Exam 1- Weeks 1 and 2 Flashcards
the study of microscopic organisms
microbiology
yeast responsible for making bread rise
saccharomyces cerevisiae
how bread rises/microbial fermentation
- metabolize the carbohydrates in flour and produce carbon dioxide
- sugars convert to CO2 and organic acids
improve food safety and preserve foods
beneficial microbes (preservation of organic acids)
study of the relationship between microorganisms and their environment
microbial ecology
first to show how bacteria help recycle vital elements between soil and atmosphere
Martinus Beijerinck and Sergei Winogradsky
convert elements carbon, nitrogen, oxygen, sulfur and phosphorous into forms that plants and animals can use
responsibility of microorganisms
microbial cleanup of oil, toxic chemicals, or other environmental pollutants
bioremediation
increase in bacteria to help do something; ex- increase in oil-degrading bacteria
bioenhancers
increasing the amount of genetically modified bacteria; specifically adapted to metabolize petroleum products
bioaugmentation
live in close association with bacteria, from nodules on their roots (ex- beans, peas, etc.)
legumes
tiny factories where bacteria come and stay on legumes and convert atmospheric nitrogen to ammonium
nodule
causes crown gall on a burning bush
Agrobacterium tumefaciens
toxic protein in digestive tract of insects; helps protect plants
bacillus thurigensis
graze on cellulose rich plants; bacteria in the rumen ferment the cellulose
ruminants such as cattle and sheep
genetically modified organisms used to synthesize products of high value; naturally occurring microorganisms grown on a massive scale to make large amounts of products at a relatively low cost; ex- insulin
biotechnology
microbes normally present in and on the human body; prevents growth of pathogens
microbiota
intestines- digestion
skin- protection
-number increases from stomach to large intestine (colon)
role of microbiota
microbes that cause disease
pathogens
fungal toxins, can cause organ damage
mycotoxins
infections acquired by patients while in a hospital or other clinical care facility
healthcare-associated infections (HAI)
infection while in the hospital
nosocomial infection
leading cause of HAI, antibiotic resistant organism, causes diarrhea and colitis; fecal transplant used as treatment when probiotics do not work
clostridium difficile
4.6 billion years
age of earth
~3.7/4.3 billion years ago
microbial cells first appeared
first phototrophs, non-oxygen producing, ex- purple and green sulfur bacteria
anoxygenic
bacteria, archaea, eukarya
domains
earliest oxygen producing (oxygenic phototroph), ~2 bya
cyanobacteria
gave evidence of microbes preserved in structures; fossilized microbial formations ~3.5 bya
stromatolites
cyanobacteria, used to compare modern and ancient
modern stromatolite
multicellular life forms
eukaryotes
common ancestor from which all domains have descended from
last universal common ancestor (LUCA)
sent an electrical charge through a flask of a chemical solution of methane (CH4), ammonia (NH3), hydrogen (H2), and water (1953)
Stanley Miller’s experiment
created organic compounds including amino acids (experiment)
results of stanley miller’s experiment
causative agent for the plague, gram-negative, rod-shaped bacterium
Yersinia pestis
fatal pandemic of medieval period, known as the black death because of black skin spots
the plague
where bacteria sits and travels
reservior
urban rats and ground squirrels
reservoir for the plague
transmit organism
vector
fleas- to humans and animals
vector for the plague
main species of rat flea as plague vector; bacteria replicated in the gut, flea regurgitates blood in next bite transmitting bacteria
Xenopsylla cheopis
infectious disease hosted by animals
zoonosis
accidental hosts, ex- plague
not in typical chain of hosts but become part of it
-flea bites
-contact with contaminated fluid or tissue
-infectious droplets (animals –> humans)
methods of transmission of the plague
an endemic disease present in an animal population
enzootic
already running in an area but at a low rate
endemic
an epidemic disease present in an animal population
epizootic
disease to a new population that kills off many- vector finds new population when the first dies off
epidemic
-most common plague
-results from infected flea
-bacteria multiply in lymph node near entrance to human body
-buboes, fever, headache develop
bubonic plague (black death)
blocks phagocytosis, helps massive colonization in immune system
capsule
flea bites human –> bacteria trapped at sit of bite in blood clot –> secretes proteases, activates host plasmin –> dissolves blood clot –> bacteria enters bloodstream
activation series of bubonic plague
2-8 days
incubation period of bubonic plague
swollen, painful lymph nodes (usually in groin area first from lower limb bite)
buboes
if bubonic plague not treated properly, bacteria spread to lungs
pneumonic plague
-incubation period 1-3 days
-transmitted person to person by infectious droplets (coughing)
-only type transmitted person to person
pneumonic plague
-rapid spread of bubonic plague via bloodstream if untreated
-severe, cause bleeding into the skin and other organs and septic shock
septicemic plague
-take blood sample from blood or swollen lymph node
-visualization of gram-negative rods with gram stain
-bipolar staining (safety pin appearance)
-known flea bite or present bubo
-ELISA/serologic testing
how to diagnose bubonic plague
-intravenous or oral antimicrobials
-no vaccine available in US
treatment for the plague
good control between reservoir and vector
prevention of the plague
using a bacteria/infectious disease as a biological weapon
bioterrorism
father of western medicine
- believed diseases had natural causes from within patients or their environments
Hippocrates
“greatest sewer”- ran through ancient Rome, carried waste away from the city
Cloaca Maxima
the first person to observe microbes, including bacteria which he called “animalcules” and “wee little beasties”
Antonie van Leeuwenhoek (16-32-1723)
credited with the following innovations:
-microbial basis of fermentation
-work on spontaneous generation
-development of vaccines
Louis Pasteur (1822-1895)
first to demonstrate the connection between a single, isolated microbe and a known human disease
-anthrax, cholera, tuberculosis
Robert Koch (1843-1910)
golden age of microbiology (people)
Louis Pasteur and Robert Koch
classification, description, identification, and naming of living organisms
taxonomy
Swedish botanist, zoologist, and physician who developed a new system (taxonomy) for categorizing plants and animals
-published Systema Naturae
Carolus Linnaeus
system of categorizing and naming organisms using a standard format and consistent terminology
Linnaean taxonomy
evolving trees of life, more refined based on similarities
phylogenies
-studied the role of genetics in modern taxonomy
-used small unit rRNA
Carl Woese
closer evolutionary relationship between ___ and ___ than they have to ___
archaea, eukarya; bacteria
animals, fungi, plants
groups in domain eukarya
used to name microbes
- every organism assigned genus name and specific epithet (species), both printed underlined or italicized
Ex- Escherichia coli
= E. coli
binomial nomenclature
first of two names for an organism- always capitalied
genus
second of two names for an organism- lowercase
species
organism-
-genus- saltwater habitat and arrangement clusters of four cells
-species- named after Anthony Edward Walsby, discoverer
Haloquadratum walsbyi
no true nucleus or nuclear membrane, including bacteria and archaea
prokaryotic microbial cells
have a true nucleus, include fungi, protozoa, and algae
eukaryotic microbial cells
-prokaryotic
-cell walls contain peptidoglycan
-common shaped include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, vibrio)
bacteria
-associated with extreme environments (but not all are)
-lack any known pathogens or parasites
archaea
common in the gut of animals (and humans), responsible for methane production (can be measured with breath analysis- CEBO)
Methanogenic Archaea
informal grouping of eukaryotes that are not plants, animal, or fungi
-include algae and protozoa
protists
-photosynthetic protist
-either unicellular or multicellular
-cellulose cell walls
algae
-diverse protist
-some are free-living, some are parasitic
-some photosynthetic, some feed on organic material
-mostly harmless, some pathogens
-move by pseudopods, flagella, or cilia
protozoa
-eukaryotes
-unicellular or multicellular
-reproduce sexually or asexually
-chitin cell walls
fungi
-unicellular fungi
-causes bread to rise and drinks to ferment
-diseases- vaginal infections, oral thrush
yeasts
-multicellular, filamentous fungi
-decomposition of dead plants and animals
-cause allergies, mycotoxins
molds
-multicellular parasitic worms
-two major groups- roundworms, flatworms
helminths
guinea worm
-caused by nematode roundworm parasite
-after person drinks water containing water fleas infected by guinea-worm larvae
Dracunculus medinensis
-not cells, acellular
-either DNA or RNA, not both
-only seen with electron microscope
-obligate parasites- can only replicate in a host
viruses
-not cells, acellular
-obligate intracellular “parasites”
-misfolded form of a normal proteins (PrPc)
-infectious protein, forms plaques
-cause transmissible spongiform encephalopathy (TSE) in humans and animals
prions
metabolism, reproduction, differentiation, communication, movement, evolution
6 activities/rules that make something an “organism”
cell is an open system
metabolism
modifications in genome for adaptations
evolution
transfer of genetic material from one organism to another, ex- donor –> recipient
horizontal gene transfer
round shaped bacterial cells
cocci
pairs of cocci
diplococci
chainlike pattern of cocci
streptococci
grape-like clusters of cocci
staphylococci
keep one shape
monomorphic
changes shape
pleomorphic
used to identify what causes a disease when looking under a microscope
shape of bacterial cells
causes anthrax
bacillus anthracis
free-living __ cells tend to grow faster than free-living __ cells
smaller, larger
supports a faster rate of nutrient and waste exchange per unit of cell volume compared with large cells
higher surface-to-volume ratio
have a greater surface-to-volume ratio, increased exchange rate, better adapt to environment
smaller organisms
helps define types of electromagnetic radiation, used as a major factor in resolution
wavelength
__ wavelength = greater resolution
shorter; relationship between wavelength and resolution
the capacity of a microscope to enlarge an image (objective and ocular)
magnification
ability to distinguish two adjacent objects as distinct and separate
resolution
light gathering ability of the objective lens
numerical aperature
0.2 um- objects that are closer together than 0.2 um cannot be resolved as distinct and separate
limit of resolution for a light microscope
when light passes through the two materials (specimen and medium) the rays change direction at the boundary between the materials
refraction
measure of the light-bending ability of a medium
refractive index
change the refractive index of specimens from that of their medium
attain contrast
D = wavelength / NAcondenser + NAobjective
NA- numerical aperature
units- nm
formula for limit of resolution for specific microscope
-contrast between object and surroundings
-wavelength smaller than the object
-detector with sufficient resolution for given wavelength
conditions needed to resolve object from its surroundings
-same refractive index as glass
-increases the maximum angle at which light leaving the specimen can strike the glass
-makes image more clear
immersion oil
blocks most of the light from the illuminator in dark-field microscopy
opaque disk
bright objects on a dark background
-can see living organisms
dark-field microscopy
causes syphilis
Treponema pallidum
2 sets of light- one from the light source, one from rays reflected or diffracted from the specimen
phase-contrast microscopy
produces image by exciting a specimen with a wavelength of light that triggers it to emit fluorescence
fluorescence microscope
-used to stain microbe
-absorb light and emit visible fluorescent light
fluorochromes
gets rid of U.V rays- leaves fluorescence to be seen
excitation filter
-uses an electron beam to create an image, with electromagnets acting as lenses
-resolution levels up to 1000-fold greater than light microscope
-used to observe sub-cellular structures/organelles, and viruses
electron microscopy
transmission electron microscope
scanning electron microscope
two types of electron microscopy
-uses electron beams that pass through a specimen
-visualize small, thin specimens such as tissue sections and sub-cellular structures
transmission electron microscopy (TEM)
uses electron beams to visualize 3D surface details of specimens
scanning electron microscopy (SEM)
drop of liquid placed on slide
wet mount
dried preparation of bacterial cells on a glass slide
smear
-smear is fixed on the slide by heat so it doesn’t wash away during the staining process
-coagulate bacterial proteins so bacteria stick to the slide surface
heat fixation
coloring microbes with a dye that creates a contrast between the bacteria and the background and emphasizes certain structures
staining
solutions consisting of a solvent (usually water or ethanol) and a colored molecule (often a benzene derivative)- the chromogen
stain
benzene (organic colorless solvent) and chromophore (chemical group that imparts color to benzene)
chromogen
basic stain with a positive chromogen- cell is stained
cationic stain
acidic stain with a negative chromogen- background is stained
anionic stain
gives ionization to the chromogen, allows binding to fibers or tissues (second part of the stain)
auxochrome
-use a single dye
-do not distinguish organisms or structures
simple stains
use two or more dyes that react differently with various kinds/parts of bacteria allowing them to be distinguished
differential stains
danish bacteriologist who developed the gram stain in 1884
Hans Christian Gram
gram-positive and gram-negative
two groups of bacteria on the basis of their reaction in the gram stain
appears purple-violet after gram stain, thick cell wall
gram-positive bacteria
appears pink after gram stain, thin cell wall
gram-negative bacteria
arises from differences in cell wall structure
color difference in gram stain
primary stain in gram staining
crystal violet
iodine, binds to the primary stain forming an insoluble complex, increases the affinity of the cell wall for the gram stain
mordant
decolorizing agent in gram staining
alcohol-acetone
-safranin
-purple gram-positive cells (thick cell walls) won’t take
-red/pink cells (thin cell walls) will take
counterstain in gram staining
contains notable human pathogens causing tuberculosis and leprosy
genus Mycobacterium
causes leprosy
M. leprae
causes tuberculosis
M. tuberculosis
gram-positive bacteria that are acid fast because of the waxy mycolic acid in their cell walls
mycobacteria
detects the presence of cell walls that are rich in mycolic acid
acid-fast staining (Ziehl-Neelsen Method)
-stain used in acid-fast protocol
-stains everything reddish-purple strongly
-heat enhances entry into cells
carbol fuchsin
-decolorizing agent in acid-fast stain
-removes stain from acid-fast negative cells
acid alcohol
-counterstain in acid-fast protocol
-stains non acid-fast cells
methylene blue
structures that protect the bacterial genome in a dormant state when environmental conditions are unfavorable
endosporee
endospore-forming, gram-positive bacteria
genera Bacillus and Clostridium
causes tetanus
Clostridium tetani
causes pseudomembranous colitis
Clostridium difficile
causes gas gangrene
Clostridium perfringens
causes botulism
Clostridium botulinum
-endospore stain
-uses heat to push primary stain malachite green into endospore
-wash with water to decolorize the cell but endospore retains green stain
-cell counterstained pink with safranin
Schaeffer-Fulton Method
cells come from other cells
modern cell theory
maggots were the offspring of flies, not the product of spontaneous generation
conclusion of Francesco Redi’s Experiment (1668)
boiled broth infused with plant or animal matter hoping to kill preexisting microbes- sealed flasks
-argued that new microbes must have arisen spontaneously
-likely did not boil broth enough to kill all preexisting microbes
John Needham (1745)
nutrient broth placed in flask, heated, then sealed - no microbial growth
Lazzaro Spallanzani (1729-1799)
disproved spontaneous generation through “swan-neck flask” experiments
Louis Pasteur (1862)
no growth in swan-neck flasks- demonstrates microbes come from air (growth in open flasks)
results of swan-neck flask experiment
popularized theory of biogenesis
Rudolf Virchow in 1858
cell theory that all cells arise from cells
biogenesis
diseases may result from microbial infection
germ theory of disease
-proposed that physicians were transferring disease to their patients
-importance of hand-washing to prevent transfer
Ignaz Semmelweis 1847
-began using carbolic acid (phenol) spray disinfectant/antiseptic during surgery
-successful efforts to reduce post-surgical infection, became common practice
Joseph Lister (1827-1912)
-believed a specific disease could be caused by a specific microbe = “one microbe, one disease”
-able to identify causative pathogens, ex- anthrax, tuberculosis, cholera
Robert Koch (1843-1910)
-coined vaccination
-based on smallpox immunity
Edward Jenner (18th century)
immunization to prevent disease
vaccination
made rabies vaccine
Louis Pasteur (1800s) -vaccine
developed antibiotics
Alexander Fleming 1928
produced by Penicillium chrysogenum
Penicillin
changes in genetic material from indiscriminate use of antibiotics- becomes resistant
superbug
resemble bacteria in size and shape and have similar traits to prokaryotes
mitochondria and chloroplasts
argued prokaryotic origin of mitochondria and chloroplasts
Lynn Margulis, 1967
theory that mitochondria and chloroplasts arose from prokaryotic cells establishing a symbiotic relationship within a eukaryotic host
The Endosymbiotic Theory
gel-like network of proteins and other macromolecules contained by a cell membrane
cytoplasm of bacterial cell
cell membrane, cell wall, and outer membrane (for gram-negative)
create cell envelope
system of looped coils of chromosomes within cytoplasm
nucleoid
plasma membrane structure
fluid mosaic model
-separates the cytoplasm from the outside environment
-phospholipid bilayer with proteins
-barrier to the diffusion of substances such as polar or charged molecules
cell/plasma membrane
spans whole membrane for transport
integral/transmembrane protein
completes the protein channel on the end of a transmembrane protein
peripheral protein
allowing some molecules to enter or leave the cell while restricting passage of others
selective permeability
moves nutrients with the concentration gradient
passive transport
moves nutrients against the concentration gradient
active transport
the use of energy from one gradient to drive transport up another gradient
-symport and antiport
coupled transport
integral proteins that function as water channels
aquaporins
passive transport, no energy required, down concentration high > low
simple diffusion
-passive transport, no energy required BUT use transport channel to move molecules (specific and non-specific)
-follows concentration gradient high –> low
facilitated diffusion
-consists of symport, antiport, group translocation, and ABC transporters
-energy required- energy released by movement down a concentration gradient can be used to transfer another molecule inside
active transport
-unique to prokaryotes
-high energy organic compounds give energy to transport sugars
-phosphorylation cascase, substrate modification
group translocation
-periplasmic binding protein has high affinity for substrate, transport channel forms, cytoplasmic ATP-hydrolyzing proteins supply energy for transport event
-ATP casette
ABC systems
-bacterium secretes siderophore that binds iron
-ABC transporter brings Fe+ across the membrane
-inside the cell, the iron is released- required for pathogen to grow
-host- human
Iron transport by a siderophore and an ABC transport complex
