Exam 2 Flashcards
(183 cards)
1
Q
bacterial nutritional categories are based on
A
how cells get energy, electrons, and carbon
2
Q
use reduced, pre-formed organic molecules as their carbon source
ex: us many bacteria
A
heterotrophs
3
Q
use CO2 as their carbon source
A
autotrophs
4
Q
most autotrophs are
A
photosynthetic organisms
5
Q
what are typical problems with carbon dioxide as a carbon source
A
- lacks hydrogen
- most oxidized form of carbon
- cannot be used as a source of protons, electrons, or energy
6
Q
chemical energy
organic e- source
organic carbon source
A
chemoorganoheterotroph
7
Q
chemical energy source
organic electron source
inorganic carbon source
A
chemoorganoautotroph
8
Q
chemical energy source
inorganic electron source
organic carbon source
A
chemolithoheterotroph
9
Q
chemical energy source
inorganic electron source
inorganic carbon source
A
chemolithoautotroph
10
Q
light energy source
organic electron source
inorganic carbon source
A
photoorganoautotroph
10
Q
light energy source
organic electron source
organic carbon source
A
photoorganoheterotroph
11
Q
light energy source
inorganic electron source
organic carbon source
A
photolithoheterotroph
12
Q
light energy source
inorganic electron source
inorganic carbon source
A
photolithoautotroph
13
Q
- required in relatively large amounts
- C, O, H, N, S, and P (carbs, lipids, proteins, and nucleic acids)
- ions such as sodium, potassium, calcium, magnesium, iron, and chloride ions
A
macronutrients / macroelements
14
Q
roles of ionic macroelements
A
enzyme cofactors, osmotic balance, ATP synthesis, etc
15
Q
- required in very small amounts
- act as enzyme cofactors
- Mn2+, Zn2+ Co2+, Mo2+, Ni2+, Cu2+
A
micronutrients / trace elements
16
Q
we need electrons for
A
biosynthesis and metabolic pathways
17
Q
organotrophs get their electrons from
A
reduced organic molecules (e.g. glucose)
18
Q
lithotrophs get their electrons from
A
- water, reduced inorganic molecules (sulfur, iron, nitrogen-based molecules, ferrous iron, ammonia, hyddrogen sulfide)
- “rock eaters”
19
Q
capture energy from oxidation or organic or inorganic compounds/chemicals
A
chemotrophs
20
Q
capture light energy to produce ATP
A
phototroph
21
Q
- occurs when pre-formed bacterial toxins are ingested
- pathogen doesn’t grow in host, symptoms occur quickly
A
foodborne intoxication
22
Q
- natural reservoir in soil
- home-canned foods, baked potatoes in foil
- inhibits synaptic vesicle fusion in motor neurons by targeting SNARE proteins in motor neurons
- paralysis and respiratory failure
A
Clostridium botulinum (botulism)
23
Q
- main reservoir is nasal cavities
- high protein foods: meat and dairy
- extracellular enterotoxins
- nausea, vomiting, cramps
A
Staphylococcus aureus
24
how does *C. botulinum* impact SNARE proteins in motor neurons
* if the SNARE protein is not synthesized or turned on, acetylcholine is not secreted, and therefore no muscle contraction occurs
* can lead to flaccid paralysis --> death
25
* found in raw oysters
* 10^8 ingested cells for illness
* marine organism
* incubation time 6-96h
Vibrio parahaemolyticus
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* from under or uncooked poultry (half of sold poultry)
* < 10 ingested cells can cause illness
* symptoms arise in 2-5 days
*Campylobacter jejuni*
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* very common
* disease lasts 1-2 days, includes vomiting, diarrhea, abdominal pain
* infection rates highest under crowded conditions
* incubation time: 12-48h
norovirus
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occur via ingestion of pathogen followed by growth in intestines
food-borne infections
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* most pathogens
* organic carbon source (C, O, H), energy source, and e-
chemoorganoheterotrophs
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* cyanobacteria, sulfur bacteria
* more flexible in metabolism
* CO2 as carbon, light energy source, inorganic e- source (H2O)
photolithoautotrophs
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* comprised of catabolism and anabolism
* all of the chemical reactions in an organism
metabolism
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breaking down large molecules into smaller molecules and releasing energy
catabolism
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building biomolecules from precursors using energy
anabolism
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aspects of metabolism are common to all organisms
1. life obeys the laws of thermodynamics
2. energy cells obtain from their environment is often conserved as ATP
3. redox rxns play a critical role in energy conservation
4. chemical rxns that occur in cells are organized into pathway
5. each rxn of a pathway is catalyzed by an enzyme
6. functioning of biochemical pathways is regulated
35
why is the catalysis of each reaction of a pathway by an enzyme so important
critical for survival because enzymes decrease activation energy
36
laws of thermodynamics
energy is only transformed not created or destroyed
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living organisms need energy to build
biomass
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bacterial growth biomass depends on
energy change of catabolic rxns
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dG (Gibbs free energy) depends on
the enthalpy and entropy changes associated with the rxn
40
* acquired thru meat, fruits, veggies
* ~500 cells ingested can cause illness
* 3-4 day incubation pd
* vomiting, diarrhea, and/or fever
*E. coli* 0157:H7 (acquired *Shiga* toxin)
41
how does the Shiga toxin work?
* cleaves rRNA, blocking protein synthesis
* binds receptors on kidney and blood vessel cells causing bloody diarrhea and kidney failure
42
* acquired thru meat, poultry, eggs
* > 10^5 ingested cells for illness
* incubation time as short as 8 hours, often longer (12-72h)
* typhoidal or nontyphoidal
* g- and bacillus shaped
*Salmonella enterica*
43
how do we prevent food spoilage
* reduction of water activity
* acidity
* chemical preservatives
* controling temp
* irradiation
* modified atmosphere packaging
44
removes oxygen or floods packaging w/ CO2
modified atmosphere packaging
45
UV, gamma, or X-rays used to kill microbes damaging DNA
irradiation
46
how do we control temperature to prevent food spoilage
pasteurization + refrigeration, freezing
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intrinsic factors that impact the likelihood of food spoilage
* water availability
* osmolarity
* nutrient content
* pH and buffering capacity
* antimicrobial constituents
* biological structures such as rinds or shells
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extrinsic factors that impact food spoilage
* temperature
* humidity
* presence and concentration of gases
49
steps to milk spoilage
1. acid production by *Lactobacillus* fermentation
2. yeasts and molds degrade the lactic acid
3. protein-digesting bacteria (cadaverine, putrescine putrefy the milk)
50
refers to microbial changes that render a product unpalatable for consumption
spoilage
51
acid fermentation products produce what taste
sour
52
alkaline fermentation products produce a what taste
bitter
53
oxidation of fats promotes
rancidity
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decomposition of proteins promotes
putrefaction
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* pathogenic bacteria typically
* you cannot tell if it will make you sick
contamination
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consists of visible microbial growth, gross
spoilage
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* amino acids, certain ions that increase osmolarity inside cell to prevent water loss
* help microbes survive high salt environments
compatible solutes
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* adapted to salty (3.5%), low water environments
* ocean, skin surface
halophiles
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more than 30% salt, use compatible solutes to survive
extreme halophiles
60
a measure of the number of solutes in a solution and is inversely related to water activity
osmolarity
61
more solute =
less water activity
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more water activity =
less solute
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* requires high pressure to grow, though they die at still higher temperatures
* pressure adapted internal structures, unsaturated membrane lipids
* greater than 380 atm
barophiles
64
organisms die as pressure increases
barosensitive
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* organisms grow to a certain pressure, but die at higher pressure
* 10-500 atm
barotolerant
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* cannot eliminate ROS
* die in presence of oxygen, cannot use or be near
* (-) SOD, - Catalase, - Peroxidase
## Footnote
ex: *Clostridium*
strict anaerobe
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* grow oxygen using anaerobic metabolism
* can't use oxygen but don't care, aren't harmed by oxygen but don't use it
* (+) SOD, + Catalase or Peroxidase
## Footnote
ex: *Lactobacillus*
aerotolerant aerobes
68
* can live without oxygen
* can use oxygen or not, grow best in oxygen but can grow anaerobically
* (+) SOD, + Catalase, + Peroxidase
## Footnote
ex: *E. coli*
facultative anaerobe
69
* grow only at low O2 concentrations
* use oxygen, grow best when there is 2-10% oxygen
* (+) SOD (low levels), + Catalase, - Peroxidase
## Footnote
ex: *Streptococcus*
microaerophiles
70
* can only grow oxygen is available, absolute requirement
* grow in atmospheric oxygen (20%)
* (+) SOD, + Catalase, + Peroxidase
## Footnote
Ex: *Pseudomonas*
obligate aerobes
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the production of reactive oxygen species (ROS) often begins w/
FAD moving an electron to oxygen
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generate ROS
* superoxide radical union
* hydrogen peroxide
* peroxide radical
73
enzymes reactions that destroy ROS
* superoxide dismutase (H2O2 into hydroxide radical)
* catalase (H2O2 into water and oxygen)
* peroxidase (H2O2 into water and NAD+)
74
* much more efficient for ATP synthesis
* uses oxygen as an FEA
aerobic respiration
75
use non-oxygen molecules as a final electron acceptor
anaerobic respiration and fermentation
76
out of which methods of respiration use ATP most efficiently (most to least)
aerobic > anaerobic > fermentation
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* rely heavily on sodium ion gradients
* growth above pH 9
alkaliphiles
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1. respiratory chain pumps H+
2. H+ import through F1F0 ATP synthase drives ATP synthesis
3. Na+ driven ATPases export Na+
Na+ transport gradient
79
sodium ion motive force powers
* motility
* symport of some substrates
* pH homeostasis
80
* altered membrane lipids to prevent protons from leaking out of the cell
* reliance on Na+ gradients
alkaliphiles
81
* altered membrane lipids that decrease proton permeability
* contains ill-defined proton extrusion mechanisms
* thrive in lower pHs
* growth below pH 3
acidophiles
82
what is a con of having a high proton concentrated environment
protons can leak into the cell and damage enzymes
83
what is a con of having a low proton concentrated environment
really hard to build proton motive force
84
most enzymes function best between pHs of
5-8.5
85
* live in fridges
* optimum around 15 degrees Celsius (below 15 degrees C)
* more flexible proteins (glycines) and unsaturated membrane lipids
psychrophiles
86
* most like us
* pathogens, human microbiota
* have an optimum temperature of about 35 degrees Celsius (15-45 C)
mesophiles
87
* have an optimum temp of about 60 degrees Celsius (50-80 C)
thermophiles
88
* often archaea
* saturated membrane lipids, archaeal monolayers
* fewer glycines = more rigid proteins
* more chaperones
* optimum temp around 90 degrees Celsius (growth above 80 C)
extreme thermophiles
89
help proteins fold
chaperone proteins
90
fewer glycines in the membrane =
more rigid proteins
91
an organism's cardinal temperature is influenced mainly by
* enzyme function
* membrane integrity
92
growth between pH 5 and pH 8
neutralophile
93
species specific time for doubling a population (doubling time)
generation time
94
bacterial growth phases
1. lag phase
2. log phase
3. stationary phase
4. death phase
95
bacteria are preparing their cell machinery for their growth
lag phase
96
growth approximates an exponential curve (straight line, on a logarithmic scale)
log phase
97
* cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability
* not dying, just arresting growth
* endospore formation commonly occurs during this phase
stationary phase
98
* cells die with a half-life similar to that of radioactive decay, a negative exponential curve
* incredibly prolonged and unpredictable
death phase
99
* used to detect bacterial-induced lysis (hemolysis) of RBCs
* complex and differential
blood agar
100
gamma hemolysis
no hemolysis / clearing
101
* partial hemolysis
* partial clearing
* bacteria makes hydrogen peroxide that oxidizes hemoglobin
alpha hemolysis
102
* otherwise known as true hemolysis, complete clearing where bacteria was streaked
* bacteria secrete toxins that lyse RBCs and degrade hemoglobin
beta hemolysis
103
brilliant green dye inhibits growth of what bacteria
gram positive
104
organisms that ferment are what color on Brilliant Green agar
yellow
104
* distinguishes Gram-negative fermenters form non-fermenters
* complex, and selective and differential
Brilliant Green Agar
105
isolates microbes with specific properties by only allowing certain species to grow
selective media
106
* exploits differences between two species that grow equally well
* recognize certain microbes based on visual reactions in the medium
differential media
107
adds fresh nutrients and removes waste
continuous culture
108
* a closed system for adding specific bacterial in liquid media
* no nutrients replenished, no waste removed
batch culture
109
* important for studying a single bacterial species
* a culture in which only one strain or clone is present
pure culture
110
liquid growth media
broth
111
solid growth media
agar
112
considerations we need to have when deciding which type of growth media to use in the lab
* sterilization
* environmental conditions (i.e. incubation)
113
nutrient rich, poorly defined
complex media
114
* minimal nutrients, known composition
* useful when we are specifically studying microbial physiology
defined media
115
growth media must contain
* sources of energy, carbon, and electrons
* sources of other macroelements for macromolecules (N, P, S)
* salts
* growth factors (amino acids, vitamins, purines, and pyrimidines, etc)
116
acid fermentation of milk produces
yogurt and cheese
117
classes of fermentation commonly used in food production
* alkaline fermentation (pidan)
* acid fermentation of vegetables (kimchi, miso)
* acid fermentation of dairy products, meat, and fish
* ethanolic (alcoholic) fermentation (beer, wine, tequila)
* propionic acid fermentation (bread)
118
fermented foods depend on
* indigenous flora
OR
* starter cultures
119
purposes of food fermentation
* preservation (by limiting microbial growth)
* improving digestibility
* adding nutrients and flavor molecules
120
every fermentation pathway has what happening
NADH being reoxidized into NAD+
121
* an organic molecules is FEA (pyruvate, acetaldehyde)
* no electron transport chain, allows oxidation of NAD+ thru generation of NADH
* catabolic
fermentation
122
* used typically in photoorganoheterotrophs
* a single-protein, light driven protein pump
bacteriorhodopsin
123
mechanism of action (in order) of bacteriorhodopsin
1. Retinal, in the all trans form, is covalently attached to the lysine of bacteriorhodopsin; nitrogen to which it is attached is protonated
2. light absorption causes one double bond to isomerize to the cis form
3. isomerization of the retinal causes the proton to be lost to the outside
4. when the retinal spontaneously isomerizes back to the ground state, the lysine is re-protonated from the cytoplasm
124
types of phototrophy
chlorophyll-based and rhodopsin-based
125
what types of phototrophs use chlorophyll-based phototrophy
photolithoautotrophs
## Footnote
ex: cyanobacteria, green sulfur bacteria, purple sulfur bacteria
126
127
capture energy from the sun to create PMF and synthesize ATP
phototrophs
128
* electrons from Fe2+ must be passed up to NADP+ by this
* the transfer of electrons through the electron transport chain through the reverse redox reactions, requires a lot of energy
reverse electron flow
129
use reduced inorganic compounds for energy and electrons
chemolithotrophs
130
more energy captured =
more ATP synthesized
131
aerobic ETCs pump how many protons across the membrane
10
132
anaerobic ETCs pump how many protons across the membrane
4
## Footnote
due to nitrate being reduced to nitrite
133
build a proton gradient that is used to make ATP
electron transport systems
134
why does anaerobic respiration yield less energy
because it uses an FEA with a lower reduction potential than O2
135
a redox reaction is favored by ... values of dE, which yields negative values of dG
positive
136
ETC components are arranged in order of
increasing reduction potential
137
larger E =
better electron acceptor
## Footnote
holds e- more tightly, at a lower energy state
138
the amount of energy captured from an ETC depends on
the FEA used
139
what does a negative dG value mean
bond energy decreases and/or disorder increases, and the reaction will go forward spontaneously
140
a change in enthalpy (bond energy) is favorable if
negative
## Footnote
reaction forms molecules with more favorable/more stable/lower bond energy bonds than reactants
141
142
what happens when a change in entropy is positive
rxn increases disorder
143
which law of thermodynamics states that thermodynamically favorable processes increase disorder
2nd law
144
how do we make dG negative?
* change temperature
* increase concentration of reactants
* product concentration kept low by removal
145
couples metabolic species across species by removing product by another species
syntrophic relationship
146
heterotrophs catabolize carbohydrates through which three main metabolic strategies
* aerobic respiration
* anaerobic respiration
* fermentation
147
which pathway of glycolysis is:
* highly conserved
* involves glucose undergoing a 10-step breakdown to pyruvate
* gains energy from the rxn
EMP pathway of glycolysis
148
* unique to bacteria and archaea
* catabolizes sugar acids (not necessarily glucose, produces NADPH for biosynthesis
* source of energy and electrons simultaneously
ED pathway of glycolysis
149
* shunts carbon from glucose into biosynthesis
* a source of carbon and electrons
PPP pathway of glycolysis
150
what is the net yield of the EMP pathway of glycolysis
* 2 three carbon pyruvate
* 2 ATP
* 2 NADH
151
what is the net yield of the ED pathway of glycolysis
* 2 three carbon pyruvate
* ATP
* NADH, NADPH
152
what is the net yield of the PPP pathway of glycolysis
* biosynthesis
* ATP
* 2 NADPH
153
if a final electron acceptor is available post-glycolysis, pyruvate is oxidized to
Acetyl CoA and enters the citric acid cycle
154
the bacterial glyoxylate shunt requires
two additional CAC enzymes
## Footnote
isocitrate lyase and malate synthase
155
benefits of using a glyoxylate shunt
* prevents loss of carbon via carbonn dioxide
* creates more starting material for biosynthesis
156
In the pentose phosphate pathway, glucose 6-phosphate is oxidized to 6-phosphogluconate, which is then decarboxylated to ribulose 5-phosphate. What is the main metabolic role of this pathway?
production of carbohydrates with three to seven carbon atoms, which can be utilized in biosynthesis
157
Identify the oxidant in the following coupled redox reaction: Malate + NAD+ --> Oxaloacetate + NADH + H+
NAD+
158
Because the reduction potential of the CO2/glucose redox pair is more negative than the Fe3+/Fe2+ redox pair, energy is released as electrons flow
from glucose (the donor) to Fe3+ (the acceptor)
159
For a given electron donor, the most energy will be released when oxygen serves as the final electron acceptor because
oxygen is a stronger oxidizing agent than most other electron acceptors.
160
The relationship between the reduction potential, E, and the change in free energy, ΔG is such that if E is ___...______, then ΔG is ____..._____ and the reaction is __..._______
positive; negative; unfavorable
161
how is ATP primarily produced in chemolithotrophs
Electrons moving through an electron transport system to generate a proton motive force
162
which type of metabolism does not use a membrane-associated ETS
fermentation
163
lactic acid is a common fermentation product and is produced when ... is reduced by electrons received from NADH
pyruvate
164
bacteria that express bacteriorhodopsin protein are typically classified as
photoorganoheterotrophs
165
a complex medium is one that
is nutrient rich, but the amounts and identity of specific nutrients are unknown
166
which ingredient makes Mannitol Salt Agar a selective medium
NaCl
167
which ingredients make Mannitol Salt Agar a differential media
mannitol and phenol red
168
How would the growth curve change relative to the curve shown above if you used a medium that was 1 pH unit more acidic than optimal?
the slope of the log phase would decrease
169
How would the growth curve change relative to the curve shown above if you diluted the growth medium so that the carbon source is half strength.
The cell yield would decrease by half
170
How would the growth curve change relative to the curve shown above if you used an inoculum of exponentially growing cells instead of old cells from the refrigerator?
There would be a shorter lag phase
171
How would the growth curve change relative to the curve shown if you omit all nitrogen from the medium?
There would be no growth at all.
172
inactivates hydrogen peroxide
catalase
173
inactivates superoxide
superoxide dismutase
174
utilizes NADH to reduce peroxide
peroxidase
175
an organism living under high pressure
barophile
176
optimal growth at a pH below 5.5 describes
acidophile
177
optimal growth at a pH above 8 describes
alkaliphile
178
an organism able to grow over a wide range of solute concentrations is
halotolerant
179
an organism that requires high levels of salt
halophile
180
mechanisms halophiles typically employ to grow in habitats with high concentrations of salt
* increase internal concentration of organic molecules such as chlorine
* maintain high intracellular levels of potassium chloride and other inorganic solutes
181
MAP helps to preserve food by
removing oxygen from the atmosphere
