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