Gene Regulation Flashcards
How goes transcription occur in bacteria?
RNA polymerase binds to the promoter region
Constitutive Genes
Genes that are always expressed in the cell. Housekeeping genes.
Where does the majority of regulation in bacteria take place?
Transcriptional level
The operator
Area upstream of the promoter. Binding site for proteins that help to regulate gene expression.
Repressors
Bind to operator to prevent RNA polymerase from initiating transcription
Activators
Bind to an operator and allow RNA polymerase to initiate transcription
LacZ
Beta-galactosidase. Protein that is produced when lactose is present. Hydrolyzes lactose to glucose and galactose
LacY
Permease. Allows for active transports of lactose across cell membrane.
LacA
Transacetylase. Acetylase lactose.
LacZ, LacY, LacA
Genes that code for products that are involved in the catabolism of lactose.
What is the role of lac?
To break down lactose
LacI
Encodes a protein that shuts the system down when lactose is not present
What is the inducer for the lac operon?
Allolactose (isomer of lactose)
LacZ-, LacY-, LacA-
Structural gene mutations that lead to non-functional proteins
LacP-
Non-functional promoter, RNA polymerase can’t bind
LacOc
Nonfunctional operator, repressor can’t bind. Constitutive mutation.
LacI-
Non functional repressor, unable to bind the operator and turn off transcription
LacIs
Super repressor, unable to dissociate from operator. System is always off.
Negative control
When a repressor is used to turn the system off (Lac repressor)
Positive Control
When an activator protein is used to increase the efficiency of transcription
What is e.colis favorite carbon source?
Glucose, it is more efficient. lac is not on in presence of glucose
The hunger signal
Binding of CAP/CRP to the promoter, allowing transcription to occurs . CAP or CRP is first activated by cAMP. Lac operon is not expressed without the hunger signal. Must have lactose and the hunger signal for it to be expressed.
Cis regulatory elements
DNA binding sites. On the actual DNA. Can bind transcription factor or enhancers.
Trans regulatory elements
Modify expression of genes that are distract from the gene that created them. Typically transcription factors or enhancer binding proteins. Bind to Cis. Analogues to LacI
Consensus Sequence
Sequence among many genes that isn’t exact, but it is similar
Basal promoter sequence
Cis regulatory element. Bind transcription factor proteins which are associated with RNA polymerase. Include that CAAT and TATA box.
Proximal control regions
These bind transcription factor proteins and are near the promoter
Enhancer sequence
Are found far away from the promoter
What does the basal transcription machinery do?
Allows a low level of expression
What do proximal promoters do?
Increase expression and provide specificity
What do enhancer binding transcription factors do?
Provide more specificity and amplify expression further
Bending of DNA
Allows an enhancer binding protein to interact with the transcription factor and enhance transcription by RNA polymerase II
DNA Binding Domain
Area on trans element transcription factor that only binds specific DNA
Dimerization Domain
Two transcription factors that have been bound together to form a functional DNA binding unit.
Activator/repressor Domain
Binds to the enhancer binding protein and modulates their function
What are the three transcription factors that must dimerize to function?
Zinc finger, helix-turn-helix, and leucine zipper
What are the three modes by which transcription factors can act as repressors?
Competition, quenching, and blocking
Competition
Binding of the repressor to the enhancer sequence competes for the DNA binding site of the activator
Quenching
Repressor protein binds to and interferes with the DNA binding domain of an activator protein. Now the activator cannot bind the enhancer sequence.
Blocking
Repressor binds to the activation domain of activator protein and prevent it from interacting with the basal transcription machinery. May reduce transcription levels
Response elements
Short sequences of DNA within a gene promoter region that are able to bind a specific transcription factor and regulate transcription of gene. Turn on/off genes
Hypoxia Response Elelements
HIf1-a and HIF1-b dimerize and bind to DNA sequences to regulate expression of genes. HIF1a is degraded in the cytosolic under normoxia. Binds to DNA in the nucleus.
Mac/myc
Regulatory system for switching between gene activation or repression.
In the absence of Myc…
Max form a homodimer and it represses gene transcription
In the presence of Myc…
A Myc/Max heterodimer if formed to activate gene expression
Myc Overexpression
Distrusts the equilibrium between activation and repression of genes and can lead to cancer. Impairs differentiation and promotes cell proliferation.
Burkitt Lymphoma
Caused if Myc is controlling the immunoglobulin promoter and enhancer control system.
Drosha
Processes long primary miRNA to pre-miRNA hairpin structures
Dicer
Further processes the pre-miRNA to ssRNA and initiates the formation of the RNA induced silencing complex (RISC)
What is the main function of miRNA?
To silence genes by preventing translational machinery
What are the two modes by which miRNA regulates translation?
Inhibition of translation on the ribosome or degradation of the target mRNA
siRNA
Short interfering RNA. Regulates expression at the mRNA level. Processed by dicer.
What is the main function of the activated GR?
Up-regulates the expression of anti-inflammatory genes in the nucleus and repressed the expression of pro-inflammatory proteins in the cytosol.
