Gene Regulation Flashcards
In regards to the lac operon in the presence of lactose, will the genes be transcribed in large amounts?
Possible Answers:
Yes; the lactose sugars bind transcription factors that turn on transcription
Yes; the lactose sugars remove the repressor and the genes will be transcribed rigorously
Maybe; it depends on the concentration of glucose
No; the lac operon does not utilize lactose sugars in its regulatory mechanism
Maybe; it depends on the concentration of glucose
Explanation:
Activation of the lac operon is necessary for the transport and metabolism of lactose sugars by E. coli. Lactose sugars actively work to remove a repressor that statically inhibits transcription; however, high concentrations of glucose (and, thus, low concentrations of cAMP) will prevent these genes from being transcribed rigorously. In order for the lac operon to be active at high levels, lactose must be present and glucose must be absent.
Which of the following conditions are crucial to maintain high activation of the lac operon?
Possible Answers:
Large concentrations of cAMP and large concentrations of lactose
Large concentrations of cAMP and large concentrations of glucose
Low concentrations of cAMP and large concentrations of lactose
Large concentrations of glucose and large concentrations of lactose
Large concentrations of cAMP and large concentrations of lactose
Explanation:
The lac operon is a system designed to only express particular proteins when the concentration of glucose is low and the concentration of lactose is high. The common cellular response to a low concentration of glucose is to increase the concentration of cAMP in order to activate various alternative metabolic pathways. Both a high concentration of cAMP and a high concentration of lactose are necessary to get sustained expression of the lac operon. When glucose levels begin to rise, the cAMP concentration will begin to fall and the operon function will deteriorate.
Which of the following choices best represents the phenotype of a cell containing a mutation in the lac I gene?
Possible Answers:
No expression of the operon; RNA polymerase cannot bind properly
Lactose cannot enter the cell
Lactose can enter the cell, but cannot be broken down
Constitutive expression of the lac operon
Constitutive expression of the lac operon
Explanation:
lac I is the gene that encodes for the repressor of the lac operon. If there is no repressor, the cell will constantly express the genes present in the lac operon whether or not the typical conditions are present.
A mutation of the gene encoding β-galactosidase permease (lac Y) would prevent lactose from entering the cell. A mutation in the gene encoding β-galactosidase (lac Z) would prevent the breakdown of lactose. A mutation in the promoter region would prevent RNA polymerase from binding.
In prokaryotes, functionally related genes are sometimes position adjacent to each other in the genome and can under the control of the same regulatory machinery. What are these called?
Possible Answers:
Operons
Promoters
Operators
Activators
Repressors
Operons
Explanation:
Prokaryotic organisms often have functionally related genes joined together on the chromosome under the direction of a single promoter. These structures are called operons. Operons have additional sequences, called operators that can be bound by either repressor or activator proteins, which will repress or activate transcription of the operon. One commonly studied example is the lac operon, whose genes encodes products required for lactose metabolism.
Inducible operons are bound by a repressor and turned off under normal conditions. How are these operons turned on?
Possible Answers:
The transcription of the repressor protein is inactivated
A second repressor protein binds to and represses the repressor
An inducer molecule binds to and inactivates the repressor
An inducer molecule competes with the repressor for binding to the operator
An activator protein displaces the repressor on the operator
An inducer molecule binds to and inactivates the repressor
Explanation:
Negatively regulated operons that are said to be inducible have their operator sequence bound by a repressor molecule normally. That leads to these operons being off normally. For these operons to be turned on and transcribed, a small molecule called an inducer has to bind to and inactivate the repressor protein.
Where are promoters typically found in DNA?
Possible Answers:
In the 3’ UTR
Upstream of the coding region of a gene
In the middle of the coding region of a gene
Downstream of the coding region of a gene
Upstream of the coding region of a gene
Explanation:
Promoters are the sites where transcription factors and RNA polymerase bind to initiate transcription. It makes sense that the promoter would be found upstream of a gene (i.e. before a gene). “Downstream of the coding region” and “in the middle of the coding region” are redundant answers, and neither describes a location where a promoter would normally be located. The 3’ UTR describes a region of mRNA and, thus, has nothing to do with promoters.
__________ are regions of DNA, located __________ of a gene, that will increase its expression.
Possible Answers:
Silencers . . . either upstream or downstream
Enhancers . . . either upstream or downstream
Silencers . . . upstream
Enhancers . . . upstream
Enhancers . . . either upstream or downstream
Explanation:
As the name suggests, enhancers enhance the expression of a gene; they increase the number of mRNA transcripts produced from said gene. Silencers do the opposite, and repress the expression of a gene by serving as a binding site for repressors. It does not matter exactly how far enhancers are from the gene (either upstream or downstream) as long as they are geometrically close.
Which of the following does not represent a feature of bacterial transcription that is not found in eukaryotic transcription?
Possible Answers:
Bacterial transcription occurs in the cytoplasm
Transcription and translation are coupled in bacteria
Bacteria rely on a single RNA polymerase
The bacterial genome utilizes 3 kinds of promoter elements
Bacterial RNA polymerase has a number of subunits that interact with initiation factors to form a holoenzyme
Bacterial RNA polymerase has a number of subunits that interact with initiation factors to form a holoenzyme
Explanation:
Bacterial RNA polymerase is very similar to eukaryotic RNA Polymerase II in that both have many subunits and form a holoenzyme with cofactors. The rest of the answers are in fact unique to bacterial transcription.
What proteins enhance transcription by promoting the recruitment of transcription factors and stabilizing the RNA polymerase holoenzyme at the promoter?
Possible Answers:
Histone acetyltransferases
Coactivators
Corepressors
DNA methyltransferases
Histone acetyltransferases
Coactivators
Explanation:
Coactivators increase gene expression by binding to a transcription factor, recruiting other transcription factors and cofactors, and stabilizing the RNA polymerase holoenzyme to ensure that it can pass the promoter and begin transcribing coding sequence. Corepressors repress transcription, while histone methyl/acetlytransferases act on histone proteins. DNA methyltransferases methylate DNA to establish epigenetic marks that generally inhibit transcription.
What regulatory element promotes RNA polymerase II binding as well as binding of factors that facilitate the unwinding of DNA prior to translation?
Possible Answers:
5’ untranslated region
TATA box
3’ untranslated region
None of the other answers
Translation start site
TATA box
Explanation:
The correct answer is TATA box. Found in about 24% of human gene promoters, this regulatory element is mostly found in genes transcribed by RNA polymerase II, and as such, recruits this enzyme to the promoter. Additionally, the TATA binding protein aids in unwinding DNA.
In a hypothetical situation, the enhancer region of gene X, which controls tail length in mice, is mutated such that transcription factors bind to the enhancer region at a much higher efficiency than if the region were wild-type. What is a reasonable phenotypic outcome possible from this mutation in gene X’s enhancer region?
Possible Answers:
The mouse will be globally larger because increased transcription at the enhancer will impact any gene behind the enhancer.
Tail length is increased due to increased activity of the gene’s promoter.
There will be no phenotype because enhancers are not coding regions.
Tail length is decreased because any mutation will cause a loss-of-function of these regulatory regions.
Tail length is not changed because the enhancer region does not dictate gene expression.
Tail length is increased due to increased activity of the gene’s promoter.
Explanation:
This question is inspired by a real life example, in which if you put a bat enhancer region in front of the gene that controls limb development in mice, the limbs are longer due to changes in the enhancer activity, which increases the activity of the promoter. By permitting more transcription factor interaction with the regulatory region, one might expect that this type of mutation may increase the tail length of the mouse because more “pro-tail length” protein is being made.
Histone acetyltransferases (HATs) transfer acetyl groups from acetyl CoA to lysine residues on histones. What is the purpose of this transfer?
Possible Answers:
Facilitate phosphorylation of these lysines by kinases
Promote formation of euchromatin and increase gene expression
Prevent DNA degredation by endonucleases
Signal for ubiquitin-mediated degredation of histones
Prevent transcription factors from binding to DNA
Promote formation of euchromatin and increase gene expression
Explanation:
The correct answer is to promote formation of euchromatin and increase gene expression. Acetylation of histones “relaxes” DNA coiling around histones by reducing the affinity between histones and DNA. This allows transcription factors to bind promoter regions and promote increased gene expression via transcription.
What is the role of mediator in gene expression?
Possible Answers:
Mediator is a thermostable DNA polymerase that replicates DNA in extreme temperatures
Mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II
Mediator facilitates alternative splicing of newly synthesized mRNA transcripts
Mediator suppresses transcription by methylating histone lysines
Mediator is not involved in gene expression
Mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II
Explanation:
The correct answer is that mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II. Mediator does not directly initiate transcription; however, by protein-protein interactions, it recruits the necessary proteins to sites of transcription.
NFkB is a transcription factor that is held inactive in the cytoplasm when bound by its inhibitor, IkB. Upstream signaling that activates NFkB causes what effect?
Possible Answers:
Ubiquitin-mediated degradation of IkB, causing a conformational shift in NFkB that renders its DNA-binding domain inaccessible
Ubiquitin-mediated degradation of NFkB
Ubiquitin-mediated degradation of NFkB, allowing IkB to translocate to the nucleus and initiate transcription
Ubiquitin-mediated degradation of IkB, allowing NFkB to translocate to the nucleus and initiate transcription
Recruitment of transcription factors and coactivators of transcription to the cytoplasmically sequestered NFkB
Ubiquitin-mediated degradation of IkB, allowing NFkB to translocate to the nucleus and initiate transcription
Explanation:
Upstream signaling, such as from a toll-like receptor, causes IKK to phosphorylate IkB, signaling for its ubiquitin-mediated degradation. Since NFkB is no longer bound by its inhibitor, IkB, it translocates to the nucleus where it binds specific motifs in the genome to recruit other transcriptional machinery and initiate transcription.
Which of the following is not a way in which transcription factors influence gene-specific transcription?
Possible Answers:
Binding transcription factor-specific DNA motifs
Recruiting DNA polymerase
Recruiting other transcription factors
Promoting euchromatin formation
Recruiting RNA polymerase holoenzyme
Recruiting DNA polymerase
Explanation:
The correct answer is recruiting DNA polymerase. DNA polymerase is involved in DNA replication, not transcription. Pioneer transcription factors can bind specific DNA motifs and promote euchromatin formation, allowing other transcription factors to bind the less organized DNA. Transcription factors can recruit other transcription factors and the RNA polymerase holoenzyme to promoters to promote gene-specific transcription.
