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80 Cards in this Set
- Front
- Back
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What is the difference between inducible and repressible genes?
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Inducible = usually off, can turn on
Repressible = usually on, can turn off |
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What is the major effector molecule involved in inducing the Lac operon and how does it work?
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allolactose: binds LacI to make it release operator
produced by b-galactosidase in small quantities |
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What is the difference between an operator and a promoter?
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Operators are binding sites for gene repressors; usually downstream of promoters
Promoters are binding sites for RNA sigma subunits and usually promote gene expression |
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What is the role of CAP in the lac operon?
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CAP = catabolite activator protein, global regulator
CAP binds upstream of operator when bound by cAMP, strengthens weak Lac operon promoter. |
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How are levels of cAMP modulated in the cell?
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B subunit of glucose Phosphotransferase system.
High [B-P] = low glucose --> make cAMP with adenyl cyclase Low [B-P] = high glucose b/c B gives its P away to glucose --> no cAMP |
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Why is the lac operon not expressed when both glucose and lactose are present?
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Glucose suppresses production of cAMP --> no active CAP --> Lac operon has weak promoter and doesn't get expressed much.
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How is allosteric/feedback regulation involved in controlling the tryptophan biosynthesis operon?
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Trp inhibits anthranilate synthetase from making chorismic acid into Trp precursors.
~1000x decrease in anth.synthetase activity |
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How is the Lac operon positively regulated? How is it negatively regulated?
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Positive: CAP-cAMP binding to initiate transcription
Negative: removal of LacI repressor by allolactose |
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How is transcriptional regulation involved in controlling the tryptophan biosynthesis operon?
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Trp repressor synthesized in inactive form
High Trp levels activate repressor protein --> repressor binds operator, prevents transcription. |
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How is attenuation involved in controlling the tryptophan biosynthesis operon?
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leader peptide before Trp synthesis genes w/2 Trp residues and 4 internal basepairing regions
high trp --> ribosome makes entire leader peptide, 3/4 terminator loop forms and dislodges RNA Pol to stop transcription low trp --> ribosome pauses at 2 trps (no trp-TRNA's), antiterminator loop forms and RNA Pol transcribes Trp operon. |
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What is sequential feedback inhibition?
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Different end products control different points of the reaction flow through a branched pathway.
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How are isofunctional enzymes involved in gene regulation?
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Isozymes = same rxn, different enzyme, different effectors.
3 DAHP synthases, each inhibited by Trp, Tyr, or Phe, so that an excess of one does not inhibit synthesis of the others. |
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What is concerted feedback inhibition?
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Multiple allosteric effector molecules each have a percentage of effect on enzyme; multiple effectors needed to have full inhibition/activation.
Also allows different degrees of activity |
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How is Glutamine Synthase regulated?
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12 subunits w/8 allosteric sites each = 96 sites
covalent: attach AMP to each subunit (12 AMP), decrease activity allosteric: PII/UMP somethingsomething |
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How does Salmonella regulate flagellins with phase variation?
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Normally H2 promoter --> transcribe H2 + H1 repressor --> no H1 expression
Site Specific Recombination: flip H2 promoter around Flipped promoter --> no H2/H1 repressor --> H1 gene expressed. |
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How are RNAs involved in post-transcriptional regulation?
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short (~170 bases) regulatory mRNAs bind 5' end of the target mRNA --> ribosome cannot bind and translate
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What are riboswitches and how do they work?
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Specific metabolite binds target mRNA and interacts to either promote or inhibit translation.
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What are the parts of a typical 2-component environmental sensing scheme?
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1. sensor kinase w/His residue
input domain + transmitter domain phosphorylates Asp on response regulator usually transmembrane 2. response regulator w/Asp residue receiver + output (DNA binding) domains Asp phosphorylated by sensor His residue. |
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How does EnvZ control porin size?
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high turgor pressure = low osmolarity
low OmpR-P --> only bind high affinity DNA, transcribes OmpF low TP = high osm high OmpR-P --> binds high AND low affinity DNA sites, repress OmpF, activate OmpC + MicF |
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What is the role of MicF in regulation of E. coli porin size?
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MicF = inhibitory mRNA, binds OmpF mRNA and inhibits translation
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How does the Bobtail Squid utilize Vibrio fischeri?
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grows them in ventral surface light organs to produce counterillumination --> confuse predators that hunt by looking for shadows
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How does AHL quorum sensing work?
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LuxI makes AHL
LuxR detects AHL, binds DNA to activate quorum-controlled genes |
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What is the advantage of the AHL molecular structure?
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Has both hydrophobic and hydrophilic domains --> freely diffusible in a range of environments.
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How does AI-1/AI-2 signaling work?
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LuxS codes for DPD synthesis enzyme
DPD --> AI-2 signal molecule AI-2 --> LuxP membrane sensor --> LuxQ transducer --> LuxR regulator (DNA binding protein) LuxM makes AI-1 --> LuxN membrane sensor detects --> LuxR regulator binds DNA |
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What is thought to be the difference between AI-1 and AI-2 signaling?
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AI-1 is for intraspecies communication
AI-2 is for interspecies communication |
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What types of organisms use AHL signaling?
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Primarily gram-negative bacteria
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What types of organisms use AI signaling?
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both gram + and -
more widespread than AHL system |
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What types of organisms use signal peptides?
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primarily gram positive bacteria.
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How does AIP signaling work? (signal peptides)
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AgrD = signal peptide
AgrB = processes and exports peptide from cell via ABC transporter system AgrC = membrane sensor/histidine sensor kinase AgrA = aspartate response regulator, activates Agr operon transcription. |
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What are advantages of living in a biofilm?
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-interspecies metabolic interactions (byproducts of one are food for another)
-facilitate gene transfer (abx resistance, etc.) -increased resistance to antimicrobial stress -increased access to nutrients |
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What is an advantage of studying biofilms rather than pure cultures?
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Biofilm = natural environment, can see how organism behaves as part of ecosystem and observe species interactions
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What example was presented to illustrate metabolic interactions in biofilms?
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Burkholderia: 3-chlorobiphenyl --> chlorobenzoate
Pseudomonas: chlorobenzoate --> TCA intermediates flow cell culture fed 3-chlorobiphenyl: B/P growing in association with ea/o rather than in separate colonies |
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How do biofilms confer resistance to antimicrobial stress?
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-extracellular matrix (ECM) = diffusion barrier or reactive sink/buffer for antagonistic molecules
-slow growing subpopulations below surface are less susceptible to abx -"biofilm phenotype:" high cell density so "bilge pumps" are on to deal with high concentration of bacterial waste |
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What domain is conserved in cyclases such as the ones involved in formation of cyclic di-GMP?
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GGDEF
gly-gly-asp-glu-phe 2 GTP --> cdGMP + 2 PPi |
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What domain is conserved in phosphodiesterases such as the ones involved in degradation of cyclic di-GMP?
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EAL
glu-ala-lys cdGMP --> 2 GMP |
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What type of genome does phage MS2 have?
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linear ssRNA
small icosahedral capsid |
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What type of genome does phage ΦX174 have?
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+ strand circular ssDNA
icosahedral capsid |
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What type of genome does phage T4 have?
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linear dsDNA
tailed with icosahedral capsid |
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What type of genome does phage Λ have?
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linear dsDNA
simple tail with icosahedral capsid |
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What type of genome does phage M13 have?
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+ strand circular ssDNA
long, filamentous |
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What is the major distinction between generalized and specialized transducing phages?
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specialized: only xfer DNA adjacent to prophage
generalized: xfer any DNA segment that fits in capsid. |
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What is phage conversion?
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presence of prophage causes phenotypic changes in host cell
specifically, lysogen becomes immune to superinfection by same type of phage, become more pathogenic/make toxins |
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What types of lambda specialized transducing phages are possible?
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Lambda Bio or Lambda Gal: only xfer genes directly adjacent to prophage.
not capable of host lysis b/c phage genome incomplete; only xfer genes to new host. |
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What types of phages can be generalized transducing phages?
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only those that pack nonspecific DNA into capsid using the "headful" method
always dsDNA must be able to inject DNA into host |
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Why is T4 not a generalized transducing phage?
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It degrades the host genome so there is no host DNA left to mistakenly package into T4 capsids.
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What determines whether phage enters lytic or lysogenic cycle?
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Ratio of C1:Cro; C1 > Cro.
Cro protein activates lysis genes C1 is Cro repressor |
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What enzyme is critical for formation of a lysogen/prophage association?
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INTEGRASE enzyme: inserts lambda genome at a specific "att" (attachment) site on host chromosome.
E. coli: att site between gal/bio genes |
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What are typical early phage proteins and what are typical late phage proteins?
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early: replication of viral genome and parts (capsid, etc)
late: assembly of phage particles, host cell lysis |
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What is unique about all ssRNA phage replication?
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host cells lack RNA pol that can use RNA template
--> RNA phages must bring own RNA pol with them into host cell. |
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How do phages M13 and ΦX174 replicate its genome?
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Rolling circle replication
CisA cuts RF1 + strand and stays attached to 5' end 3' -OH exposed: host DNA pol makes new + strand by attaching nt's to it 5' end of old + strand is "rolled" off as DNA pol progresses - strand not replicated, only new + genomes made |
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How does phage T4 replicate its genome?
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degrades host genome and σ
makes new T4-only σ and DNA pol replicate genome + combine into concatermers, then chop into "headful" lengths & package glucosylates dCMP to protect new T4 genomes from own nucleases. |
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How does phage Lambda replicate its genome?
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linear ssDNA has sticky ends --> circularizes
does θ replication early on later: modified rolling circle same as M13 but host DNA pol makes new - strand as + strand is rolled off separate concatamers only at Cos sequence --> sticky ends no circular permutation like in T4 |
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What is the difference in DNA uptake during transformation between gram + and gram - cells?
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gram + nonspecific: dsDNA binds 10-50 sites on cell surface, take in 6-8kb ssDNA chunks
gram - more specific: recognize 9-11bp sequence, often one that occurs frequently in own genome (uptake closely related DNA) |
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What is the difference in how DNA is transported into gram + vs gram - cells during transformation?
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gram + : ssDNA just pumped into cell through transport protein, 100nt/sec
gram - : same except that dsDNA enters outer membrane through secretin protein/transformosome that protects from OM nucleases |
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What is the advantage of gram negative organisms specifically binding particular sequences of transformative dsDNA?
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sequences recognized are usually present in own genome at unusually high frequency
if present on free DNA, it's more likely to be closely related & confer fitness advantage similarity --> easier homologous recombination |
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What is the difference between conjugative and mobilizable plasmids?
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conjugative: has all genes necessary for own transfer
mobilizable: has to hitch ride w/conjugative plasmid (no transfer genes) |
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What is the relationship between plasmid size and copy number?
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inverse
large size => fewer copies. |
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What is a cryptic plasmid?
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plasmid with ambiguous function but nonetheless highly conserved.
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How is glutamine synthetase regulated?
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AMP Adenyl Transferase must attach AMP to GS to render it susceptible to feedback inhibition by glutamine
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How does phage MS2 regulate gene expression during the infection cycle?
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ssRNA folds up --> limits access to RBS
capsid RBS always open replicase RBS only open when capsid being translated A/Maturation protein RBS at 5' end of RNA only open when replicase is making a new + strand genome. |
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Why must all ssDNA phages go through a dsDNA intermediate?
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because new + ssDNA genomes can only be transcribed from a - strand template.
must make new neg. strand before making progeny genomes |
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What is Replicative Form 1?
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supercoiled dsDNA form of M13 and ΦX174 phage genomes. can undergo rolling circle replication with CisA protein.
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What is the difference between ssRNA and ssDNA phage genome replication?
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ssRNA: no dsRNA intermediate
regulate via transcriptional control + ssRNA = mRNA, transcribe directly use own RNA pol ssDNA: use host DNA/RNA pol NEED dsDNA RF1/RF2 |
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What is the difference between chronic and acute infections?
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Chronic: untreatable, cannot eradicate, only control. does not spread
Acute: explosive, invasive, spreading growth of bacteria. treatable with abx but may be fatal. |
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What are some ways Pseudomonas aeruginosa adapts to its habitat in cystic fibrosis patients?
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lose motility
lose lipopolysaccharide antigens (avoid attack by immune system) become amino acid auxotroph (just mooch) overproduce alginate (protect from abx) |
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What mutation causes overexpression of the alginate-forming operon?
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mutation in MucA protein. MucA represses AlgU activator protein --> Alginate operon expressed.
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What are four reasons for hyperformation of cellular aggregates?
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overproduce cyclic diGMP --> extra sticky colonies, globs in liquid culture
overproduction of alginate due to mutated MucA protein --> wrinkly colonies pel/psl mutations --> xs EPS mutated WspF --> WspR remains phosphorylated and overproduces cdGMP |
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What does the Ti plasmid code for in Agrobacter tumifaciens?
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-production of opines
-opine metabolizing proteins -transfer of plasmid to plant host -rapid plant cell division |
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Which types of phages require dsDNA intermediates?
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ssDNA phages: M13 and phiX174
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What is the benefit of forming aggregate-style biofilms?
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allows flow of nutrients to lower levels of the biofilm
separation maintained with rhamnolipids |
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What is Replicative Form 1?
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a circular, supercoiled dsDNA form of dsDNA phage genomes
used for rolling circle replication. |
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What is a benefit and drawback of overlapping genes/reading frames on a genome?
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saves space
BUT one mutation --> multiple genes damaged. |
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Which phage has overlapping genes on its genome?
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phiX174.
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What is the major difference between the "T-even" phage genomes?
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genes for cell surface receptor recognition.
85% same genome except different binding sites. |
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How do ssDNA genome phages replicate their genomes?
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use host DNA polymerases
dsDNA intermediate |
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Where does lambda separate its concatameric DNA molecule?
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staggered cut to form sticky ends at cos sites.
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Which end of the F plasmid is transferred to the recipient first during conjugation of Hfr strains?
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starts at OriT
distant from Tra genes --> recipient rarely able to carry out subsequent conjugation |
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Why does conjugation rarely result in complete chromosome transfer?
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conjugation complex not stable enough; falls apart before transfer complete
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How is an F' or R' plasmid formed?
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imprecise excision from host chromosome.
Type I: F genes left behind, host genes picked up Type II: all F genes present plus extra from host |
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What allows plasmids to integrate into host chromosomes?
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Is/Tn's on plasmid allow integration.
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