Chapter 16

______ often stimulate RNA polymerase to transcribe better at weak promoters

activators

when the level of glucose is high, cAMP level are low and transcription of the lac operon is _______

reduced

when cAMP binds to the transcriptional activator protein ______ it stimulates RNA polymerase ~50X to initiate transcription

CAP

specific amino acids of a _______ interact (often through H-bonds) to specific bases in a DNA sequence

DNA binding protein

the lac repressor binds DNA at a sequence that blocks _______ access to the lac promoter

RNA polymerase

lactose must but ________ transported into the cell and broken down into galactose and glucose

actively

________ regulation may target an enzyme activity or transcriptional regulator

allosteric regulation

transcriptional activators and repressors are commonly regulated ________

allosterically

________, especially in the major groove, vary with each type of base pair

base side groups

mutation in lacZ and/or lacY

can't grow on lactose (as sole carbon source)

glucose is the preferred _________ source for E. coli

carbon

control of the lac transcription by glucose is an example of _____ repression

catabolite

which part of the lac regulatory region is the binding site

catobolite activator protin (CAP)

_________ expression is used for genes that encode products that are always needed, often in the same amount

constitutive expression (housekeeping genes)

how to control gene expression at transcription initiation through variations in intrinsic promoter strength

different promoter DNA sequences lead to different levels of transcription this can generate large differences in gene expression levels but does not permit regulation by itself

true/false: the lac promoter can be turned 100% off

false- it is never fully off, its very low basal activity level allows enough permease and B-gal activity to be made to import enough lactose to allow induction of the lac promoter

true/false: in the presence of lactose, lac repressor binds to lacO and inhibits transcription

false- its in the absence of lactose that the repressor binds

true/false: the lacY encodes B-galactoside and breaks down lactose

false- lacZ does this

true/false: most DNA binding proteins bind in the minor groove

false- most bind in the major groove

true/false: examples of trans-acting elements are regulatory DNA sites like lacO and lacP

false- these are cis-acting elements

true/false: protein forming dimers have greatly decreased binding specificty

false- they have greatly increased binding specificity

________ is the preferred energy source of E. coli

glucose

low glucose causes ______ adenylate cyclase and ____ cAMP

high and high

RNA polymerase _____ binds to the promoter via the sigma subunit

holoenzyme

when the level of glucose is low, cAMP level are high and cAMP-CAP _________ transcription of the lac operon

increases

regulatory gene is often constitutively expressed, but its binding to operator is dependent on _____ or _____ molecules

inducer or repressor molecules

predicted effects of mutations in different parts of the lac operon in partial diploids

mutations in both lacZ- phenotype can't grow on lactose mutations in one lacZ and one lacY- wild type phenotype mutations in one lacI and one lacZ- wild type phenotype

______ regulation is protein binding that decreases expression and involves a repressor of transcription

negative

______ is the regulatory sequence where regulatory proteins bind and affect transcription

operator

______ is a set of functionally related structural genes transcribed from a single promoter

operon

__________ regulation is protein binding that increases expression and involves and activator of transcription

positive

in the ________ of lactose, allolactose binds to lac repressor and makes repressor unable to bind to lacO

presence expression of lac operon is induced by lactose/allolactose

how to control gene expression at transcription initiation through regulation of promoter activity

proteins bound in or near promoter (transcription factors) can modulate promoter activity by regulating the presence and activity of transcription factors at the promoter, the transcription from that promoter can be regulated in complex ways

base side groups provide the ________ for specific-sequence protein binding to DNA

recognition codes

______ expression is used for genes that encode products only needed at certain times or in certain circumstances/environments

regulated expression

_______ are DNA sequences that do not encode gene transcripts but play a role in regulating gene expression

regulatory elements

_______ genes encode products that regulate expression of structural genes and/or their products

regulatory genes

a _______ response to a signal causes a decrease in expression

repressible

________ inhibit transcription, often by blocking RNA polymerase or an activator from binding to the promoter

repressors

repressors and activators are typically _______ DNA binding proteins

sequence-specific note that proteins occupy a greater "footprint" on DNA than the sequence they bind to

how do DNA binding proteins recognize the specific sequences that they bind to?

sequence-specific binding of proteins to DNA requires bases to have identifying features beyond those involved in base-pairing

Why does gene expression need to be regulated in bacteria?

they are single cell organisms need to rapidly respond to environmental changes need to conserve energy

lacI+ is dominant to lacI- and acts in ____

trans

________ elements can diffuse and act at target sites on any DNA molecule in the cell

trans-acting elements

mutation in lacI

transcription of operon can't be repressed

mutation in the operator of the lac operon

transcription of operon can't be repressed

mutation in the promoter of the lac operon

transcription of operon can't occur ever

mutation in the CAP site of the lac operon

transcription of operon is weak at best

true/false: a separate gene encodes a regulator protein or an operon

true

what questions did Jacob and Monod want their experiment to answer?

which lac alleles are inducible which lac mutations are dominant to wildtype which lac mutations act in cis vs trans

an _______ response to a signal causes an increase in expression

inducible

gene expression at which level of transcription is of a particular importance?

initiation

what does the lac repressor (lacI) do?

it encodes protein that can bind lac operator (lacO)

which part of the lac regulatory region binds the lac repressor protein

lac operator (lacO)

Jacob and Monod used lac mutations and partial diploids (two copies of the lac sequences) to dissect regulation of the _______

lac operon

the ______ operon encodes genes involved in utilizing the sugar lactose

lac operon

what part of the lac regulatory region binds RNA polymerase

lac promoter (lacP)

three parts of the lac regulatory region

lac promoter (lacP) lac operator (lacO) Catabolite activator protiein (CAP)

what is the third structural gene along with lacY and lacZ?

lacA encodes transacetylase, but the function is poorly understood

bacteria typically have several different ________ that each bind to very different promoter sequences

sigma factors

_________ genes encode proteins that function in metabolism, biosynthesis, or structural aspects of the cell

structural (non-regulatory) genes

the lac promoter requires activation by the _____ protein for activity

the CAP protein

true/false: In their experiment, Jacob and Monod used bacterial mating to introduce F' into cells that contained copy of lac operon

true

true/false: because bacteria have many different sigma factors, it allows many promoters to be regulated as a common group by regulating the particular sigma subunit

true

true/false: because transcriptional activators and repressors are commonly regulated allosterically, activity of the regulated gene can therefore toggle between being on and off

true

true/false: binding of inducer to lac repressor causes conformation change to lac repressor such that it no longer binds DNA

true

true/false: cis-acting elements cannot diffuse and therefore can only influence expression of adjacent genes on the same DNA molecules

true

true/false: coordinate expression of multiple genes required for a particular for a particular pathway or function

true

true/false: different amino acid sequence of the regions contacting DNA can lead to different specificity of the DNA sequence that is bound by the protein

true

true/false: examples of trans-acting elements are regulator proteins like the lac repressor

true

true/false: if an activator or a repressor were always bound, there might never e a change in the expression level of a gene

true

true/false: in E. coli alternative sugars like lactose are not used until all the glucose is sued up

true

true/false: in E. coli lactose of one of many sugars that can serve as an alternate carbon source to glucose

true

true/false: in a partial diploid with lacI+ lacZ- / lacI- ZacZ+, no transcription will occur because wildtype repressor binds to both operators

true

true/false: in the absence of glucose, cyclic AMP (cAMP) is generated

true

true/false: lac repressor is an allosteric protein that has binding side for an inducer

true

true/false: many different regulatory proteins utilize the same domains

true

true/false: many transcriptional regulatory proteins (transcription factors) have DNA-binding activity

true

true/false: regulating the activity of an activator or repressor allows regulation of the gene they act on

true

true/false: regulatory elements are usually the site of binding of regulatory proteins

true

true/false: the lacY encodes permease and transports lactose into the cell

true

true/false: the lac repressor is occasionally released from lacO

true very low level of transcription from the operon small amount of permease and B-gal even if there's no lactose present

true/false: gene expression can be regulated at many different levels

true- transcription and translation both have three stages: initiation elongation and termination

two general ways to control transcription initiation

variations in intrinsic promoter strength regulation of promoter activity

high glucose causes ______ adenylate cyclase and ____ cAMP

low and low