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201 Cards in this Set
- Front
- Back
minimal inhibitory concentration
|
lowest dilution with no turbidity.
|
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Minimal bactericidal concentration (MBC)
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lowest dilution With no growth when subbed.
|
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Factors that influence disk diffusion susceptibility in bauer kirby?
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medium, agar depth, disk potency, inoculum concentration, pH, and β-lactamase production by the test organisms.
|
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Inhibition of cell wall synthesis
|
penicillin, vancomycin, bacitracin, penicillins, cephalosporins, monobactams, carbapenems
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Combination with cell membranes
|
polymixin causes holes in cytoplasm
|
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Action on eukaryotic membranes
|
the polyenes: sterols present in the cell wall of eukaryotes. Fungi are inhibited, but dangerous for human use, as it is not as selectively toxic.
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Inhibition of protein synthesis
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chloramphenicol, streptomycin, neomycin, kanamycin, tetracyclines, erythromycin
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50S ribosome subunits
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erythromycin (macrolides), chloramphenicol, clindamycin, lincomycin
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30S ribosome subunits
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30S ribosome subunits
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Aminoglycosides
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streptomycin, gentamicin, tobramycin, kanamicin, amikacin.
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Nitrofurans
|
(urinary tract only, not antibiotic)
|
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DNA gyrase
|
nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin (quinolones) Novobiocin
|
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DNA directed RNA polymerase
|
rifampin
|
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Bacteriocines
|
compound produced by bacteria active against closely related bacteria.
|
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Ciprofloxacin
|
Ciprofloxacin is used to treat urinary tract infections and anthrax caused by penicillin-resistant bacillus anthracis.
Fluorinated derivatives of nalidixic acid are more soluble than nalidixic acid and reach clinically therapeutic levels in blood and tissues. |
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Prontosil
|
It is broken down in the body to sulfanilamide, the active agent
|
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Sulfanilamide competes with _________ which is a precursor of __________
|
para aminobenzoic acid
folic acid |
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Each year more than _____ metric tons of chemotherapeutic agents are manufactured.
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500
|
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Mechanisms of antibiotic Resistance?
|
1. Resistance may be inherent or can be acquired.
2. Organism may not have the structure affected. Ex. Mycoplasma have no cell wall - are resistant to penicillin. 3. Organism may be impermeable to antibiotic. 4. Organism alters the antibiotic to an inactive form. 5. Organism may modify the target of the antibiotic. 6. By genetic change, the organism may alter the metabolic pathway that the antibiotic blocks. 7. The organism may be able to pump out any antibiotic entering the cell (efflux). 8. Genetic change: due to plasmid transfer or at the chromosomal level. |
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Type of resistance:
inactivation of antibiotic, e.g. penicilinase; methylases, acetylases phosphoryl-ases |
penicillins, chlorampheni-col
plasmid and chromosomal |
|
Type of resistance:
reduced permeability |
penicillin
chromosomal |
|
Type of resistance:
efflux |
tetracyclines, chloramph.
plasmid chromosomal |
|
Type of resistance:
alteration of target; ribos. |
Erythro.
Strepto. chromosomal |
|
Type of resistance:
alteration of target; DNA gyrase |
quinolones
chromosomal |
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Type of resistance:
development of resistant pathway |
sulfonamides
chromosomal |
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Anti-fungals?
|
Polyenes - disrupt membrane integrity
polyoxins - inhbit chitin synthesis azoles and allyamines - inhibit ergosterol synthesis 5-fluorcytosine - nucleotide analog that inhibits na synthesis griseofulvin - inhibits microtubule formation |
|
Virion
|
complete virus particle
|
|
Capsid
complete pacakge is called? |
protein coat surrounding nucleic acid center.
nuclocapsid |
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Capsomere
|
protein subunit making up capsid
|
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Viral structure
|
technically geometrical structures called icosahedrons with 20 triangular faces and 12 corners or rod like. Some are enveloped. Roughly 30-300 nm in size.
|
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Viral quantification:
Phage overlay |
plaques due to lysis, pfu.
|
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Viral quantification:
Animal viruses |
tissue culture, cpe, count analogous to plaques.
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Viral Replication
Attachment |
(adsorption) of virion to susceptible host. High specificity for host.
|
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Viral Replication
Penetration (injection |
infectivity of the virus particles disappears, called eclipse, due to the uncoating of the virus particles
|
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Viral Replication
Early steps in replication |
host cell biosynthetic machinery is altered as prelude to virus nucleic acid synthesis, virus specific enzymes are typically made.
|
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Viral Replication
Latent Period |
Replication of virus nucleic acid and protein. No infectious virions are present extracellularly.
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Viral Replication
Assembly of structural subunits |
packaging of nucleic acid into new virus particles. Titer of active virions inside cell rises dramatically. At this time, if the cells are broken open, active virus can be detected. The protein coat forms spontaneously from protein capsomeres by self assembly.
|
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Viral Replication
Release of mature virions |
due to cell lysis, budding or excretion process. Release of virions occurs after breakdown of cw by lysozyme like protein.
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Burst size
|
the no. Of virions released, varies with virus and host cell.
|
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eclipse
|
infectivity of the virus particles disappears
|
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Viral Replication
Timing |
varies from 20-60 min in bacteria. Viruses to 8-40hr in most animal viruses.
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Early proteins
|
synthesized soon after infection, necessary for replication of viral nucleic acid
|
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Late proteins
|
synthesized later, protein coat.
|
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Temperate bacteriophages
|
Direct to lysis, or integration of the virus DNA into the host DNA – lysogenization. The lysogenic cell can also be induced to produce mature virus and lyse.
|
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Main Types of bacterial viruses
RNA ss |
MS2 (small globular)
|
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Main Types of bacterial viruses
RNA ds |
q6 (Small globular,membranous)
|
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Main Types of bacterial viruses
DNA ss |
T3,T7 (Small lander, no neck)
|
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Main Types of bacterial viruses
DNA ds |
T2, 74 (Large lander, long, coiled neck)
|
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Class I
|
ds DNA +/-
|
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Class II
|
ss DNA + or -
|
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ClassVII
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dsDNA +/-
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Class III
|
ds RNA
|
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Class IV
|
ss RNA +
Virus genome serves directly as mRNA. |
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Class V
|
ss RNA –
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RNA viruses, whether +, - or ds require a _________.
|
specific RNA -dependent RNA polymerase.
|
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RNA Replicase.
|
virus specific and RNA-dependent RNA polymerase
|
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Class VI
|
ss RNA +
Retrovirus |
|
Process of copying information from RNA into DNA is called ____, requiring an enzyme called _____.
|
reverse transcription
reverse transcriptase |
|
Codon
|
- triplet of bases in mRNA that code for an amino acid.
|
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Anti-Codon
|
triplet of bases in tRNA that code for an amino acid.
|
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degeneracy
|
A single amino acid is frequently coded for by several different but related triplets of bases.
|
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Nonsense codons
|
Those that don’t lead to amino acid production. May function as punctuation - ie termination of the growing polypeptide chain.
|
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lateral gene flow
|
genes are transferred from donor to recipient, rather than mother to daughter.
|
|
the genotype of an organism is designated by
|
3 lowercase letters followed by a capital letter all in italics indicating the gene involved, e.g. hisC
|
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The phenotype of an organism is designated by
|
a capital followed by 2 lowercase and a + or – to indicate presence or absence of property.
E.g. His+ strain is capable of making histidine, whereas his- is incapable. |
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selectable mutation
|
gives the mutant a clear advantage under certain environmental conditions
|
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Lederberg replica plating technique
|
used for screening nutritional mutants.
|
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Auxotroph
|
a mutant that has a nutritional requirement for growth.
|
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Prototroph
|
parent from which auxotroph is derived.
|
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Bulk of spontaneous mutations occur during DNA replication as result of
|
errors in pairing bases.
|
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Point mutations
|
Mutations involving a change in one base pair
|
|
silent mutations
|
Because of degeneracy, not all mutations in polypeptide encoding genes result in changes in polypeptide
|
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missense mutation
|
Changes in 1st or 2nd base more often lead to significant changes in peptide leading to an inactivity or reduced activity.
|
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nonsense mutation
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point mutation resulting in termination of translation causing incomplete polypeptide due to formation of stop codon.
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Transition
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substitution of one purine base (a or g) for another purine , or one pyrimidine (c or t) is substituted for another pyrimidine.
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Transversion
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point mutation where a purine base is substituted for a pyrimidine or vice versa.
|
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Frameshift mutation
|
deletion or insertion of a base pair causes this with serious results. This mutation is a result of replication error. Shifts in the reading frame of messenger RNA are caused by insertion or deletion mutations in DNA.
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Transposon mutagenesis
|
insertion of a transposable element occurs within a gene, loss of gene function results. Transposable elements can enter chromosome at various locations and are used by microbial geneticists as mutagenic agents.
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Back mutations or reversions
|
point mutations are reversible by process of reversion, resulting in a revertant, a strain in which the wild type phenotype that was lost in the mutant is restored. Can be due to restoration at the same site or occur at a different site (called suppressor mutation).
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mutagens
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chemical, physical, or biological agents to increase the mutation rate
|
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Nucleotide base analogs
|
molecules resembling DNA purine and pyrimidine bases in structure but with faulty pairing properties.
|
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5-bromouracil
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can base pair with guanine causing at to gc substitutions.
|
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2-aminopurine
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can base pair with cytosine, causing at to gc substitutions.
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Alkylating agents
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powerful mutagens that induce at higher frequency than analogs.
|
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mutagens:
Nitrous acid |
Deaminates a & c
AT GC, GC →AT |
|
mutagens:
Hydroxylamine |
Reacts with c
GC→AT |
|
mutagens:
Monofunctional |
Put methyl on g
GC →AT |
|
mutagens:
Bifunctional |
Cross link DNA strands
Both point mutation and deletions |
|
mutagens:
Intercalative dyes Acridines, ethidium bromide |
Inserts between 2 base pairs
Microinsertions and microdeletions |
|
mutagens:
UV |
Pyrimidine dimer
Repair may lead to error or deletion |
|
mutagens:
ionizing |
Free radical, break chain
Repair may lead to error or deletion |
|
1. Transformation
|
free DNA inserted directly into competent recipient cell.
|
|
2. Transduction
|
transfer of bacterial DNA via temperate or defective phage.
|
|
3. Conjugation
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DNA transfer via actual cell to cell contact between donor and recipient.
|
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Competence
|
the ability of the recipient to take up free DNA. Only certain strains are competent and this seems to be genetically determined.
|
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In bacillus only about ____ of the cells become transformable while in streptococcus, ____ but for only a few minutes.
|
20%
100% |
|
In ___ only about 20% of the cells become transformable while in ____, 100% but for only a few minutes.
|
bacillus
streptococcus |
|
Integration
|
DNA is bound at cell surface by a DNA binding protein, after which the entire double stranded fragment is taken up, or a nuclease degrades one and the other is taken up.
|
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Transfection
|
the bacteria transformed with DNA extracted from a bacterial virus. It has become a standard mechanism for studying transformation.
|
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Competence can be induced in non-transforming bacteria by ____
|
treatment with calcium in the cold.
|
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Generalized transduction
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host DNA from any portion of host genome becomes part of mature virus in place of virus genome. If the donor genes don’t undergo homologous recombination with host genome, they will be lost, as they can’t replicate independently and are not part of virus genome.
|
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Specialized transduction
|
only in some temperate viruses; DNA from a specific region of the host genome is integrated directly in to virus genome, usually replacing some virus genes. The virus is in both cases is usually non-infective (therefore called defective) as a virus because bacterial genes have replaced some necessary viral genes.
|
|
transducing particle
|
When infected with phage, the lytic cycle may be initiated. The enzymes responsible for packaging viral DNA, sometimes package host DNA by accident.
The resulting virion is called a transducing particle. When released, the lysate contains mixture of normal and transducing particles. |
|
conjugative plasmids
|
A process by which plasmids are transferred from donor to recipient [cell to cell transfer]. This is encoded by some plasmids themselves
|
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episomes
|
Some plasmids called episomes can integrate into the chromosome, and under these conditions their replication comes under control of the chromosome. This is similar to that of several viruses whose genome can become incorporated prophages.
|
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curing
|
Plasmids can be eliminated from cells (curing) by various treatments. This causes inhibition of plasmid replication without inhibition of chromosome replication.
|
|
Transmissibility by conjugation is controlled by set of genes within plasmid called the ____ region
|
tra
|
|
rolling circle replication
|
Process called rolling circle replication best explains DNA transfer. 1 strand of plasmid DNA circle is nicked and is transferred to recipient. The enzyme also has helicase activity and is involved in unwinding the strand to be transferred.
As this transfer occurs, DNA synthesis by rolling circle mechanism replaces the transferred strand in donor with complementary strand which is also then made in recipient. |
|
Hfr
|
– if plasmid acts like an episome and integrates with host chromosome, then chromosomal genes are mobilized and transfer of host genes takes place.
Those that have a chromosome integrated f plasmid are called hfr and are unable to take up a 2nd f plasmid. |
|
guilds
|
Metabolically related populations of microorganisms
|
|
Energy enters ecosystems in form of
|
sunlight, organic carbon, and reduced inorganic substances.
|
|
allochthonous organic matter
|
organic matter that enters from the outside
|
|
Biogeochemical cycle
|
microorganisms play a role in the recycling of several elements , the study of which is called biogeochemistry.
|
|
prime niche
|
Ecological theory states that for each organism there is a prime niche.
|
|
microenvironments
|
Small organisms live in small environments so they are called microenvironments. E.g. A 3 mm soil particle can contain several different microenvironments, different chemically and physically.
|
|
Experiments demonstrate their oxygen content can vary, even throughout such a small particle with the outer zones being fully ____, and the inner zones completely _____ with intermediate or microaerophilic zones between.
|
oxic
anoxic |
|
Biofilms
|
Organisms sticking to surface, encased in slime, usually polysaccharide. Biofilms trap nutrients essential for growth. Cell – cell communication is critical in biofilm development and maintenance. Attachment is a signal for the expression of biofilm specific genes, which encode proteins that synthesize cell to cell signaling molecules that begin polysaccharide formation.
|
|
homoserine lactones
|
The major signaling molecules in pseudomonas biofilm formation
|
|
quorum sensing
|
chemotactic agents to recruit nearby organisms,
|
|
Reasons for biofilm formation
|
1- Allows cells to remain in favorable niche.
2- Allows cells to live in close association fostering genetic exchange and quorum sensing. 3- Type of defense – resist physical force of current or phagocytosis. 4- Biofilms may be the typical way bacteria grow in nature. |
|
mineral soils
|
weathering of rock
|
|
organic soils
|
sedimentation from bogs or marshes
|
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rhizosphere
|
soil around roots
|
|
Predominant microorganisms in oxic areas
|
cyanobacteria and algae
|
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Predominant microorganisms in anoxic areas
|
anoxygenic phototrophs
|
|
Phytoplankton
|
algae floating or suspended in water
|
|
Benthic algae
|
those attached to bottom or sides.
|
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oligotrophs
|
Adapted to grow under dilute conditions.
|
|
epilimnion
|
warmer and less dense surface layer in lakes
|
|
hypolimnion
|
cold dense bottom layers in lakes
|
|
Thermocline
|
zone of transition between these two layers in lakes
|
|
Biochemical oxygen demand (bod)-
|
Oxygen consuming property of a body of water – directly related to amount of suspended organic matter.
|
|
Objective in water treatment
|
reduce bod.
|
|
often develop in response to pollution by inorganic nutrients
|
Algae, cyanobacteria, and macrophytes (aquatic weeds)
|
|
The largest carbon reservoir is
|
earth’s crust
|
|
global turnover time of carbon
|
about 40 years
|
|
humus
|
complex mixture from protoplasmic constituents of soil microorganisms.
|
|
most rapid turnover of carbon
|
Co2 of atmosphere
|
|
The single most important contribution of co2 to the atmosphere
|
microbial decomposition of dead organic material.
|
|
The only way that new organic c is synthesized
|
photosynthesis (more important), chemosynthesis (less important).
|
|
Methanogens
|
make methane
|
|
methanotrophs
|
consume methane
|
|
Methanogenesis is carried out by a group of
|
methanogens, strict anaerobes
|
|
Most methanogens use ___ as a terminal electron acceptor in ____ respiration, reducing it to ____ with h2.
|
c02, anaerobic, methane
|
|
primary fermenters.
|
decompose complex molecules
|
|
Syntrophs
|
a species that lives off another species
|
|
secondary fermenters
|
species that ferment the products of primary fermentors
|
|
homoacetogens
|
Acetate and h2 + co2 from primary fermentations can be directly converted to methane, although h2 + co2 can also be consumed by them.
|
|
Primary treatment of wastewater
|
Wastewater is pumped into the reservoir (left) where settling of solids occurs. As the water level rises, the water spills through the grates to successively lower levels. Water at the lowest level, now free of solids, enters the spillway (arrow) and is pumped to a secondary treatment facility.
|
|
Anoxic secondary wastewater treatment processes
|
Anoxic sludge digester
Trickling filter Aeration tank Activated sludge installation |
|
thalus
|
fungal body
|
|
Hypha
|
unit of structure of a mold, a tube shaped structure exhibiting cytoplasmic streaming toward tip as it grows
|
|
Mycelium
|
– hyphae forming an interwoven mat of growth consisting of vegetative hyphae extending into medium and aerial hyphae extending into the air above medium.
|
|
Rhizoid
|
root like structure
|
|
Coenocytic
|
description of hypha, a tube like structure with many nuclei.
|
|
Chlamydospore
|
asexual spore borne at the end of a conidophore.
|
|
Sporangium
|
sack like structure containing sporangiospores (asexual).
|
|
Zoospores
|
Zoospores
|
|
Gametangia
|
specialized sex hypha that grow toward each other.
|
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Ascospores
|
sexual spores borne in a sack like structure the ascus.
|
|
Basidiospores
|
spores borne on a structure called a basidium.
|
|
Basidiocarp
|
the fructification holding many basidia.
|
|
types of fungi
|
1- Ascomycetes
2- Zygomycetes 3- Basidiomycetes 4- Deuteromycetes |
|
Aerial hyphae
|
extend above surface
|
|
Vegetative hyphae
|
below surface
|
|
Aseptate hyphae
|
no cross walls
|
|
Septate hyphae
|
cross walls
|
|
Budding yeast
|
no hyphae
|
|
Asexual Fungi
|
Deuteromyces
fungi imperfecti |
|
Sexual fungi
|
Ascomycetes
Zygomycetes Basidiomycetes |
|
Traditional biotechnology
|
large scale manufacture by microorganisms of products that they normally make.
|
|
Engineered organisms or recombinant DNA
|
use of organisms with modified genome specifically selected and placed into organism.
|
|
Fermenter
|
refers to an organism that ferments
|
|
fermentor
|
to a vessel that is used for an industrial microbial process; it may be either aerobic or anaerobic
|
|
Metabolic specialists
|
microbes that have been altered by mutation to produce large amounts of metabolites.
|
|
Strain improvement
|
eg penicillium chrysogenum, 1µl/ml vs 85000 µl/ml –achieved via mutation and selection.
|
|
Ideal industrial microorganisms:
|
a. Grow rapidly – doesn’t tie up equipment, contamination less likely, easier to control environment
b. Are non-pathogenic c. Are free of toxins d. Can be removed from culture easily, e.g. Yeasts, filamentous fungi, filamentous bacteria |
|
Bioconversion
|
cells are used to chemically convert a specific substance from one form to another.
|
|
Microbial products
|
a. Cells themselves, e.g. Yeasts, lactobacillus, mushrooms.
b. Enzymes – amylases, proteases, lipases, rennin, isomerase (fructose from glucose), penicillin acylase (used in production of semisynthetic penicillins). c. Commodity metabolites – ethanol, acetic acid, lactic acid, citric acid, methanol. d. Growth factors – vitamins, amino acids, antibiotics, steroids, alkaloids |
|
use of microbial products:
Pharmaceutical |
antibiotics, steroids, steroid conversion, hormones.
|
|
use of microbial products:
Genetically engineered |
insulin, human growth hormone, antiviral, anti-tumor, e.g. Interferons, lymphokines, blood clotting, vaccines (hbv), monoclonal antibodies.
|
|
use of microbial products:
Agricultural uses |
insulin, human growth hormone, antiviral, anti-tumor, e.g. Interferons, lymphokines, blood clotting, vaccines (hbv), monoclonal antibodies.
|
|
use of microbial products:
Specialty chemicals and food additives |
amino acids, glutamic acid, lysine, tryptophan, aspartic acid, aspartame, phenylalanine, vitamins.
|
|
use of microbial products:
Commodity chemicals |
energy production.
|
|
Secondary Metabolites
Trophophase |
growth phase.
|
|
Secondary Metabolites
Iidiophase |
metabolic production phase.
|
|
fermentor probe
|
computer converts these data into microbiological or biochemical terms, and graphs the data. Processes data to measure growth, decides when and how much nutrient to add, optimal conditions maintained.
|
|
β-lactam antibiotics
|
Penicillins and cephalosporins, medically useful, contain the β-lactam ring, a complex 2 membered heterocyclic ring. They act by inhibiting peptioglycan synthesis.
|
|
Major ingredient of penicillin production is
|
corn steep liquor
|
|
Cyanocobalamin (B12)
|
synthesized in nature exclusively by microorganisms. B12 has cobalt as a central part of its structure; yields are increased by adding cobalt to the medium.
Propionibacterium yield from 19 – 23 mg/l, pseudomonas denitrificans produceds 60 mg/l in a 2 stage process using molasses as the c source. |
|
Riboflavin (B2)
|
synthesized by many organisms including bacteria, yeasts and fungi. Ashbya gossypii produces up to 7g/l
|
|
Glutamic acid
|
used as a flavor enhancer. (MSG)
|
|
Aspartic acid and Phenylalanine
|
the ingredients of Aspartame.
|
|
Lysine
|
an essential amino acid and is produced by brevibacterium flavum for use as a food additive.
|
|
steroid hormones created in microbial bioconversion
|
progesterone
11-α-hydroxyprogesterone Estrogens androgens Hydrocortisone cortisone |
|
Induced enzymes
|
inducer is present, therfore added during stationary phase.
|
|
bacterial proteases
|
used in laundry detergents that also include amylases, lipases, reductases.
|
|
Laundry enzymes
|
formed by alkaliphilic bacteria, mainly bacillus licheniformis.
|
|
Amylases and glucoamylases
|
are important in the production of glucose from starch that can then be isomerized to fructose used in the food industry as high fructose syrup, made from corn, wheat, potatoes.
|
|
Extremozymes
|
enzymes made by hyperthermophilic microorganisms, function at high temperature. Useful because many industrial processes work best at high temperature.
Ex- Taq and pfu DNA polymerases used in pcr (polymerase chain reaction). |
|
Thermostable ___, ____ and ____ isolated and characterized.
|
amylases
pullulanases xylanases |