Exam 4 Flashcards
(167 cards)
1
Q
Homologous recombination in Euk.
A
vertical gene transfer during meiosis
2
Q
Homologous recombination in Prok.
A
horizontal gene transfer by transformation, transduction, conjugation
3
Q
Genetic recombination
A
the physical exchange of genes between genetic elements
4
Q
RecA
A
promotes strand invasion
5
Q
Transformation
A
involves the uptake of naked DNA from environment
6
Q
Transformation experiment
A
Streptococcus pneumoniae
7
Q
Streptococcus pneumoniae smooth
A
Capsule and Pathogenic
8
Q
Streptococcus pneumoniae rough
A
No Capsule and Nonpathogenic
9
Q
Mechanism of transformation
A
DNA binding proteins expressed on the cell’s surface; stand cleaved by endonucleases (5-15 kilobases); while being taken up, one strand is completely degraded by exonucleases
10
Q
Competency
A
the ability to take up exogenous DNA; Bacillus, Streptococcus, Haemophilus, Neisseria; Gram +, -, Archaea
11
Q
Poorly transforming bacteria
A
Electrical shock; exposure to Calcium chloride
12
Q
Electroporation
A
usually used with Gram +, and then chill them after
13
Q
Streptococcus pneumoniae competency
A
can take up any DNA; cells must be in exp. Phase of growth; 10^7-8 bact/mL; competence factor secreted; triggers upregulation of genes involved in translation
14
Q
Bacillus competency
A
only 20% competent after competence factors secreted
15
Q
Haemophilus competency
A
will only take up its own DNA; an 11 base sequence repeated 1400 times must be recognized
16
Q
Transduction
A
DNA transfer that is mediated by bacteriophage
17
Q
lytic
A
generalized transduction
18
Q
lysogenic
A
specialized transduction
19
Q
Conjugative plasmids
A
relies on formation of a pili; mediates direct exchange between bacterial cells
20
Q
tra region
A
a plasmid must have this to transfer DNA
21
Q
R (resistance) plasmids
A
confer resistance to antibiotics and other growth inhibitors by having genes that encode for proteins that inactivate it
22
Q
Virulence plasmids
A
carry genes that allow attachment to specific cells and/or the formation of substances that cause damge to host
23
Q
Conjugation
A
the transfer of DNA by direct cell contact
24
Q
Pilus
A
thin, fragile, and hard to maintain; retracts for more stability, but still hard to keep in place
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Biofilm
on the rocks in a stream; a large community of cells create an EXOPOLYMER SUBSTANCE; aids in conjugation
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Hfr conjugation
chromosomal genes take longer to transfer than plasmids
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Transposition
recombination due to themovement of DNA sequences form one part of the genome to another; can occur in Euk.; diversifies genome
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transposons
jumping genes
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transposable elements
insertion sequences: contain only the genes for those enzymes required for its movement; transposons: carry other genes
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Discovery of Viruses
A. Mayer was trying to find the cause of Tobacco mosaic: hypothesis- either the organism was ultra-small or toxin mediated
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Viruses
average size: 10-400nm
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Enveloped virus
nucleocapsid; main component from host
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nucleocapsid
main component from host; any proteins within it will be viral
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Naked virus
lacks a envelope
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Glycoprotein spikes
used for attachment
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capsomeres
usually one expressed; MAX 4
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Viral capsid structure
copmosed of protein subunits called capsomers that spontaneously self assemble
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2 Arrangements of capsid structure
Helical and Icosahedron
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Helical structure
rigid or flexible; hollow inside
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Icosahedron
aka polyhedral capsule; much more common; 20 triangular faces and 12 vertices
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Vertices
glycoprotein spikes protrude from these in naked viruses
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Atypical/complex viruses
Pox virus: coating made up of glyco and fibral protein; Bacteriophage
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Viral nucleic acid
quite small; usually 4-100 genes; can contain either DNA or RNA, NOT BOTH
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Viral DNA
can be double stranded or single stranded; double more common
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Viral RNA
can be double stranded or single stranded; single more common
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Positive sense RNA
can act as mRNA
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Negative sense RNA
cannot act as mRNA
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Segmented viral genome
multiple pieces of genome; one gene per piece
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Viral Order
-virales
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Viral Family
-viridae
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Viral Genus
-virus
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Viral Species
_virus
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Viral Taxonomy
based on the International Committee for the Taxonomy of Viruses
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International Committee for the Taxonomy of Viruses
genome structure; life cycle; morphology; genetic relatedness
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The Baltimore classifcation system of viruses
genome and replication strategy only; 7 classes
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Adsorption
a specific glycoprotein spike binds to a specific host cell receptor protein
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Host cell receptors
tend to deal with the immune system; typically cytokine receptors
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lipid rafts
lipid microdomains that allow only certain proteins to interact; usually have more cholesterol; GPI-anchored protein found here
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Penetration and Uncoating: Endocytosis
NAKED or ENVELOPED; endocytic entrance; endosomal compartment and a decreease in pH triggers uncoating event
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Penetration and Uncoating: Fusion
ENVELOPED ONLY; viral envelope directly fused with host cell membrane; uncoating events hard to define
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Synthesis: DNA Viruses
enter host's nucleus and exert control over host's machinery
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Why can't RNA viruses use Euk's machinery?
there is no RNA-dependent RNA polymerase to read the RNA
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Synthesis: (-) RNA
a viral RNA-dependent RNA polymerase is packaged within the viral capsid
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Synthesis: (+) RNA
translation of RNA-dependent RNA polymerase is translated by host's ribosomes and enzymes
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Retroviruses
RNA is transcribed to DNA using reverse transcriptase; the DS DNA enters the nucleus where it is incorporated into host's genome using integrase
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reverse transcriptase
RNA=> DNA
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integrase
integrates viral DNA into host's genome
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Early viral proteins
for genome replicationand taking over host cell's machinery
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Late viral proteins
for capsid
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matrix proteins
line up underneath lipid domains and grab onto nucleocapsid proteins
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budding
reverse endocytosis
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Cytopathic effects of viruses
inhibition of trascription, translation, and host's replication; endosomes damaged; plasma membrane alterations (syncytia); inclusion bodies formed; build up of of viral products; chromosomal incorporation; malignant cells
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Syncytia
large multi-nucleated cells where the plasma membrane fused together (50-100 nuclei); syncytium (pl)
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Oncogenes
cancer causing genes
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Proto-oncogenes
regulate cell growth and division cycle
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dsDNA viruses
making a viral protein to inhibit a tumor suppresssor gene (pRb, p53)
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Retroviruses and cancer
either bring in their own oncogene protein or insert oncogene into genome
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Bacteriophage found...?
in both bact. and arch.; RNA, ss DNA (not common), dsDNA (common and naked)
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virulent/lytic
kill host immediately (25 minutes)
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temperent/ lysogenic
"hide out" in bacteria
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Step 1 of Lytic Attachment
tail fibers mediate interaction
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Step 2 of Lytic Attachment
retraction of tail fibers pulls base plate clos; lysozyme-like enzyme on base plate breaks peptidoglycan
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Step 3 of Lytic Attachment
tail enters cell wall and contracts
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Step 4 of Lytic Attachment
DNA is released into cytoplasm
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Early phage PROTEINS
involved in DNA replication and transcription
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Middle phage PROTEINS
involved in DNA replication and transcription
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Late phage PROTEINS
involved in the making of head and tail fibers and anything else needed for release
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Early phage GENES
transcribed using host's RNA polymerase; promoters identical to host
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Last Early Proteins
include an anti-sigma factor; make proteins that modify alpha-subunit to make host RNA polymerase bind to phage promoters; some phage proteins will bind directly to RNA polymerase
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Anti-sigma factor
interacts with sigma-factor and disables it
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Late phage GENES
make a phage sigma-factor that recognizes late gene promoters
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Phage DNA
linear not circular; must overcome th eabsence of telomerase
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concatomer
individual genes spliced together; leaving extra ensures that all genes included
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Phage endonuclease
cuts a "headful" of DNA
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Phage assembly
all parts come from different biosynthetic events and then are assembled
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Phage release
two enzymes are used to release; VERY RARE to see budding or envelopment
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Holin
puts holes in cell membrane for release
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T4 lysozyme
degrades peptidoglycan
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Characteristics of lysogenic phage
can't have late gene synthesis AND phage genome integrates into host genome
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Virulent phage
can only be lytic
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Temperent phage
can either be lytic or lysogenic
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Cohesive ends
linear genome, but the 5' ends of each strand has a 12 nucleotide sequence that are complementary
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cos sites
where the single stranded tails bind to make circular genome
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MOI
multiplicity of infection; how many other phage are in the area
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Host growing rapidly under nutrient rich conditions and has a low MOI
Lytic favored
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Host growing slowly under metabolic stress and high MOI
Lysogenic favored
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If cI wins
lysogenic cycle; aka lambda repressor
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If Cro wins
lytic cycle
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PL
makes N protein
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PR
makes Cro
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N Protein
an anti-terminator which allows RNA polymerase to go past specific termination sites to make cII and cIII
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cII
considered unstable, so targeted by bacterial protein hflA; activates transcription of cI
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hflA
degrades cII; available based on how well the cell is doing; cyclic AMP involved
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cIII
stabilizing factor for cII; 2 mechanisms: binds directly to cII and the other is unknown
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hflA activity when cAMP levels are low in glucose rich environments
hflA activity is high
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hflA activity when cAMP levels are high in glucose lacking environments
hflA activity is low
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Integrase enzyme
cleaves phage and host genome at specific sites
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Can prophage remain integrated indefinitely?
Yes
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Agents that revert phage back to a lytic cycle
UV radiation, X-rays, chemicals
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SOS Response for lytic cycle
activates a protease that destroys lambda repressor; lytic genes can now be transcribed
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Cultivating bacteriophage
broth culture containing young, actively growing cells
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Cultivating animal viruses in whole animals
hard to observe effects at cellular level; many viruses only infect one host
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Cultivating animal viruses in cell culture
animal cells can be free from surrounding tissue and grown on plastic to produce a monolayer
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Primary Cell Lines
Straight from the tissue with no passages
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Continuous Cell Lines
Have at least one passage
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Quantifying viruses
differential centrifugation or gradient centrifugation; mixed with liquid agar and a culture of host cells
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Why are Plaque Forming Units used?
cannot be sure if it was one virus or phage that started the colony of death
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Who discovered Prions?
Stanley Prusiner
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Prion definition
Proteinaceous infectious particles found composed of normal protein PrPC
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Normal PrPC
more alpha-helices
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PrPSc
more B-sheets
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If PrPSc is transmitted by animals
infectious ex) Kuru (cannibalism)
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If PrPSc is sporadic
spontaneous random misfolding of PrPC ex) Creutzfeldt-Jacob disease
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If PrPSc is inherited
mutation within the PrP gene (20 mutations linked) ex) Gerstmann-Straussler-Scheinker Disease and Fatal familial insomnia
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What do prions cause?
Transmissable spongiform encephalopathies
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Amyloids
proteinaceous fibers that are resistant to proteases and are an elongation of PrPSc
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Highest resistance of microbes
bacterial endospores
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Moderate resistance of microbes
naked viruses and bacterial cells with more resistant vegetative cells
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Least resistance of microbes
most bacterial vegetative cells, enveloped viruses
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Moist Heat
operates at lower temperates and short exposures; causes coagulation and denaturing of proteins; permeates better using moisture
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Dry Heat
operates at higher temperatures with long exposures; dehydrates cells
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Autoclave
121 degrees Celsius achieved by pressurizing steam by 15psi
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Traditional pasteurization
63 degrees C for 30 mins. BATCH
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Flash pasteurization
71 degrees C for 15 sec. THIN AMOUNT
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Ultrapasteurization
140 degrees C for 1-2 sec. THIN AMOUNT; DOES NOT NEED REFRIGERATION
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Ionizing radiation
causes DNA breakages; Gamm rays, X-rays, Electron beams
147
Nonionizing radiation
causes Thymine dimers; Germicidal lamps at 254nm wavelength UV disinfection
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Advantages of ionization
prevent food born illnesses; preservation; control of insects; delay sprouting and ripening; sterilizes food
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How many KiloGrays of ionization required depending on DNA?
the more DNA it has, the less KiloGrays necessary
150
Depth filter
liquid and air; 0.3 micrometers = 99.97% of contaminants
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Membrane filter
porous; to be sterilizing 0.2 micrometers
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Disinfectant
for a nonliving surface
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Antiseptic
for a living surface
154
Microbicidal
kills organism
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Microbiostatic
inhibits growth
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What are antimicrobials geared to target?
cell wall, cell membrane, genetic material, proteins
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Which chemical agents come closest to fulfilling all the requirements?
Hydrogen Peroxide and Glutaraldehyde
158
Chlorine as a disinfectant
hypochlorous acid
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Iodine as a disinfectant
first used as a tincture of 2% iodine and water, ethanol, mix of Potassium idodide; STAINS, ALLERGENIC
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Iodophores
common in use; water soluble; release iodine slowly
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Phenol
Joseph Lister; not widely used because of irritating effects
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Isopropyl
used at 70% isopropyl and 30% water for better permeability
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Hydrogen Peroxide
3% Hyd. Perox. Used; can be vaporized to sterilize enclosed areas
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Detergents
break down cell membrane by interacting with lipids
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Silver
effective in low concentrations
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Glutaraldehyde
used more than formaldehyde; yellow acidic liquid with a mild odor
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Why do dsDNA phage have to form a concatemer?
To overcome the absence of telomerase
