Exam 2 Flashcards
bacterial nutritional categories are based on
how cells get energy, electrons, and carbon
use reduced, pre-formed organic molecules as their carbon source
ex: us many bacteria
heterotrophs
use CO2 as their carbon source
autotrophs
most autotrophs are
photosynthetic organisms
what are typical problems with carbon dioxide as a carbon source
- lacks hydrogen
- most oxidized form of carbon
- cannot be used as a source of protons, electrons, or energy
chemical energy
organic e- source
organic carbon source
chemoorganoheterotroph
chemical energy source
organic electron source
inorganic carbon source
chemoorganoautotroph
chemical energy source
inorganic electron source
organic carbon source
chemolithoheterotroph
chemical energy source
inorganic electron source
inorganic carbon source
chemolithoautotroph
light energy source
organic electron source
inorganic carbon source
photoorganoautotroph
light energy source
organic electron source
organic carbon source
photoorganoheterotroph
light energy source
inorganic electron source
organic carbon source
photolithoheterotroph
light energy source
inorganic electron source
inorganic carbon source
photolithoautotroph
- 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
macronutrients / macroelements
roles of ionic macroelements
enzyme cofactors, osmotic balance, ATP synthesis, etc
- required in very small amounts
- act as enzyme cofactors
- Mn2+, Zn2+ Co2+, Mo2+, Ni2+, Cu2+
micronutrients / trace elements
we need electrons for
biosynthesis and metabolic pathways
organotrophs get their electrons from
reduced organic molecules (e.g. glucose)
lithotrophs get their electrons from
- water, reduced inorganic molecules (sulfur, iron, nitrogen-based molecules, ferrous iron, ammonia, hyddrogen sulfide)
- “rock eaters”
capture energy from oxidation or organic or inorganic compounds/chemicals
chemotrophs
capture light energy to produce ATP
phototroph
- occurs when pre-formed bacterial toxins are ingested
- pathogen doesn’t grow in host, symptoms occur quickly
foodborne intoxication
- 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
Clostridium botulinum (botulism)
- main reservoir is nasal cavities
- high protein foods: meat and dairy
- extracellular enterotoxins
- nausea, vomiting, cramps
Staphylococcus aureus
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
- found in raw oysters
- 10^8 ingested cells for illness
- marine organism
- incubation time 6-96h
Vibrio parahaemolyticus
- from under or uncooked poultry (half of sold poultry)
- < 10 ingested cells can cause illness
- symptoms arise in 2-5 days
Campylobacter jejuni
- very common
- disease lasts 1-2 days, includes vomiting, diarrhea, abdominal pain
- infection rates highest under crowded conditions
- incubation time: 12-48h
norovirus
occur via ingestion of pathogen followed by growth in intestines
food-borne infections
- most pathogens
- organic carbon source (C, O, H), energy source, and e-
chemoorganoheterotrophs
- cyanobacteria, sulfur bacteria
- more flexible in metabolism
- CO2 as carbon, light energy source, inorganic e- source (H2O)
photolithoautotrophs
- comprised of catabolism and anabolism
- all of the chemical reactions in an organism
metabolism
breaking down large molecules into smaller molecules and releasing energy
catabolism
building biomolecules from precursors using energy
anabolism
aspects of metabolism are common to all organisms
- life obeys the laws of thermodynamics
- energy cells obtain from their environment is often conserved as ATP
- redox rxns play a critical role in energy conservation
- chemical rxns that occur in cells are organized into pathway
- each rxn of a pathway is catalyzed by an enzyme
- functioning of biochemical pathways is regulated
why is the catalysis of each reaction of a pathway by an enzyme so important
critical for survival because enzymes decrease activation energy
laws of thermodynamics
energy is only transformed not created or destroyed
living organisms need energy to build
biomass
bacterial growth biomass depends on
energy change of catabolic rxns
dG (Gibbs free energy) depends on
the enthalpy and entropy changes associated with the rxn
- 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)
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
- 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
how do we prevent food spoilage
- reduction of water activity
- acidity
- chemical preservatives
- controling temp
- irradiation
- modified atmosphere packaging
removes oxygen or floods packaging w/ CO2
modified atmosphere packaging
UV, gamma, or X-rays used to kill microbes damaging DNA
irradiation
how do we control temperature to prevent food spoilage
pasteurization + refrigeration, freezing
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
extrinsic factors that impact food spoilage
- temperature
- humidity
- presence and concentration of gases
steps to milk spoilage
- acid production by Lactobacillus fermentation
- yeasts and molds degrade the lactic acid
- protein-digesting bacteria (cadaverine, putrescine putrefy the milk)
refers to microbial changes that render a product unpalatable for consumption
spoilage
acid fermentation products produce what taste
sour
alkaline fermentation products produce a what taste
bitter
oxidation of fats promotes
rancidity
decomposition of proteins promotes
putrefaction
- pathogenic bacteria typically
- you cannot tell if it will make you sick
contamination
consists of visible microbial growth, gross
spoilage
- amino acids, certain ions that increase osmolarity inside cell to prevent water loss
- help microbes survive high salt environments
compatible solutes
- adapted to salty (3.5%), low water environments
- ocean, skin surface
halophiles
more than 30% salt, use compatible solutes to survive
extreme halophiles
a measure of the number of solutes in a solution and is inversely related to water activity
osmolarity
more solute =
less water activity
more water activity =
less solute
- requires high pressure to grow, though they die at still higher temperatures
- pressure adapted internal structures, unsaturated membrane lipids
- greater than 380 atm
barophiles
organisms die as pressure increases
barosensitive
- organisms grow to a certain pressure, but die at higher pressure
- 10-500 atm
barotolerant
- cannot eliminate ROS
- die in presence of oxygen, cannot use or be near
- (-) SOD, - Catalase, - Peroxidase
ex: Clostridium
strict anaerobe
- 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
ex: Lactobacillus
aerotolerant aerobes
- can live without oxygen
- can use oxygen or not, grow best in oxygen but can grow anaerobically
- (+) SOD, + Catalase, + Peroxidase
ex: E. coli
facultative anaerobe
- grow only at low O2 concentrations
- use oxygen, grow best when there is 2-10% oxygen
- (+) SOD (low levels), + Catalase, - Peroxidase
ex: Streptococcus
microaerophiles
- can only grow oxygen is available, absolute requirement
- grow in atmospheric oxygen (20%)
- (+) SOD, + Catalase, + Peroxidase
Ex: Pseudomonas
obligate aerobes
the production of reactive oxygen species (ROS) often begins w/
FAD moving an electron to oxygen
generate ROS
- superoxide radical union
- hydrogen peroxide
- peroxide radical
enzymes reactions that destroy ROS
- superoxide dismutase (H2O2 into hydroxide radical)
- catalase (H2O2 into water and oxygen)
- peroxidase (H2O2 into water and NAD+)
- much more efficient for ATP synthesis
- uses oxygen as an FEA
aerobic respiration
use non-oxygen molecules as a final electron acceptor
anaerobic respiration and fermentation
out of which methods of respiration use ATP most efficiently (most to least)
aerobic > anaerobic > fermentation
- rely heavily on sodium ion gradients
- growth above pH 9
alkaliphiles
- respiratory chain pumps H+
- H+ import through F1F0 ATP synthase drives ATP synthesis
- Na+ driven ATPases export Na+
Na+ transport gradient
sodium ion motive force powers
- motility
- symport of some substrates
- pH homeostasis
- altered membrane lipids to prevent protons from leaking out of the cell
- reliance on Na+ gradients
alkaliphiles
- altered membrane lipids that decrease proton permeability
- contains ill-defined proton extrusion mechanisms
- thrive in lower pHs
- growth below pH 3
acidophiles
what is a con of having a high proton concentrated environment
protons can leak into the cell and damage enzymes
what is a con of having a low proton concentrated environment
really hard to build proton motive force
most enzymes function best between pHs of
5-8.5
- live in fridges
- optimum around 15 degrees Celsius (below 15 degrees C)
- more flexible proteins (glycines) and unsaturated membrane lipids
psychrophiles
- most like us
- pathogens, human microbiota
- have an optimum temperature of about 35 degrees Celsius (15-45 C)
mesophiles
- have an optimum temp of about 60 degrees Celsius (50-80 C)
thermophiles
- 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
help proteins fold
chaperone proteins
fewer glycines in the membrane =
more rigid proteins
an organism’s cardinal temperature is influenced mainly by
- enzyme function
- membrane integrity
growth between pH 5 and pH 8
neutralophile
species specific time for doubling a population (doubling time)
generation time
bacterial growth phases
- lag phase
- log phase
- stationary phase
- death phase
bacteria are preparing their cell machinery for their growth
lag phase
growth approximates an exponential curve (straight line, on a logarithmic scale)
log phase
- 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
- cells die with a half-life similar to that of radioactive decay, a negative exponential curve
- incredibly prolonged and unpredictable
death phase
- used to detect bacterial-induced lysis (hemolysis) of RBCs
- complex and differential
blood agar
gamma hemolysis
no hemolysis / clearing
- partial hemolysis
- partial clearing
- bacteria makes hydrogen peroxide that oxidizes hemoglobin
alpha hemolysis
- otherwise known as true hemolysis, complete clearing where bacteria was streaked
- bacteria secrete toxins that lyse RBCs and degrade hemoglobin
beta hemolysis
brilliant green dye inhibits growth of what bacteria
gram positive
organisms that ferment are what color on Brilliant Green agar
yellow
- distinguishes Gram-negative fermenters form non-fermenters
- complex, and selective and differential
Brilliant Green Agar
isolates microbes with specific properties by only allowing certain species to grow
selective media
- exploits differences between two species that grow equally well
- recognize certain microbes based on visual reactions in the medium
differential media
adds fresh nutrients and removes waste
continuous culture
- a closed system for adding specific bacterial in liquid media
- no nutrients replenished, no waste removed
batch culture
- important for studying a single bacterial species
- a culture in which only one strain or clone is present
pure culture
liquid growth media
broth
solid growth media
agar
considerations we need to have when deciding which type of growth media to use in the lab
- sterilization
- environmental conditions (i.e. incubation)
nutrient rich, poorly defined
complex media
- minimal nutrients, known composition
- useful when we are specifically studying microbial physiology
defined media
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)
acid fermentation of milk produces
yogurt and cheese
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)
fermented foods depend on
- indigenous flora
OR
- starter cultures
purposes of food fermentation
- preservation (by limiting microbial growth)
- improving digestibility
- adding nutrients and flavor molecules
every fermentation pathway has what happening
NADH being reoxidized into NAD+
- an organic molecules is FEA (pyruvate, acetaldehyde)
- no electron transport chain, allows oxidation of NAD+ thru generation of NADH
- catabolic
fermentation
- used typically in photoorganoheterotrophs
- a single-protein, light driven protein pump
bacteriorhodopsin
mechanism of action (in order) of bacteriorhodopsin
- Retinal, in the all trans form, is covalently attached to the lysine of bacteriorhodopsin; nitrogen to which it is attached is protonated
- light absorption causes one double bond to isomerize to the cis form
- isomerization of the retinal causes the proton to be lost to the outside
- when the retinal spontaneously isomerizes back to the ground state, the lysine is re-protonated from the cytoplasm
types of phototrophy
chlorophyll-based and rhodopsin-based
what types of phototrophs use chlorophyll-based phototrophy
photolithoautotrophs
ex: cyanobacteria, green sulfur bacteria, purple sulfur bacteria
capture energy from the sun to create PMF and synthesize ATP
phototrophs
- 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
use reduced inorganic compounds for energy and electrons
chemolithotrophs
more energy captured =
more ATP synthesized
aerobic ETCs pump how many protons across the membrane
10
anaerobic ETCs pump how many protons across the membrane
4
due to nitrate being reduced to nitrite
build a proton gradient that is used to make ATP
electron transport systems
why does anaerobic respiration yield less energy
because it uses an FEA with a lower reduction potential than O2
a redox reaction is favored by … values of dE, which yields negative values of dG
positive
ETC components are arranged in order of
increasing reduction potential
larger E =
better electron acceptor
holds e- more tightly, at a lower energy state
the amount of energy captured from an ETC depends on
the FEA used
what does a negative dG value mean
bond energy decreases and/or disorder increases, and the reaction will go forward spontaneously
a change in enthalpy (bond energy) is favorable if
negative
reaction forms molecules with more favorable/more stable/lower bond energy bonds than reactants
what happens when a change in entropy is positive
rxn increases disorder
which law of thermodynamics states that thermodynamically favorable processes increase disorder
2nd law
how do we make dG negative?
- change temperature
- increase concentration of reactants
- product concentration kept low by removal
couples metabolic species across species by removing product by another species
syntrophic relationship
heterotrophs catabolize carbohydrates through which three main metabolic strategies
- aerobic respiration
- anaerobic respiration
- fermentation
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
- 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
- shunts carbon from glucose into biosynthesis
- a source of carbon and electrons
PPP pathway of glycolysis
what is the net yield of the EMP pathway of glycolysis
- 2 three carbon pyruvate
- 2 ATP
- 2 NADH
what is the net yield of the ED pathway of glycolysis
- 2 three carbon pyruvate
- ATP
- NADH, NADPH
what is the net yield of the PPP pathway of glycolysis
- biosynthesis
- ATP
- 2 NADPH
if a final electron acceptor is available post-glycolysis, pyruvate is oxidized to
Acetyl CoA and enters the citric acid cycle
the bacterial glyoxylate shunt requires
two additional CAC enzymes
isocitrate lyase and malate synthase
benefits of using a glyoxylate shunt
- prevents loss of carbon via carbonn dioxide
- creates more starting material for biosynthesis
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
Identify the oxidant in the following coupled redox reaction: Malate + NAD+ –> Oxaloacetate + NADH + H+
NAD+
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)
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.
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
how is ATP primarily produced in chemolithotrophs
Electrons moving through an electron transport system to generate a proton motive force
which type of metabolism does not use a membrane-associated ETS
fermentation
lactic acid is a common fermentation product and is produced when … is reduced by electrons received from NADH
pyruvate
bacteria that express bacteriorhodopsin protein are typically classified as
photoorganoheterotrophs
a complex medium is one that
is nutrient rich, but the amounts and identity of specific nutrients are unknown
which ingredient makes Mannitol Salt Agar a selective medium
NaCl
which ingredients make Mannitol Salt Agar a differential media
mannitol and phenol red
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
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
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
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.
inactivates hydrogen peroxide
catalase
inactivates superoxide
superoxide dismutase
utilizes NADH to reduce peroxide
peroxidase
an organism living under high pressure
barophile
optimal growth at a pH below 5.5 describes
acidophile
optimal growth at a pH above 8 describes
alkaliphile
an organism able to grow over a wide range of solute concentrations is
halotolerant
an organism that requires high levels of salt
halophile
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
MAP helps to preserve food by
removing oxygen from the atmosphere
