CH. 10 Prokaryotic Gene Regulation Flashcards
How are genes organized in bacteria, specifically what is: (a) an operon; (b) structural and control genes; (c) mono‐cistronic & polycistronic; and (d) a regulon?
Operon: a cluster of functionally-related genes that are controlled by a shared operator
Structural Genes: genes that code for proteins and most RNAs except regulatory factors
Control Genes: genes that code for proteins or factors that control the expression of structural genes (turning other genes on and off)
Monocistronic/Polycistronic: one gene (monocirstronic) or multiple genes (polycistronic)
Regulon: a group or multiple operons
What is the role of regulatory proteins in a bacterial cell? Describe the levels at which control of gene expression can occur in a bacterium.
Regulatory Proteins: repressors and activators to regulate gene expression (repression/induction/corepressor/derepression)
Levels:
-DNA (methylation and phase variation)
-Transcription (affects RNA polymerase function)
-mRNA Stability (mRNA half-life)
-Translational (affect ribosome function)
-Post-translational (affect protein function; modify or degrade protein)
What are constitutive genes?
They are genes that are always active and expressed
Describe inducible and repressible operons. What is a co‐repressor? An inducer? What is derepression?
Inducible operons turn on transcriptional genes based on an inducer or enhancer (ex. lac operon)
-Inducers is a substance that is capable of activating the transcription of a gene by combining with and inactivating a genetic repressor (ex. allolactose)
-De-repression is the blockage/removal of the repressor
Repressible operons is the binding of a repressor to the operator that shuts off transcription
-Co-repressor is a molecule that binds to the repressor and turns off the transcription
Review the operon model of gene organization; describe the components and regulatory elements.
Promoter - DNA segment that allows the region of DNA to be transcribed and helps RNA polymerase to find where a gene starts
Operon - A group of closely linked genes that produces a single messenger RNA molecule
Regulatory Protein - Regulates operon via operator sequence
-Induction/De-repression: inducible - gene expression initiated (ON)
-Repression/Co-repressor: repressible - gene expression stopped (OFF)
Describe what the lactose operon is, and how the lactose operon functions in both the presence and absence of lactose.
A lac operon is a series of three genes (lacZ, lacY, & lacA) in bacteria to encode proteins/enzymes that allow bacteria to use lactose as an energy source
-LacZYA is a structural gene that code for the proteins for the transportation and metabolism of lactose. Low levels of lacZYA transcription always occur
-LacY transports and detects lactose
-LacZ at low levels converts the lactose into allolactose (an inducer that binds to the repressor to allow transcription of the lac operon to occur)
-LacI is a repressor that binds to the operator if lactose is absent
What is the cAMP-CRP complex? How does the cAMP‐CRP complex affect the expression of the lactose operon?
Cyclic AMP (cAMP) is a regulatory molecule that binds to cAMP regulatory protein (CRP) to form the cAMP-CRP complexes. These complexes bind to the lac promoter to increase transcription
cAMP levels fluctuate based on the cell’s energy level based on levels of glucose:
High glucose = low cAMP levels
Low glucose = high cAMP levels
How does the presence of glucose affect the expression of the lac genes?
Glucose can block the transport of lactose, meaning high glucose levels reduce levels of lac expression.
-Maximal lac expression will be if lactose is present & glucose absent
Glucose & lactose both present = catabolite repression occurs (repression of the lac operon, resulting in the resort to the secondary sources of carbon by glucose)
-Yield diauxic growth (growth in two phases); glucose is first consumed, cell growth pauses to turn on expression of lac operon, then lactose is consumed
-Glucose is a more favorable & efficient energy source
Describe what the tryptophan operon is, and how the tryptophan operon functions in both the presence and absence of tryptophan.
A tryptophan operon is a group of genes of a biosynthetic pathway that codes for enzymes for tryptophan synthesis. Regulation occurs via repressor (TrpR) and co-repressor (tryptophan)
Trp operon is expressed when low/no tryptophan presents; derepression occurs and transcription proceeds
Trp operon is turned off at high tryptophan levels; tryptophan acts as co-repressor and binds aporepressor; active holorepressor forms to block transcription of trp operon
What is transcriptional attenuation? How does this work in the presence/absence of tryptophan?
Transcriptional attenuation is a secondary strategy for regulating tryptophan synthesis. Attenuation relies on the formation of competing for stem-loop structures in the leader mRNA. TrpL (leader sequence) determines whether transcription can proceed through the genes in the trp operon
Presence of tryptophan:
-The attenuator loop forms at 3:4 after the translation of the trpL leader sequence
-The ribosome stalls at the stop codon
-Has charged trp tRNAs present
-Transcription of trp operon is prevented
Absence of tryptophan:
-Anti-attenuator loop forms at 2:3
-Ribosome stalls at trp codons before the translation of the trpL leader sequence
-Has uncharged trp tRNAs
-Transcription is continued
What is phase variation? How does this work in the expression of Salmonella enterica flagellar protein?
It is the alteration of protein-coding DNA sequences. It results in immune avoidance where the pathogens bypass host immune systems
In Salmonella enterica flagellar proteins, within the host, can switch between flagellin proteins H2 and H1 via recombination causing gene inversion (inactivation of one gene to activate another)
What is small regulatory RNA? How do these function in regulation?
They are untranslated RNAs with regulatory functions that occur between genes. Their features are that they are efficient due to not needing protein synthesis and can act on pre-existing messages
Some translational control mechanisms of sRNA include:
-Inhibiting/activating translation
-Promoting/preventing mRNA degradation
-Promoting processing
-Alters activity of regulatory protein
What are anti‐sense RNA’s? How do these function in regulating gene expression?
They arise from the transcription of sense DNA strands from protein-coding genes and are the complementary/template strand for producing mRNA
They reside and originate from the protein-coding gene and only affect the expression of that gene by binding to the mRNA segment to block translation (translational control mechanism)
What is the stringent response? How does this occur?
A reduction in energy sources requires a slowdown in ribosome formation due to the reduced cellular growth rate which stringent response decreases ribosomal RNA transcripts and increases starvation-induced responses
Components:
-ATP
-GTP
-RelA
-ppGpp (decreases expression of different genes)
How do sigma factors figure into gene regulation?
The regulation of sigma factors in bacteria can coordinate the gene expression of several genes at once in response to changing growth conditions or different stresses such as temperature
