of the 3-4 stem loop causes the rna .. to pause and dissociation of the .. machinery

u rich, dna, translation, trpl mrna, high, no, repression, low, coupled, expression, high, coupled, repression, attenuation

• the formation of the 3-4 stem loop causes rna pol to pause allowing …-… sequence to dissociate from the …

• conditions that favor the formation of the 3-4 stem loop rely on the … of the … ..

• 3 possibel scenarios

  • 1) … tryptophan levels and …. coupled transcription/translation = ….

  • 2) .. levels of tryptophan levels and … transcription/translation = …

  • 3) … levels of tryptophan levels, but …. transcription/translation = … through …..

no, not, attenuation, repression, not, 1 hydrogen, 2, 3, 4, 3-4 terminator, u, rich attenuator, 1, 2, no

• high tryptophan levels = …. ribosome associated with the rna = transcription/translation is … coupled = … via 3-4 stem loop = ….

• picture

  • when translation is .. coupled with transcription, region … … bonds to region … and region .. hydrogen bonds to region …

  • because a … -… … stem loop forms, transcription will be terminated at the ..-.. attenuator

  • most stable form of mrna occurs rapidly as region … pairs with region ….

  • … translation, 1-2 and 3-4 stem loop forms

ribosome, blocked, 2, 2, 3, no, no, expression, structural, coupled, low, ribosome, codons, trpl, charged, trp, 1, 2, 3, cannot, not, rest

• low tryptophan levels = … associates with mrna = region 1 …. bc ribosome stalls at the … tryptophan codons = pairing between regions … and .. = … 3-4 stem loop = no … = … of trp … genes

• picture

  • …. transcription and translation occur under conditions in which the tryptophan concentration is very ….

  • the …. pauses at the trp … in the .. gene because insufficient amounts of … trna .. are present

  • this pause blocks region … of the mrna so region .. can hydrogen bond only with region …

  • when this happens, the 3-4 stem loop structure … form

  • transcriptional termination does … occur and rna polymerase transcribes the … of the operon

  • 2-3 stem loop forms

full, ribosome, stop, 2, 3, 4, attenuation, repression, sufficient, trpl, stop, pauses, 2, 3, 4, terminations, u, rich attenuator

• high tryptophan but coupled transcription/translation = … trpl gene transcribed/translated = ribosome comes to … codon and pauses at region … = stem loop forms between region …/…. = … and …

• picture

  • coupled transcription and translation occur under conditions in which a … amount of tryptophan is present in the cell

  • translation of the … gene processes to its … codon, where the ribosome …

  • this blocks region .. from hydrogen bonding with any region and enables region … to hydrogen bond to region …

  • this … transcription at the ..-.. …

attenuation, not

if region 3 pairs with region 4, … occurs = the full trp operon is … transcribed

catabolism, inducible, broken, inducer, anabolism, repressible, small, product, operon

• inducible vs repressible regulation

  • the study of many operons revealed a general trend concerning inducible vs repressible regulation

    • operons involved in …. (breakdown of a substance) are typically ….

      • the substance to be broken down (or a related compound) acts as the …. (like allolactose)

    • operons involved in … (biosynthesis of a substance) are typically ….

      • the inhibitor or corepressor is the … molecule that is the … of the … (like tryptophan)

proteins, mrna, inhibit, repressors, next, start, ribosome, translation, outside, secondary, initiation

• translational regulation: proteins

  • for some bacterial genes, the translation of mrna is regulated by the binding of … which recognizes mrna sequences

    • in most cases, these proteins act to …. translation

  • these translational … can act in one of 2 ways:

    • 1) bind …. to the shine-delgarno sequence and or the … codon

      • this weill sterically hinder the … from initiating ….

    • 2) bind … the shine-delgarno sequence/start codon region

      • this will stabilize an mrna …. structure that prevents ….

micf, ompf, high osmolarity, low, complementary, antisense

• translational regulation: antisense rna

  • the expression of .. gene, is responsible for inhibiting the …. gene at … … (ompF is needed during … osmolarity)

    • micF encodes an rna that is … to ompF mrna

      • called an …. rna

allosteric, 2, catalytic, substrate, regulatory, final, high, 1, inhibit, intermediate 1

• posttranslational regulation: feedback inhibition

  • enzyme 1 is an … enzyme, which means it contains …. different binding sites

    • …. site → binds …

    • ….. site → binds .. product of the pathway

  • if the conc of the final product becomes …., it will bind to enzyme … and … its ability to convert the substrate into … …

proteolytic processing, sugars, lipids, function

• posttranslational regulation: covalent modification

  • some modifications are irreversible like .. .. or attachment of prosthetic groups (…. or …)

  • other modifications arr reversible and transiently affect protein …..

2, secondary, active, expression, small molecule, 3, 5, transcription, splicing, stability, translation

• riboswitches, another forms of gene regulation

  • first discovered in 2001

  • rna exists in … different … conformations

    • one is …

    • the other inhibits gene ….

    • conversion between forms is due to the binding of a … molecule

    • … - … % of all bacterial genes may be regulated by riboswitches

  • riboswitches can regulate at various levels

    • ….

    • rna .. and …

    • ….

tpp, rna, high, secondary, termination, transcription, tpp synthesis

• transcriptional regulation of thiamin pyrophosphate (tpp) synthesis (vitamin b1)

  • binding of tpp to the … will occur when it is present at … levels, causing a change in the .. structure of the rna

  • the tpp-bound conformation causes … of … for the genes involved in … …

mrna, stem, loop, shine, delgarno, blocked

• translation regulation of thiamin pyrophosphate (tpp) synthesis

  • binding of tpp to this … allows the formation of …-… that sequesters the …-… sequence

  • translation is ….