exam #1 Flashcards
1
Q
microbe
A
living organism that requires a microscope to be seen
2
Q
most microbes consist of how many cells?
A
a single cell
3
Q
how big are microbes?
A
0.2 um to just a few mm
4
Q
each microbe contains in its own genome the capacity to what?
A
reproduce its own kind
5
Q
is a virus considered a microbe?
A
yes, even though it doesn’t perfectly fit the definition
6
Q
prokaryote
A
-type of microbial organism
-cells lacking a nucleus
-bacteria and archaea
7
Q
eukaryote
A
-type of microbial organism
-cells with a nucleus
-algae, fungi, and protists
8
Q
type of microbial organisms: prokaryotes, eukaryotes, and ?
A
viruses and prions (acellular entities)
9
Q
three domains of life
A
-all come from common ancestor
-bacteria = prokaryote
-archaea = prokaryote
-eukarya = algae and plants, fungi and animals, protists = eukaryotes
10
Q
order these form least to most recent
-microbes observed under a microscope
-food and drink are produced by microbial fermentation
-koch’s postulates are established
-first immunization (smallpox)
-first microbial genome sequenced
-penicillin antibiotic first isolated
-first mRNA vaccine approved (covid)
-crispr-cas9 bacterial self-defense mechanism is used for programmable gene editing
A
-food and drink are produced by microbial fermentation
-microbes observed under a microscope
-first immunization (smallpox)
-koch’s postulates are established
-penicillin antibiotic first isolated
-first microbial genome sequenced
-crispr-cas9 bacterial self-defense mechanism is used for programmable gene editing
-first mRNA vaccine approved (covid)
11
Q
Robert Hooke (1635-1703)
-built the first _____
-used it to observe ____
-coined the term ____
-published micrographia, the first manuscript that illustrated ____
A
-built the first compound microscope
-used it to observe mold
-coined the term “cell”
-published micrographia, the first manuscript that illustrated objects observed with a microscope
12
Q
Antonie can Leeuwenhoek (1632-1723)
-built ______, complete with sample holder and ___ adjustment
-first to observed ____: he called them ____
A
-built single-lens magnifiers, complete with sample holder and focus adjustment
-first to observed single-celled microbes: he called them “small animals”
13
Q
spontaneous generation
A
theory that living organisms could arise without parents
14
Q
Francesco Redi (1660s)
showed that maggots in decaying meat were ____= refuted ___
A
showed that maggots in decaying meat were the offspring of flies = refuted spontaneous generation
15
Q
Lazzaro Spallanzani (1760s)
showed that a sealed flask of meat broth sterilized by boiling ______ = refuted ____
A
showed that a sealed flask of meat broth sterilized by boiling failed to grow microbes = refuted spontaneous generation
16
Q
Louis Pasteur (1822-1895)
-showed that a broth boiled in a swan-neck flask _____, despite being exposed to air = refuted ____
-discovered the microbial basis of ____
A
-showed that a broth boiled in a swan-neck flask remained free of microbial growth, despite being exposed to air = refuted spontaneous generation
-discovered the microbial basis of fermentation
17
Q
Pasteur experiment
1. the broth was boiled to ___
2. after a year, ____ and the old ones were trapped in curve
3. the flask was tipped to allow the ____
4. microbes quickly ____
A
- the broth was boiled to kill all microbes
- after a year, no microbes appeared and the old ones were trapped in curve
- the flask was tipped to allow the broth to reach the microbes
- microbes quickly multiplied
18
Q
germ theory of disease
A
suggests that many diseases are caused by microbes
19
Q
Robert Koch (1843-1910)
-German physician
-founder of the _____ of microbiology
-applied his methods to the study of several ____
A
-German physician
-founder of the scientific method of microbiology
-applied his methods to the study of several lethal diseases
20
Q
working with anthrax, ____ demonstrated an important principle of epidemiology: ____
A
working with anthrax, Koch demonstrated an important principle of epidemiology: the chain of infection, or transmission of disease
21
Q
to prove that mycobacterium caused TB, ___ needed to establish a ____ of the microbes being studied
A
to prove that mycobacterium caused TB, Koch needed to establish a pure culture of the microbes being studied
22
Q
Koch’s colleagues contributed important tools for the generation of _____
-Angelina and Walther Hesse = ____
-Julius Petri = ____
A
Koch’s colleagues contributed important tools for the generation of pure cultures
-Angelina and Walther Hesse = agar to solidify culture medium
-Julius Petri = double-sided Petri dish
23
Q
Koch’s postulates
A
- the microbe is found in all cases of the disease but is absent from healthy individuals
- the microbe is isolated from the diseased host and grown in pure culture
- when the microbe is introduced into a healthy, susceptible host, the same disease occurs
- the same strain of microbe is obtained from the newly diseased host
24
Q
immunization
-observation: milkmaids had ___ to smallpox
-hypothesis: ____ due to exposure to ____
-experiment: Edward ____ (1749-1823) ___ with material he collected from cowpox lesions
—the practice of cowpox inoculation was called ____
A
-observation: milkmaids had natural immunity to smallpox
-hypothesis: immunity due to exposure to cowpox infected cows
-experiment: Edward Jenner (1749-1823) deliberately infected patients with material he collected from cowpox lesions
—the practice of cowpox inoculation was called vaccination
25
_____ developed the first vaccines based on _____ strains of microbes: ____ and ____
Louis Pasteur developed the first vaccines based on attenuated (weakened) strains of microbes: fowl cholera and rabies
26
immunization
the stimulation of an immune response by deliberate inoculation with an attenuated pathogen
27
(1847) Ignaz ___ ordered doctors to ____ with chlorine, an ___ agent = mortality rates rose/fell
(1847) Ignaz Semmelweis ordered doctors to wash their hands with chlorine, an antiseptic agent = mortality rates fell
28
(1865) Joseph ___ developed ___ to treat wounds and clean surgical instruments
(1865) Joseph Lister developed carbolic acid to treat wounds and clean surgical instruments
29
in the twentieth century, ____ surgery was developed
-environments completely ____-free
in the twentieth century, aseptic surgery was developed
-environments completely microbe-free
30
(1929) _____ discovered that ____ mold generated a substance that kills bacteria
(1929) Fleming discovered that Penicillium mold generated a substance that kills bacteria
31
(1941) Florey and Chain purified ____
-_____ quickly became the first commercial ____ used to save human lives
(1941) Florey and Chain purified penicillin
-penicillin quickly became the first commercial antibiotic used to save human lives
32
microbes cycle the many nutrients essential for life, including all global __ and most of the __ in earth's atmosphere
-less than 0.1% of all microbial species can be ___
-the remainder make up the majority of earth's ___
microbes cycle the many nutrients essential for life, including all global N2 and most of the O2 in earth's atmosphere
-less than 0.1% of all microbial species can be cultured in the laboratory
-the remainder make up the majority of earth's biosphere
33
bacteria are important for ____ cycling
bacteria are important for geochemical cycling
34
endosymbionts
microbes that partner with a larger host organism
35
Linnaeus (1707-1778) called the microbial world ___
-early taxonomists faced two challenges as they attempted to classify microbes
1. ___ of the microscope was too low = overcome via advances in ___
2. microbial species are ___ = 95% similarity of ___ sequence
Linnaeus (1707-1778) called the microbial world "chaos"
-early taxonomists faced two challenges as they attempted to classify microbes
1. resolution of the microscope was too low = overcome via advances in biochemistry and microscopy
2. microbial species are hard to define = 95% similarity of DNA sequence
36
(1977) ___ studied recently discovered ___that live in hot springs and produce methane
-analysis of their ____ revealed that these prokaryotes were a ___
-called these new prokaryotes the ___
(1977) Woese studied recently discovered prokaryotes that live in hot springs and produce methane
-analysis of their 16S rRNA revealed that these prokaryotes were a distinct form of life
-called these new prokaryotes the archaea
37
____ discovery replaced the classification scheme of five kingdoms with ___ groups called ___
-list them
Woese's discovery replaced the classification scheme of five kingdoms with three equally distinct groups called domains
-bacteria, archaea, and eukarya
38
(1938-2011) ___ proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by ____ from prokaryotic cells ___ by pre-eukaryotes
(1938-2011) Margulis proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes
39
advances in biochemistry and microscopy revealed the fundamental structure and function of ____
cell membranes and proteins
40
the revelation of the ___ and ___ structures led to the discovery of the ___ of model organisms
the revelation of the DNA and RNA structures led to the discovery of the genetic programs of model organisms
41
a heat-stable bacterial DNA ____ was used for amplifying DNA via the ____
a heat-stable bacterial DNA polymerase was used for amplifying DNA via the polymerase chain reaction (PCR)
42
the size at which objects become visible depends on the ___ of the observer's eye
the size at which objects become visible depends on the resolution of the observer's eye
43
resolution
the smallest distance by which two objects can be separated and still be distinguished
44
detection
the ability to determine the presence of an object
45
magnification
an increase in the apparent size of an image to resolve smaller separations between objects
46
light is part of the spectrum of
electromagnetic radiation
47
for electromagnetic radiation to resolve an object, 3 conditions must exist
1. contrast between object and its medium
2. wavelength smaller than the object
3. magnification
48
absorption
the photon's energy is acquired by the absorbing object
49
reflection
wavefront bounces off the surface of an object
50
scattering
wavefront interacts with an object smaller than the wavelength of light
51
refraction
-our goal
-bending of light as it enters a substance that slows its speed
52
bright field microscopy
-what it is
-how to increase resolution
-generates a dark image of an object over a light background
-to increase resolution: use shorter-wavelength light, use immersion oil, use wider lens closer to specimens
53
immersion oil has a ____ comparable to that of the ____ (n=1.5)
-it minimizes the _____ by refraction and makes it possible to reach 100x _____ with minimal ___
immersion oil has a refractive index comparable to that of the lens (n=1.5)
-it minimizes the loss of light rays by refraction and makes it possible to reach 100x magnification with minimal distortion
54
higher ___ increases resolution
numerical aperture (10x v.s 100x)
55
compound microscope
-parts
-total magnification (TM)
compound microscope: a system of multiple lenses designed to correct or compensate for aberration
-ocular lens, objective lens, needs to be parafocal (focus doesn't change when lens switches)
-total magnification: magnification of the ocular multiplied by the objective
56
wet mount
-advantages
-disadvantages
wet mount preparation: a simple way to observe microbes by placing them in a drop of water on a slide with a coverslip
-advantages: observation of cells in natural state
-disadvantages: little contrast between cell and background and sample may dry out quickly
57
the detection and ___ of cells under a microscope are enhanced by: fixation and staining
-give definitions
the detection and resolution of cells under a microscope are enhanced by: fixation and staining
-fixation: cells are made to adhere to a slide in a fixed position
-staining: cells are given a distinct color
58
simple stain
-what is most commonly used?
adds dark color specifically to cells, but not to the external medium or surrounding tissue
-methylene blue
59
differential stain
-what is most commonly used?
stains one kind of cell but not another
-gram stain
60
gram stain (+ vs -)
-gram positive bacteria retain the crystal violet stain because of their thicker cell wall
-gram negative bacteria do not, thin cell wall
61
acid-fast stain
carbofluchsin used to stain mycobacterium species
62
spore stain
malachite green use to detect spores of bacillus and clostridium
63
negative stain
colors the background, which makes capsules more visible
64
fluorescence microscopy
the specimen absorbs light of a defined wavelength and then emits light of lower energy, thus longer wavelength = the specimens fluoresces
65
fluorophore
-fluorescent chemical compound
-cell specificity can be determined by: chemical affinity, labeled antibodies, DNA hybridization, gene fusion reporter
66
immunofluorescence microscopy determines what?
co-localization of labeled proteins
67
electron microscopy
the foremost tool for observing the shapes of macromolecular structures
68
X-ray crystallography or X-ray diffraction analysis
-tool of choice for atom-level detail of a macromolecule
-protein resolution
-for samples that can be crystallized (limitation), X-ray diffraction makes it possible to fix the position of individual atoms in a molecule
69
electron microscopy
-electrons behave like ___: very high ____and allow very great ___
-sample must absorb ____: coated with heavy ___
-electron beam and sample are in a ___: lenses are ___ fields
-electrons behave like light waves: very high frequency and allow very great resolution
-sample must absorb electrons: coated with heavy metal
-electron beam and sample are in a vacuum: lenses are magnetic fields
70
transmission electron microscopy
-electrons pass through specimen
-reveals internal structures in 2D
-can look at thin slices
71
scanning electron microscopy
-electrons scan the specimen surface
-reveals external features in 3D
-electrons bounce off surface of specimens and reflect back
72
cryo-electron microscopy
-high-strength____ now permit low-temperature cryo-EM
-the specimen does not require ___
-specimen must be ___ in water solution
-high-strength electron beams now permit low-temperature cryo-EM
-the specimen does not require staining
-specimen must be flash-frozen in water solution
73
cryo-electron tomography or electron cryotomography
-acquisition of ___ from different angles of a _____
-avoid the need to physically ___ the sample for thin-section ___
-images are combined digitally to visualize the ___
-acquisition of projected images from different angles of a transparent specimen
-avoid the need to physically slice the sample for thin-section TEM
-images are combined digitally to visualize the entire 3D object
74
X-ray diffraction analysis/crystallography: how it works
-a beam of x-rays is shot at a crystallized sample
-many molecules are identical in conformation
-x-rays diffract according to position of atoms
-pattern of scattered x-rays can compute positions of atoms
75
bacteria shared fundamental traits
-thick, complex outer envelope
-compact genome
-prokaryote
76
archaea shared fundamental traits
-have unique membrane and envelope structures
-prokaryote
77
eurkaryotic cells shared fundamental traits
have a nucleus and extensive membranous organelles
78
bacterial cell
-cytoplasm:
-cell (plasma) membrane:
-cell wall:
- nucleoid:
-flagellum:
-cytoplasm: consists of a gel-like network
-cell (plasma) membrane: encloses the cytoplasm
-cell wall: rigid structure external to the cell membrane (unique to bacteria)
- nucleoid: non-membrane-bound area of the cytoplasm that contains the chromosome in the form of looped coils
-flagellum: external helical filament whose rotary motor propels the cell (some but not all have it)
79
all cells share 4 common chemical components
-water
-essential ions
-small organic molecules
-macromolecules
80
membranes have approximately equal volumes of what?
phospholipids and proteins
81
phospholipid
-consists of what?
-two layers called?
-glycerol with ester links to two fatty acids and a phosphoryl group
-two layers of phospholipids in the bilayer are called leaflets
82
membrane lipid diversity
-fatty acid chains may be ____, ____, or ___
-may also contain __ structures
-membranes also include ___ molecules that ___ between hydrocarbon chains
-in eukaryotic membranes, the ___ agents are sterols, such as ___
-^in bacteria, ___ or ___
-fatty acid chains may be saturated, unsaturated, or polyunsaturated
-may also contain cyclic structures
-membranes also include planar molecules that fill gaps between hydrocarbon chains
-in eukaryotic membranes, the reinforcing agents are sterols, such as cholesterol
-^in bacteria, hopanoids or hopanes
83
membrane proteins serve numerous functions:
-____support
-detection of ___
-secretion of ___ and___
-__ transport and __ storage
-structural support
-detection of environmental signals
-secretion of virulence factors and communication signals
-ion transport and energy storage
84
how do prokaryotes protect the cell membrane?
-the cell envelope includes at least one structural supporting layer - most commonly, the cell wall
-exception: mycoplasmas
85
-the cell wall confers shape and rigidity to the cell and helps it withstand ___
-the bacterial cell wall, or the ___, consists of a single ___
-the cell wall confers shape and rigidity to the cell and helps it withstand turgor pressure
-the bacterial cell wall, or the sacculus, consists of a single interlinked molecule
86
most bacterial cell walls are made of ____ (unique to bacteria)
-long polymers of repeating disaccharides called N-acetyl____ and N-acetyl____ acid bound to a peptide of amino acids
-the peptides can form ____ connecting the parallel ___ strands
-enzymes responsible for its biosynthesis make excellent targets for ____
peptidoglycan
-long polymers of repeating disaccharides called N-acetylglucosamine and N-acetylmuramic acid bound to a peptide of amino acids
-the peptides can form cross-bridges connecting the parallel glycan strands
-enzymes responsible for its biosynthesis make excellent targets for antibiotic
87
antibiotics
-penicillin inhibits the ____ that ___ the peptides
-vancomycin prevents ____ by binding to the terminal d-Ala-d-Ala ___
-penicillin inhibits the transpeptidase that cross-links the peptides
-vancomycin prevents cross-bridge formation by binding to the terminal d-Ala-d-Ala dipeptide
88
gram positive cell envelope
-very thick layer of ____
-contains ___ and often some ___
-retains the ___ of gram stain even after addition of ___
-very thick layer of peptidoglycan
-contains techoic acid and often some proteins
-retains the crystal violet dye of gram stain even after addition of alcohol
89
gram negative cell envelope
-____ is much thinner
-covered by an outer membrane: ___ and ___
-___ of gram stain easily washed off with alcohol = counterstain with ___
-peptidoglycan is much thinner
-covered by an outer membrane: lipopolysaccharide and porins
-crystal violet stain of gram stain easily washed off with alcohol = counterstain with safranin
90
lipopolysaccharide (LPS) of gram negatives
-important medically: signals immune system of invasion by ____
-___levels elicit appropriate response to eliminate
-___ amounts of accumulating in bloodstream can yield ___ response
-called ____
-important medically: signals immune system of invasion by gram-negative bacteria
-small levels elicit appropriate response to eliminate
-large amounts of accumulating in bloodstream can yield deadly response
-called endotoxin
91
capsule
-made of
-function
-found where
-polysaccharide and glycoprotein
-protects cells from phagocytosis
-gram positive and gram negative cells
92
s-layer
-function
-found where
-consists of
-additional protective layer that may contribute to cell shape and help protect the cell from osmotic stress
-free-living gram positive and gram negative bacteria and archaea
-crystalline layer of thick subunits consisting of protein or glycoprotein
93
bacterial cytoskeleton
-proteins are reveled by ___ that drastically alter the cell shape
-shape-determining proteins
-proteins are reveled by gene defects that drastically alter the cell shape
-FtsZ: forms a "Z-ring" in spherical cells
-MreB: forms a coil inside rod-shaped cells
-CreS "crescentin" forms a polymer along the inner side of crescent-shaped bacteria
94
membrane vesicles
-some microbial cells continually export bits of ___ in membrane vesicles
---these carry __ and ___
-vesicles may function as?
-some microbial cells continually export bits of cytoplasm in membrane vesicles
---these carry proteins and nucleic acids
-vesicles may function as
---attractors of partner heterotrophs
-phage decoys
-vehicles for DNA transfer
95
nanotubules
-some bacteria and archaea can form ___that ____ with the membranes of neighboring organisms
-these nanotubules allow bacteria to directly share __ and __ useful under ___ conditions, such as when exposed to ___
-some bacteria and archaea can form membrane extensions that merge directly with the membranes of neighboring organisms
-these nanotubules allow bacteria to directly share proteins and mRNA useful under hostile conditions, such as when exposed to antibiotics
96
thylakoids: extensively folded ___ found in ___ bacteria
extensively folded intracellular membranes found in photosynthetic bacteria
97
carboxysomes: polyhedral ___ packed with the enzyme ___ for __ fixation
polyhedral bodies packed with the enzyme rubisco for CO2 fixation
98
storage granules
-glycogen
-energy resources
-sulfur globules (for oxidation)
99
pili
-also called fimbriae
-straight filaments of pilin protein
-used in attachment
-gram-negative enteric bacteria use sex pili for conjugation
100
stalks
membrane-embedded extensions of the cytoplasm
101
holdfasts
adhesion factors that tips secrete
102
rotary flagella
-prokaryotes that are motile generally swim by means of rotary flagella
-peritrichous cells have flagella randomly distributed around cell
-flagella rotate together in a bundle behind the swimming cell
103
like all living things, microorganisms need sources of ___ and ___ to grow
carbon, energy
104
over eons, bacteria have evolved ingenious strategies to find, acquire, and ___ a wide assortment of ____ sources
metabolize, food
105
understanding how bacteria use ___ to increase cell mass, and ultimately cell ___ enables us to control their ___
-it even allows us to manipulate them to make useful products
food, number, growth
106
essential nutrients
those that must be supplied from the environment
107
macronutrients
-major elements in cell macromolecules
-cations necessary for protein function
micronutrients
-major elements in cell macromolecules: C H N O P S
-cations necessary for protein function: Mg2+, Fe2+, K+, Ca2+
-micronutrients: necessary for enzyme function: Co,Cu,Mn,Mo,Ni,Zn
108
all of earth's life-forms are based on ___, which they acquire in different ways
-autotrophs
-heterotrophs
carbon
-autotrophs: fix CO2 and assemble into organic molecules (mainly sugars) = C from CO2
-heterotrophs: use preformed organic molecules = C from organic (carbohydrates, lipids, glucose, etc.)
109
energy source: phototroph v.s chemotroph
-phototroph: obtain energy from chemical reactions triggered by light
-chemotroph: obtain energy from oxidation-reduction reactions (bond breaking)
110
electron source: lithotroph v.s organotroph
-lithotroph: use inorganic molecules (H2, HS-, S, NH4, Fe2, etc.)
-organotroph: use organic molecules (carbohydrates, lipids, glucose, etc.)
111
freshwater cyanobacteria are ____trophs
photoautotrophs
112
"black smoker" dwelling bacteria and archaea and soil bacterium nitrobacter are ____trophs
chemoautotrophs (or lithoautotrophs)
113
oceanic cyanobacteria are ___trophs
photoheterotrophs
114
human pathogens are ____trophs
chemoheterotrophs (or organotrophs)
115
eukaryotic microbes such as protists and fungi are ____ consumers
-their lifestyle involves predation, parasitism, and scavenging the dead
-fungi possess the exceptional ability to digest complex organic compounds such as lignin
heterotrophic
116
algae are ___ that produce biomass through photosynthesis
-protist algae, such as single-celled Euglena, are ___
photoautotrophs
-mixotrophic
117
nitrogen cycle
-N2 makes up nearly 79% of earth's atmosphere but is ____ for use by most organisms
-nitrogen fixers possess?
-denitrifiers convert?
-unavailable
-nitrogenase, which converts N2 to ammonium ions (NH4+)
-nitrate to N2
118
selective permeability achieved in 3 ways:
-membrane-spanning protein channels or ___
-substrate-specific carrier proteins, or ___
-dedicated ___ that patrol the periplasmic space
-membrane-spanning protein channels or pores
-substrate-specific carrier proteins, or permeases
-dedicated nutrient-binding proteins that patrol the periplasmic space
119
aquaporins transports water and ___ via facilitated diffusion
small polar molecules such as glycerol
120
the largest family of energy-driven transports systems are the ___ transporters
-they are found in 1, 2, or 3 domains of life
-two main types: uptake are efflux
ATP-Binding Cassette or ABC
-all 3
-uptake: critical for transporting nutrients
-efflux: used as hazardous chemical efflux pumps
121
siderophores
-specialized molecules secreted to find ferric iron ___ and transport it into/out of the cell
-the iron is released into the ____ and ___ to the more useful ferrous form ___
-specialized molecules secreted to find ferric iron (Fe3+) and transport it into the cell
-the iron is released into the cytoplasm and reduced to the more useful ferrous form (Fe2+)
122
group translocation
-a process that uses energy to ----- the substrate during its transport
-the --- system (PTS) uses energy from ---- (PEP) to attach a --- to specific sugars
-since the substrate is altered upon entrance, the substrate is always move up/down the concentration gradient
-a process that uses energy to chemically alter the substrate during its transport
-the phosphotransferase system (PTS) uses energy from phosphoenolpyruvate (PEP) to attach a phosphate to specific sugars
-since the substrate is altered upon entrance, the substrate is always move down the concentration gradient
123
microbes in nature exist in complex, multispecies communities, but for detailed studies they myst be grown separately in ____
-succeeded at culturing __% of the microorganisms around us
pure culture
-1%
124
bacteria are grown in culture media
-liquid or broth used for?
-solid used for?
-liquid or broth useful for studying the growth characteristics of a pure culture
-solid (usually gelled with agar) useful for trying to separate mixed cultures from clinical specimens or natural environments
125
pure colonies are isolated via two main techniques
-dilution streaking (quadrant streak, T-streak): a loop is dragged across the surface of an agar plate
-spread plate: tenfold serial dilutions are performed on a liquid culture, a small amount of each dilution is then plated
126
one colony means how many cells were originally on that location of the plate?
one cell
127
complex media (rich media)
-enriched media
complex: nutrient rich but poorly defined components
-enriched: complex media to which specific blood components are added
128
defined (or synthetic) media
-minimal defined media
defined: have known concentrations of each chemical component
-minimal defined: contain only those nutrients that are essential for growth of a given microbe
129
selective media
favor the growth of one organism over another
130
differential media
exploit differences between two species that grow
131
the ____, or rate of increase in cell numbers or biomass, is proportional to the population size at a given time
-if a cell (like bacteria) divides by binary fission, the number of cells is proportional to __
growth rate
-2n
132
generation time definition and calculation
generation time is the time it takes for a population to double
-Nt = N0 x 2^n
-Nt = final cell number
-N0 = original cell number
-n = number of generations
133
the simplest way to model the effects of a changing environment is to culture bacteria in a ____
-a liquid medium within a(n) open/closed system
batch culture
-closed
134
bacterial growth curves
-lag phase
-log phase
-stationary phase
-death phase
-lag phase: bacteria are preparing their cell machinery for growth = nutrients are high, but cell needs time to switch gears to new environment
-log phase: growth approximates an exponential curve = nutrients are high and growth rate is exponential
-stationary phase: cell stops growing and shut down their machinery while turning on stress responses to help retain viability = nutrients are low and rate of replication is now equal to death rate
-death phase: cells die with a half-life similar to that of radioactive decay, a negative exponential curve = nutrients are depleted and waste levels are high
135
in a _____, all cells in a population achieve a steady state, which allows detailed study of bacterial physiology
-the ___ ensures logarithmic growth by constantly ____ equal amounts of culture medium
continuous culture
-chemostat, adding and removing
136
antibiotics are ___ metabolites and amino acids are ___ metabolites
antibiotics = secondary
amino acids = primary
137
in nature many bacteria form specialized, surface-attached communities called ____
-these can be constructed by __ or __ species and can form on a range of __ or __ surfaces
biofilms
-one or multiple, organic or inorganic
138
the formation of ___ can be cued by different environmental signals in different species
-chemical signals enable bacteria to communicate = ___
-bacteria growing in ___ also exhibit a type of cell ___ limited by physiological conditions that develop in different layers of the biofilm
biofilms
-quorom sensing
-biofilms, differentiation
139
endospores
-clostridium and bacillus species can produce dormant spores that are ___
-___ initiates an elaborate 8-hour genetic program that involves: a ____ cell division process that produces a ____ and ultimately an ____
-heat resistant
-starvation
-asymmetrically, forespore, endospore
140
microbes have both the fastest and slowest growth rates of any known organisms and these differences are determined by?
nutrition and niche-specific physical parameters like temperature and pH
141
extremophiles are what?
-when life on earth began, conditions were extreme, so the ____ microbes would likely have been extremophiles
-the "normal" growth conditions are (4 things)
---any ecological niche inside/outside this window are "extreme" and organisms inhabiting them are called extremophiles
extremophiles are microbes (bacteria, archaea, and a few eukaryotes) that are able to grow in conditions very different from those for humans
-earliest
-normal growth conditions: sea level, temperature 20-40C, near-neutral pH, 0.9% salt and ample nutrients
---outside
142
the environmental habitat that a species inhabits is based on the ___ of that organism's proteins and other macromolecular structures to the ___ conditions within that niche
the environmental habitat that a species inhabits is based on the tolerance of that organism's proteins and other macromolecular structures to the physical conditions within that niche
143
-a species grows most quickly at temperatures where____ work most efficiently; growth stops when __ temperatures cause critical proteins or cell structures to fail
-microbes that grow at __ temperatures typically can achieve higher rates of growth
-microbial growth rates roughly ___ for every 10C rise in temperature
-a species grows most quickly at temperatures where all of the cell's proteins work most efficiently; growth stops when rising temperatures cause critical proteins or cell structures to fail
-microbes that grow at high temperatures typically can achieve higher rates of growth
-microbial growth rates roughly double for every 10C rise in temperature
144
psychrophile
-temerpature
-example
->15C
-refrigerator spoilage
145
mesophile
-temperature
-example
-15-45C
-pathogens and most environmental oragnisms
146
thermophile
-temperature
-example
-50-80C
-compost heaps
147
hyperthermophile
-temperature
-example
-80-120C
-hot springs, thermal vents
148
thermotolerant
-temperature
-example
able to survive exposure to low or high temps for a while, but don't grow
149
adaptation to pressure
-leaving creatures at earth's surface (sea level) are subject to a pressure of ____
-many ____ philes are also ___philes because the average temperature at the ocean floor is 2C
-1 atm
-barophiles, psychophiles
150
in addition to moving water, microbes have at least two mechanisms to minimize osmotic stress:
-in ____ media, bacteria protect their internal water by synthesizing or importing ____ solutes (proline, glutamic acid, or K+)
-in ____ media, pressure-sensitive or ____ channels can be used to __ solutes out of the cell
-outside their osmotic comfort range, these housekeeping strategies become ___ at controlling internal osmolarity
-hypertonic, compatible
-hypotonic, mechanosensitive, leak
-ineffective
151
halophiles
-growth at what osmolarity
-note
-10-20% NaCl
-seawater is 3.5% as a reference
152
extreme halophiles
-growth at what osmolarity
-note
->15% salt
-will not grow at larger concentrations
153
osmotolerant
-growth at what osmolarity
-note
-0-8% salt
-can grow across a wide range of salinities
154
saccharophiles
-growth at what osmolarity
-note
-high sugar
-thrive in high sugar concentrations: jams and jellies, often yeasts and molds
155
to achieve a low internal concentration of Na+ ___ microbes use special ion pumps to ___ sodium and replace it with other ___, such as K+
halophilic
excrete
cations
156
similar to temperature, __ also has a direct effect on the cell's macromolecular structures
-extreme concentrations of either __ or __ in a solution will limit growth
-all enzyme activities exhibit optima, minima, and maxima with regard to __
-biological membranes are relatively impermeable to ___. however, ___ organic acids can readily cross the membrane then dissociate inside the cell, releasing a __ and disrupting internal ___
pH
-hydrogen ions (H+), hydroxide ions (OH-)
-pH
-protons, uncharged, proton, pH
157
acidophiles
-pH
-example
-pH<5
-often chemoautotrophs
-fermenting bacteria that produce acids as by-products of carbohydrate metabolism
-corrosion of metals by thiobacillus sulfuric acid production
158
neutrophiles
-pH
-example
-pH 5-8
-most bacteria, including pathogens
159
alkaphiles
-pH
-example
-pH > 8
-putrefying bacteria degrade proteins to amines and ammonia, increasing pH (particularly in meats)
160
acidotolerant
-pH
-example
some neutrophils can survive pH < 5.5 < 8.5, but won't grow
161
need to to keep internal cell pH near neutral even though surrounding environment is high or low pH
-in acidic environments, microbes can prevent the unwanted influx of protons by exchanging ___ for __ when the internal pH becomes too low
-under extremely alkaline conditions, the cells can use the ____ to bring H+ into the cell in exchange for ____
-extracellular K+ for intracellular H+
-Na+/H+ antiporter, expelling Na+
162
aerobic respiration with ___ serving as the terminal electron acceptor of the electron transport chain required for ____ and other key cell processes
oxygen, ATP synthase
163
-oxygen is toxic to cells unless the cells has enzymes capable of efficiently ___ oxygen's breakdown products, called ____
---ROS seriously damage DNA, RNA, proteins, and lipids by ___
-strict anaerobes lack these enzymes, while aerobes have:
-____: superoxide --> oxygen + hydrogen peroxide
-___: hydrogen peroxide --> oxygen + water
-destroying, reactive oxygen species (ROS)
-stripping them of electrons
-superoxide dismutase
-catalase
164
growth characteristic: strict aerobe
grows only when O2 is available
165
growth characteristic: facultative anaerobe
grows best when O2 is available, but also grows without it
166
growth characteristic: strict anaerobe
cannot grow when O2 is present
167
growth characteristic: microaerophile
grows only if small amounts of O2 are available
168
growth characteristic: aerotolerant anaerobe
grows equally well with or without O2
169
sterilization
killing of all living cells, spores, and viruses
170
disinfection
killing or removal of pathogens from inanimate objects; does not necessarily result in sterilization
171
antisepsis
killing or removal of pathogens from the surface of living tissues
172
sanitation
reducing the microbial population to safe levels
173
cells treated with antimicrobials die at a ___ rate
-microbes die accord to a ___ curve, where cell numbers are reduced in greater/equal/lesser fractions at constant intervals
-___ = the length of time it takes an agent or condition to kill __% of the population
logarithmic
-negative exponential, equal
-decimal reduction time (D-value), 90%
174
other methods of growth control
-filtration
-irradiation
-chemicals that damage macromolecules
-filtration: liquid or air
-irradiation: UV light, gamma rays, electron beams, x-rays
-chemicals that damage macromolecules: ethanol, iodine, chlorine
175
bacteria can develop resistance to disinfectants
-altering ___ protein normally targeted by triclosan
-producing membrane-spanning, ____ pumps
-forming ___, which offer collaborative protection
-fatty acid synthesis
-multidrug efflux
-multispecies biofilms
176
barophiles
require high pressure to grow, though they die at still higher pressures
176
barotolerant
organisms grow up to a certain pressure, but die at high pressures
177
barosensitive
organisms die as pressure increases
