Unit 2 Flashcards
What is generation time?
Time to double in cell number; varies depending on species
What type of cells typically have a longer generation time?
Cells with hard cell waxes
What is the log phase of a growth curve?
Where bacteria are mainly taken from
What is the stationary phase of a growth curve?
Where cell death = cell death and nutrients becomes limited
what is the death phase of a growth curve?
Where cell death is greater than replication, cells are still replicating and dead cells become nutrients for living ones
What are the four stages of the growth curve?
Lag phase, log phase, stationary phase, and death phase
what is quorum sensing?
when bacteria are able to detect population density and alter gene expression
How does quoroum sensing work in gram negative bacteria
AHLs are specific for each species and diffuse throughout the cell. AHLS bind to LuxR proteins in the cell causing them to from a dimer. LuxR binds to genome causing synthesization of molecules and decrease in synthesization of others.
How does quorum sensing work in gram positive bacteria
Peptides are sensing molecules that never come back into the cell but attach to a kinase that can phosphorylate response regulators to affect gene expression
How agr operon work in Staph aureus
toxic materials are made when high pop. agrB makes molecules that are secreted to the membrane to secrete AIP that bind to kinases to upregulate kinase activity. Phosphates are then transferred to agrA that upregulates operon and blocks protein synthesis
Explain the realtionship between squids and vibrio fischeri
bacteria produce light via Lux operon which protect the squid from predators. Use of the Lux operon produces a lot of waste products so when sunrise hits the squid expel 95% of bacteria to allow regrowth during the day
How does the Lux operon work
Luxl produces HSL at low levels so that when high pop density LuxR binds to HSLs then to Lux box. Genes to the right of the box are tuned on (LuxL to upregulate itself and Lux CDAE to produce light)
What are cardinal temperatures
the maximum, minimum, and optimal temperatures for bacteria
What are psychotrophs
optimal at room temp and can survive at refrigerated temperatures
what are mesophiles
mostly cause disease most common ones
What is the process of PCR
dsDNA temperature is raised to cause annealing, atrificial pieces of DNA are put into DNA, temperature is raised to Taq to make new DNA, now DNA is doubled
What are the differences between prokaryotes and eukaryotes for transcription and translation
prokaryotes have polycistronic mRNA that encodes multiple protein but eukaryotes can’t have this due to nucleus. Archaea have so many more RNAP compared to bacteria making them more related to eukaryotes than bacteria.
How is RNAP made in bacteria
alpha one and two bind to large beta protein, beta prime and omega subunit bind, alpha subunit and beta protein bind to make core enzyme, sigma binds to core enzyme to make holoenzyme
What part of the holoenzyme engages with DNA
Sigma protein which binds to the -10 and -35 elements of DNA
what are the landmarks of RNAP in bacteria
+1: where transcription starts, spacer region (17 random bps used to separate promoters so they are on the same face of helix) and UP element that interacts with alpha subunits to help transcription
What is the transcription process
core RNAP melts DNA to make open complex, RNAP kicks sigma off, core enzyme slides down DNA to make mRNA (5’ to 3’)
What starts mRNAs
leader mRNA that has a Shine Dalgarno sequence to ensure proper binding of ribosome
What is the 30s subunit of polymerase do and how does it work
Has a piece of rRNA in it to hold subunits of RNAP together, binds to mRNA via a RNA-RNA interaction, is used to identify where translation starts and helps ribosomes bind to rRNA
What is the difference between prokaryotic and eukaryotic translation initiation
5’ leader is eukaryotes is extensive while in prokaryotes it is short. Multiple proteins are used to translate a protein then will fall off and another will translate next protein
In eukaryotes there are multiple polymerases but bacteria don’t have as many why?
bacteria have multiple sigma factors that are dropped and added as conditions change allowing different genes to be expressed
How are sigmas used in the act of transcription?
bacteria hold sigma factors in reserve that are bound by proteins when not needed. When needed, protein is bound to casuing a conformational change so it releases sigma which binds to core enzyme to begin transcription for needed proteins and also makes more sigma and anti sigma factors
How does the trp operon work?
Five different genes are encoded on gene to allow bacteria easy control over entire pathway. repressor gene is located to the left of operon that only works when trp is bound to it (negative control)
What are the two ways to end transcription
Factor dependent and factor independent
How does factor dependent ending of transcription work
Two factors; NusA binds to RNAP as it moves along DNA causing it to slow down so that Rho can bind to the mRNA and “chase” it. If it catches it, RNAP is pushed off but ribosomes block it, slowing it down
How does factor independent transcription termination work?
Inverted repeats allow a secondary structure to form in mRNA that causes RNAP to fall off.
What are inverted repeats?
Direct copy in a different area on complimentary DNA and when being used for terminatino will always be followed by a poly T tail
what is the significange of the first amino acid of bacteria
Is used a sort of signal if the amino acid is misfolded. If misfolded PDF won’t be able to remove the first amino acid thus the protein will be degraded
What is a missense mutation
single nucleotide change affecting the sequence of following nucleotides
What is phase variation
when a bacterial population is expressing two alterntive forms of a gene: on or off
What is the advantage of using phase variation
There is always a subpopulation of bacteria that are expressing the opposite of the others thus, if a sudden change causes the main population to be selected agaisnt then the subpopulation will live
What is the process of slipped strand DNA
DNA becomes dissasociated from template so strands no longer match up codon wise, This can cause a shift in the reading frame which can result in phase variation
Explain the relation between phase variation, slipped strand DNA, and the sabA protein
When phase off the stop codon is 15 codon in due to a dinucleotide repeat resulting in no sabA protein. But a mutation can occur due to slipped strand DNA where there there are more dinucleotide repeats causing a reading frame shift so that there is no stop codon anytime soon thus sabA protein is expresssed
What is antigenic variation
form of phase variation where bacteria can express on of multiple genes and can actively switch btwn them
What is the use of antigenic variation
genes can be switched out to evade the immune system thus there can be a higher infection rate
Explain how S enterica can have two forms of flagellin
When the host immune system becomes resistant to one form of flagellin the bacteria will switch to the other one. Random inversion is done. Promoter causes production of fljB and fljA genes (fljB creates H2 protein while fljA makes repressor for H1). When switching, the hin gene is expressed to make hin proteins that attach to the hixL and hixR (right and left) to flip hin gene causing the promoter to face the left and not the right like before. This causes H1 to be to be expressed since repressor isn’t expressed
explain how the N gonorrhoeae pilli works
The pilli have two loci: pilE results in expression while pilS results in supression. There are numerous pilS genes that can be switched out or mixed together to evade the immune system
Explain how the lexA operon works
Is a regulon that controls gene repair. When a mutation occurs making ssDNA recA attaches to it and lexA (repressor) so that lexA then degrades itself so that the regulon is then on causing transcription and DNA repair
What is a regulon
group of genes that are under control of one regulatory molecule
Explain tranlesion systhesis
The umuDC operon repairs DNA damaged by UV lights. recA stimulates lexA cleavage causing umuDC proteins to be made which allow DNAP to occur across from the damaged DNA dimer. The nucleotides put in are random so mutations are very common
How does enzyme repression work
Transcriptional control via a co-repressor. Enzymes stop being produced once there are enough but stopping is not rapid so resources are unnecesarily used and transcripts are made that do not become enzymes
Explain how arginine repression works
RNAP binds to the promoter that will cause transcription if there is a lack of agrinine. If there is enough, then the repressor protein will be bound by a co-repressor so that the repressor can bind to the operon
How does enzyme induction occur in the lac operon?`
Repressor allow a minor amount of transcription which is needed to allow some lactose into the cell. When beta galactosidase is low lactose is isomerized to form allolactose. This binds to the repressor to act as an inducer. The inducer causes a conformational change in the repressor which then cannot bind to the operon
How does the CAP protein work in the lac operon
When bound by cAMP, CAP site promotes transcription by making the RNAP more stable. But when there is a lot of glucose, cAMP is not being produced so there is a lack of transcription and lactose is not being brought into the cell though some is being transcribed
How does the phospho-transferase system work in the lac operon
If there is no glucose then enzmyes 2B and 2A become phosphorylated. 2A binds to adenyl cyclase causing cAMP production and affecting the production of glycerol and other carbs. When glucose is present the phosphate goes from 2B to 2A to glucose causing no production of cAMP and 2A to block lactose permease and glycerol transport (inducer exlusion)
How does the maltose utilization operon work
3 genes are needed to break maltose down. The activator protein binds to maltose to activate RNAP. The activator protein only works when maltose is bound to it. When there is not maltose the genes are not activated
How does attenuation works in the trp operon
It gets rid of leaking by stopping transcripts from going to completion. A leader peptide is formed by using tandem trps. When there are low levels of trp the ribosome has to wait for the two trps to come indicating that there is a lack of them. When this happens the ribosome covers region one creating a stem loop in regions 2 and 3 which becomes an antiterminator to prevent termination and keep transcription going. When there is a lot of trp, the peptide is easily made thus the ribosome covers region 2 making a stem loop in regions 3 and 4 which becomes a terminator.
How does post translational control work
Form of feedback inhibition that allows for efficient and rapid control and alters the activity of pre-existing enzymes. In this, the end product inhibits the first enzyme to conserve energy and resources
How does the two component signal transduction system work
sensory arm is used alongside a ligand to sense changes in the environment which then transfer that information to a response regulator that goes through allosteric modification to bind to DNA
How does osmotic regulation work
Porin proteins, OmpF and OmpC are different sizes. OmpF is larger for aqueous environments while OmpC is smaller for the colon due to a higher concentration of nutrients. An increase in osmolarity will cause more pressure on EnvZ so a phosphate is transferred to OmpR causing it to bind to high affinity sites when in low concentration and high and low affinity sites when in high concentrations.
what are the low and high affinity sites in E. coli
high affinity site is the promoter of OmpF while low affinity is repressor of OmpF and promoter of OmpC
What are plasmids
extra chromosomal elements of DNA that are usually circular
What are the two ways that plasmids can replicate
theta replication where there are two replication forks and DNA is made in two directions. rolling circle replication uses nuclease to nick a strand of the plasmid, polymerase binds to the 3’ side to add nucelotides, and a single strand is created while the other strand just makes copies of itself
How does the pR1 system work
LCP (low copy plasmids) use ParC on the plasmid to bind to a ParR polymer. ParM binds to form polymers that can bind to parR so polymers betweent the plasmids grow to push them to the sides of the cell then degrades
How does post translation killing occur
Used to ensure that any daugher cells that don’t have a plasmid are killed. CcdA encodes an antidote while CcdB encodes a toxin. The toxin can only be broken down the antidote which has a short half life than the toxin. Thus, if there is no plasmid then there is no way for the antidote to be made so that the toxins will be degraded
What are transfer genes
Genes that give the plamsid the ability to be transferred from one bacteria to another
How do transfer genes work
transfer gene encodes sex pilus that binds to other cells. Via rolling circle replication the plasmid is passed into the new cell. plasmid then goes from ssDNA to dsDNA
How does OriT replication work
Uses rolling circle replication only when an F- cell is present. The sex pilus grows from the root of the F+ cell
How does OriV replication work
uses F+ cell and replicated via theta replication
What is an episome
genetic elements that exist outside/inside the chromosome and switches between them
What is an Hfr cell and how does it occur
When F plamids is integrated into the bacterial chromosome
How is Hfr conjugation different from regular plasmid conjugation
The sex pilus is weak so an incomplete f plasmid is transferred along with bacterial DNA which can result in some extra genes that could be beneficial.
