Exam #3
merozygote
(by Jacob, Monod, and Pardee) a partial diploid strain of bacteria containing F' factor genes, the two strains of bacteria can share their genetic codes
gene regulation
(by jacob and monod) the phenomenon in which the level of gene expression can vary under different conditions (regulated so that the proteins they encode can be produced at the proper times and in the proper amounts- produce proteins only when required to save energy)
trp (trip) operon
-encodes enzymes involved with the synthesis of the amino acid tryptophan -regulated by a repressor protein and another mechanism called attenuation -involves the genes trpE, trpD, trpC, trpB, and trpA
when translation is not coupled with transcription
1-2 stem loop and 3-4 stem loop and translation doesn't occur
when coupled and low tryptophan levels
2-3. stem-loop forms and translation occurs, insufficient levels of tryptophan so it pauses at 1 which shields it so 2 and 3 connect
allolactose
4 of them acts as a small effector molecule for regulating the lac operon, attaches to the lac repressor and allows transcription (inducer)
CAP site
a DNA sequence that is recognized by the activator protein CAP (catabolite activator protein)
inducible gene
a gene that is regulated by an inducer, which is a small effector molecule that causes the rate of transcription to increase
attenuation
a mechanism of genetic regulation seen in the trp operon in which a short RNA is made but its synthesis is terminated before RNA polymerase can transcribe the rest of the operon; early termination of translation; coupling of transcription and translation has to be quick so it only works in prokaryotes
lactose permease
a membrane protein required for the active transport of lactose into the cytoplasm of the bacterium
translational repressor
a protein that binds to an mRNA and inhibits its ability to be translated. (bind to either the shine-dalgarno sequence or start codon- translational repressor can stabilize an mRNA secondary structure which is unacceptable to shine-dalgarno)
trp repressor
a protein that binds to the operator site of the trp operon and inhibits transcription, it's a protein encoded by the trpR gene
translational regulatory protein
a protein that regulates translation
osmoregulation
ability of a cell to control the amount of water inside it
lactose makes
allolactose, galactose, and glucose from b-galactosidase
lactose permease
allows lactose enter the cell as a secondary active transport
2-3 stem loop
allows transcription to occur because a 3-4 stem-loop can't be formed
allosteric enzyme
also known as a regulatory site; an enzyme that contains two binding sites: a catalytic site and a regulatory site; catalytic site is responsible for the binding of the substrate and its conversion to intermediate 1; the second site is a regulatory/ allosteric site that binds the final product of the metabolic pathway which inhibits the catalytic ability of enzyme 1
antisense RNA
an RNA strand that is complementary to a strand of mRNA, another way that regulates bacteria translation; the two strands of RNA come together to form a double-stranded structure that prevents mRNA from being translated
operon
an arrangement in DNA in which two or more genes are found within a regulatory unit that is under the transcriptional control of a single promoter
cis-effect
an effect on gene expression due to a genetic sequence within the same chromosome and often immediately adjacent to the gene of interest
trans-effect
an effect on gene expression that occurs even though two DNA segments are not physically adjacent to each other. trans-effects are mediated by diffusible genetic regulatory proteins
b-galactosidase
an enzyme that cleaves lactose into galactose and glucose, converts small percentages of lactose into allolactose, a structurally similar sugar
polycistronic mRNA
an mRNA that is transcribed from an operon and encodes two or more proteins
where can gene regulation occur
anywhere in the formation from a gene to a functional protein (transcription, translation, or postranslation)
response to environmental stress
certain proteins help a bacterium to survive an environmental stress (example is osmotic shock or heat, proteins required only when the bacterium is confronted with the stress)
repressible operons
commonly encode anabolic enzymes
lacO- or lacOc
constitutive expression of the lac operon even in strains that make a normal lac repressor protein, nonfunctioning set of operators not recognized by repressor proteins
posttranslational
describes events that occur after translation is completed
lacZ gene
encodes b-galactosidase
lacA gene
encodes encodes galactoside transacetylase
lacY gene
encodes lactose permaease
effector molecules
exerts its effects by binding to a repressor or activator causing a conformational change in the regulatory protein thereby influences whether or not the protein can bind to the DNA
stem loops
form in the mRNA because there are four regions complementary to each other (region 2 is complementary to region 1 and also region 3. region 3 is complementary to region 2 as well as to region 4) three stem loops possible, 1-2, 2-3, and 3-4 each region can only for one stem loop with another though
trpE, trpD, trpC, trpB, and trpA genes
genes required for tryptophan biosynthesis
trpR
has its own promoter and is not part of the trp operon encodes the trp repressor
3-4 stem loop
in combination with the u-rich attenuator sequence results in intrinsic termination (p-independent termination) relys on the translation of the trpL gene and on the amount of tryptophan in the cell
camp
inducer that binds to the activator CAP
lac operon
inducible operon, regulated by sugar molecules, digest lactose when presented in the cell
in bacteria, the most common way to regulate gene expression
influencing the rate at which transcription is initiated
trans element in lac operon
lacI (lac repressor gene) changes merozygotes
O2
located farther downstream in the lacZ coding sequence
O3
located slightly upstream from the promoter
processes regulated at the genetic level in bacterium
metabolism, response to environmental stress, and cell division
lacIs
mutation which doesn't allow allolactose to bind to the lac repressor
lacI
not part of the lac operon, encodes lac repressor
omF gene
ompF protein is produced at low osmolarity and its synthesis is decreased at high osmolarity
lactose and glucose (low cAMP)
once glucose is used up, CAP can bind and lactose starts repressor is inactive CAP is inactive transcription is low diauxic growth
induced
refers to a gene that has been transcriptionally activated by an inducer
when the trpL gene is being transcribed
region 1 rapidly hydrogen bonds to region 2 and region 3 is left hydrogen bond to region 4
trpR and trpL
regulate the trp operon
trp oeron
repressible operon regulated by tryptophan
lactose, no glucose (high cAMP)
repressor is inactive CAP/ cAMP binds to CAP site transcription is very high
no lactose, no glucose (high cAMP)
repressor on the operon CAP/cAMP on CAP site transcription is very low
micF
responsible for inhibiting the expression of the ompF gene at high osmolarity (micF is complementary to ompF; it's an antisense strand and when it's transcribed its it's RNA product binds to the ompF mRNA via hydrogen bonding and prevents it from being translated); blocker ncRNA
lacI-
results in the synthesis of an internal activator, making it unnecessary for cells to be exposed to lactose for the expression of the lac operon
Binding of allolactose to LacI is
reversible
inducer
small effector molecule that causes the rate of transcription to increase (bind to repressor to prevent it from binding to DNA or bind to activator and cause it to bind to the DNA)
trp operon
synthesize tryptophan; anabolic; normally constitutively expressed; feedback inhibition
covalent modification
the chemical alteration of a protein or the covalent attachment of a molecule or functional group to a protein after it has been synthesized via ribosomes; often reversible; phosphorylation/ acetylation/ methylation are examples
posttranslational regulation
the functional control of proteins that are already present in the cell
genes under the control of lac promoter
the lac Z, lacY, and lac A
O1
the operator site slightly downstream from the promoter
catabolite repression
the phenomenon in which a catabolite (glucose) represses the expression of certain genes (the lac operon)
allosteric site
the site on a protein where a small effector molecule binds to regulate the function of the protein
gene's aren't just turned on or turned off
they're expression is increased or decreased
glucose, no lactose (low cAMP)
CAP inactive repressor on operator transcription is very low
lac operon contains
CAP site, lac promoter (lacP), an operator site (lacO), three protein-encoding genes (lacZ, lacY, and lacA), and a terminator catabolic
regulatory protein binding sites
DNA binding site and effector molecule binding site
lac repressor can bind to
O1 and O2 or O1 and O3, so if O1 is missing, repression is nearly abolished because lac repressor cannot bind to O2 and O3
pseudo-operators
O2 and O3; substantial repression occurred in the absence of either one of them
constitutive gene
a gene that is not regulated and has essentially constant levels of expression over time (encode proteins that are continuously needed for survival)
repressible genes
a gene that is regulated by a corepressor or inhibitor, which are small effector molecules that cause the rate of transcription to decrease
riboswitches
a mechanism for regulating transcription, translation, RNA stability, and splicing in which an RNA molecule can switch between two secondary conformations based on whether or not a small molecule, such as TPP, binds to the RNA; secondary RNA structures that switch between one another depending on different conditions ex) low TPP: antiterminator stem-loop forms high TPP: terminator stem-loop
lac repressor
a protein that regulates the lac operon by binding to the operator site and repressing transcription, normally bound when lactose is not present
activator
a regulatory protein that binds to DNA and increases the rate of translation
repressor
a regulatory protein that binds to DNA and inhibits transcription
trans-acting factor
a regulatory protein that binds to a regulatory element in DNA and exerts a trans-effect (lacI)
attenuator sequence
a sequence found in certain operons (trp operon) in bacteria that stop transcription soon after it has begun it's not far off from the trpL and is before trpE, trpD, trpC, trpB, and trpA genes and inhibits the production of tryptophan in the cell typically U-rich
cis-acting element
a sequence of DNA, such as a regulatory element, that exerts a cis-effect (operon)
operator site
a sequence of nucleotides in bacterial DNA that provides a binding site for a genetic regulatory protein
promoter
a sequence within a gene that initiates transcription
terminator
a sequence within a gene that signals the end of transcription
corepressor
a small effector molecule that binds to a repressor protein, thereby causing the repressor protein to bind to DNA and inhibit transcription
inhibitor
a small effector molecule that binds to an activator protein, preventing the protein from binding to the DNA and thereby inhibiting transcription
galactose transacetylase
an enzyme that covalently modifies lactose and lactose analogs by the attachment of hydrophobic acetyl groups. the acetylation of nonmetabolizable lactose analogs prevents their toxic buildup within the bacterial cytoplasm by allowing them to diffuse out of the cell
cis element in lac operon
operator, promoter sequence doesn't change merozygotes
trpL
part of the trp operon contains codons for 14 amino acids that form the trp leader peptide encourages 2-3 stem-loop or 1-2 and 3-4 stem-loop
cell division
some proteins are needed for cell division. these are necessary only when the bacterial cell is getting ready to. divide
metabolism
some proteins function in the metabolism of small molecules (example is certain enzymes are needed for a bacterium to metabolize particular sugars, enzymes required when sugars are present in bacterium's environment)
acetylation
stimulates transcription; reduces electrostatic attraction between DNA and histones (negative tail and negative charge of the histones so opens up and allows transcription to occur)
enzyme adaptation
the phenomenon in which a particular enzyme appears within a living cell only after the cell has been exposed to the substrate for that enzyme- due to the synthesis of specific proteins in response to lactose in the environment
allosteric regulation
the phenomenon in which a small effector molecule binds to a non-catalytic site on a protein and causes a conformational change that regulates the protein's function
feedback inhibition
the phenomenon in which the final product of a metabolic pathway inhibits an enzyme that acts early in the pathway; prevents a bacterium from overproducing the product of a metabolic pathway; when there's too much of the final product it binds to the enzyme 1
diauxic growth
the sequential use of two sugars by a bacterium (glucose is metabolized preferentially)
negative control
transcriptional regulation by a repressor protein
positive control
transcriptional regulation by an activator protein
when coupled and high trpytophan levels
trpL gene progresses to its stop codon when there's a sufficient amount of trpytophan already allowing 2 to be too far gone and the ribosome pauses which enables region 3 to hydrogen bond with region 4
inducible operons
usually encode catabolic enzymes
tryptophan
when it's high (2), it acts as a corepressor that binds to trp repressor which binds to the operator site and inhibits transcription