Term
|
Definition
| a stable and heritable change in genotype of an organism. mutations ALWAYS change the genotype, but they may not affect the phenotype. |
|
|
Term
|
Definition
| a segment of DNA that encodes for a protein |
|
|
Term
|
Definition
| the genetic makeup of an organism. in bacteria, this includes plasmids. |
|
|
Term
|
Definition
| the observable properties of an organism. in bacteria, an example of this would be the ability to use histidine as a carbon source. if the bacteria can't use histadine, it is a His- strain phenotype with a hisA- genotype. |
|
|
Term
|
Definition
| if a protein is decreased in function or no longer functions as intended. EXAMPLE: hisA-. |
|
|
Term
|
Definition
| if a protein is more active or more efficient |
|
|
Term
|
Definition
| the mutation goes unnoticed because protein function is unchanged. this occurs because the genetic code is redundant. |
|
|
Term
|
Definition
| 1 base is changed. base subs can be silent (no impact), missense, or nonsense. |
|
|
Term
|
Definition
| no change in final protein structure. the codons may be altered slightly (by 1 base) but the amino acid they encode for remains the same. |
|
|
Term
|
Definition
| changes the amino acid sequence, and thus leads to altered protein function. EXAMPLE: sickle cell disease |
|
|
Term
|
Definition
| base substitution results in early stop codon, creating fragments of genes and therefore fragments of protein. if the new stop codon is at the end of the strand, the effect is lessened. nonsense mutations are deleterious. |
|
|
Term
|
Definition
| bases are added (insertion) or removed (deletion). this shifts the "reading frame" and changes protein function. |
|
|
Term
| causes of mutation (2 major types, 4 subtypes) |
|
Definition
| spontaneous: random mistakes by DNA pol during replication. mutagenic (nonspontaneous): caused by environmental, chemical, or radiation factors or plasmids. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| can mimic a base, causing mismatch between base pairs. can cause frameshift mutations. radiation can cause mismatch or breaks in the DNA phosphodiester bonds. in the case of UV radiation, crosslinks between thymines, called thymine dimers, can be formed in the DNA. |
|
|
Term
| major test for carcinogens |
|
Definition
|
|
Term
|
Definition
| in one example, a histidine auxotroph (hisA- mutant) is plated with rat liver cells and no histidine in the media, along with the suspected carcinogen. if the culture has the ability to grow, we know the suspected carcinogen caused a back mutation. |
|
|
Term
|
Definition
| the uptake of DNA from environment by a competent cell |
|
|
Term
|
Definition
| DNA is transferred between bacteria mediated by a bacteriophage |
|
|
Term
|
Definition
| bacterial "sex"; transfer of DNA between 2 cells via cell-cell contact. plasmid mediated. |
|
|
Term
| how do we artificially induce transformation in naturally non-competent cells? |
|
Definition
| heat shock, high calcium chloride levels. |
|
|
Term
|
Definition
| phage attaches to host cell and injects its DNA into the cell. the phage DNA uses the host machinery to make viral progeny. when the phage is done replicating itself, the cell is lysed and the bacterium dies. during the replication process, there may be errors which cause the phage DNA to pick up chunks of bacterial DNA. these are called transducing particles. when the progeny are made, they may have transducing particles, which they take with them after the cell lyses. |
|
|
Term
|
Definition
| mixture of phage DNA with bacterial DNA. found in viral progeny. |
|
|
Term
|
Definition
| the phage attaches to the host cell and injects its DNA. the phage DNA is incoportated into the host chromosome, becoming a prophage. the prophage then lies in wait, sometimes for a very long time, until an event in the host cell triggers it (e.g., cell distress). the phage then cuts itself out and continues with the lytic cycle. during the excision of prophage from host DNA, the phage may take some host DNA with it. in the case of phage lambda, the host genes will always be either gal or bio (never both). |
|
|
Term
|
Definition
| the type of transduction phage lambda can get up to. lambda always inserts its DNA between the host genes gal and bio, and when it leaves, it may take either gal or bio with it (never both). |
|
|
Term
|
Definition
| davis took a long U-shaped tube and filled it with media. at the bottom of the tube, he put a filter which would allow media to pass through but not bacteria. then he added 2 types of bacteria to the cell: an A-/D- auxotroph and a C-/D- auxotroph. the bacteria could not physically come together, so they could not trade DNA. thus, the A-/B- auxotroph could not grow on media without A- and B- supplied, and the C-/D- auxotroph could not grow on media without C- and D- supplied. |
|
|
Term
| Lederberg's discovery of conjugation |
|
Definition
| lederberg used 2 strains of E. coli. one strain was auxotrophic for Bio-, Phe-, and Cys-. the other was auxotrophic for Thr-, Leu-, and Thi-. this meant that they would not grow on media that didn't have those nutrients supplied for them. but when he mixed them together, they could grow on nutrient-free media because they were sharing plasmids which let them utilise the nutrients they were auxotrophic for. |
|
|
Term
| transfer of DNA between bacteria |
|
Definition
| this is a 1-way transfer from a donor (D) to recipient (R). mediated by a self-transmissible plasmid or F-plasmid (fertility plasmid). |
|
|
Term
|
Definition
| an F-plasmid is one which has all the genetic info needed to engage in conjugation. F-plasmids may also contain other traits, like antibiotic resistance. |
|
|
Term
| the process of conjugation |
|
Definition
| begins at the origin of transfer, oriT. the donor cell makes a structure called a sex pilus which contacts the recipient cell and draws the 2 cells closer together. relaxase nicks 1 strand in oriT and an intact strand of DNA is turned into a double stranded copy of the plasmid DNA. the leftover single stranded plasmid DNA is passed to the recipient cell, who immediately circularises it and makes a copy of the genes. both cells are now considered F+, and the recipient can no longer receive from the donor cell (but it can pass its plasmid on to a different recipient cell). |
|
|
Term
|
Definition
| high refrequency of recombination organism. this occurs when F-plasmids are incorporated into host chromosome. these organisms are F+ but even if they manage to transfer their chromosome to another cell, the recipient does not become F+. to transfer an entire chromosome between bacteria is time and energy consuming, and never happens in nature. |
|
|
Term
| general requirements for bacterial growth |
|
Definition
| pH, temperature, atmosphere, nutrients, and water |
|
|
Term
|
Definition
| stops bacterial growth without killing the organism. if the organism is removed from the bacteriostatic substance or environment (e.g., the cold), growth resumes as normal. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| to kill all forms of life, prokaryotic and eukaryotic alike. includes spores. |
|
|
Term
|
Definition
| only kills vegetative cells, not spores. applies to inanimate objects ONLY |
|
|
Term
|
Definition
| does the same thing as a disinfectant, but is safe for use on skin, etc. applies to animate objects/live surfaces. |
|
|
Term
|
Definition
| reduce microbial population to a safe level, e.g., pasteurisation. |
|
|
Term
|
Definition
| amount of time it takes microbial cells to be reduced by 90% (tenfold, 1 log) |
|
|
Term
|
Definition
| the tenfold reduction rate |
|
|
Term
| factors affecting D value |
|
Definition
| population size at time 0, population composition (mixed cultures vs pure), intensity and concentration of the agent, time of exposure, temperature, and physical/chemical environment. |
|
|
Term
|
Definition
| DNA, ribosomes, key enzymes, cell walls, membranes -- anything and everything a cell might need to grow. |
|
|
Term
| physical agents: autoclave |
|
Definition
| uses steam under pressure (so water can be pushed above boiling point). denatures proteins and nucleic acids, disrupts cell membrane. the more microbes involved, the more time you need. standard time, temp, and pressure: 121C, 15 psi, 15 minutes. kills spores, vegetative cells, and viruses. not for use on live surfaces or objects which could not withstand high heat (e.g., milk). 2 ways to tell it's successful: autoclave tape which changes colour when conditions are met properly; use of Bacillus stearothermophilus, an indicator strain whose failure to thrive post-autoclave means the autoclave was successful. |
|
|
Term
|
Definition
| disinfects but not sterilises (kills only vegetative cells). used when autoclaving is impossible. |
|
|
Term
|
Definition
| works below boiling point (50-60C). used for milk, juice, and other liquids which can't be boiled or autoclaved. |
|
|
Term
|
Definition
| for material unable to withstand steam. examples: incineration, flaming a loop. |
|
|
Term
|
Definition
| bacteriostatic only, commonly used for food and antibiotic storage. |
|
|
Term
|
Definition
| bacteriostatic. dehydrate material to inhibit microbial growth, for example dry noodles or spices. |
|
|
Term
|
Definition
| bacteriostatic. food preservation like high salt or sugar content. |
|
|
Term
|
Definition
| ionising: gamma and x-rays (wavelength < 1nm). waves penetrate deeply and sterilise objects. nonionising: UV (wavelength > 1nm). good for surface sterilisation, can't penetrate like ionising radiation. |
|
|
Term
|
Definition
| separates bacteria from liquid, and also air (HEPA filters). filters push the sample through a membrane with holes smaller than bacteria and other microbes; can be effective against viruses also so long as they aren't smaller than the pores. useful for liquids that can't be autoclaved (antibiotics, vaccines, enzymes). |
|
|
Term
|
Definition
| used primarily by hospitals to kill gram-. when gram- are autoclaved, they will die but their LPS can remain behind. so autoclaved materials can be ultrafiltered to remove LPS. |
|
|
Term
|
Definition
| inhibits growth of strict aerobes; vacuum packaging of meat. |
|
|
Term
| properties of an ideal chemical disinfecting agent (12) |
|
Definition
| 1. it should be broad spectrum: effective against gram+ and gram-, acid fast, viruses, etc. 2. soluble in H2O and lipids so it can penetrate cell membranes and kill the microbe. 3. stable; should not require a fume hood or special equipment; easy to use for households. 4. nontoxic to people and animals as well as surfaces (noncorrosive). 5. uniform in composition (homogenous solution). 6. must work in presence of other organic matter besides microbes. 7. active at room temp. 8. ability to penetrate cells and surfaces (e.g., layers of organic material on surface). 9. can't cause damage to things like clothes or metals. 10. deodorising ability; shouldn't smell bad. 11. detergent ability; remove dirt and stuff stuck on the surface being cleans. 12. low cost. |
|
|
Term
| types of disinfectants and antiseptics (6) |
|
Definition
| phenols; alcohols; halogens; heavy metals; surfactants; quaternary ammonium compounds |
|
|
Term
|
Definition
| disinfectant (smells bad and has some toxicity to people) only. bactericidal in high concentrations, but bacteristatic in lower. used as the standard for all disinfectants. a phenol coefficient of 1 means as good as phenol; above 1 means better than phenol; less than 1 means worse than phenol. MODE OF ACTION: changes membrane permeability and denatures proteins. |
|
|
Term
|
Definition
| can be antiseptic or disinfectant. works in lower dilutions (e.g., 70% is better than 90%). MODE OF ACTION: dry out cells, dissolves lipids, denatures proteins. DOES NOT KILL SPORES. can kill some viruses, like the flu. examples: ethanol, isopropyl (no methanol). |
|
|
Term
|
Definition
| iodine and chlorine. MODE OF ACTION: oxidation agent, inactivates key proteins. efficacy is decreased in presence of other organic compounds, so sometimes they need an organic carrier to increase their efficacy. |
|
|
Term
|
Definition
| Ag, Cu, Hg, Pb, Zn. antibacterial, but also work against algae and fungi. MODE OF ACTION: inactivate enzymes that have -SH groups; bacteriostatic. sometimes used as antiseptics, but they can be toxic. examples of use: AgNO3 drops in newborn infants' eyes to prevent gonorrheal infections; copper and zinc in ship hulls or pipes to repel algae buildup. heavy metals form zones of inhibition in petri dishes, which is a clearance around the heavy metal where bacteria does not grow. |
|
|
Term
| surface active compounds (surfactants) |
|
Definition
| make hydrophobic molecules soluble. MODE OF ACTION: damages cell membrane and denatures proteins. |
|
|
Term
| quaternary ammonium compounds |
|
Definition
| high concentration: antiseptic, disinfectant. low concentration: sanitising. P. aeruginosa is resistant to quats. |
|
|
Term
|
Definition
| ethylene oxide, hydrogen peroxide, aldehydes. |
|
|
Term
|
Definition
| used in gas form for things that can't be autoclaved; works slower than autoclave. sterilises surface, kills spores. used in hospitals to sterilise catheters. downside: very reactive and poisonous to people (diluted with CO2 to make it safer). |
|
|
Term
|
Definition
| liquid: antiseptic. vapor: sterilant (under pressure only). nontoxic to people, safer alternative to ethylene oxide. |
|
|
Term
|
Definition
| formaldehyde and glutaraldehyde. sterilises medical instruments, kills spores and inactivates nucleic acids. |
|
|
Term
|
Definition
| compounds (either natural or synthetic in origin) which target microbes and inhibit metabolic processes. |
|
|
Term
| role of antibiotics in nature |
|
Definition
| symbiosis with plants; competition for resources (crowd out other microbes); signal compounds (in lower concentrations) |
|
|
Term
|
Definition
| minimal inhibitory concentration: lowest concentration of an antibiotic that inhibits the growth of a given organism. |
|
|
Term
|
Definition
| determines MIC. plate organism with disks of varying antibiotics at different concentrations; the size of the zone of inhibition around the disks (place where no microbes grow) is an indication of how effective the antibiotic is. |
|
|
Term
| broad spectrum antibiotics |
|
Definition
| target lots of different organisms |
|
|
Term
| narrow spectrum antibiotics |
|
Definition
| targets only a few types of organisms |
|
|
Term
| antibiotic modes of action |
|
Definition
| cell wall synthesis, protein, nucleic acid synthesis inhibition; metabolite antagonism |
|
|
Term
| cell wall synthesis inhibition |
|
Definition
| beta-lactam rings inhibit cell wall synthesis by mimicking the final amino acid in the peptide chain of the pg layer. crosslinks fail to form and the cell wall destabilises. very effective on log phase cells and gram+ (only some gram-). EXAMPLES: penicillin, cephalosporins, vancomycin. |
|
|
Term
|
Definition
| bacterial enzyme that breaks down penicillin at the beta-lactam ring; one method a microbe may defend itself against antibiotics |
|
|
Term
|
Definition
| increase membrane porosity and disrupt concentration gradients, effectively removing the proton motive force. these antibiotics are toxic to people, as they won't differentiate between eukaryotic and prokaryotic cells. last resort type molecules (e.g., P. aeruginosa infections). EXAMPLES: polymyxins |
|
|
Term
|
Definition
| form cross links with DNA and cause endonucleases to become active and chop up DNA. toxic to people, as it cannot differentiate between proke and euke cells/DNA. EXAMPLES: mitomycin. |
|
|
Term
|
Definition
| broad spectrum bactericides that target DNA gyrase. useful for MRSA, UTIs (gram-), P. aeruginosa. EXAMPLES: nalidixic acid, ciprofloxacin. |
|
|
Term
| protein synthesis inhibitors |
|
Definition
| indirectly inhibit transcription. works on gram+/-. toxic to humans, unable to differentiate proke and euke cells. EXAMPLES: actinomycin, rifampin (TB infections). direction translation inhibitors: very broad spectrum bacteriostatics (reversible). bind to 30S subunit and inhibits initiation. EXAMPLES: tetracyclines. you might know them from acne creams; they reduce the efficacy of the acne microbes so that the immune system can kick in and take acne out. |
|
|
Term
|
Definition
| enzyme inhibition; inhibit folic acid synthesis by mimicking the desired substrate. bactericidal. EXAMPLES: trimethoprim. |
|
|
Term
| problems with antibiotics (2) |
|
Definition
| toxicity/allergy: we don't want to cause harm to host tissues. teratogenicity: we don't want to cause birth defects. |
|
|
Term
| microbial defense against antibiotics |
|
Definition
| inactivation (beta-lactamase); block entry (waxy cell walls, efflux pumps); alter target cells/structures. |
|
|
Term
|
Definition
| a structure in microbes which can pump undesired materials out of the cell (e.g., antibiotics). P. aeruginosa is a specimen with a lot of efflux pumps, which is part of why it's so resistant to antibiotics. |
|
|
Term
|
Definition
| genomes: RNA or DNA (never both). protein coat: capsid. use host machinery to replicate their genomes and produce progeny. |
|
|
Term
|
Definition
| the protein coat and nucleic acids together |
|
|
Term
|
Definition
| the spectrum of host cells the virus can infect. can be limited to types of cells (e.g., flu to respiratory cells) or species (e.g., swine and bird flu). |
|
|
Term
| viral taxonomy: nucleic acids |
|
Definition
| can be ss/dsDNA or ss/dsRNA. never both RNA and DNA or ds and ss. |
|
|
Term
|
Definition
| made up of capsomere proteins, which are self assembling. sometimes covered by an envelope. may have spikes, which are used to recognise host proteins. |
|
|
Term
|
Definition
| derived from host cell membranes, acquired when the virus buds off of the cell and leaves the host. |
|
|
Term
|
Definition
| tube-like with spiraling nucleic acid inside the capsid tube. EXAMPLE: ebola. helical viruses can have envelopes as well. EXAMPLE: influenza. |
|
|
Term
|
Definition
| cube shaped nucleic acids inside a highly angular and multifaceted capsid. an icosahedral virus has 20 equilateral triangles in capsid. |
|
|
Term
|
Definition
| icosahedral head with a tube tail. the capsid head contains the DNA. the tube tail fits into a baseplate that fits to tail fibers (the virus "legs"). these fibers recognise e. coli and attach to bacteria. EXAMPLE: phage. |
|
|
Term
| growing bacteriophages vs growing animal viruses |
|
Definition
| bacteriophages must be grown in bacterial plates. their presence is confirmed via plaques that form on the agar surface, where bacteria have been killed by the virus. conversely, animal viruses must be grown in live, susceptible host animals, chicken eggs, or in live cell cultures. |
|
|
Term
|
Definition
| need host; electron microscopes; genetic sequencing. |
|
|
Term
| after the virus enters host cell, it HAS to: |
|
Definition
| either replicate itself or enter the host chromosome. |
|
|
Term
|
Definition
| new virus particles made in the cell, "baby viruses" |
|
|
Term
| bacteriophage infection process: lytic (T-even phages) |
|
Definition
| 1. virus attaches to bacteria receptors (e.g., LPS in e. coli); 2. virus injects its DNA into host. capsid remains on cell surface and will eventually degrade. 3. biosynthesis of new viral DNA commences using host machinery. 4. maturation: new pieces of capsids, tails, etc., are made and assembled to make virions. 5. all virions leave the cell. in bacteria, the phage virions excrete lysozyme or use "teeth" on their baseplates to tear holes in the cell wall to escape through. the cell lyses and dies as the virions leave. |
|
|
Term
| bacteriophage infection process: lysogenic cycle (lambda) |
|
Definition
| 1. attachment and entry are the same for lambda. 2. phage DNA circularises immediately upon entry, to avoid detection and destruction by endonucleases. 3. phage enters the host chromosome and becomes a prophage in a latent infection. the prophage will be replicated each time the bacterial DNA replicates normally. 5. a spontaneous external event triggers the lytic cycle. the prophage is excised from the host chromosome. sometimes it takes host DNA with it (gal and/or bio), which can be integrated into the next host cell. |
|
|
Term
| toxins derived from transduction |
|
Definition
| botulinum; toxic shock syndrome in S. aureus |
|
|
Term
| viral infection process in animals |
|
Definition
| 1. attachment to host receptors. 2. entry: pinocytosis or fusion. envelope is degraded in both processes. 3. uncoating: capsid is disassembled. 4. biosynthesis (more or less the same as in bacteria). 5. maturation (ibid). 6. release: the host cell is not killed. the virions leave via "budding," wherein nubbins form on the cell wall containing the virus. this is how viruses get their envelopes. |
|
|
Term
|
Definition
| RNA genomes. use reverse transcriptase to turn their genomes into DNA. if the vDNA enters the host chromosome, it becomes a provirus and may never leave the host (but they can be expressed and create virions to pass on to other hosts). |
|
|
Term
|
Definition
| a general term for a cell taking particles into its cytoplasm. the cell forms an invagination around the virus and brings the virus in via a vesicle, which will perform the uncoating. |
|
|
Term
|
Definition
| the virus (usually enveloped) fuses membrane-to-membrane with the host cell and is slowly drawn into the cytoplasm of the host cell. |
|
|
Term
|
Definition
| cancer-causing genes. sometimes switched on by oncogene viruses. |
|
|
Term
|
Definition
| no antibiotics! use vaccines, normal immunity. fever, interferons and normal host immune response can take care of viruses. antivirals can target the difference between host and virus (i.e., reverse transcriptase), but they are a last resort option. |
|
|
Term
|
Definition
| plant virus that consists only of ssRNA and no capsid/envelope. |
|
|
Term
|
Definition
| infectious proteins without nucleic acids that infect brain cells. this is the only form of life where heredity is caused by proteins and not nucleic acids. in cows, healthy prions can spontaneously turn into infectious prions and thus herald the zombie apocalypse. |
|
|
