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90 Cards in this Set

  • Front
  • Back
microbiology
the science (study/knowledge) of microorganisms
taxonomy
-naming, describing, and classifying organisms
- grouped according to
Genetics
Ecology-> soil/water microbio.
Morphology-> shape/structure
Physiology->enzymes, functions
macroscopic life
-things visible to the naked eye
-anything bigger than:
0.2 mm
200 micrometers
200,000 nanometers
-most are unicellular (single-celled, more primative)
rhizopus
-macroscopic
-black bread mold
microscopic life
-anything too small to see with the naked eye
-anything smaller than
0.2mm
200 micrometers
200,000 nanometers
light microscopes
-ranges from 0.2mm-0.2micrometers
-ranges from 200 micrometers to 200 nanometers

-can see most:
-Larger bacteria
-Algae
-Mycoplasma
-Protozoa
mycoplasma
-smallest bacteria
electron microscopes
- range from 0.2micrometers to 0.5nanometers under the best conditions
3 Domains of Life
-Archaea
-Bacteria
-Eukarya

-DKPCOFGS
R.H. Whittaker
- developed old system that used 5 kingdoms in 1969

- 5 kingdoms:
1 Fungi
2 Animalia
3 Monera
4 Protista
5 Plantae

-FAPP: eukaryotic, membrane bound organelles
-Monera: bacteria, prokaryotic, have ribosomes
Woese
-developed new system that uses 3 domains in 1978

-3 domains:
1 Archaea
2 Bacteria
3 Eukarya

-classified organisms by examining their DNA to see relationships/differences

-Monera: 2 kingdoms are the following:
i. Archaea
ii.Bacteria
----> there are no kingdoms in these 2 domains!
archaea
-NOT BACTERIA!!
-prokaryotic
-no murein in cell walls
-cell membrane phospholipids have ETHER links
-unicellular
-NOT pathogenic

-ex) thermophiles, methanogens, halophiles
bacteria
-prokaryotic
-contain murein in cell walls
-cell membrane phospholipids have ESTER links

ex)
-tuberculosis (Genus Mycobacterium)
-cholera (salty water flooding)
-bacillary dysentery (Genus Shigella); severe diarrhea where stool has blood
eukarya
-eukaryotic
-possess nuclei, mitochondria, ribosomes, some have chloroplasts
-made up of 4 different kingdoms

ex) Protists-->eukaryotic, mostly unicellular
-simple plants (algae)
-simple animals (protozoa)
-simple molds (water molds)
---->WAP

-Protozoans eat via PHAGOCYTOSIS
ex) Amoebic dysentery
fungi
-eukaryotic
-mostly multicellular
-ABSORPTIVE HETEROTROPHS

ex's)
-Mushrooms
-Molds
>ringworms & athlete's foot
-Yeasts(single-celled)
>Candida Albicans- causes candidiasis and thrush (yeast infections) which is candidiasis in the throat
plants
-eukaryotic
-multicellular
-PHOTOSYNTHETIC AUTOTROPHS

ex)
-bryophytes (mosses)
-gymnosperms (pines)
-angiosperms(flowering plants)
animals
-eukaryotic
-ALL multicellular
-INGESTIVE HETEROTROPHS

ex)
-sponges
-mammals
-worms
>helminthes(worms) cause diseases
>roundworms: ex)Ascaris-caught from eating undercooked meat
>flatworms: tapeworms, flukes
evolution
prokaryotes->protists->plants, animals, fungi
viruses
- NOT CONSIDERED IN ANY DOMAIN
-not considered living because they are ACELLULAR (w/o cells)
>Cell Theory: cells are composed of:
-cell membrane
-cytoplasm (ribosomes)
-nucleus (nucleoid in prokaryotes)

-Viruses lack...
-nucleus
-mitochondria
-ribosomes
-INFECTIOUS AGENTS
ex) colds, flu, measles, AIDS, hepatits, herpes
phycology
-the study of algae
mycology
-the study of fungi
protozoology
-the study of protozoans

ex's) Amoebic Dysentery, Giardia
parasitology
-the study of all parasites

ex's)
-protozoans
-helminthes
-certain insects involved in transmitting diseases i.e.mosquitoes
immunology
-the study of defense against diseases, antibodies, antigens, allergy/hypersensitivity
antigens
-anything your body recognizes as foreign
antibodies
-fight antigens
molecular biology
-study of DNA, RNA, and the SEQUENCING of them
-study of RECOMBINANT DNA>>moving genes from one organism to another
microbial ecology
-the study of microbes in ecology and how they break down substances and release them into the ecosystem
-study of how microbes act in soil and water

-ex) carbon cycle, nitrogen cycle
microbial physiology
-the study of the metabolism (enzymes) of microbes, fermentations (ex-production of antibiotics), & biosynthetic pathways
4 Beneficial Aspects of Microorganisms
-Other chemicals and drugs
-Decomposers
-Antibiotics
-Research
medical microbiology
-study of microorganisms and their relationships to diseases
-deals with all kingdoms except plants and animals because they don't affect us
decomposers
-are absorptive heterotrophs
-are saprobes or saprophytes, meaning they feed off of dead material
>break them down for nutrients
>important ecologically
parasites
-are absorptive heterotrophs
- live off of living organisms
-are HARMFUL

-are important medically
antibiotics
-a chemical produced by a microbe that, in small amounts, will inhibit the growth of another microbe

ex) Pennicillium- attacks murein in bacterial cell wall, which means it won't hurt human cells
Penicillium
-a mold that produces penicillin
- can be used to fight Streptococci (bacteria) and Gram + Infectrions
- can also be used to fight Streptococci Pneumonia
other chemicals and drugs from microorganisms
-alcohol (may be used for fuel)
-ethanol
-acetic acid
-insulin
-cheeses
-bread, beer, wine->all from yeasts
research tools
-bacteria have only 1 CHROMOSOME, whereas humans have 46; thus they are easier to study
>biochemical studies
>DNA/RNA studies
detrimental effects of microorganisms
-spoilage- molds
-plant diseases
>blueberries
-animal diseases
>tetanus
>tb
>AIDS
>malaria
light microscopes
-used to see eukaryotes
-uses visible light
radiation
-defined by its wavelength, which is the distance between the tops of two curves of a wave
visible light
- ranges from 400 nm-800 nm
- VIGBYOR
UV light
-ranges from 100 nm-400 nm
x-ray, gamma ray
-below 100 nm
above visible light
-infrared, microwaves
resolving power of the human eye
- 0.2 mm
- 200 micrometers
amount of energy
- is inversely proportional to wavelength
bright-field microscopes
- either 1 or 2 oculars, each withe magnification of 5x, 10x, 15x, or 20x
-objectives are located below oculars (which makes it compound b/c 2 mag. lenses are used)

-range from....
4x (scanning)
10x (low power)
40x (high power)
100x (oil immersion)

- below the objectives lies the specimen, then the condense, then the light source
-magnification range of light microscopes is 20x-2000x
-slide must be stained
resolution
-is resolving power.
-smallest size you can see either with your eyes or with the microscope
-resolution of eyes is 0.2mm

RP= Wavelength/2A
(NA is numerical aperture)

- the smaller the wavelength, the smaller the resolving power, the better the resolution
dark field microscope
-similar to field microscope, except it has a dark-field stop
-if no specimen is present, the field of view is black

-ADVANTAGES
>good for looking at living organisms that are unstained
>good for looking at motility and artifacts (which are things that should not be present)
>good for looking at mycoplasma b/c they lack cell walls but they move by gliding; the increased contrast helps display bacterium
dark-field stop
- a piece of material with a circular center and an outer ring that is placed b/w the condenser and the light source so that the light must bend at angles around the stop; light will only bend to the objectives if a specimen is present
Phase-Contrast Microscope
-similar to bright-field, except it has an annular diaphragm and a PHASE SHIFTING ELEMENT (ring)
-annular setup is placed below the condenser; produces a ring of light to be passed up; initiates the effect (bending of light)
- phase plate can advance light (make it go faster) or retard light (make it slower); this is due to refractive index
-phase shifting element in the oculars forces the direct rays and NOT the incident rays

--direct rays: light rays that shine head-on with the target
--incident rays: light rays that shine at some angle away from the target

-increases contrast due to focusing of direct rays
-contrast is increased/decreased based on the density of the bacteria

-USE
>good for looking at living organisms and their motility
>good for looking inside the cells
>morphology
>mycoplasma
>inclusions
Fluorescence Microscope
-easy, rapid diagnosis

-has.......
>intense light source: mercury vapor lamp
>an exiter filter: filters out everything greater than 400 nm, so it blocks out visible light and only lets light in that is close to UV light
>a barrier filter: blocks out anything less than 500 nm, so humans can observe without eyes burning; lets things through that are >500nm

-dye absorbs energy from UV lights, then emits light at a longer wavelength, makes it shine a yellow color

-USES
>mycobacterium- has high amounts of wax, which absorbs fluorescent dyes>>diagnosis of tb

ex) auramine O (a fluorescent dye) emits yellow light on high power
>fluorescent dye
refractive index
-the difference between the speed of light in vacuum and speed of light in the medium
immunofluorescence (fluorescent antibody technique)
-used to view organisms without the waxy lipids

-antibodies (y-shaped) are grown when an organism is infected with a microorganism, then some of the antibodies are removed and a dye is attached to the antibodies

-ex's of antigens that produce antibodies:
>Syphilis (Treponema palladium)
>Streptococcus pyogenes

- a swab is smeared on slide, then dye complex is smeared also: antibody will stick to organism, if the human has disease, then it will shine
if there is no infection, the dye complex will wash off
Differential Interference Contrast Microscope (DIC)
-very expensive $$$$
-has a prism, which splits the light up and then recombines it
-similar to phase contrast b/c you get high contrast with very sharp detail. Also b/c prism splits light into individual colors so you get false color and a 3D image

USE
-LIVE specimens
-morphology
-inside microorganisms
-3D image
Transmission Electron Microscope (TEM)
-base shoots our a stream of electrons, then has a vacuum, which pass through the condenser magnet, then pass through the specimen, then reach the objective magnet (lens), where they display an image on the fluorescent screen

-if no specimen, appears white
-if specimen is present, it will scatter the electrons
-the denser the object, the darker the image!!
-Resolving power
= 0.0005 micrometers
= 0.5 nm
= 5 Angstroms
= 500 pm
-USE:
>look at dead organisms
>to see inside bacteria
>to see viruses
electron
- 0.1-0.2 nm
-increase resolution
Scanning Electron Microscope (SEM)
- basic setup is similar to TEM
- has a 3D effect, so there is SURFACE DETAIL

-USE
>RP =0.1 micrometers
= 10 nm
>surface details of bacteria
classification
-giving things names
-describing them
-putting them in groups based on similarities and differences

Used to.....
1- identify
2- see relationships to increase understanding, solve problems, and control them
artificial classification
- based on 1 or very few EASILY RECOGNIZABLE CHARACTERISTICS
- does NOT show relationships

ex's)
birds have feathers
mammals have hair
WHITTAKER SCHEME: all prokaryotes were placed in monera, and they were all bacteria
natural classification
-shows relationships with sexual reproduction, common ancestry, DNA, phylogenic
-Used to help control diseases and prevent other ailments
-EX) CARL WOESE'S DOMAINS
Woese's 3 Domains
- showed relationships
- examination of DNA and RNA shows relationships between organisms
Bergey's Manual of Systematic Bacteriology- 1st Edition
-artificial, not based on DNA
- separated bacteria based on the chemistry of their cell wall by GRAM STAINING
-4 phylums/divisions
>Gracilicutes
>Firmicutes
>Tenericutes
>Mendosicutes
Gracilicutes
- gracili = thin
- cute = skin
- Gram (-) negative

ex's)
> E.coli
>Klebsiella (causes nosocomial pneumonia, from being in the hospital)
>Neisseria
>Spirochetes
>Rickettsiae (bacteria, rocky mountain spotted fever, from ticks)
>chlamydia
>treponema (syphilis)
>borrelia (lime disease)
Firmicutes
-thick skin
- Gram (+) positive
- have LOW G-C Ratio

ex's)
>Clostridium (tetanus)
>Staphylococcus
>Streptococcus (sore throat, pneumonia)
>Bacillus (anthrax)
> Mycobacterium (TB, leprosy)-->does not stain well!
>Corynebacterium (diptheria)
Tenericutes
-soft skin
- NO CELL WALL, so it's GRAM (-) NEGATIVE

ex) Mycoplasma!!!
Mendosicutes
- faulty skin
- NO MUREIN in cell walls, so it's GRAM VARIABLE~~

ex) Archaeabacteria
Bergey's 2nd Edition
- recognized 2 domains of prokaryotes (Archaea and Bacteria)
- Archaea were NO LONGER CONSIDERED BACTERIA
-based this analysis on DNA (natural classification)
-did NOT recognize any kingdoms, but recognized about 40 different phyla!

ex's)
>Cyanobacteria
>Actinobacteria
>Firmicutes
>Proteobacteria
>Chlamydia
>Spirochetes
Cyanobacteria
- blue-green bacteria
- used to be considered algae
- photosynthetic
- gram (-) negative
Actinobacteria
- gram (+) positive
- have high G+C ratio

ex's)
>Mycobacterium (does not stain well; use acid-fast stain)
>Cornyebacterium (causes diptheria)

-stains purple
Proteobacteria
- all are Gram (-) Negative

ex's)
>E.coli
>Klebsiella
>Neisseria (meningitis and gonorrhea)
>Rickettsiae
>took out Treponema, Borrelia, Chlamydia b/c DNA differs
Chlamydia
-has its own phylum
-Gram (-)
- ex: Chlamydia trachomatis (STD)
Spirochetes
-has its own phylum
-Gram (-)
Cocci
-sphere shaped
-avg size: 1 micrometer
-ex)
>Staphylococcus: causes boils, carbuncles, food poisoning
>streptococcus: causes strep throat, pneumonia
>Neisseria: causes gonorrhea, meningitis
Bacillus
-rod shaped
-avg. size: 0.5micrometers x 2 micrometers
-ex's)
>Clostridium: causes tetanus, botulism
>E.coli: causes diarrhea
>Klebsiella: causes pneumonia (nosocomial)
>Corynebacteria: causes diphtheria
>Bacillus: causes anthrax
Spirilli
-spiral shaped (curved)
-ex's)
>Treponema: causes syphilis
>Borrelia: causes lyme disease

-avg. size:
0.5micrometers x 1-14 micrometers
glycocalyx
- outermost layer of the bacterium
- the nonliving, extracellular, nonessential part of the cell
- not all bacteria have the glycocalyx
slime layer
-a think layer of slime
ex)Staphylococcus aureus-MRSA
- slime layers look shiny and small
capsule
- thick layer; big

ex's)
>Klebsiella pneumoniae (nosocomial pneumonia)
>Streptococcus pneumoniae (typical pneumonia)
>Streptococcus pyogenes (strep-sore throat)
>Bacillus anthrasis (anthrax)
>Haemophilus influenzae (secondary infection after you get the flu; causes meningitis)
-capsules are MUCOID
chemistry of glycocalyx
- some are proteins
-some are polysaccharides
-used to be thought it has was because it was thick and gooey
Regulation
-primarily regulated by genes
-GENETICS (DNA) & ENVIRONMENT (based on nutrition) determine whether bacteria will develop glycocalyx
Colonial appearance
-visible to the eyes so you can see on agar plate
-capsules have a mucoid appearance; difficult to see
-slime layers look shiny and wet
negative staining technique
-stain everything EXCEPT for what you're looking for and capsule
- India ink is placed on glycocalyx, then crystal violet is placed on the slide. When it's rinsed, the inside of the bacterium will be violet, the outside of the cell will be black (b/c of the India ink)
-the glycocalyx will be clear, shine like a HAAAAAAAALO
-capsule does not get stained (it's clear) because of the proteins and polysaccharides that repel the dye

ex) Klebsiella pnumonia
background=stained black
capsule=clear
bacteria=purple
Importance in Identification
-Go through 3 levels to identify genes and species
1: shape/morphology
2: gram staining
3: enzymes (physiology) at biochemical level
Serology-SEROVARS
-serological varieties
=races
=strains
-serology is the classification by serotypes based on GLYCOCALX
-affects antibiotic sensitivity
-important in development in vaccines (23 most common varieties)>>ex there are more than 92 varieties of streptococcus pneumoniae that can affect humans
-antibodies and vaccines only affect a few certain varieties
Functions of Capsules
- allow organisms to stick together, forming a MICROCOLONY

BENEFITS:
-provides protection
-inner bacterium are protected against dryness and chemicals
-white blood cells have difficulty engulfing the larger microcolonies
-however the outside bacteria may die
-protection against phagocytosis, which works well against 1 organism but NOT against a colony
-allow bacteria to adhere to contaminate, inanimate objects (like anything inserted into the body, like a catheter) and adhere to the animate hosts
virulent/pathogenic; pathogenicity
-able to adhere/cause disease
avirulent/non-pathogenic
-no capsule/no sticking
General Properties of the Cell Wall
-nonliving
-NOT extracellular
- 20%-40% of dry weight of microbe (weight when water is removed)
Functions of the Cell Wall
-prevents plasmoptysis: lysis, or bursting of the cell
-prevents plasmolysis: shrinking of cell, and flaccid


osmotic pressure: water flows from high concentration to low concentration
>environment = low osmotic pressure
>inside of cell= hypotonic/hypoosmotic, which means it has a high concentration of solutes, low water
>outside of the cell= hypotonic/hypoosmotic, meaning it has a low concentration of solutes and low osmotic pressure, high water