Chapter 1,2,3 Flashcards
What is Microbiology?
The study of organisms too small to be seen by the unaided eye (can see object 1 nm in Diameter,cannot perceive less than 0.1in Diameter)
Bacteriology?
study of Bacteria & Archaea
Mycology?
study of Fungi,yeast,molds,macro fungi
Phycology?
Study of Algae
Protozoology?
Study of Protozoa
Virology?
Study of Viruses, viroids, Prions
Antony Van Leeuwenhoek(1684)(Dutch)
-Amateur lens maker -made simple microscopes -discovered bacteria,yeast,algae and protozoa(“animacules”) -advancements from Robert hooke)
Fredinand Cohn(1876)(German)
-Father of bacteriology -accurate observations of bacteria -dis. endospores -proved monomorphism of microbes
Louis Pasteur (french)(mid-late,1800’s)
-saved the french beer industry(developed mechanism of fermentation) -chemist(studied optical activity) -Anthrax, rabies vaccine(tried on kid) -Transformation of organic matter due to microbes -discovered anaerobic life -crushed the theory of spontaneous generation(swan necked flask experiment) -early development of germ theory
Pasteur’s Swan necked flask experiment
1- nonsterile liquid poured into flask(neck of flask drawn out in flame, & liquid sterilized by extensive heating) 2-liquid cooled slowly(flask upright position where dust and microorganisms trapped in bend-open end-liquid remains sterile indefinitely 3-Flasked tipped so microorganism-laden dust contacts sterile liquid (liquid putrefies(contamination))
Robert Koch(physician) (German)(late 1800’s)
-proved causation of anthrax -demonstrated biological specificity of disease agents -experimental application of Henle’s principles of infection(“koch’s Postulates”)
Koch’s Postulates
- The suspected pathogen must be present in all cases of the disease and absent from healthy animals. 2. The suspected pathogen must be grown in pure culture. 3. Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal. 4. The suspected pathogen must be reisolated and shown to be the same as the original.
Development of Pure Culture Methods
-Koch first used solid nutrients as potato slice (not everything can grow on)(overgrown molds) -Later used gelatin(drawback was only solid at certain temp.) -finally, agar( from seaweed) which remain with us to this day. (koch got from hesse)
Golden age of Medical Microbiology
-rise -(1876-1900) -Beijerinck & Winogradski
Sergei Winogradsky (Russin)(late 1800-early 1900)
Chemolithotrophy and Chemoautrophy, nitrogen fixation (described the cycles), sulfur bacteria (autotrophic bac.)
Martinus Beijerinck (Dutch)(late 1800-early 1900)
Enrichment culture technique, discovery of many metabolic groups of bacteria, concept of virus(smaller than bac.)
Growth of microbiology in 20th century
-characterizing agents of infectious disease -study of immunity and relation to disease -search of chemotheraputic agents -chemical activities of microorganisms -Contributed significantly to the rise of biochem.
1941- Beadle & Tatum
Biochemical mutants of the fungus (Neurospora)
1943- Delbruck & Luria
Mutations in bacteria( inheritance characteristics)
1944- Avery, Mcleod, & McCarty
Bacterial transformation, DNA is hereditary material
Six characteristics of Living Cells(cell based systems)
- Metabolism 2.Reproduction 3.Differentiation 4.Communication 5.Movement 6. Evolution
1.Metabolism
uptake of chemicals from the environment, their transformation within the cell and elimination of wastes into the environment. The cell is thus an open system.
- Reproduction(growth)
chemicals from the environment are turned into new cells under the direction of preexisting cells.(mother cell to daughter cells)
- Differentiation
Formation of a new cell structure such as a spore usually as part of a cellular life cycle.(life boats-no increase in population - survival mechanism)
- Communication
Cells communicate or interact primarily by means of chemicals that are released or taken up. (quorum sensing and biofilms)
- Movement
living organisms are often capable of self-propulsion. (optional) (flagellum)
- Evolution
cells evolve to display new biological properties.(descent through modification)
Classification of Living Organisms
Taxonomy (systematics)-the art of biological classification -which is made up of Classification, Nomenclature, Identification
Classification types
-Artificial(great for id) vs Natural (phylogenetic) classifications -Phenotypic – based on observable characteristics(artificial) -Genotypic – based on nucleic acid sequence data(natural) -Polyphasic – uses both phenotypic and genotypic data (accurate description used today)
Classification
Domain,Kingdom,phylum,class,order,family,genus,species (dear king Philip came over for green spaghetti)
Carl Linnaean
gave us first binomial system (genus name + Specific epithet) -two kingdoms-1. plant(algae & Fungi) and Animal(infusoria)
Haekel(1866)
three kingdom system- plants, animals, protist
Whittaker (1969)
5 Kingdom System- Eukaryotic- 1.Multicelluar- plants, fungi, animal 2.Unicellular-protist Prokaryotic- 1. Unicellular- Monera
Woess(1977)
Prokaryotes- 1.bacteria 2. archaea Eukaryotes- 1.Eukarya (choose rRNA as an evolutionary chronometer)
Conditions on Early Earth
-No significant O2 -Water, methane, carbon dioxide, nitrogen, ammonia, trace carbon monoxide and hydrogen cyanide -Much hotter
Early life-forms
-Heat-tolerant -Resemble Hyperthermophilic prokaryotes -anoxygenic phototrophic bacteria-then origin of cyanobacteria(02 waste product)-modern eukaryotes
LUCA( population of cells)
Last Universal Common Ancestor(all cells have descended from a common ancestral cell)
dominant structure 3 billion yrs ago?(ancient rocks)
Stromatolites- cynobacteria grow onto sand and make a layer cake structure( in high saline)
Prebiotic Accumluation of Organic Materials
-Polymerization of macromolecules -Exposed surfaces as supports 1.Clays 2.Pyrites 3.Basaltic glasses -Stable, dry environment -Synthesis, accumulation, film formation -Primitive, self-replicating structures
Primative OrganismsMolecular Coding & Energy Generation
-Predict certain requirements -Obtain energy -Make copies (self-replicating) -Certain RNAs are catalytic (ribozymes) (didn’t need enzymes) -RNA life -Catalytic functions (ribozymes) -Genetic coding( unstable and easily mutated) -The “RNA World”
The Modern Cell
-Origin of DNA genetic coding molecule 1.Saved energy 2.Higher replication fidelity 3.More compatible with increasing complexity
Change from RNA to DNA?
Less precise RNA life-forms eliminated
Central dogma
DNA to RNA to Protein
Metabolism in primitive cells
-Required energy, anoxic environment 1.Chemoorganotrophs, chemolithotrophs, anoxygenic phototrophs 2.Ferrous iron redox reactions -Carbon assimilation 1.Organic prebiotic carbon 2.CO2 3. autotrophy -Oxygenic photosynthesis (cyanobacteria) 1.Oxidative metabolism 2.Ozone shield
The theory of Endosymbiosis
explains the origin of chloroplasts and mitochondria and their double membranes. 1.There are two prokaryotic cells 2.One cell “engulfs” the other cell 3. A double membrane the other cell can be found inside
Evolutionary Chronometers
serves as measures of evolutionary change. (ex: amino acid sequence of HOMOLOGOUS molecules) (# of sequence differences is proportional to the # of mutations fixed in the DNA)
Ribosomal RNA(evo. chronometer)
-ancient molecules -functionally constant -universally distributed -phylogenetically conserved -degree of similarity
rRNA
Carl Woes -small subunit sequencing= 16s(1500bp) or 182s
Generating Phylogenetic Trees (rRNA)
Methods: 1.Distance-bp mutations(evolutionary distance) 2.Parsimony-minimum amount of sequence change occurred for divergence
Light Microscopy
-Total magnification = objective x ocular ~ 1500x is upper limit -Resolution: depends of wavelength of light and numerical aperture (NA)(lower the light the higher res.) -Oil-immersion lenses -Staining: increases contrast
Compound light microscope
bright field,phase-contrast,dark field,fluorescence(2-D) differential interference contrast and confocal scanning laser (3-D)
Phase Contrast
-improves contrast between cells and medium -relies on differences in refractive index -useful for viewing living samples
Darkfield
-light reaches specimens from the side -specimen scatters light -high resolution possible, motility observation
Fluorescence
-specimen either natural or treated(DAPI-4,6 diamidino-2-pheylindole0 -tagged antibodies -tagged nucleic acid probes
Differential interference contrast
-Two beams of polarized light(single plane) -Intensifies subtle differences in cell structure -Creates a pseudo- 3-D effect -useful for living cells
Atomic Force
-stylus scans surface of specimen -weak atomic repulsive forces recorded -high resolution with living, hydrated specimens
Confocal Scanning Laser
-computerized microscope with a laser light source -records one thin plane of the specimen in one scan -software combines scans into 3-D image -often used with fluorescent dyes -microbial ecology, cell bio
Electron Microscopy
-use of electrons instead of visible light(the shorter wavelength gives better resolution) (black and white) -TEM(Transmission electron microscope) -SEM(scanning electron microscope)
TEM(transmission electron microscope
-internal structure of cells -thin sections required -high magnifications, high resolution
SEM(scanning electron microscopy)
-external features -intact cells -coated with heavy metal
Prokaryotes
-~3.5 billion years ago -Prokaryotic unicells alone for ~1 billion years -a persisting “age of bacteria” -dominant creatures on earth (biochem diversity,range of habitats,resistance to extinction,biomass)
Phenotypic properities(prokaryotes)
-Ferdinand Cohen -Phenotypic Characteristics 1.morphology 2.Metabolism -Phenotypic classifications 1.artificial classifications(linnaean binomials)
asexual species
a group whose divergence(genetic variation) is constrained and occasionally rest to zero by intermittent bouts of natural selection
biological species concept
a species as members of populations that actually or potentially interbreed in nature, not according to similarity of appearance. Although appearance is helpful in identifying species, it does not define species.
ecotype
species that uses the same resources(ex.glucose)
what are bacterial species?
(Fredrick Cohan, Weslyian U) -Bacterial taxa called “ecotypes” have the dynamic properties of eukaryotic species -Each currently named bacterial “species” is actually composed of many ecotypes -A currently named prokaryotic species is more like genus than a species
Quorum Sensing
the regulation of gene expression in response to fluctuations in cell-population density
Quorum Sensing(Autoinducers)
-Chemical signal molecules that increase in concentration as a function of cell density 1.Gram positives-secreted oligo-peptides 2.Gram negative-acylated homoserine lactones
Quorum Sensing(diverse physiological activités it regulates)
-symbiosis -virulence -competence -conjugation -antibiotic production -motility -sporulation -biofilm production
biofilms
a highly differentiated matrix-enclosed community whose cells express a phenotype profoundly different from planktonic cells (biological unique,superorganism,functional multicellular)
origins of cells and multicellular communities
-Surfaces are sites for absorbed nutrients and cells to interact -Biofilms are an ancient development -Dominance in both Bacteria and Archaea suggest early, independent development -Found in most ancient bacterial, archaeal lineages -Dominant form of prokaryotic life
Characteristics of biofilm communities
1.Highly structured -Position and spatial relationships predetermined -Coordinated developmental cycle -Signal molecules/positioning mechanisms 2.Self-assembly -Biofilms form wherever, whenever nutrient events occur -Phenotypic plasticity of bacterial genomes -Ubiquity of bacterial genomes
biofilm formation
Made of EPS(extracellular polymeric substance) -provides structural support(controls structure) -produced by bacteria in the film -genetically controlled & by quorum sensing
Four stages of biofilm formation
- reversible attachement 2. Irreversible attachement 3.maturation 4.detachment
low flow conditions(biofilms)
no directionality to microcolonies(easy to pick apart)
high flow unidirectional flow(biofilms)
-filamentous streamers -filamentous mats(water flow)
Biofilm disadvantages
-overcrowding -limited access to nutrients -starvation
Microbial ecology
how microbial communities interact with each other and their environment
microbial ecology organization levels
-populations -guilds -communities -ecosystems
guilds
metabolically similar microbial populations that exploit the same resources in a similar way
niche
the habitat that is shared by a guild and that supplies the nutrients and conditions the cells require for growth.
Microenviroments
-very spatially small -physical/chemical conditions can change rapidly
soil aggregate
-comes from polysaccharides from fungi that glue together mircocolonies with different metabolic needs
nutrient levels and growth rates
-nutrients are in short supply -nutrient distribution not uniform -competition with other organism -periods of optimal growth are rare
symbiosis
cooperation with complementary metabolism
Fluorescent Stainning
- Acrindine Orange
- DAPI
Genetic Stains
Fluorescent in situ hybridization (FISH) phylogenetic probes
- species specific signature sequences
- highly specific
- simple to perform
- mulitple probing of single sample
FISH Chromosomal Painting
- Identify specific genes
- locate, count specific metabolic population
In Situ Reverse Transcriptase FISH
- locate specific genes
- detects expression specific genes
PCR & Microbial Community Analysis
- Terminal Restriction Length Polymorphism
- Denaturing Gradient Gel Electrophoresis
Microbial Activity Measurements
- Radioisopes
- high sensitivity
- turnover rates
- fate of substrate
- killed cell control - Microelectrodes
- 2-100 micro in diameter
- micromanipulator
- microbial mats
- multiple electrodes
covalent bonds
from strong bonds in which electrons are shared more or less equally between atoms
monomers
small molecules that in turn bond with each other to from larger molecules called polymers
macromolecules
covalently bonded polymers in living things
hydrocarbons
carbon and hydrogen make stable compounds that are nonpolar, do no form hydrogen bonds and are generally insoluble in water
covalent bonding(double or triple bonds)
hydrogen bonds
form as the result of weak electrostatic interactions between hydrogen atoms and more electronegative atoms(oxygen or nitrogen)
alcohol
the -OH is called hyroxyl group
aldehyde
carbonyl group(c=o)
ketone
carbonyl group (c=o)
carboxylic acid
The-COOH is called a carboxyl group.
esters
formed by combining an acid and an alcohol
Amines
in water combine with an H+ ion to become positively charged
amides
are formed by combining an acid and an amine. Unlike amines, amides are uncharged in water.
phosphates
H3PO4
