what is microbiology?
the study of small things; strudy of entities too small to be seen with the unaided human eye
-first to see microorganisms
-coined the word 'cell'
-published book- Micrographia
Antoni van Leeuwenhoek
-made his own microscope
-"Father of Microbiology"
-developed taxonomic system
-every oragnism has a two-name designation (binomial nomenclature) Genus species (italicized)
what are the three domains?
Bacteria, Archaea, Eukarya
what domains do prokaryotes fall under?
Bacteria and Archaea
what did Leeuwenhoek first describe microoraganisms as?
what are the 4 questions that scientists searched for the answers to?
1. is spontaneuous generation of microbial life possible?
2. what causes fermentation?
3. what causes disease?
4. how can we prevent infection and disease?
what is spontaneous generation? who was it proposed by?
-proposes that living organisms can arise from nonliving matter
-proposed by Aristotle
describe what Francesco Redi did and if he supported spontaneous generation
-he took meat and put it into a flask so that flies could get at it. one flask had been unsealed and maggots were present on the meat; the second flask was sealed and there were no maggots; the third flask was covered with gauze and maggots were present on top of the gauze (not the meat)
-therefore, did NOT support spontaneous generation
describe what John Needham did and if he supported spontaneous generation
-he took a flask with broth and briefly boiled it then sealed it with cork, waited days later and there was bacterial growth
-he DID support spontaneous generation
describe what Lazarro Spellanzani did and if he supported spontaneous generation
-he did the same thing as Needham but boiled it much longer and sealed it with wax and there was no bacterial growth
-he did NOT support spontaneous generation
-"Father of Modern Microbiology"
-he used swan neck flaks and heated broth then lets it sits for months (air can freely go in and out) and it remains sterile; dust had collected in the bend and the dust contain the microbes
-RIP spontaneous generation
describe the scientific method
1. observations lead to a question
2. a question leads to a hypothesis
3. a hypothesis leads to an experiment with control groups and that leads to observations
4. these observations either support or do not support your hypothesis
5. if supported, repeat experiment with accepted hypotheiss to get similar results then it becomes theory or law
6. if not supported, either reject hypothesis or modify hypothesis and run new experiment
fermentation: what was the observation?
that fermentating grape juice contains bacteria and yeast (review slide about hypotheses and experiments)
what was the microbiological event that was the most important one? what bacteria did this?
-the domestication of yeast
-presence of enzymes
-began the field of biochemistry
what is the germ theory of disease?
discovery: bacteria responsible for spoiling wine + hypothesis: microbes responsible for diseases
-determine cause of anthrax (bacillus anthracis)
-investigations of etiology
-discovered cause of tuberculosis
-method of isolation
Koch's Postulates (steps that must be taken to prove the cause of any infectious disease)
1. suspected causative agent must be found in every case of the disease be absent from healthy hosts
2. agent must be isolated and grown outside the host
3. when agent is introduced into a healthy, susceptible host, the host must get the disease
4. same agent must be found int he diseased experimental host
-hypothesized that cadaver particles from the hands of medical students caused puerperal fever
-required handwashing in chlorinated lime water
-began spraying wounds, surgical inscisions and dressings with carbolic acid
-reduced deaths by 2/3
-known as antisepsis
-introduced cleanliness into nursing
-determined the cause of cholera transmission
-foundation for two branches of microbiology: infection control and epidemiology
-influential in field of immunology
-injected push collected from cowpox to prevent smallpox
-search for 'magic bullet' that could kill microorganisms without being toxic to humans
-discovered chmicals effective against sleeping sickness and syphilis
-uses living bacteria, fungi and algae to detoxify polluted environments
-recycling of chemicals such as carbon, nitrogen, sulfur
-study of blood serum
-Von Behring and Kitasato
-study of body's defense against specific pathogens
-Fleming discovered penicillin
-Domagk discovered sulfa drugs
what are the general principles of microscopy?
1. wavelength of radiation
what is resolution?
-shortest distance between two points on a specimen that can still be distinguised by the observer as separate entities
what is contrast?
-differences in intensity between two objects, or between an object and background
-important in determining resolution
-staining increases contrast
staining ____ contrast and resolution
what are the three simple stains?
1. crystal violet
3. methylene blue
what are differential stains?
1. gram stain
2. acid-fast stain
3. endospore stain
what are special stains?
1. negative (capsule) stain
2. flagellar stain
describe the Gram stain procedure
1. slide is flooded with crystal violet for 1 min, then rinsed with water. Result: all cells are stained purple
2. slide is flooded with iodine for 1 min, then rinsed with water. Result: iodine acts as a mordant; all cells remain purple
3. slide is flooded with solution of ethanol and acetone for 10-30 sec, then rinsed with water. Result: smear is decolorized; gram + cells remain purple but Gram - cells are now colorless
4. slide is flooded with safranin (counterstain) for 1 min, then rinsed with water and blotted dry. Result: gram + are purple, gram - are pink
Ziehl-Neelsen acid-fast stain
-Mycobacteria (waxy cell wall)
-red primary stain, then decolorize then use counterstain with methylene blue
-acid fast cells are red and non acid fast cells are blue
Schaeffer-Fulton endospore stain
-primary stain with malachite green
-decolorized with water
-counterstain with safranin
-green colored endospores and red colored vegetative cells
what are negative (capsule) stains used for?
primarily used to reveal the presence of negatively charged bacterial capsules
what is a flagellar stain used for?
stains bind to flagella, increase their diameter and change their color, all of which increases contrast and makes them visible
-used binomial nomenclature in his system
-proposed only two kingdoms
proposed taxonomic approach based on five kingdoms (animalia, plantae, fungi, protista and prokaryotae)
why did they add a domain?
based on comparisons of genetic material
-compared nucleotide sequences of rRNA subunits
-proposed three domains (eukarya, bacteria and archaea)
what are dicotomous keys?
-series of paired statements where only one of two either/or choices applies to any particular organism
-key directs user to another pair of statements, or provides name of organism
what are the four processes of life?
1. growth (changing in size)
2. reproduction (changing in number)
3. responsiveness (react to environment to different stimulus--chemicals, food, light)
general characteristics of prokaryotes: genetic material? organelles? size? composed of what organisms?
1. circular DNA
2. lack nucleus and membrane bound organelles
3. smaller in size (about 1.0 micrometers)
4. simple structure
5. bacteria and archea compose prokaryotes
general characteristics of eurkaryotes: genetic material? organelles? size? composed of what organisms?
1. linear DNA
2. nucleus and internal membrane-bound organelles
3. larger (10-100 micrometers)
4. more complex structure
5. composed of algae, protozoa, fungi, animals and plants
what are glycocalyces?
-gelatinous, stick substance surrounding the outside of a cell
-composed of polysaccharides, polypeptides or both
what are the two types of glycocalyces? describe them.
1. capsule- firmly attached to cell surface; may prevent bacteria from being recognized by host
2. slime layer- loosely attached to cell surface; sticky layer allows prokaryotes to attach to surfaces
what are flagella?
-responsible for movement
-composed of filament, hook and basal body
-NOT present in all bacteria
what are the functions of flagella?
-rotation propels bacterium through environment
-rotation reversible; can be counterclockwise or clockwise
-bacteria move in response to stimuli (taxis)
runs and tumbles
what are fimbriae and pili in general?
rod-like proteinaceous extensions
what are fimbriae specifically?
-sticky, bristlelike projections
-used to bacteria to adhere to one anothe, to hosts and to substances in environment
-shorter than flagella
-serve an important function in biofilms
what are pili specifically?
-tubules composed of pillin
-also known as conjugation pili
-longer than fimbriae but shorter than flagella
-bacteria typically only have one of two per cell
-mediate the transfer of DNA from one cell to another (conjugation)
what do bacterial cell walls do? what are they composed of? what are the two types?
-provide structure and shape and protect cell from osmotic forces
-composed of peptidoglycan
-two types: gram-positive (thicker; purple) and gram-negative (thinner; red)
describe the gram-positive cell walls
-thick layer of peptidoglycan
-contain teichoic acids
-appear purple following Gram stain
describe the gram-negative cell walls
-thin layer of peptidoglycan
-bilayer membrane containing phospholipids, proteins and lipopolysaccharides (LPS)
-appear red following Gram stain
what is Lipid A?
-a potent endotoxin
-dead cells release Lipid A, which may trigger fever, vasodilation, inflammation, shock, blood clotting
what is the structure of the bacterial cytoplasmic membrane?
what are the functions of the bacterial cytoplasmic membrane?
-harvest light energy for phosynthetic bacteria
-*maintain concentration and electrical gradient
what are the passive processes of the cytoplasmic membrane?
2. facilitated diffusion
what are the active processes of the cytoplasmic membrane?
1. active transport
2. group translocation (substance chemically modified during transport)
what is diffusion?
-passive process of transport
-just passes through the phospholipid bilayer
what are the two types of facilitated diffusion?
-passive process of transport
1. substances go through a nonspecific channel protein
2. substances go through a specific channel protein for one chemical; binding of chemical causes shape change in channel protein
what is osmosis?
-diffusion of water through a specific channel protein or through a phospholipid bilayer
-water flows to area of higher solute concentration
what will happen if the concentration is the same inside the cell and outside in a animal cell and plant cell?
you are in an isotonic solution so there is not net diffusion of water
what will happen if the concentration is higher outside the cell than inside in a animal cell? a plant cell?
youre in a hypertonic solution
1. in an animal cell, water will leave the cell causing the cell to shrink (crenation)
2. in a plant cell, water will leave the cell but the cell wall keeps the entire cell from crenating...only the inside will
what will happen if the concentration is higher inside the cell than outside in a animal cell? a plant cell?
you are in a hypotonic solution
1. in an animal cell, water will enter the cell and it will swell and possible lysis
2. in a plant cell, water will enter the cell but the cell wall protects it from damage
what are the three methods of active transport?
1. uniport- one direction
2. antiport- two substances in two different directions using same channel
3. coupled transport: (one using another ones energy) uniport and symport- two channels; the symport one is bringing two substances in the same channel in the same direction
what is group translocation?
-a substance comes in a channel and changes structure and then can't be taken back up
what are endospores?
-unique structures produced by some bacteria that are a defensive strategy against unfavorable conditions
-most resistant and enduring cells
what are the size of prokaryotic ribosomes?
composed of 30S and 50S subunits
what are the external structures of archaea?
-glycocalyces: function in formation of biofilm; adhere cells to one another and inanimate objects
-flagella: consist of basal body, hook and filament
do archaea cell walls have peptidoglycan?
do animals and protozoan have cell walls?
no...they lack cell walls
what are plant cell walls made of?
what are fungi cell walls made of?
cellulose, chitin, and/or glucomannan
what are algae cell walls made of?
variety of polysaccharides
what is endocytosis?
physical manipulation of cytoplasmic membrane around cytoskeleton....form pseudopodia
what are the two types of endocytosis?
1. phagocytosis- solid imported into cell
2. pinocytosis- liquid imported into cell
what is exocytosis?
substances exported from cell
what type of cells have cilia?
no prokaryotic cells have cilia
what are the size of eukaryotic ribosomes?
they have a 60S and 40S subunits
what are centrioles? what type of cells have them?
-centrioles play a role in mitosis, cytokinesis and formation of flagella and cilia
-plants, algae, most fungi and prokaryotes LACK centrioles
what is often the largest organelle in a eukaryotic cell?
what are mitochondria? describe their ribosome size
-mitochondria are composed of 2 membranes of phospholipid bilayer
-produce most of cell's ATP
-they have 70S ribosomes and circular molecule of DNA
what are chloroplasts? what are the size of their ribosomes? do prokaryotes have chloroplasts?
-light-harvesting structures found in photosynthetic eukaryotes
-have 70S ribosomes
-prokaryotes lack chloroplasts
what group is the most numerous and diverse group of cellular microbes?
what are the 7 different typical prokaryote morphologies?
1. coccus (round)
3. bacillus (rod-like)
4. vibrio (comma-shaped)
5. spirillum (stiff)
6. spirochete (flexible)
7. pleomorphic (bizarre shape or multiple shapes)
what are the three main methods of reproduction in prokaryotic cells?
1. binary fission (most common)
2. snapping division
describe binary fission
-parent cell replicates its DNA
-cell elongates and DNA separates to opposite ends
-a cross wall forms and the membrane invaginates
-cross wall forms completely and daughter cells separate
describe snapping division
-modified binary fission
-daughter cells remain connected and a hinge is formed
-new nucleoid moved into bud
-young bud develops into daughter cell
-parent cell is maintained
what is viviparity? what genus performs this type of reproduction?
-viviparity is live offspring emerge from the body of the dead mother cell
-Epulopiscium and some of its relatives have this unique reproduction
what are the five different arrangements of cocci?
2. streptococci (chain)
3. tetrads (two vertical planes)
4. sacinae (2 vertical and a horizontal plane)
5. staphylococci (grape-like clusters)
what are the 5 different arrangements of bacilli?
1. single bacillus
3. streptobacilli (chain)
4. palisade (results from snapping division)
5. V-shape (results from snapping division)
what two genuses produce endospores?
what is something unique about bacteria that produce endospores?
they usually produce deadly toxins that cause fatal diseases such as anthrax, botulism, tetanus and gangrene
what is Bergey's Manual?
-manual for classification of prokaryotes
what are the four major divisions that Bergey's manual organizes prokaryotes into?
1. Gracilicutes (gram -, thin skinned)
2. firmicutes (gram +, thick and strong)
3. tenericutes (lack cell wall, soft)
4. mendosicutes (archaea)
what is distinguishable about bacteria with no cell wall? what are two examples?
-lack cell walls and therefore stain red on gram stain
-when grown on media, form distinctive 'fried egg' appearance
-colonize osmotically protected habitats such as animal and human bodies
ex: mycoplasma (pneumonia) and ureaplasma (urinary infection)
what is unique about archaea in relation to disease?
they are not known to cause disease
archaea: characteristics of methanogens
-largest group of archaea
-convert CO2 and H2 into methane gas
-one of primary sources of environmental methane
archaea: what is the basic defintion of extremophiles? what are the 4 types?
require extreme conditions to survive (temp, pH, salinity)
-thermophiles, psychrophiles, halophiles, acidophiles
-require high temps to survive
-do not function properly below 45 C/113 F
-require temps over 80 C/ 176 F
-require low temps to survive
-between -15 C/5 F to 10 C/50 F
-inhabit extremely saline habitats
-greater than 9% NaCl
-thrive under highly acidic conditions (less than 2.0 pH)
what are the major groups of eukaryotes for microbiology?
4. water molds
-parasitic helminths and arthropod vectors
reproduction of eukaryotes
can be asexually, sexually or both (see slide 4 on page 1)
what are eukaryotic organisms with haploid DNA?
-most fungi, many algae, and some protozoa
what are eukaryotic organisms with diploid DNA?
-remaining fungi, algae and protozoa
-most plants and animals
protozoa are a diverse group of organisms defined by three characterists....
3. typically lack a cell wall
protozoa require ___ environments. ___ ___ are pathogens.
moist; very few
describe the unique morphology of protozoa (also give definitions)
-all produce trophozoites (motile feeding stage)
-some produce cysts (hardy resting stage
-some have contractile vacuoles (actively pump water from the cells, protecting them from osmotic lysis)
-most reproduce asexually
what are dinoflagellates?
-large proportion of freshwater and marine plankton
-many are bioluminescent
-many produce neurotoxins that can affect humans who ingest fish or shellfish that have been infected
what are characterisitics of fungi?
-have cell walls typically composed of chitin
-do not perform photosynthesis
what is the significance of fungi?
-30% cause diseases of plants, animals and humans (mycoses)
-can spoil fruit, pickles, jams and jellies
fungal morphology: thallus
fungal morphology: hyphae
long, branched, tubular filaments
fungal morphology: dimorphic
generally, yeast form of dimophics cause diseases
fungal morphology: mycelium
-tangled mass of hyphae
reproduction of fungi
-all have some means of asexual reproduction
-most also reproduce sexually
-buddying and asexual spore formation
-series of buds that remain attached to one another and to parent cell
-found in Candida albicans (yeast infections)
what are lichens?
symbiotic partnerships between fungi and photosynthetic microbes
what are algae?
-simple, eukaryotic phototrophs that carry out oxygenic photosynthesis using chlorophyll a
-most are aquatic and live in the photic zone of fresh, brackish and saltwater
how to water molds differ from fungi?
cell walls are cellulose, not chitin
what do water molds do?
decompose dead animals and return nutrients to environment; some are detrimental to crops
what are arthropod vectors?
animals that carry pathogens
what are the two types of arthropod vectors?
mechanical- only carry the pathogen
biological- serve as host for pathogen
what are the two arthropod vectors classified under arachnids?
what is the most important arachnid vector?
what are the five arthropod vectors classified under insects?
4. kissing bugs (true bugs)
what is the most important insect vector?
what is the most important of ALL vectors?
are all viruses harmful to humans?
what are bacteriophages?
attack pathogens and have clinical use
what are characteristics of viruses?
miniscule, aceulluar, infectious agent having either DNA and RNA
viruses ___ ___ have any processes of life on their own.
-cannot carry out any metabolic pathway
-cannot reproduce independently (require host cell)
what are capsids?
protein coat that provides protection for viral nucleic acid and means of attachment to host's cells
-composed of proteinaceous subunits called capsomeres
what is the name of the extracellular state of a virus?
what is the strucutre of a virion?
central nucleoid surrounded by capsid (aka nucleocapsid)
-some have phospholipid envelope
what is the intracellular state of the virus?
the capside is removed and the virus exists as nucleic acid
what is the genetic material of viruses?
(primary way to categorize and classify viruses)
-may be DNA or RNA but never both
hosts of viruses may be specific or generalists. what does this mean?
-specific means they only infect particular kind of cell in a particular host
-generalists means they infect many kinds of cells in many different hosts
what types of organisms are susceptible to some sort of viral attack?
ALL types of organisms
what are the three basic viral shapes?
2. polyhedral (icosahedron- 20 sides)
describe the viral envelope
-acquired from host cell during viral replication or release
-with envelope= enveloped virion
-no envelope= nonenveloped/naked virion
what is lytic replication?
replication cycle usually results in death and lysis of host cell
describe the 5 steps in lytic replication
1. attachment of the virion to host cell
2. entry of the virion or its genome into host cell
3. synthesis of new nucleic acids and viral proteins by the host cell's enzymes and ribosomes
4. assembly of the new virions within the host cell
5. release of the new virions from the host cell
what is lysogeny?
-modified replication cycle of viruses
-infected host cells grow and reproduce normally for generations before they lyse
-temperate phages- prophages (inactive phages)
-lysogenic conversion results when phages carry genes that alter phenotype of a bacterium
what are the three mechanisms of entry of animal viruses?
1. direct penetration
2. membrane fusion
what is direct penetration?
-insert genetic material directly into animal cell
-only has capsid
what is membrane fusion?
-fuses to membrane (envelope stays part of human cell membrane)
-release capsid then uncoating to release genetic material
what is endocytosis?
-engulf entire virus (envelope, capsid and genetic material)
-envelope opens then capsid uncoats and material released
what is latency of animal viruses?
when animal viruses remain dormant in host cells
what is neoplasia?
-uncontrolled cell division in multicellular animal
-mass of neoplastic cells is tumor (neoplasm)
what does benign mean?
does not cause any harm
what does malignant mean?
has the ability to cause harm/cancer and metastasize
what is metastasis?
grow and inhibit other tissues than the source
what are environmental factors that contribute to the activation of oncogenes?
viruses cause _____% of human cancer
what are viroids?
-extremely small, circular pieces of RNA that are infectious and pathogenic in plants
what are viroidlike agents?
infections, pathogenic RNA particles that lack capsides but do not infect plants (affect some fungi)
what are prions?
-proteinaceous infectious agents
-lack nucleic acid
-can affect humans
prion diseases cause what?
-predominant in nervous system
what are the 7 growth requirements for microbial growth?
2. moisture requirements
3. oxygen requirements
4. temp requirements (most important factor)
5. pH requirements (work best near 7)
6. light requirements (most pathogens are killed by direct sunlight)
7. osmotic pressure (hypertonic, hypotonic and isotonic solutions)
what are autotrophic organisms?
-thrive in areas where organic matter is scarce
-self-nourishing (capable of surviving in the absence of organic compounds)
-algae and some bacteria are autotrophic
what are heterotrophic organisms? and what are the three types?
-use organic matter for entergy and synthesis of cell materials
1. strict (obligate) saprophytes- obtain nutritional need from non-living sources
2. strict (obligate) parasites- only grow on other organisms
3. facultative- live and adapt in food conditions that may vary
what are strict (obligate) aerobes?
only grow in the presence of oxygen
what are strict (obligate) anaerobes?
require total absence of oxygen
what are facultative organisms when it comes to oxygen requirements?
grow in absence or presence of oxygen
what are microaerophilic organisms?
require very little free oxygen to maintain growth
what are psychrophilic organisms?
prefer cold temps
what are mesophilic organisms?
prefer moderate temps (usually around human body temp) [most pathogenic organisms are this]
what are thermophilic organisms?
prefer high temps
what is genetics?
study of inheritance and inheritable traits as expressed in an organisms genetic material
what is a genome?
entire genetic complement of an organism; includes its genes and nucleotide sequences
what is the strucutre of nucleic acids?
G with C
A with T
A with U
describe prokaryotic chromosomes
-circular molecule of DNA in nucleoid
what are plasmids?
-small molecules of DNA that replicate independently
-not essential for normal metabolism, growth or reproduction
what are the 4 types of plasmids?
1. fertility factors (F plasmids)
2. ressitance factors (R plasmids)
3. bacteriocin factors
4. virulence plasmids
what are F plasmids for?
carry instructions for conjugation
what are R plasmids for?
carry genes for resistance to one or more antimicrobial drugs or heavy metals
what are bacteriocin factors?
carry genes for proteinaceous toxins called bacteriocins-- can kill its competitors
what are virulence plasmids?
carry instructions for structures, enzymes or toxins that enable bacterium to become pathogenic
describe eukaryotic chromosomes
-linear and sequestered within nucleus
extranuclear DNA of eukaryotes resemble chromosomes of _____
what is a genotype?
-actual set of information
-internally coded, inheritable info
what is a phenotype?
-outward, physical manifestation
-physical features and functional traits of the organism
what determines phenotype?
what is vertical gene transfer?
organisms replicate their genomes and provide copies to descendants
what is horizontal gene transfer? what are the three types?
-acquire genes from other microbes of the same generations
-donor cell contributes part of genome to recipient cell
-types: 1. transformation
3. bacterial conjugation
what is transformation?
-recipient cell takes up DNA from environment (may be from dead organisms)
-cells have to be competent
what is transduction?
-transfer of DNA from one cell to another via a replicating virus
what is conjugation?
-F+ cell has F plasmid
-F plasmid tells cell to conjugate
-has sex pilus
-attaches to F- cell and then draws it near with pilus and confers one strand of F plasmid DNA
-now both cells are F+ cells
what is conjugation involving Hfr cell?
-F plasmid incoporated into chromosome
-conjugate with F- cell
-part of F plasmid moves into F- cell plus some of F+ chromosome
-doesnt have full F plasmid; stays F- cell
what are the 5 emerging diseases?
1. variant creutzfeldt Jakob disease
5. vibrio vulnificus infection