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