Ch 16 Control of Gene Expression in Bacteria Flashcards
the mechanisms and systems that control the expression of genes
gene regulation
genes that encode proteins that are used in metabolism or biosynthesis or play a structural role in the cell
structural genes
genes that encode RNA or proteins that interact with other DNA sequences and affect transcription/translation of the sequences
regulatory genes
structural genes that are not regulated and are expressed continually
constitutive genes
genes that are not transcribed; affect the expression of DNA sequences to which they’re physically linked to
regulatory elements
processes that stimulate gene expression
positive control
processes that inhibit gene expression
negative control
list the levels of gene regulations
alteration of DNA or chromatin structure
regulation of transcription
mRNA processing
regulation of mRNA stability
regulation of translation
posttranslational modification
why is regulation of transcription important in both bacterial and eukaryotic cells?
it allows for limited production of a protein early
functional parts of a protein, usually consisting of 60 to 90 amino acids
domains
what part of regulatory proteins are responsible for binding to DNA
the domains (functional parts)
what are the most common amino acids within a domain that bind with the DNA?
asparagine, glutamine, glycine, lysine, and arginine
how do amino acids within a domain of DNA-binding proteins interact with DNA?
by forming hydrogen bonds with the bases or interacting with the sugar-phosphate backbone of DNA
characteristic structures found within the binding domain that allow proteins to bind to DNA
motifs
motif characterized by two alpha helices and binds into the major groove of the DNA double helix
helix-turn-helix
motif characterized by a loop of amino acids with zinc at base, and binds into the major groove of the DNA double helix
zinc finger
motif characterized by two perpendicular alpha helices with zinc surrounded by four cysteines; binds into the major groove and DNA backbone
steroid receptor
motif characterized by helix of leucine and a basic arm and two leucines interdigitate; binds into two adjacent major grooved
leucine zipper
motif characterized by two alpha helices separated by a loop of amino acids; binds into the major groove of the DNA double helix
helix-loop-helix
motif characterized by three alpha helices; binds into the major groove of the DNA double helix
homeodomain
how are genes regulated in bacteria?
bacterial genes w/ related functions are clustered, controlled, and transcribed together into a single mRNA, by using operons
a group of bacterial structural genes that are transcribed together, along with their promoter and additional sequences that control their transcription
operon
which level of gene regulation is the most important in bacteria?
transcription
describe and label the structure of an operon
promoter: upstream of first structural gene, where RNA polymerase binds and starts transcription
operator: where regulator protein binds
structural genes: genes transcribed into mRNA and translated to produce proteins/enzymes
gene that helps control expression of structural genes by encoding the regulatory protein
regulatory gene
is the regulator gene part of the operon?
no, it is not part of the operon. it has its own promoter
protein that binds to the operator in operon, affecting the rate of transcription
regulatory protein
region of operon where regulatory protein binds and affects whether transcription takes place
operator
what are the two types of transcriptional control
negative control and positive control
transcription control in which regulatory protein is a repressor, which binds to DNA to inhibit transcription
negative control
transcription control in which regulatory protein is an activator, which binds to DNA to stimulate transcription
positive control
operon in which transcription is normally off and must be turned on
inducible operon
operon in which transcription is normally on and must be turned off
repressible operon
what does the regulator gene for a negative inducible operon encode for?
an active repressor protein
what does the regulator gene for a negative repressible operon encode for?
an inactive repressor protein
what does the regulator gene for a positive inducible operon encode for?
an inactive activator protein
what does the regulator gene for a positive repressible operon encode for?
an active activator protein
small molecule that binds to repressor protein and inactivates it, therefore protein cannot bind and transcription turns on
inducer
small molecule that binds to repressor protein and activates it, therefore protein can bind and transcription turns off
corepressor
how does the binding of an inducer or corepressor to a regulatory protein affect it?
it alters the proteins shape
in a negative inducible operon, if the inducer is absent, what happens?
if the inducer is absent, transcription remains off, due to the repressor protein remaining active and binding to the operator
what kind of processes do negative inducible operons usually control?
they usually control proteins that carry out degradative processes
the proteins synthesized from the operon break down the substrate
in a negative repressible operon, if the corepressor is absent, what happens?
if the corepressor is absent, transcription remains on, due to the repressor protein being inactive and cannot bind to the operator
what kind of processes do negative repressible operons usually control?
they usually control proteins that carry out biosynthesis of molecules needed in the cell
the product produced by the proteins synthesized from the operons are always needed by the cell, and operon is only turned off when there’s an adequate amount of the product present
in a positive inducible operon, if the inducer is absent, what happens?
if the inducer is absent, transcription remains off, due to the activator protein being inactive and cannot bind to the operator
in a positive repressible operon, if the corepressor is absent, what happens?
if the corepressor is absent, transcription remains on, due to the activator protein being active, binding to the operator
what kind of operon is the lac operon? what does it regulate? what are the structural genes and what do they encode?
negative inducible operon
regulates lactose metabolism
structural genes:
lacZ - ß-galactosidase
lacY - permease
lacA - transacetylase
what is the purpose of the protein lactose permease?
since lactose cannot easily diffuse across cell membranes, permease actively transports it
what is the purpose of the enzyme ß-galactosidase?
ß-galactosidase catalyzes the reaction that breaks down lactose into glucose and galactose, to use as energy sources
also converts lactose into allolactose
how is coordinate induction demonstrated in the lac operon, by the presence of lactose?
when lactose is present, the rate of synthesis of the protein produces increases
what is the inducer molecule in the lac operon
allolactose
if the lac operon is repressed and no proteins are being produced, how does lactose get into the cell, convert into allolactose in order to turn on transcription?
repression is never fully off; when the repressor is bound, only low levels of transcription are performed, which allows some permease to transports small amounts of lactose in, which is converted to allolactose by some ß-galactosidase, which then inactivates the repressor
cells that possess two copies of the lac operon, one on a chromosome and another on an extra piece piece of DNA
partial diploid
what does it mean when some parts of an operon are cis-acting?
they are able to control the expression of genes only on the same piece of DNA
what does it mean when some parts of an operon are trans-acting?
they are able to control the expression of genes on other DNA molecules
what are the effect of lacZ & lacY mutations?
they affect structure of the proteins (permease and ß-galactosidase), making them nonfunctional; they don’t regulate the synthesis of them
if a partial diploid had: lacZ+ lac Y- / lac Z- lac Y+ , would galactosidase and permease still be synthesized?
yes, a single functional lacZ+ and lacY+ (despite presence of mutations) are sufficient to produce ß-galactosidase and permease
what are the effect of lacI mutations?
they are mutations in the regulatory gene, thus affected regulation of protein production
describe the affect of lacI- and how it differs from lacI+
lacI- : irregular production; the regulatory protein (repressor) would not be synthesized, therefore transcription remains on and proteins are produced all the time
lacI+ : normal production; repressor is synthesized
is lacI+ cis- or trans-acting
trans-acting
describe superrepressors (lacI s)
produce defective repressor proteins that could not be inactivated by an inducer, therefore repressor always remains attached to operator, preventing transcription
which is dominant? lacI s or lacI+
lacI(s) is dominant over lacI+
what are the effect of lacO mutations?
operator DNA sequence altered and repressor protein cannot bind, therefore transcription transcription is always on
which is dominant? lacOc or lacO+
lacOc is dominant over lacO+
is lacO cis- or trans-acting?
lacO is cis-acting
what are the effect of lacP mutations?
they interfere with binding of RNA polymerase to the promoter, therefore transcription cannot occur
is lacP cis-or trans-acting?
lacP is cis-acting
why do bacteria prefer to metabolize glucose?
glucose requires less energy to metabolize than other sugars
explain catabolite repression
what type of control is it?
genes that participate in metabolism of other sugars are turned off when glucose is present
positive control - when there are low glucose levels, transcription turns on
what is CAP? what does it bind with to form a complex?
explain its importance in catabolite repression
CAP - catabolite activator protein
forms a complex with cAMP
must bind to DNA first in order for RNA polymerase to bind efficiently to the promoter
describe the relationship of concentration of cAMP to glucose, and how they effect transcription
concentration of cAMP is inversely proportional to glucose levels
high concentrations of glucose = low cAMP-CAP complexes that bind to DNA –> little transcription
low concentrations of glucose = high cAMP-CAP complexes that bind to DNA –> lots of transcription
what in CAP allows RNA polymerase to have better affinity at the promoter?
CAP has a helix-turn-helix DNA-binding motif that when it binds to DNA, the DNA helix bends, enabling RNA polymerase to bind
what kind of operon is the trp operon? what does it regulate? what do the structural genes encode?
negative repressible operon
regulates biosynthesis of the amino acid tryptophan
structural genes: trp E, trp D, trp C, trp B, and trp A –> produce components to convert chorismate into tryptophan
describe the trp operon when there are low and high levels of tryptophan
when there are low levels of tryptophan, the repressor molecule is inactive and transcription turns on, increasing tryptophan levels
when there are high levels of tryptophan, the repressor molecule is active and transcription turns off
describe attenuation
transcription begins at the transcription start site but terminates prematurely, before RNA polymerase reaches the structural genes
what kind of operons is attenuation associated with?
operons that encode enzymes participating in biosynthesis of amino acids
what region of the trp operon is responsible for attenuation?
the long 5’ UTR region in the trpE gene
describe the four regions in the 5’UTR of the trpE and their complementaries
region 1 complementary to region 2
region 2 complementary to region 3
region 3 complementary to region 4
explain why tryptophan is required for the translation of the 5’UTR region in the trpE gene and how this relates to attenuation?
the ribosome binding site is located upstream of region 1
within the coding sequence of region 1, there are two UGG codons, that specify the amino acid tryptophan
tryptophan must be added to the developing amino acid chain
if there are low levels of tryptophan, transcription proceeds to synthesize more tryptophan
describe transcription when tryptophan levels are low
ribosome binds to 5’ UTR and begins translation as RNA polymerase transcribes downstream
ribosome stops at region 1 at Trp (UGG) codons, since there are low levels of tryptophan, the ribosome stalls
RNA polymerase continues transcription, and region 2 base pairs with region 3, forming antiterminator, preventing termination
transcription continues, and translation of the mRNA into enzymes synthesizes tryptophan
secondary structure formed in 5’ UTR when region 2 base pairs with region 3, preventing termination of transcription
antiterminator
describe transcription when tryptophan levels are high
ribosome binds to 5’ UTR and begins translation as RNA polymerase transcribes downstream
ribosome is able to translate region 1 due to abundant tryptophan and keep up with RNA polymerase
hairpin forms by pairing of regions 1 & 2, and hairpin forms between 3 &4, producing the attenuator, and transcription terminates, causing no additional tryptophan to be synthesized
secondary structure formed in 5’UTR when region 3 base pairs with region 4, followed by a string of uracil nucleotides, causing termination of transcription
attenuator
RNA molecules that control gene expression by binding to complementary sequences on mRNA and inhibiting translation
antisense RNA
describe how antisense RNA affects gene expression
a regulator gene is activated to produce an antisense RNA
the antisense RNA pairs with complementary sequence in 5’UTR of target mRNA to inhibit the binding of a ribosome, therefore preventing translation
regulatory sequences in mRNA where regulator molecules can bind and affect gene expression by influencing the formation of secondary structures in mRNA
riboswitches
describe how riboswitches affect gene expression
riboswitches fold into secondary structures within the mRNA molecule
when a regulatory protein binds, it may stabilize the structure, and may lead to premature termination of transcription or prevent initiation of translation
when no regulatory protein binds, the riboswitch changes to another structure that allows transcription/translation
