Chapter 15.2: Regulation of Transcription Initiation via DNA-Binding Proteins Flashcards
Does DNA act in trans or cis?
cis
What is the order of ZYA on the lac operon?
Order on bacterial chromosome is lacZ-lacY-lacA
Describe the helix-turn-helix (HTF) motif
• Two α-helical regions are separated by a turn
o One of the α helixes in each HTH-containing transcription factor carries unique amino acids that recognize a specific DNA sequence of nucleotides. As a result, various HTH-containing proteins can bind to unique DNA sequences
What does it mean to act in trans?
Elements that act in trans can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell
What is induction?
The process by which a specific molecule stimulates synthesis of a given protein
The process by which a specific molecule stimulates synthesis of a given protein is known as?
induction
What are pathways in which complicated molecules are broken down for the use of the cell?
catabolic pathways
What are pathways that allow cells to construct end product molecules they need from simple constituents?
anabolic pathways
What is the effect of lacI- mutations?
Mutations in a gene called lacI, located near but not within the lac operon, produce constitutive mutants that synthesize β-galactosidase and Lac permease even in the absence of lactose
What is the function of the repressor encoded by the lacI gene?
• The repressor protein prevents further transcription of lacY and lacZ by binding to a hypothetical operator site
What is the effect of supperrepressor (lacI^s) mutations?
The lacIS mutants, although they cannot bind inducer, can still bind to DNA and repress transcription of the operon
Define operon theory
o The operon theory suggests that a single signal can simultaneously regulate the expression of several genes that are clustered together on a chromosome and are involved in the same process
What is the effect of operator mutants?
When mutations change the nucleotide sequence of the operator, the repressor is unable to recognize and bind to the site; the resulting phenotype is the constitutive synthesis of the lactose-utilization proteins
• They call the constitutive operator DNA alterations oc mutations
What is the relationship between glucose and levels of cAMP?
When glucose is present, the level of cAMP remains low; when glucose is absent, cAMP synthesis increases
What are the 5 gene in order on the E. coli tryptophan operon?
o The E.coli tryptophan (trp) operon is composed of a group of five genes—trpE, trpD, trpC, trpB, and trpA—required for biosynthesis of the amino acid tryptophan
What does the lacA gene code for?
lacA encode a transacetylase enzyme that adds an acetyl group to lactose and other sugars
• not required for the breakdown of lactose
Define effector
a small molecule that binds to an allosteric protein or an RNA molecule and causes a conformational change
What is the function of the promoter site in the lactose operon in E. coli?
A promoter site, from which RNA polymerase initiates transcription of a polycistronic mRNA. The promoter acts in cis, affecting the expression of only downstream structural lac genes on the same DNA molecule
What is the function of the promoter site in the lactose operon in E. coli?
An inducer (allolactose) that prevents the repressor’s binding to the operator.
Define repressible regulation
the pathway should be turned on only when the cell does not have enough of the needed end product. If the end product is present in sufficient quantities, the pathway should be turned off/repressed so the cell does not waste resources trying to make molecules that it already has.
What means the pathway should be turned on/induced only when the complex molecules to be broken down (catabolites) are present in the cell’s environment?
inducible regulation
What is the function of B-galactosidase?
There the enzyme β-galactosidase splits the lactose into galactose and glucose (catabolic)
Define lac operon
a single DNA unit enabling the simultaneous regulation of the three structural genes in response to environmental changes
What type of regulation do catabolic pathways require?
inducible regulation
Define inducible regulation
the pathway should be turned on/induced only when the complex molecules to be broken down (catabolites) are present in the cell’s environment
What are catabolic pathways?
pathways in which complicated molecules are broken down for the use of the cell
Describe the levels of lac permease and B-galactosidase without lactose present?
The two proteins Lac permease and β-galactosidase are present at very low levels in cells grown without lactose
Where does the inducer bind?
to the repressor
What makes up the lac operon?
o Structural genes (lacZ, lacY, lacA) encoding proteins needed for lactose utilization, together with two regulatory elements—the promoter (P) and the operator (o)—make up the lac operon
Describe induction in the lac operon in E. coli
- When lactose is present, allolactose, an inducer derived from the sugar, binds to the repressor. This binding changes the shape of the repressor, making it unable to bind to the operator.
- With the release of the repressor from the operator, RNA polymerase gains access to the lac operon and initiates transcription of the three lactose-utilization genes into a single polycistronic mRNA
What does the lacZ gene code for?
LacZ encodes β-galactosidase
What are the two molecules that interact with the operon in prokaryotes?
repressor and inducer
Where does the repressor bind?
binds to the operon’s operator
What does the lacY gene code for?
LacY encodes Lac permease
Do proteins act in trans or cis?
trans
When does maximal expression the trp genes occur?
o Maximal expression of the trp genes occurs when tryptophan is absent from the growth medium
What is the function of lac permease?
A membrane protein, Lac permease, transports lactose in the medium in the E. coli cell
What are anabolic pathways?
pathways that allow cells to construct end product molecules they need from simple constituents
How does an inducer trigger enzyme synthesis?
The binding of inducer to repressor thus causes an allosteric effect that abolishes the repressor’s ability to bind the operator
• The inducer is an effector molecule that releases repression without itself binding to the DNA
Describe the dominance pattern of lacI gene mutations
lacI^s > lacI+ > lacI- in trans
Define operator site
a DNA sequence near the promoter of the lactose-utilization genes
Describe repression in the lac operon in E. coli
• In the absence of lactose, the repressor binds to the DNA of the operator, and this binding prevents transcription. The repressor this serves as a negative regulatory element
How is the trp operon controlled?
o The trp operon is controlled in part at the level of transcription initiation trough the action of a repressor protein that is the product of the trpR gene
Tryptophan functions as a corepressor for the TrpR repressor protein
What do constitutive mutants do?
• Constitutive mutants synthesize certain mutants all the time, irrespective of environmental conditions
What does it mean to act in cis?
Elements that act in cis can influence only the expression of adjacent genes on the same DNA molecule
What suggests that a single signal can simultaneously regulate the expression of several genes that are clustered together on a chromosome and are involved in the same process?
operon theory
What is The molecule responsible for stimulating production of the protein called?
inducer
What are the 3 domains of the lac repressor protein?
- Inducer-binding domain
- DNA-binding domain
- Multimerization domain
What is the function of the cAMP-CRP complex?
When bound to DNA, CRP helps recruit RNA polymerase to the promoter by making physical contacts with the polymerase enzyme; in essence, then, the DNA binding of CRP increases the ability of RNA polymerase to transcribe the lac genes
CRP thus function as a positive regulator that enhances the transcriptional activity of RNA polymerase at the lac promoter, while cAMP is an effector whose binding to CRP enables CRP to bind to DNA near the promoter and carry out its regulatory function
What is the function of the operator site in the lactose operon in E. coli?
A cis-acting DNA operator site lying very near the lac operon promoter on the same DNA molecule
What type of regulation do anabolic pathways require?
repressible regulation
What means the pathway should be turned on only when the cell does not have enough of the needed end product. If the end product is present in sufficient quantities, the pathway should be turned off/repressed so the cell does not waste resources trying to make molecules that it already has.?
repressible regulation
What does the lacI gene code for?
lacI encodes a negative regulator, or repressor
What is a protein that undergoes a reversible change in conformation when bound to another molecule?
allosteric protein
What is a DNA sequence near the promoter of the lactose-utilization genes?
operator site
How are partial diploid made?
The merodiploids (partial diploids) were made using F’ plasmids that carry a few chromosomal bacterial genes.
• When F’ (lac) plasmids are present in a bacterium, the cell has two copies of the region containing both the lactose-utilization genes and lacI—one on the plasmid and one on the bacterial chromosome
What is the function of the inducer?
prevents repressor from binding to the operator
What is allolactose and what is its purpose?
Lactose modified to a derivative known as allolactose is the inducer of the genes for lactose utilization
What is a result of helix-turn-helix motifs (HTF)?
Helix-turn-helix (HTF) motif in the protein fits well into the major groove of the DNA
What is a small molecule that binds to an allosteric protein or an RNA molecule and causes a conformational change?
effector
What is a single DNA unit enabling the simultaneous regulation of the three structural genes in response to environmental changes?
lac operon
What is the function of the repressor in the lactose operon in E. coli?
A trans-acting repressor that can bind to the operator. The repressor is encoded by the lacI gene, which is separate from the operon and is unregulated. After synthesis, the repressor diffuses through the cytoplasm and binds with its target
What sugars is lactose composed of?
o Lactose is composed of glucose and galactose
Define operons
o Clusters of genes regulated through mRNA transcription
What are o Clusters of genes regulated through mRNA transcription ?
operons
Define inducer
The molecule responsible for stimulating production of the protein
Define allosteric protein
a protein that undergoes a reversible change in conformation when bound to another molecule
Why is the overall effect of glucose in preventing lac gene transcription known as catabolite repression?
The overall effect of glucose in preventing lac gene transcription is known as catabolite repression, because the presence of a preferred catabolite (glucose) represses transcription of the operon
Describe the cAMP-CRP complex
Inside bacterial cells, the small nucleotide known as cAMP (cyclic adenosine monophosphate) binds to a protein called cAMP receptor protein, or CRP
The binding of cAMP to CRP enables CRP to bind to DNA in the regulatory region of the lac operon near the promoter
