Exam 1- Weeks 1 and 2 Flashcards by Jesse Barer

the study of microscopic organisms

microbiology

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yeast responsible for making bread rise

saccharomyces cerevisiae

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how bread rises/microbial fermentation

metabolize the carbohydrates in flour and produce carbon dioxide
sugars convert to CO2 and organic acids

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improve food safety and preserve foods

beneficial microbes (preservation of organic acids)

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study of the relationship between microorganisms and their environment

microbial ecology

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first to show how bacteria help recycle vital elements between soil and atmosphere

Martinus Beijerinck and Sergei Winogradsky

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convert elements carbon, nitrogen, oxygen, sulfur and phosphorous into forms that plants and animals can use

responsibility of microorganisms

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microbial cleanup of oil, toxic chemicals, or other environmental pollutants

bioremediation

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increase in bacteria to help do something; ex- increase in oil-degrading bacteria

bioenhancers

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increasing the amount of genetically modified bacteria; specifically adapted to metabolize petroleum products

bioaugmentation

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live in close association with bacteria, from nodules on their roots (ex- beans, peas, etc.)

legumes

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tiny factories where bacteria come and stay on legumes and convert atmospheric nitrogen to ammonium

nodule

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causes crown gall on a burning bush

Agrobacterium tumefaciens

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toxic protein in digestive tract of insects; helps protect plants

bacillus thurigensis

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graze on cellulose rich plants; bacteria in the rumen ferment the cellulose

ruminants such as cattle and sheep

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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

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microbes normally present in and on the human body; prevents growth of pathogens

microbiota

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intestines- digestion
skin- protection
-number increases from stomach to large intestine (colon)

role of microbiota

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microbes that cause disease

pathogens

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fungal toxins, can cause organ damage

mycotoxins

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infections acquired by patients while in a hospital or other clinical care facility

healthcare-associated infections (HAI)

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infection while in the hospital

nosocomial infection

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leading cause of HAI, antibiotic resistant organism, causes diarrhea and colitis; fecal transplant used as treatment when probiotics do not work

clostridium difficile

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4.6 billion years

age of earth

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~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

Exam 1- Weeks 1 and 2 Flashcards

(205 cards)