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57 Cards in this Set
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genetic elements found in bac |
chromosome(s), insertion sequences of IS elements, transposons, plasmids, and bacterial viruses |
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2 types of mobile genetic elements |
insertion (IS) elements and transposon (Tn) elements; are not autonomous replicons; move by tranposition via transposases; provide portable regions of homology (may bring about DNA rearrangements= deletions, translocations, fusions or replicons etc); may inactivate genes (i.e. disrupts gene); may activate inactive genes (i.e. provides functional promoter) |
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insertion (IS) elements |
small (about 1000 bp's) discrete genetic elements able to insert into new DNA sites on the same or different replicon=transposition; have 2 genes= one for its transposition (aka movement) and one to regulate the transposition gene target sequence are direct repeats in the DNA; can move from one replicon to another or from one position in the replicon to another; transposase recognizes inverted repeats on either end of the IS element and a sequence in the DNA, then cuts and places the IS element, and then DNA polymerase I fills in gaps and DNA ligase glues the nicks; how can you identify IS elements in a genome? look for those direct repeats |
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transposon (Tn) elements |
larger (may carry multiple genes) discrete genetic elements able to insert into new DNA sites on the same or different replicon; usually have IS elements on either end; can move from one replicon to another or from one position in the replicon to another; this is a way that antibiotic resistance can move between bacteria; how did these come about? 2 IS elements come fairly close to one another and then start to move at the same time taking the genetic info that was between them with them |
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mechanisms of transposition of Tn's |
non-replicative transposition (moves from one location to another via a cut and paste mechanism); replicative transposition (leaves a copy of itself) |
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transposons may carry a wide variety of genes including |
viral genes, antibiotic resistance genes, catabolic genes, and genes for virulence factors |
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classification of transposons is according to |
their overall structure, their transposition mechanisms, their similarities among their transposases, the function(s) they provide their hosts (i.e. antibiotic resistance or ability to utilize/metabolize new food sources) |
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plasmids characteristics |
are autonomous replicons; usually are DNA (5-40 mDa aka 7-200 genes); may carry transposons/IS elements; may integrate into chromosomes (at sites of DNA sequence homology) or exist as an autonomous replicon=episome |
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typing of plasmids according to |
their ability to co-exist in the same cell (compatibility groups); according to their copy number (number/cell)(relaxed plasmids= high copy number (10-200) and stringent plasmids= low copy number (1-2)); according to the functions they provide their host (antibiotic resistance (R factors), conjugative plasmids (DNA transfer), bacteriocin or colicin plasmids (antibacterial), toxigenic plasmids (toxin production), virulence plasmids (adherence factors), and cryptic (no identifiable function)) |
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drug resistance (R) plasmids |
provide multiple drug resistance to pathogens; are transmissible between different pathogens; are found with increasing numbers of antibiotic resistance genes (Tn's); are found with increasing frequency among increasingly different types of bacteria; increase in frequency corresponds with the increase of antibiotic therapy; genetically and structurally can be divided into 2 functional components= RTF or resistance transfer factor (carrier the tra (aka transfer) genes) and R-determinant (carries the drug resistant genes, transposons, and IS elements); RTF and R determinants may dissociate and associate with each other to form an R factor |
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molecular structure of R100 |
NEED TO FINISH THIS ONE |
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medical significance of R-factors |
multiple antibiotic resistance (reduces effectiveness of antibiotic therapy); transfer of multiple antibiotic resistance (may be an infective process (conjugation), i.e. normal flora reservoir --> to transient pathogen) |
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virulence plasmids- production of |
invasion factors (type III translocation systems (like the creation of flagella so this can be like a hypodermic needle that injects things), various hydrolytic enzymes); toxins (haemolysins, enterotoxins); adhesions (pili, common surface antigen) |
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integrons characteristics |
2 component gene capture and dissemination system; found in plasmids, chromosome, and transposons; consists of a gene encoding a site specific recombinase (Int) along with a specific site for recombination (Att) and a second component that comprises fragments of DNA called gene cassettes which can be incorporated or shuffled; the gene cassettes do not contain their own promoters and are expressed from a promoter that is at the Att site |
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bacterial viruses characteristics |
are obligate intracellular parasites of bacteria; are infective agents producing about 100 phage/infected host; are very small (electron microscope); contain either DNA (ds or ss) or RNA as genetic material; are specific for their hosts |
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phage structures |
can come as an icosahedral tailless (just a head), an icosahedral failed (head with tail)(most common and what you recognize), and filamentous (looks like just a tail but in this case the nucleic acid would have to be in the tail instead of the head because there is no head) |
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phage multiplication cycle |
adsorption then penetration then replication |
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types of phage |
virulent (lysis of host only choice); temperate (lysis or lysogeny) |
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phage life styles- virulent phage |
only have lytic cycle; usually lyse host producing many progeny phage (about 100-200 phage/cell)=burst size; free phage/lysed cells=lysate |
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phage life styles- temperate phage |
has choice of lysing host (lytic cycle) or replicating their genome along with replication of host (lysogenic cycle)=prophage; host in such a relationship=lysogen; this relationship between phage and bacteria is called lysogeny; can be induced into the lytic cycle of phage multiplication |
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lysogenic conversion definition |
the process by which a temperate phage carrying nonessential genes which when expressed changes (converts) its host's phenotype; can happen by activating these = diptheria toxin (corynebacterium, phage B), erythrogenic toxin (streptococcus pygenes), and protease in flesh eating bacteria (streptococcus pyogenes (group A)) |
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phage therapy |
self replicating antibiotic; self limiting; specific |
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unlike antibiotics, bacteriophage are discriminatory about |
the bac they kill, multiply exponentially, and are rapidly removed when their host is depleted |
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fluctuation analysis |
showed that it was a random mutation that was selected for (a bacteria doesn't say hey we need to overcome this thing); took tubes with the same number of bac then added the same amount of antibiotic then plates; saw that there were different numbers of living colonies on the plates (different numbers that gained the resistance gene) showing that it was random and not directed by the bac; so proved that it was a random mutation that is then selected for by the pressure |
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replica plating experminent |
took a plate with bac colonies and several mutated colonies and used velveteen cloth to make replica plates with these colonies and saw that the colonies were in the same positions on the new plates; proved that the mutation is random and then selected for |
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mutation definition |
any stable inherited change in the nucleotide sequence of an organisms genome |
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mutation frequency definition |
number of mutants/population |
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mutation rate definition |
probability of a mutation occurring during a given time interval (i.e. per cell doubling time) |
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types of DNA damage |
double strand break (from ionizing radiation and this is often a lethal event); thymine dimer (form ultraviolet radiation); mismatch (incorporation error or deamination of C to U); single strand break; a purinic site |
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when are mutations expressed in bacteria |
bacteria are haploid organisms and hence any mutation which alters the function of a gene product (i.e. enzyme, structural protein, regulatory protein, etc) will eventually be expressed (ie mutant phenotype) however this change may take several cell doublings because of segregation lag and phenotypic lag (might NEED a little help on these because he didn't explain them well) |
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classification of mutations |
according to phenotypic result or according to DNA changes or according to codon usage/translation |
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2 types of base pair substitutions |
transitions and transversions |
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transitions |
purine/purine or pyrimidine/pyrimidine |
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transversions |
purine/pyrimidine or pyrimidine/purine |
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types of rearrangement mutations |
duplications or inversions |
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classification of mutations- DNA structural changes |
base pair substitution, insertions and deletions, rearrangements |
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mutation classifications- according to codon usage/translation |
missense (codes for different aa), same sense (codes for same aa), nonsense (codes for translational termination, frameshift (shifts the reading frame of codons |
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repair of potential mutations in the bac DNA can be why what 3 ways |
direct repair, dark repair, and postreplication repair |
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direct repair |
photoreactivation enzymes; photolyase recognizes helix distortion; photolyase is activated by light and the dimer is uncoupled; photolyase is released |
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dark repair |
can use this to remove thymine dimers; DNA pol I, DNA ligase, UvrA, B, C; incision(s) made by Uvr ABC endonuclease then DNA pol I so single stranded gap is filled in then gap is sealed by ligation (ligase) |
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postreplication repair |
DNA pol I, DNA ligase, rec system; unexcised dimers in paternal DNA; you are using recombination; post dimer initiation leaves gaps; undamaged parental is nicked and dissociated and is assimilated into gap of newly synthesized daughter molecule; gap is repaired |
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suppression of mutations definition and types |
when the effects of a primary mutation are eliminated without correcting (repairing) the mutation the phenomenon is called suppression; genotypic suppression (involves the DNA) and phenotypic suppression (very rare) |
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genotypic supression |
intragenic suppressor mutations (so you have a mutation that maybe misfolds the protein so you make another mutation to correct this misfolding)(want to do the second mutation within the affected gene); intergenic suppressor mutations (second mutation to correct first is within a DIFFERENT gene)(direct=correct the problem created by the first mutation, indirect=circumvent the problem created by the first mutation), examples of these can be nonsense suppressors, missense suppressors, and frameshift suppressors |
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phenotypic suppression |
very rare that this happens; alterations of the protein synthesizing machinery (transcription/translation) which causes misreading of genetic code and may allow missense or nonsense codons to be read and translated as sense codons; nongenetic; very rare; transient |
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3 types of gene transfer in bac |
transformation (uptake of naked DNA), transduction (transfer of DNA via a phage), and conjugation (cell cell contact); when DNA is taken up into the DNA of a bac by any of these methods the bac is called a recombinant (because it has gone through DNA recombination) |
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the direction of gene transfer in bac |
unidirectional from donor to recipient; endogenote=entire genome of recipient; exogenote=partial genome of donor |
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diploid zygotes? |
no; but can have (under certain circumstances) partial diploids (2 alleles for the same gene)= meridiploid, merozygote, or partial diploids |
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transformation procedure |
free DNA is released from a cell (alive or dead cell) and this can be absorbed into living cells which have competence factors on their surface (the factors take up the DNA but make it single stranded in the process) and then the DNA is recombined into the genome and you get a transformant which is heterozygous for the gene and therefore you may not get the phenotype until you have segregation of the replicating chromosomes; steps= competence factor accumulates as cells reach high density, absorption, entry (eclipse stage), incorporation, transformant |
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transduction definition |
the transfer of bacterial DNA from a donor to a recipient via a bacterial virus; is the result of an error in phage maturation (either uptake of DNA into phage package or excision of phage DNA from bac DNA) |
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generalized transduction |
involves a lytic phage; capsid DNA packaging error; random bacterial DNA fragments, size dependent upon capsid capacity; transducing phage has no phage DNA, only bacterial phage, random sequences, head full packaging; ok so in this case the virus infects the bac and breaks down the bac DNA then commands cell to make more of the virus DNA and plenty of packaging material but when it is packaging the DNA some of the package material takes up one of the bac segments instead of virus DNA (so full of ONLY bac DNA and no phage DNA) and this "fake" virus "infects" a new bac all it is doing is injecting a piece of some other bacs DNA which can then recombine with the new bacs genome (although most of the virus that is released will be normal phage virus) |
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specialized transduction |
involves temperate phage; contains both phage and specific bacterial DNA sequences; error in excision of prophage; transduced sequence is not random; when it enters the DNA of the host it always enters at a specific site and when it is cut out it can take host DNA with it and/or leave phage DNA behind and this is what brings DNA between cells (will only transfer genes that are near its integration site); lambda phage is an example; so in this the virus DNA actually integrates into the bac DNA instead of breaking it down into pieces and the possible innacurracy in its excision leads to the transfer of bacterial DNA |
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life cycle of lysogenic bacterial virus |
can either do lytic cycle or integrate into the DNA of their host (lysogenic cycle) (then the region of the DNA were they are is called prophage) and when they want to come out they are induced into the lytic cycle |
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conjugation definition |
ssDNA is transferred unidirectionally from donor to recipient; mediated by conjugative plasmids; best characterized in gram negative enteric bacteria= E. coli and S. typhimerium |
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nature of F factor |
plasmid of about 50x10^6 daltons; contains 40-50 genes; tra operon=13 genes; F pilus mediated cell cell adherence; OmpA acts as receptor for F pilus; carries IS elements |
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F+ x F- matings |
when an F+ mates with an F- cell = the F plasmid is transferred very efficiently (approaches 100% efficiency), the F- cell is converted to an F+ cell (the infective process), the F+ cell remains F+ (i.e. the F plasmid is replicated during conjugation)(it is double stranded and one strand gets transferred and then it becomes double stranded in both)(rolling circle DNA replication- as one strand is transferred it is being replicated(the replication fork is right behind it as it is being peeled off so there is very little single strandedness (only a very small segment) in the donor bac)) |
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formation of Hfr |
F factor contains 4 IS elements which are homologous with IS elements found in the E. coli chromosome; recombination between one of these IS sequences on the F factor and the E. coli chromosome=Hfr (high frequency recombinant); Hfr donors transfer chromosomal genes during conjugation; so if the F factor has an IS element with homology in the bac chromosome then recombination can occur and this means that there can be transfer of bac DNA when the F factor leaves to be transferred to another bac; origin of transfer means that there can be counter clockwise or clockwise transfer of DNA (the orientation of insertion of the F factor determines whether the bac DNA to the right or left of it gets taken out when it excises) |
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F' |
if the plasmid takes out a gene from a bac and then is transferred to another bac and remains as a plasmid and the new bac already has that gene then there are 2 copies of the gene; the cell is now called a meridiploid (look at the above slide that gives the 3 names for this) (so it is a partial diploid) |
