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273 Cards in this Set
- Front
- Back
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Methanogens - oxygen & temperature requirements
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obligate anaerobes, usually mesophiles
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Staphylococcus and Micrococcus - catalase activity
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catalase positive
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Staphylococcus and Micrococcus are resistant to what extreme conditions?
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drying & high salt
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These acid tolerant obligate anaerobes grow in "packets" of eight cells.
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Sarcina
sometimes in stomach! |
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Micrococcus resembles Staphylococcus, but is actually a member of ...
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Actinobacteria
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morphology of lactic acid bacteria
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rods and cocci - Lactococcus
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These bacteria are aerotolerant but lack an electron transport system and only perform substrate level phosphorylation.
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Lactic acid bacteria
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Most of these fastidious organisms can only catabolize sugars.
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Lactic acid bacteria
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2 groups of endospore-forming bacteria & their usual environment
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Bacillus and Clostridium - live in soil
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These spore-forming, gram positive bacteria are strict anaerobes, and some fix N2
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Clostridium
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These organisms are facultative or obligate aerobes that can break down polymers
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Bacillus
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Some species of this group can produce crystal protein toxins that kill insect larvae.
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Bacillus
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Streptomyces are species of ______ .
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filamentous Actinobacteria
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These form branching mycelia.
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filamentous Actinobacteria
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Conidia are ____ that are formed in ____, which are ____.
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spores, formed in sporophores which are aerial filaments (hyphae) found in filamentous Actinobacteria
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This genus is found mostly in the soil & produce many important antibiotics.
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Streptomyces
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This phylum is oxygenic, usually obligate, phototrophs.
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Cyanobacteria
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The cyanobacteria have what sort of motility?
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gliding - no flagella
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What kind of chlorophyll is in Cyanobacteria?
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chlorophyll A
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Some Cyanobacteria filaments contain differentiated cells called _______ distributed along the _____.
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heterocysts along the filament
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heterocysts
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N2 fixation takes place in these differentiated cells - they lack the O2-evolving photosystem II found in undifferentiated Cyanobacterial cells
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Heterocysts have ______ that slows the diffusion of O2 into the cell.
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thick cell wall
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______ forms tumours and hairy roots with dicot plants.
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Agrobacterium
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____ form N2 fixing symbioses with legume plants.
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root nodule bacteria
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Agrobacterium and root nodule bacteria are members of _____.
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The Rhizobiaceae
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Agrobacterium are a natural example of what?
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Trans-Domain genetic transfer (Bacteria to Plant)
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Agrobacteria only express bacterial virulence genes when ...
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signals are produced by a wounded (susceptible) host plant:
low pH, monosaccharides, phenolic compounds |
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What are the stages of in Agrobacterium infection process?
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1) wounding; 2) attachment to plant; 3)vir gene induced; 4) T-DNA processing; 5) T-DNA integrated into plant nuclear genome & expression of genes; 6) tumour formation, opine synthesis
opine - modified amino acids for Agrobacteria energy |
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What signals from a plant induce the vir gene?
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phenolics, monosaccharides, acidic pH, (temperature)
wound juice invites Agrobacteria |
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Rhizobia are Gram _____.
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negative
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As the nodule is developing, the rhizobia infect through plant cell wall invaginations which form tubes called ____.
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infection threads
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bacteroids
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N2-fixing cells , differentiated rhizobia inside plant cells
only starts N2 fixation after gets membrane & becomes symbiosome |
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____ are required for nodule formation to take place.
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nod
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The products of the nod genes are enzymes that carry out ____>
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the formation of lipo-chito-oligosaccharides
(Nod factors) |
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______ signal nodule induction in plants.
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lipo-chito-oligosaccharides
Nod factors - induce root hair curling & lead to nodule formation |
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What are used by the bacteroid to generate energy and reducing power?
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C4-dicarboxylic acids such as malate
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______ cells prey on other gram-negative bacteria. They stick to the surface of the "victim" cells, then replicate inside the ______. They are members of the ____.
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Bdellovibrio, periplasmic space, Spirilla
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Example of a budding cell.
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Hyphomicrobium
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Example of a stalked cell
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Caulobacter
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What is unusual about cell division in budding & prosthecate/stalked bacteria?
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unequal => daughter cell (swarmer cell) is distinct from mother cell
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Hyphomicrobium cell division
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mother initially has no extrusion, grows hypha, one copy of DNA goes into hypha, bud forms at end of hypha, daughter cell is a flagellated swarmer cell
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This bacteria has a very large chromosome and obtain nutrients by lysing other cells in its vegetative state.
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Gliding Myxobacteria
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This bacteria has gliding motility in its vegetative state, but when nutrients are limited they differentiate to form multicellular pigmented fruiting bodies that are visible to the eye.
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Gliding Myxobacteria
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The fruiting bodies of gliding myxobacteria are filled with
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myxospores
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"
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Bacteriochlorophylls and carotenoid pigments
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Proteobacteria are Gram
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negative
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These photoautotrophs oxidize H2S to S0 during photosynthetic CO2 reduction
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Purple sulfur bacteria
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Purple Sulfur Bacteria store S^0 in ...
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The periplasm
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These organisms are photoheterotrophs and N2 fixers, can do a little H2S oxidation.
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Purple Nonsulfur Bacteria
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___ are the only organisms which are able to oxidize methane and other C1 compounds which lack carbon-carbon bonds
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methanotrophs
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Methanotrophs convert methane to methanol using ...
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methane monooxygenase
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Oxygen requirements of Methanotrophs
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obligate aerobes, often microaerophiles
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Some ____ are symbionts of marine mussels and are found in mussel lung tissue.
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methanotrophs - the mussels live near geological sources of methane
mussel lungs absorb methane! |
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Azotobacter is an example of ...
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Free Living Aerobic N2-Fixing Bacteria, forms cysts that make it resistant to drying, radiation & mechanical disruption
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The nitrogenase enzyme reduces ___ to ___, and is irreversibly inactivated by ____. Found in ____.
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N2 to NH3 ... O2 ... Free Living Aerobic N2-Fixing Bacteria
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What keeps the intracellular O2 concentration low during N2 fixation in free living aerobic N2-fixing bacteria?
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thick slime layer + very high rate of respiration
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These nonmotile aerobes are examples of gram-negative cocci.
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Neisseria, Chromobacterium, and Relatives
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2 enteric bacteria
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Escherichia coli, Salmonella
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What can be described as follows: Peritrichous flagella, facultative aerobes, oxidase negative, simple nutritional requirements
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Enteric bacteria
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Enteric bacteria are oxidase ___ and Photobacterium are oxidase ___.
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negative; positive
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Bioluminescence requires ...
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luciferase enzyme (LuxA gene) and a long chain aliphatic aldehyde (acylated homoserine lactone) signal (high cell concentration)
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Obligate intracellular parasites with restricted energy metabolism
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Rickettsias
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Rocky Mountain spotted fever & Q fever are caused by
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Rickettsias
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Rickettsias are often transmitted by ____ and are closely related to ____.
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arthropod vectors; mitochondria
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The synthesis of luciferase is induced at the ___ level.
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transcriptional
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______________ is the time required for a ten-fold reduction in the population density.
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Decimal reduction time (D)
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D is/is not dependent on the initial cell concentration.
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not!
D = decimal reduction time (time required for 10-fold reduction in population density) |
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How long would endospores last in an autoclave?
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4-5 minutes at 121 degrees
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Milk can be pasteurized by what treatment conditions?
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71ºC for 15 seconds
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Pasteurization does what?
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Doesn't sterilize, just reduces cell numbers without wrecking the product.
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There is what kind of relationship between radiation dose and survival?
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exponential
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Sterilization by radiation is appropriate for what applications?
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anytime objects are heat sensitive or would be ruined by heat sterilization -> spices, pharmaceuticals, medical equipment
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Filtration is used to sterilize ____.
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liquids and gases but they don't remove virus-sized particles.
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Distinguish between bacteriostatic and bacteriocidal.
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static - inhibits growth; cidal kills organism
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A bacteriolytic agent is a _____ that kills cells by ...
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bacteriocidal/antimicrobial agent that kills by causing lysis
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The minimal inhibitory concentration (MIC) is ...
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smallest amount needed to inhibit growth - measure of sensitivity of a microorganism to a particular antimicrobial agent
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The agar diffusion method is used to determine ...
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sensitivity to an antimicrobial agent
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Distinguish between antiseptics and disinfectants.
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antiseptic -> living tissue, disinfectant -> non-living objects
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_____ can be designed to differentiate between RNA signature sequences
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oligonucleotide probes
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lateral gene transfer definition
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when genes transfer between organisms
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evidence that lateral gene transfer occurs
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phylogeny determined using small subunit rRNA sometimes differs from that found using other gene sequences
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similarities and differences between protein synthesis in Bacteria and Archaea
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ribosome binding sites like Bacteria, but synthesis is inhibited by antibiotics & toxins that act on Eukarya but not those that inhibit Bacteria
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Traditionally, taxonomy relied on ___.
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phenotypic analysis
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Comparison of WHAT can be used to differentiate between organisms that are phenotypically similar but not phylogenetically related?
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GC base ratios
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Hybridization values above ___ indicate same species, and above __ indicate the same genus.
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70%, 30%
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How are species of prokaryotes identified?
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hybridization above 70%, direct comparison of small subunit rRNA sequence - should be at least 97% identical in this sequence
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Criteria for classification as a new species
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fully described; sufficiently different from known species; culture deposited in an approved culture collection available to the scientific community
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_______ of gaseous mixtures resembling the atmosphere of early Earth can result in the formation of organic macromolecules.
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UV irradiation
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the “great oxidation event”
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transition of the Earth's atmosphere from an anoxic, reducing environment to an oxic environment caused by oxygenic prokaryotic organisms
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2 versions of endosymbiotic theory
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1) archaeal organism swallowed aerobic bacteria; 2) nuclear line diverged first then acquired the mitochondrion ancestor
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Evidence for endosymbiotic theory.
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1) eukaryotes that lack organelles close to root of tree, 2) ribosomes of chloroplast and mitochondrion inhibited by bacterial but not eukaryal ribosome inhibiting antibiotics
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molecular chronometers
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homologous sequences compared between organisms to measure evolutionary distance
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What rRNA molecule is used most often for determination of phylogenetic relationships between prokaryotic organisms? Eukaryotes?
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16S rRNA (= small subunit (SSU) rRNA), 18S rRNA molecule that is found in the SSU of eukaryal ribosomes
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How does one obtain the 16S rRNA sequence of a given organism?
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First, primers to conserved regions of the 16S gene are used in a PCR reaction to amplify the gene from genomic DNA of the organism, then the 16S rDNA is sequenced directly (it encodes the rRNA)
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This heterogeneous group is made up of aerobic chemoorganotrophs that are nutritionally versatile.
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Pseudomonads
unlike Bacillus, they can't break down polymers |
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What determines which wavelengths of light are used for photosynthesis in purple phototrophic bacteria?
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Bacteriochlorophylls and carotenoid pigments
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Distinguish between lophotrichous and peritrichous flagella.
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lopho - tuft on end
peri - all over |
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Oxygen requirements: methanogens are _____, the extreme halophiles are___.
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obligate anaerobes;
obligate aerobes. |
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T/F: The purple nonsulfur bacteria
use light as an energy source and an organic compound as a carbon source. |
True - they're photoheterotrophs
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One genus of free-living nitrogen-fixing bacteria is:
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Azotobacter
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The genus Proteus is characterized by what enzyme activity?
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urease
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Caulobacter are typically found in what type of habitat?
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aquatic
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Cytoplasmic extrusions that are smaller in diameter than a mature cell, contain cytoplasm, and are bounded by the cell wall are collectively called:
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prosthecae
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The purple sulfur bacteria utilize __________ as an electron donor for carbon dioxide reduction in photosynthesis.
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hydrogen sulfide
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The key enzyme found in methanotrophs is __________.
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methane monooxygenase
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Chromobacterium violaceum produces a water-insoluble pigment that has antibiotic-like properties and is known as __________.
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violacein - only made if tryptophan is in the medium
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Multicellular structures formed by the fruiting myxobacteria are called __________.
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fruiting bodies
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All Proteobacteria are Gram-what?
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negative
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The use of some sulfur compounds, such as H2S, S0, and S2O32-, as electron donors in chemolithotrophic metabolism generates large amounts of:
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sulfuric acid
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Certain species of Pseudomonas, Ralstonia, and Burkholderia, and the genus Xanthomonas are well-known:
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plant pathogens
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Organisms of the genus Neisseria are always what shape?
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cocci
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What types of cells are capable of being attacked by Bdellovibrio?
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gram-negative (remember the space!)
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The product of both SO42- and S0 reduction is:
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hydrogen sulfide.
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__________ function as internal magnets that orient magnetic spirilla along a specific magnetic field.
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magnetosomes
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The cytoplasmic extrusions formed by the budding and prosthecate/stalked Bacteria include ________, ________, and ________.
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stalks, hyphae, and appendages.
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Bacteria that lack flagella but can move when in contact with surfaces are called __________.
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gliding
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A major factor in heat resistance of endospores is:
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the amount and state of water within the endospore.
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The tube dilution technique is useful for determining the:
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MIC of an agent
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Antimicrobial resistance is typically the result of genes on an R plasmid that:
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causes the organism to modify and inactivate the drug.
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Microbial death is more rapid at __________ pH.
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acidic
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Bacteriostatic agents are frequently inhibitors of
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protein synthesis
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The reaction that results in the cross-linking of two glycan-linked peptide chains is:
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transpeptidation
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A(n) __________ is a strand of nucleic acid that can be labeled and used to hybridize to a complementary nucleic acid from a mixture.
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a probe
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Distinguish transcriptome, proteome & metabolome.
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t = complement of mRNA under given conditions, p = complement of proteins at given time, m= complete set of metabolic intermediates & small molecules produced in organism
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How to study transcriptome?
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microarrays/DNA chips
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How do microarrays & DNA chips work?
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fix genes or genome on surface, label mRNAs - they are complementary to genes transcribed from, so will stick.
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What is shotgun sequencing?
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make many copies of whole genome and cut them up, sequence, computer matches overlapping sequences
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How much redundancy is required for shotgun sequencing?
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7-10 fold redundancy of any given region
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What's an ORF?
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open reading frame - if transcribed, translates to protein of known length & composition
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How do you study a proteome (in lab)?
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2D gel polyacrylamide gel electrophoresis (2D-PAGE)
separates protein by charge and mass (denatured) |
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How does 2D-PAGE work?
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pH gradient under denaturing conditions - proteins stop moving at isoelectric point (net charge is 0), then separate denatured bits by mass - smaller move further
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How does Thermatoga maritima's metabolome reflect its environment?
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-many genes for transport of carbs & a.a.s
-many genes for metabolism of sugars -suggests environment is rich in organic material -flagellar genes -chemotaxis genes -Thermatoga loves in marine sediments |
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What were conditions on earth like before the great oxidation event?
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No free o2, atmosphere rich in H2O, CH4, CO2, N2, NH3
temp >100 C |
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What's a stromatolite?
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biofilms, especially of cyanobacteria, trapped sediment to form layered structures in shallow water -> ancient signs o' life
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The ___ hypothesis holds that life began at hydrothermal springs on ocean floor. Why was this plausible?
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subsurface origin hypothesis - conditions would be more stable & steady supply of energy (reduced inorganic compounds like H2, H2S) at these sites
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RNA-based theory of origin of life
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RNA can bind small molecules & has catalytic activity - could replicate itself;
RNA -> RNA + protein -> DNA -> diversified biochemical processes -> LUCA |
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How did cellular life evolve after LUCA?
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lipid biosynthesis diverges, cell wall biochemistry diverges -> Bacteria + Archea -> disperse to new habitats
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Surface origin hypothesis for LIFE.
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UV irradiation can cause AAs to form from chemicals in ponds on Earth's surface; BUT temperature fluctuations + atmosphere was reducing -> hostile environment
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What is FAME for?
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fatty acid methyl ester analysis
to differentiate between prokaryotes: take fatty acids from cell, amake the methyl esters, then gas chromatography to see if saturated, unsaturated, branched, etc. |
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Describe possible energy-yielding reactions for organisms living in anoxic conditions.
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1) Hydrogenase
Ferrous iron FeS + H2S -> FeS2 + H2 -exergonic or UV rays hook up some H2 Hydrogenase oxidises the H2 to get protons to get proton motive force 2) use force to drive primitive ATPase |
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Compare 2 models eukaryotic origins.
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1) nucleated line diverges from Archaea; endosymbiosis with mitochondrion and chloroplast
2) endosymbiosis by Archaea (mitochondrial ancestor), nucleus emerges, later endosymbiotic acquisition of chloroplast ancestor |
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Steps of PCR.
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1) isolate DNA
2) separate with heat, add primers 3) extend primers with DNAp 4) repeat to get many copies 5) agarose gel - look for product of right size 6) purify & sequence product |
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What is cladistics?
What are some principles used in cladistics? |
methods of constructing phylogenetic trees by looking at nucleotide changes at "phylogenetically informative" sites (conserved) in aligned sequences; principles of parsimony, maximum likelihood, Bayesian analysis
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What are terminal nodes in a phylogenetic tree? Internal nodes?
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internal - ancestor diverged into 2 new entities; terminal - species that exist now
branch length ~ number of changes |
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What are signature sequences? How are they used?
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Sequences from rRNA that are used to identify microbes - specific to group, genus or domain - used in fluorescent in situ hybridization (FISH)
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What's FISH?
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fluorescent in situ hybridization - bind labelled probe to cellular ribosomes - can detect specific microbes (probe based on signature sequence)
e.g. detecting a microbe in mixed culture, or studying community structure (have to get all DNA & amplify it) |
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What pressures lead to genetic differences between domains?
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-barriers to unrestricted gene flow
e.g. physicochemical - selective colonization of habitats enzymatic - restriction endonucleases |
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What genes are shared across all domains?
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core cellular functions: transcription, translation
-may results from lateral gene transfer before primary domains diverge |
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What features group Bacteria with Eukarya?
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ester-linked membrane lipids
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What features group Archaea with Eukarya?
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-no muramic acid in cell wall
-RNAPs have more subunits -TATA box promoters -not sensitive to antimicrobial agents that work on bacteria |
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What features distinguish prokarotes from eukaryotes?
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-cell structure
-circular DNA in P -membrane-enclosed nucleus in E -ribosomes 70s in P, 80s in E -introns in most E genes -no operons in E -plasmids rare in E -no nitrogen fixation in E -no chemolithotrophy in E -no gas vesicles in E -no carbon storage granules in E -E can't grow over 70 C |
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Systematics links together __ & ___.
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phylogeny & taxonomy
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Polyphasic approach to taxonomy means what?
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using phenotypic, genotypic & phylogenetic info to classify organisms & group them according to natural relationships; ecology may help
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Requirements of classical identification methods.
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-pure culture
-isolation -look at physiology -detailed physiology with biochemical tests |
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Microscopic characteristics used for identification.
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morphology, flagellar arrangement,endospores, staining reactions
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Growth characteristics used for identification.
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appearance in liquid culture, colony morphology, pigment, habitat, symbiotic relationships
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Biochemical characteristics used for identification.
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cell wall chemistry, pigment, storage inculsions, antigen, fatty acids, polar lipids, respiratory quinones
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Physiological characteristics used for identification.
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temperature ragnge & optimum, O2, relationship, pH range & optimum, osmotic tolerance, salt requirement/tolerance, antibiotic sensitivity
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Nutritional characteristics used for identification.
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energy sources, carbon source, nirtrogen source, fermentation product, modes of metabolism
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Classes of fatty acids in bacteria
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saturated
unsaturated - double bonds cyclopropane - circle of Cs (roundest damned triangle I ever ...) branched - look at the Cs! hydroxy - has OH on the chain |
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What method of DNA comparison has better resolving power for species?
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DNA-DNA hybridization
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The genealogical species concept for prokaryotes.
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group of strains that based on DNA sequences of multiple genes cluster closely together phylogenetically and are distinct from other groups of strains
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What's a nosocomial infection?
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infection you pick up from health care whatevers
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What measures of the effect of temperature on the viability of an organism is dependent on population size?
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thermal death time (TDT)
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Compare rates of heating & cooling for the autoclave and object being sterilized.
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object lags behind autoclave for heating and cooling after steam stops
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Why does the drying oven have limited usefulness?
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moist heat penetrates better than dry
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What's the HTST method?
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for pasteurizing milk
high temperature, short time 71 C, 15 seconds |
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Comment on the radiation sensitivity of spore-formers, non-sporeformers, viruses, mold, yeasts & enzymes.
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enzymes>viruses>spore-formers>mold = yeast>non-spore formers
(generally - Lactobacillus & Deinococcus radiodurans more resistant than mold/yeast) |
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How does hydrogen peroxide kill microbes?
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oxidizin agent
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Match the function to the agent: oxidizing, alkylating; chlorine gas, ethylene oxide.
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chlorine is an oxidizing agent, ethylene oxide is an alkylating agent
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T/F: Triclosan disrupts cell membranes
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True. P.S. Triclosan is phenolic.
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What does the size of a zone of inhibition depend on?
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nature of antibiotic, diffusion coefficient, amount of antibiotic
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What is the agar diffusion method?
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assay for antimicrobial activity
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What is minimal inhibitory concentration? How do you measure it?
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smallest amount of agent needed to inhibit growth; put the same amount of bacteria into tubes with different concentrations of the agent
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3 types of antimicrobial agent
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static (inhibits growth); cidal (kills cells); lytic (kills cells by lysing them)
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What type of antimicrobial agent is in use if you observe that the viable cell count and total cell count decrease?
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Lytic – if it were cidal, the total cell count would stay constant
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How do you identify static activity?
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viable cell count and total cell count stay constant
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A ___ filter is a thin polycarbonate film with size-controlled holes.
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Nucleopore – pores formed using nuclear radiation + a chemical to enlarge them
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Cellulose acetate and cellulose nitrate are polymeric compounds use to make _____ filters.
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conventional membrane filters – act like a sieve
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What kind of filter is useful for microscopy? Why?
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nucleopore filter – material is in a single plane on surface
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How is the diameter of the pores in a conventional membrane filter controlled?
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changing the conditions of polymerization
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A ___ filter is a fibrous sheet or mat of overlapping fibers.
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depth filter – traps stuff in the fiber network – for large particles
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A pore size of __ is usual for sterilization.
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0.2 micrometres – viruses still fit through
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One application of radiation sterilization.
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biological containment cabinet in a lab – decontaminates surfaces after use
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Radiation intensity is measured in ___, while heat intensity is measured in ___.
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grays, minutes
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Spores are ___ to radiation, while viruses are ___.
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sensitive, resistant
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What tool is used for pasteurization?
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a heat exchanger – milk passes through tubes in contact with a heat source
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____ involves raising the temperature for brief periods of time to reduce the number of microorganisms.
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pasteurization
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How do you test if an autoclave is working?
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could use a piece of tape with a chemical indicator for temperature, pressure; testing kits containing spores that will survive & germinate if autoclave isn't working
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What is “exhaust time”?
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When the steam in an autoclave stops, the period of temperature decrease.
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What would a graph of temp vs. Time for the autoclave and an object look like?
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Temperature of the object rises later than the autoclave temperature but it catches up, both level out around 121 degrees, steam stops so autclave temperature drops and object trails behind.
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What is an advantage of moist heat? Why is there moist heat in an autoclave?
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faster penetration of endospores, pressure is so high there can't be complete evaporation
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decimal reduction time of an endospore
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4-5 minutes
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2 values used to describe heat sensitivity of an organism
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decimal reduction time, thermal death time
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decimal reduction time
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time require for a 10-fold reduction in population density at a given temperature (not dependent on population size)
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thermal death time
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time required to kill all cells at a given temperature
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4 main strategies for preventing microbial growth
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heat sterilization, radiation, filtration, chemical sterilization
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biofouling
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bacteria can cover insides of oil pipelines & obstruct flow of oil
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Staphylococci and micrococcus can be differentiated by the ___ test, or by ___.
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Oxidation-fermentation test – Staph can make acid from glucose aerobically and anaerobically (it's facultative); micrococcus only aerobically (obligate aerobe); GC content – micrococcus has high GC%
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Sarcina packets have what shape?
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Cubic – they divide in 3 planes
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Distinguish between homofermenters and heterofermenters.
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Homo – just lactic acid -> 2 ATP per glucose b/c have aldolase (glycolysis); hetero – lactic acid + ethanol + CO2 -> 1 ATP/glucose because lack aldolase --> ATP can only come from substrate level phosphorylation
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Lactic acid oxygen requirements.
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anaerobes, but they are aerotolerant
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Shape of lactic acid bacteria.
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bacilli and cocci
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What do Streptococcus, Lactococcus & Enterococcus have in common?
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They're all lactic acid streptococci.
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What do Sarcina, lactic acid bacteria and Staphylococcus have in common?
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Non-sporulating, Gram-positive, low GC%
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If you're using 7.5% NaCl medium to select for something, what might you be looking for?
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micrococcus, Staphylococcus
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What's the significance of BT-toxin?
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crystalline protoxiin made by B. Thurungiensis during sporulation as va paraporal body is coverted to the toxin in insect's gut so we put it in plants
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These species can make industrially important products like butyrate, acetone and butanol.
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Clostridium
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An important genus within Actinomyces that produces important antibiotics and unusual spore production.
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Streptomyces – makes antibiotics like tetracycline, produces conidia spores
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3 phyla within the bacterial domain
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Cyanobacteria, proteobacteria (all Gram-neg), Gram-positive + actinobacteria (splits into low-GC and high-GC)
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M. tuberculosis and M. Leprae are part of what genus?
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Mycobacterium
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___ can break down polymers while Pseudomonads cannot.
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Bacilli
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Life cycle of gliding myxobacteria.
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live on their own in vegetative state, but aggregate when nutrient are scarce and differentiate to form a fruiting body in which myxospores germinate & are relased
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Structure of Caulobacter
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Stalked – has a “holdfast” on end to attach to surfaces, and swarmer cell which has a flagella for motillity – swarmer cell loses its flagellum, grows a stalk to atach to a surface while replicating its DNA, regrows a flagella & the two cells break apart (unequal binary fission), daughter swarmer cell swims around and reproduces elsewhere
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Prosthecates discussed in class
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hyphomicrobium, Caulobacter
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4 ways to get unequal cell division, with examples.
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simple budding (from cytoplasm) – non-prosthecates, budding from hyphae - Hyphomicrobium, division of stalked organism (buds from the regular part of the cell) - Caulobacter, polar growth without differentiation of cell size
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Relate the function of prosthecates to their environment.
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increases surface/volume ration (maximizes nutrient uptake) & can attach to things – helps survive in nutrient-poor aquatic habitats so they can climg to solid surfaces where food is, and take up as much as possible
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Prosthecae describes what structures?
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cytomplasmic extrusions like stalks, hyphae & appendages – they are different from flagella and pili because they are still part of the cytoplasm
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Budding/stalked bacteria are part of a subdivision of ___.
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Proteobacteria
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What's unusual about spirilla as a group?
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They are not a phylogenetic group – they just look alike; huge diversity in %GC - span all sub-divisions of proteobacteria
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A vibrio human pathogen associated with poor water sanitation.
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Vibrio cholerae
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How did Barry Marshall prove what caused ulcers?
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drank a culture of H. Pylori after an endoscopic exam of his stomach showing no prior infection, experienced nausea/vomiting within a week, endoscopic exam & biopsy showed inflammation & colonization by H. Pylori of the gastric mucosa
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Significance of flavinoids
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induce nod gene expression – bind to receptors & inhibit or activate nod gene expression – introduce another leel of bacteria-plant specificity: not all bacteria recognize the same flavinoids
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Significance of NodD
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activates transcription of all the other nod genes
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What's the Sym plasmid?
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symbiosis plasmid – in rhizobia, has genes coding for nod factors and nif genes for nitrogenase
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What happens inside the symbiosome?
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plant cell provides intermediates of the TCA cycle (succinate, malate, fumarate) use by symbiosome to make ATP & donate electrons to reduce N2
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ATP requirement of nitrogen fixation
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Big – 16 to 24 ATP
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Typical pore size for filter sterilization of gases, fluids.
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0.2 microm
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applications of filtration
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isolating/distinguishing organisms, sterilization
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depth filter mode of action
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trapping in overlapping fibers (prefilter for suspended particles)
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conventional membrane filter
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like a sieve – polymers like cellulose acetate or nitrate – pore sizes vary
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nucleopore filter
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polycarbonate film – pores formed by chemical etching – good for microscopy
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Distinguish between germicides and sterilants.
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Both disinfectants – Germicide – decontaminates surfaces; sterilants are suitable for sterilization
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action of iodine
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iodinates tyrosine residues of proteins, oxidizing agent
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Match to mode of action: phenol-containing antiseptics, cationic detergents, phenolic sterilants .... interaction with phosopholipids, of cell membrane, denatures proteins, cell membrane disruption
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Phenol antiseptic– disrupts cell membrane, cationic interacts with phospholipids, phenolic disinfectant denatures proteins
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How many phyla of bacteria are there?
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80+
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Which proteobacteria don't have photosynthetic ability?
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epsilon purple bacteria & delta purple bacteria -> all are chemoorganotrophs
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Which subdivisions of proteobacteria contain both chemolithotrophs and chemoorganotrophs?
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alpha, beta, gamma, all are phototrophs, some grow aerobically using chemotropic respiration
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What colors are bacteriochlorophyll a &carotenoid pigments?
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bca is blue, carotenoids are red-orange-yellow
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What subdivision of Proteobacteria are purple sulfur bacteria in?
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gamma
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What characteristics vary within the purple sulfur bacteria
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whether S is deposited inside or outside cell, cell shape, presence/absence of gas vesicles, halophilic?
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What division of Proteobacteria are purple nonsulfur bacteria in?
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alpha, beta
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distinguish between methylotrophs and methanotrophs
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all methanotrophs are methylotrophs, but they have methane monooxygenase to metabolize methane, none can use C=C
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methylotrophs & methanotrophs are in what phylogenetic groups
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alpha and gamma Proteobacteria
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How do alpha and gamma methylotrophs differ?
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C assimilation paths, different types of internal membranes, gamma have incomplete citric acid cycle, alpha complete, some of both groups can do N2 fixation
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Can Pseudomonads ferment? Are they motile? Infect plants & animals?
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nope, but may produce small amounts of acid from glucose; yes, all are motile; sure do
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Resting structure of Azotobacter
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Cyst – not resistant to heat
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Gram-negative pathogenic (and fastidious) cocci.
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Neisseria – meningitis, gonorrhea
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A penicillin-resistant, oxidase negative genera of gram-negative cocci.
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Acinetobacter
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Enterics can/can't ferment glucose.
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Can – distinguishes them from obligately aerobic bacteria
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Examples of bacteria that use mixed acid fermentation and butanediol fermentation.
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mixed acid – E coli; Enterobacter aerogenes --> so E coli makes mostly acidic products, Enterobacter mostly neutral
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What do enterics, pseudomonas & vibrios have in common? How do you tell them apart?
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all gram negative rods; enterics have peritrichous flagella (not polar) and are oxidase negative, pseudomonads can't ferment sugar but E and V can.
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Obligate intracellular parasites.
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Rickettsias
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All Rhizobia have what features?
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Alpha-Proteobacteria, Gram negative, aerobic, motile
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Why do some believe Agro & Rhizo are members of same genus?
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distinguishing features are plasmid-borne
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What's encoded by theTi plasmid
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transmissibility, opine catabolism, vir genes, and the T-DNA to put in plant – oncogenes and genes for opine synthesis
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Example of N2 fixation by rhizobium-legume symbiosis
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soybean root nodules form with infection by Bradyrhizobium japonicum
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What causes pinkish color of root nodules in legume
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Leghemoglobin – LB is blue, turns pink when complexed with O2 from end of electron transport chain
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What happens in nitrogen fixation?
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N2 gas reduced to 2NH3 (ammonia) which is incorporated into organic N compounds, also produces H2, requires ATP; overall; 8H+ + 8e- + N2 -> 2NH3 + H2
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How do bacteroids look different from free-living rhizobia
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free living are rod-shaped, bacteroids are swollen, x or y-shaped
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What N compound is sent to plant from the bacteroid?
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Glutamine, Asparagine
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Describe Sym plasmid
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nif genes for nitrogenase flank nod genes
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What determines specificity of Nod factors?
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R groups on the ring
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inducer of nod genes vs. Inhibitor of nodulation
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5,7,3',4'-tetrahydroxyflavone vs. 5,7,4'-Trihydroxyisoflavone -> inhibitor has one less -OH group
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Magnetosomes contain ___.
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magnetite- Fe3O4
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Stages of Caulobacter cell cycle
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swarmer loses flagellum, grows stalk & starts DNA synthesis, elongates and synthesizes flagellin, cross-band forms, cell divides.
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chemical test distinguishing micrococcus from staphylococcus
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oxidation/fermentation
Staph produces acid frm glucose aerobically & anaerobically, Micro only aerobically |
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Where is BT protoxin?
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parasporal body of B thuringiensis
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What kind of fermentation does butyric acid group of clostridia use
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acetone-butanol fermentation (acetone & butanol biproducts)
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phycobilins are found in what phylum? what are they?
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accessory pigments used in photosynthesis by Cyanobacteria
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nitrogen product from heterocyst
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glutamine
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Restriction enzyme that leaves sticky ends, and enzyme that prevents it from working.
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EcoRI, EcoRI methylase
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