Chapter Eighteen: Gene Regulation in Prokaryotes Flashcards
bacteria are ___ and ___ their environment
in contact with and respond to
the ability to coordinate the expression of many genes leads to ___ and ___
survival and energy savings
luminescent bacteria protect squid from predators by controlling the ___
light level to match the moonlight
___ of ATP being used does into protein synthesis, don’t want to ___ when its not necessary
80%
make protein
___ participates in all three phases of prokaryotic transcription
RNA polymerase
in transcription initiation, RNA polymerase has four subunits (___, ___, and ___); ___ binds to RNA polymerase and recognizes the promoter site and also binds to it
two alpha, one beta, and one beta prime
sigma factor
in transcription elongation, RNA polymerase is not bound to ___, but moves along DNA until ___
sigma factor
it reaches a termination sequence
there are two kinds of termination in bacteria: ___ and ___
rho-dependent and rho-independent
in rho-dependent termination, ___ binds to RNA polymerase and ___
rho protein
removes it from RNA
in rho-independent termination, RNA forms a ___
hairpin loop
transcription and translation occur ___ in prokaryotes
simultaneously
sequences for start and stop of transcription are ___ from sequences for start and stop of translation
distinct
mRNA are often ___, meaning multiple genes together can be controlled by one promoter
polycistronic
three levels of transcriptional control
- binding of RNA polymerase to promoter
- shift from initiation to elongation
- release of mRNA at termination
three levels of posttranscriptional control
- stability of mRNA
- efficient of translation initiation
- stability of polypeptide
in a catabolic pathway, molecules are ___
broken down
catabolic pathways require ___
inducible regulation
inducible regulation means that the pathway is ___ when ___
only turned on when molecules to be broken down are present
in an anabolic pathway, molecules are ___
built from simpler constituents
anabolic pathways require ___
repressible regulation
repressible regulation means that the pathway is ___ unless the cell ___
turned off
needs more of the larger molecule
utilization of lactose by E. coli provides a model system of ___
gene regulation
two enzymes required for lactose utilization
permease and beta-galactosidase (B-gal)
transports lactose into cells
permease
splits lactose into glucose and galactose
beta-galactosidase
lactose is a disaccharide of ___ and ___
glucose and galactose
are permease and B-gal present when lactose is not present
yes, in very low levels
lactose is an ___ of the genes encoding permease and B-Gal
inducer
stimulation of the synthesis of a specific promoter
induction
molecule responsible for induction
inducer
lac- mutants can be maintained on media with ___, so lac genes are not ___ for survival
glucose
essential
if both glucose and lactose are present, E. coli cells will use ___ first; if there is a lot of ___ present, lactose does not need to be ___
glucose
glucose
broken down
lactose induces a ___ increase in B-gal activity
1000 fold
studies of lac mutants revealed the ___ of gene regulation
operon theory
one signal can simultaneously regulate expression of several clustered genes
operon theory
three structural genes in the lac operon
lacZ, lacY, and lacA
site to which RNA polymerase binds
promoter
controls transcription and translation
operator
in the absence of lactose, a ___ binds to the ___ and functions to ___
repressor protein
operator
prevent transcription
the lac repressor is a ___ regulatory element
negative
when lactose is present, it binds to the ___, which moves off of the ___ because it ___; this allows for ___
repressor protein
operator
changes shape
transcription of the structural genes
type of repressor that reversibly changes shape and cannot bind to operator
allosteric repressor
when lactose is bound to the repressor protein, RNA polymerase binds to the ___ and initiates ___ of the ___ lac mRNA
promoter
transcription
polycistronic
lacZ encodes ___
B-galactosidase
lacY encodes ___
permease
lacA encodes ___
transacetylase
lacI encodes ___
the repressor protein
a mutation in lacI that stops the repressor protein from being made causes ___ of the structural genes
constitutive expression
mutations of the lacO (operator) sequence would cause ___ of the structural genes
constitutive expression
lacIc mutants have a super repressor that binds to the ___ but cannot bind to the ___; causes ___ in the presence or absence of lactose
operator
inducer
repression
can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell
trans-acting elements
can only influence expression of adjacent genes on the same DNA molecule
cis-acting elements
lacI+ proteins act in ___
trans
lacO acts in ___
cis
lacZYA are ___
polycistronic
lac repressor binds to the ___
operator
lac repressor domains correspond to ___
functions
operator and promoter can be identified by ___
DNAse footprinting
structure of operator and repressor allows for ___ in binding
cooperativity
the lac repressor ___ motif binds DNA
helix-turn-helix (HTH)
the HTH motif is found in hundreds of ___
DNA binding proteins
duplication and divergence means each HTH motif recognizes a ___
different DNA sequence
the lac repressor HTH motif recognizes the ___
lac operator
DNAse footprinting identified the DNA sequence bound by the ___
repressor
DNAse digests DNA not bound by a ___
protein
digesting DNA not bound to protein forms ___ on a gel, with a break occurring when ___
bands
bound proteins protect the DNA from digestion
when he lac repressor is bound to the lac operator, functional binding of ___ to ___ is blocked
RNA polymerase to promoter
lac repressor tetramer binds to ___
two sites
the lac operon has ___ operators, each of which contains two recognition sequences for ___
three
lac repressor
___ has the strongest binding affinity for lac repressor
O1
maximal repression occurs when ___
all four repressor subunits are bound
___ repressor subunits bind to O1
two
two repressor subunits bind to either ___ or ___
O2 or O3
the lac operon of E. coli is regulated by both ___ and ___
lactose and glucose
when both lactose and glucose are present, only ___ is utilized
glucose
lactose induces ___ expression, but only in the ___ of glucose
lac mRNA
absence
lactose prevents ___ from binding to ___
repressor
lacO (operator)
lac repressor is a ___ regulator of lac transcription
negative
lac mRNA expression cannot be induced if ___ is present
glucose
in the absence of glucose, levels of ___ increase
cAMP
cAMP binds to ___
cAMP receptor protein (CRP)
CRP-cAMP is a __ regulator of lac transcription
positive
CRP-cAMP complex makes ___ with RNA polymerase
direct contact
without interaction from CRP-cAMP, RNA polymerase can ___ but is less likely to ___
bind the promoter
unwind the DNA and initiate transcription
overall effect of glucose is to prevent ___
lac gene expression
anabolic synthesis of tryptophan (trp) is regulated by the ___
trp operon
structural genes for tryptophan (trp) biosynthesis are expressed only ___
in the absence of trp
transcription from the trp promoter produces two ___
alternative transcripts
tryptophan acts as a ___
corepressor
binding of trp to TrpR repressor allows ___ to bind to ___ and inhibit transcription of the five structural genes
TrpR
TrpO
in the absence of trp, TrpR repressor cannot ___
bind to TrpO to induce transcription
gene regulation after transcription ignition occurs by several ___
RNA-based mechanisms
RNA leader sequences act in ___
cis
small RNAs (sRNA) act in ___
trans
two examples of RNA leader sequences
attenuation
riboswitches
after transcription initiation, RNA ___ can regulate gene expression
structure
controls termination of transcription in the trp leader
attenuation
when trp is present, transcription ___ in the trp leader; when trp is absent, transcription ___ in the trp leader
terminates
doesn’t terminate
RNA leader sequence forms alternate ___ structures
stem loop
the ___ is a transcription terminator; the ___ prevents formation of the ___, so it is an antiterminator
3-4 stem loop
2-3 stem loop
3-4 stem loop
a terminator may halt ___ or prevent access to the ___
transcription
ribosome
when trp is present, transcription ___ due to the formation of ___
terminates
3-4 stem loop
movement of ribosomes depends on the availability of ___
tRNAtrp
when trp is present, tRNAtrp is ___ and ___ ribosome movement allows for formation of a ___
available
rapid
3-4 stem loop
riboswitches bind ___ to regulate ___
small molecules
gene expression
a riboswitch is an RNA leader with ___, it binds small molecules through a short sequence called an ___, conformation of a second region called the ___ changes in response to first region configuration
several conformations
aptamer
expression platform
small RNAs usually ___ translation by ___
inhibit
base-pairing with the ribosome site
small RNAs can also ___ transcription by disrupting ___
activate
stem loops
some small RNAs lead to mRNA ___
degradation
___ is produced by transcription of the strand of DNA opposite the template strand
antisense RNA
antisense RNA may ___ translation by base pairing with the sense strand
inhibit
