Biology – 261

Chapter 8
- Major modes of regulation
o Gene expression: transcription of gene into mRNA followed by translation of mRNA into
a protein
 Genes for proteins and when the genes are transcribed and translated it is called
gene expression
o Most proteins are enzymes that carry out biochemical reactions essential for cell growth
 Cell will make proteins when they are needed and to do that the genes are
transcribed and translated (expressed)
o Constitutive proteins are needed at the same level all the time
 Enzymes like the ones that are needed for glycolysis are needed all the time are
called constitutive genes
o Microbial genomes encode many proteins than are present at any one time
 Enzymes for lactose fermentation are not needed when a cell has glucose and
does not lactose so those genes would only be expressed when they are needed
o Regulation is important in all cells and helps conserve energy and resources
 Repression of genes is called regulation
 Lac operon: lactose fermentation expression
 Lac operon considered inducible operon because can be turned on and off
- Two major levels of regulation in cell
o One controls the activity of preexisting enzymes
 Posttranslational regulation
 Very rapid process (seconds)
 Feedback inhibition
o One controls the amount of an enzyme
 Regulate level of transcription
 Regulate translation
 Slower process (minutes)
o Remember cell only needs to make proteins when it needs them
- DNA binding proteins
o Multiple outcomes after DNA binding are possible
 DNA binding protein may catalyze a specific reaction one the DNA molecule
(transcription by RNA polymerase)
 The binding event can block transcription (negative regulation)
 If it is a repressor protein and binds to the operator region of a gene then it
will block transcription  negative regulation
 The binding event can activate transcription (positive regulation)
 If a protein binds so that transcription occurs and protein is not a polypeptide
 positive regulation
- DNA binding proteins: Many such proteins are dimers that combine specifically with two sites
on the DNA
- Inverted repeats: specific DNA sequences that interact with the protein
- RNA polymerase: binds to promoter sequence then promoter sequence then operator
(repressor protein binds here)
- Negative control of transcription: Repression and induction
o Negative control: a regulatory mechanism that stops transcription
 Repression: prevention the synthesis of an enzyme in response to a signal
 Enzymes affected by any repression make up a small fraction of total proteins
in the cell
 Typically affects anabolic enzymes (biosynthesis)
 Enzyme repression: cell makes things when it needs them then turns them
off when it doesn’t
 o Note: that negative control is when repressor protein binds to operator
region on the gene  repressor is almost like the polymerase so it
stops the polymerase from making the mRNA
o Regulatory gene: makes the repressor proteins which are inactive
unless activated and then bind to operator
 Induction: production of an enzyme in response to a signal (making it happen)
 Typically affects catabolic enzymes (lac operon)
 Enzymes are synthesized only when they are needed
o No wasted energy
o Allolactose: inducer because stimulates lactose production
o When gene is repressed, it is because cell doesn’t need gene product
o When inducer is present it will cause induction of operon so that cell
will have enzymes to do what it needs
 Enzyme induction: lactose  allolactose  binds to repressor proteins which
inactivate them and allow lactose to be made
 Inducer: substance that induces enzyme synthesis
 Corepressor: substance that represses enzymes enzyme synthesis
 Effectors: collective term for inducers and repressors
 Effectors affect transcription indirectly by binding to specific DNA-binding proteins
 Repressor molecules bind to an allosteric repressor protein
 Allosteric repressor becomes active and binds to region of DNA near
promoter called the operator
 Operator: cluster of genes arranged in a linear fashion whose expression is under
control of a single operator
 Operator is located downstream of the promoter
 Transcription is physically blocked when repressor binds to operator
 Enzyme induction can also be controlled by a repressor
 Addition of inducer inactivates and transcription can proceed
 Repressor’s role is inhibitory so it is called negative control
o Steps: RNA poly binds to promoter followed by operator, repressor protein binds to
operator to block transcription (repression/negative control), if the inducer (allolactose)
is preset then it binds to the repressor protein which changes its shape and prevents it
from binding to operator, with nothing blocking polymerase it is able to copy structural
genes to make mRNA for proteins coded for by gene
- Positive control of transcription
o Positive control: regulator protein activates the binding of RNA poly to DNA (making
transcription happen)
 Example: Maltose catabolism in E coli
 Maltose activator protein cannot bind to DNA unless it first binds to maltose
o Activator proteins bind specifically to certain DNA sequence (There is a activator protein
that binds to the DNA at the activator binding site and then the RNA poly binds and
trans or expression of gene beings/ helps poly recognize promoter)
 Called activator binding site, not operator
o Promoters of positively controlled operons only weakly bind RNA poly
o Activator protein helps RNA poly recognize promoter and several mechanism
 May cause a change in DNA structure
 May interact directly with RNA polymerase
o Activator-binding site may be close to the promoter or several hundred base pairs away
- Positive control of enzyme induction in maltose operon
o Absence of an inducer, neither activator protein nor the RNA poly can bind to the DNA
o An inducer molecule (maltose) binds to the activator protein, which in turn binds to the
activator – binding site. This allows the RNA poly to bind to the promoter and begin
transcription
 o Genes for maltose are spread out over the chromosome in several operons (Maltose
operons: positively controlled operon because activator binding sites and activator
proteins)
 Each operon has an activator-binding site
 Multiple operons controlled by the same regulatory protein are called regulon
o Regulons also exist for negatively controlled systems
- Activator protein interactions with RNA poly
o Activator binding site is near the promoter
o Activator binding site is several is several hundred base pairs from promoter
 In this case, DNA must be looped to allow the activator and the RNA poly to
contract
- Global control and the Lac Operon
o Global control systems: regulate expression of many different genes simultaneously
o Catabolite repression is an example of global control because many different genes are
regulated at the same time  once glucose gets used up then the cell needs the
enzymes to break down the other sugars like lactose to get the glucose that it needs to
make ATPs  lac operon will be induces and cells will be able to grow
 Explains when cells use glucose first
 Cells does not need to express te genes for the metabolism of any other sugars
 Synthesis of unrelated catabolic enzymes is repressed if glucose is present in
growth medium
 Lac operon is under control of catabolite repression
 Ensures the “best” carbon and energy source is used first
o Diauxic growth: two exponential growth phases (switching of growth on just glucose to
using lactose results in two exponential growth phases)
o Cyclic AMP and CRP
 In catabolic repression, transcription is controlled by an activator protein and is a
form of positive control
 Cyclic AMP receptor protein (CRP) is the activator protein
 Cyclic AMP is a key molecule in many metabolic control systems (made from ATP
by enzyme adenylyl cyclase)
 It is derived from a nucleic acid precursor
 It is a regulatory nucleotide
 Note: cells will only use glucose over other sugars and thus will only trans genes
to make enzymes to use other sugars when glucose is not available
o Dozens of catabolic operons affected by catabolite repression
 Enzymes for degrading lactose, maltose, and other common carbon sources
o Flagellar genes are also controlled by catabolite repression
 No need to swim in search of nutrients
o Note: goal for cell is to get nutrients, primarily glucose, that it needs to grow and all the
control mechanisms help the cell to achieve this goal
- Two-component regulatory systems
o Prokaryotes regulate cellular metabolism in response to environmental fluctuations
(temperature, pH, nutrients, etc)
o In order to adapt to change, cells have mechanisms to take the info and signal cell to
make needed proteins or to stop making proteins
 External signals is not always transmitted directly to the target to be regulated
 External signal can be detected by a sensor and transmitted to regulatory
machinery  signal transduction
 Most signal transduction systems are two-component regulatory systems
o Made up of two different proteins
 Sensor kinase (cytoplasmic membrane): detects environmental signals and
sutophosphorylates
 Response regulators (cytoplasm) DNA-binding protein that regulates transcription
o Absent in bacteria that live as parasites of higher organisms
 o Almost 50 different two component systems in E coli
 Examples include phosphate assimilation, nitrogen metabolism, and osmotic
response!
o Some signal transduction systems have multiple regulatory elements
o Some Archaea also have two component regulatory systems
- Quorum sensing
o Several different classes of autoinducers
 Acyl homoserine lactone was the first autoinducer to be identified
o Quorum sensing first discovered as mechanism regulating light production in bacteria
including V. fischeri
 Lux operon encodes bioluminescence
 Bioluminescence: enzyme responsible for this is luciferase and gene that codes for
this is lux operon
 Luciferase: bacteria make it unless there is enough of the cells to male luciferase
they will not make it
 Bacteria that makes it is gram negative curved rod, Vibrio fischeri
o Examples of quorum sensing
 P. aeruginosa (gram neg rod) switches from free living to growing as a biofilm
 Example: scum across top of bucket that has been out a long time
 Virulence factors of S. aureus
o Quorum sensing is present in some microbial eu (switching from being free living to
growing as a biofilm)
o Quorum sensing likely exists in archaea
o Staphylococcus aureus is a gram pos cocci that is pathogen
o Some of it virulence factors like toxin production are controlled by quorum sensing
- Other global control networks
o Several other global control systems
 Aerobic and anaerobic respiration
 Catabolic repression
 Nitrogen utilization
 Oxidation stress
 SOS response
 Heat shock response
 Another global control mechanism
- Attenuation
o Transcriptional control that functions by premature termination of mRNA synthesis
 Control exerted after the initiation of transcription but before its complete
 First example was the tryptophah operon in E coli
 mRNA stem-loop structure and synthesis of leader peptide are determining factors
in attenuation
o Genomic evidence suggest attenuation exists in archaea