Lecture 16 -- Principles of Regulation Flashcards
_____ encompasses a range of mechanisms to increase or decrease the production of a specific gene products (protein/RNA/metabolites)
regulation
What are the three basic levels of regulation?
1) Gene expression (transcription)
2) Protein production (translation)
3) Protein function
Name at least three causes of adaptation
- changes in temp, osmotic stress, pH, oxygen
- fluctuations in nutrient supply/starvation
- loss or build up of metabolic intermediates
- in vivo/in vitro environment
- change in population size
Name at least three outcomes of adaptation
- altered metabolic activity
- macromolecule synthesis
- cell morphology changes
- changes in transcription
- altered fitness
What are the main three adaptation through signal transduction systems
- two component
- c-di-GMP-dependent regulation
- quorum-sensing
Name the concept: certain proteins, secondary metabolites, or processes are only required at particular stages or under certain conditions
conservation of energy
Name the concept: changes in the environment require activation/suppression of specific pathways or mechanisms
survival
the process by which information encoded in a gene is synthesized into a functional gene product
gene expression
genes that encode cellular components that perform housekeeping functions
constitutive
genes that are expressed only when their products are required for growth (inducible and repressible)
non-constitutive
characteristics of inducible genes (for lactose utilization)
- induced when glucose is absent and lactose is present
- occurs at the level of transcription (alters the rate of enzyme synthesis)
- often enzymes involved in catabolic pathways
characteristics of repression genes for tryptophan biosynthesis
- turned on in the absence of tryptophan/turned off when available
- occurs at the transcriptional level
- often enzymes involved in anabolic pathways
name the characteristics of allosteric regulation
- rapid response
- does not require inhibition or promotion of gene expression
- primary metabolic pathways
name the characteristics of protein modification
- rapid
- leads to alteration of activity or interaction
name the characteristics of protein modification + transcriptional regulation
- slower
- used in response to stressed or altered environmental conditions
- can be global
name the characteristics of signaling among bacteria
- used to alter the activities of a bacterial community
the alteration of DNA structure via modification; results in stable phenotypes that can be transferred from parent to offspring
epigenetic regulation
name the step these mechanisms control: promoter structure/sigma factor, activator, repressor, termination
transcription
name the step these mechanisms control: attenuation, autogenous translational repression, mRNA stability
translation
name the step these mechanisms control: feedback inhibition/activation, chemical/physical modification, degredation
enzyme activity
when a single regulator (transcription factor) regulates multiple genes at the same time
coordinate/simultaneous regulation
when a single regulator or cascade of regulators (transcription factor) regulates multiple genes in a defined temporal series of events
sequential regulation
- interact with RNA polymerase
- positions RNA pol on the promoter region upstream of genes
- contain alternative forms
Sigma factors
- bind to the promoter region of genes
- can repress or induce genes based on where they bind the promoter region and how they interact with RNA pol
- can be turned off or on by binding small molecule metabolites or by post translational modification
- ex: lac operon
activators and repressors
- interaction of products with mRNA to impact the completion of transcription
- ex: tryptophan regulation
termination/antitermination
- interacting with mRNA to affect stability
- interaction to impact function of the ribosome
- asRNA interaction with mRNA to regulate translation
post-transcriptional/translational regulation
- the different RNA structures undergoing cleavage events and modifications during maturation
- the selective breakdown RNAs to regulate gene expression
RNA processing; RNA degradation
- a metabolite binds, stabilizes a secondary mRNA structure, leaves the SD and initiation codon in base-paired region
- note high temperatures can overcome this
repression of translation
- a metabolite binds, secondary structure mRNA is stabilized, leaves SD and AUG in unpaired region allowing for ribosomal access
activation of translation
list whether these are enzyme mediated or nonenzymatic: phosphorylation, methylation, adenylation
enzyme mediated
list whether these are enzyme mediated or nonenzymatic: redox, nitrosylation, glycation
nonenzymatic
What type of enzyme mediated adaptation do histidine kinases illustrate?
phosphorylation (the addition of a phosphoryl group)
- CheB removes these groups from glutamate residues
- CheR adds these groups to the same glutamate residues
- memory is encoded in the protein, enzyme-mediated
methylation (through methyl-accepting chemotaxis proteins)
- when an AMP molecule is covalently attached to the side chain of a protein, altering its function
- virulence factors secreted by bacteria carry this out on GTPases, causing actin cytoskeleton changes
Adenylation/AMPylation
- covalent bonding of sugar molecule to protein or lipid molecule without the controlling action of an enzyme
glycation
- changing protein structure through binding of second messenger or activator
- protein-protein interaction changes
- protein localization changes (cell division/septum formation)
physical modification
