Exam 2: Microbial Metabolism; Fermentation and Respiration; Bacterial Growth; Microbial Ecosystems; Nutrient Cycles; Antibiotics and Chemotherapy; (Bio 286 - Microbiology) Flashcards
all life requires
electron flow (to drive all life processes), energy (to move electrons), materials (to make cell parts)
electron flow
drives all life processes; drives ions into and out of cells; used to create ATP
materials to make cell parts
nutrients, which must be supplied from environment
macronutrients
major elements in cell macromolecules; INCLUDES C, O, H, N, P, S and Mg2+. Ca2+, Fe2+, and K+ (ions necessary for protein function)
micronutrients
trace elements necessary for enzyme function; INCLUDES Ni, Co, and other trace metals
complex media
ensures growth of a newly discovered bacterium with unknown nutritional requirements
heterotroph
microbes using organic carbon (contains at least 1 carbon-hydrogen bond)
autotroph
microbes using carbon dioxide (CO2) or inorganic carbon (contains no carbon-hydrogen bond)
typical bacterial cell is ____% carbon (by dry weight)
50
phototroph
light energy excites electrons; excited molecules are electron donors
chemotroph
chemicals are electron donors; chemical is oxidized
oxidation
donation of electrons; loss of electrons; loss of H
reduction
acceptance of electrons; gain of electrons; gain of H
lithotroph
inorganic molecules are electron donors
organotroph
organic molecules are electron donors
ultimate electron acceptor - inorganic molecules
respiration
ultimate electron acceptor - organic molecules
fermentation
different additional nutrients required by different microbes
amino acids; N from air (N2) or soil or other organisms; electron acceptors in aerobic vs anaerobic organisms; light vs organic energy source
passive diffusion
some gases freely pass through membranes (O2, CO2); follows gradient of material; does not require a protein carrier
facilitated diffusion
transporters pass material into and out of cell; follows gradient of material
passive diffusion - require energy
NO
passive diffusion - require carrier
NO
passive diffusion - accumulate inside
NO
facilitated diffusion - require energy
NO
facilitated diffusion - require carrier
YES
facilitated diffusion - accumulate inside
NO
(active transport) ABC transport - require energy
YES - ATP
(active transport) ABC transport - require carrier
YES
(active transport) ABC transport - accumulate inside
YES
(active transport) gradient (symport or antiport) - require energy
YES - Ions
(active transport) gradient (symport or antiport) - require carrier
YES
(active transport) gradient (symport or antiport) - accumulate inside
YES
(active transport) group translocation - require energy
YES - PEP
(active transport) group translocation - require carrier
YES
(active transport) group translocation - accumulate inside
NO
active transport
ABC transporters, Symport/Antiport, group translocation
ABC transporters
use ATP energy to pass material into cell; transport material against gradient
symport
gradient of molecules in same direction
antiport
gradient of molecules in opposite directions
symport and antiport
gradient of one molecule transports another– electron transport creates Proton-Motive Force, which transports the other molecule; transports material against its gradient
phosphotransferase system (PTS)
(group translocation) uses high energy phosphate to pass material into cell – modifies material as it enters cell, allowing gradient to be maintained and continue pushing material into cell (ex: glucose enters to be phosphorylated into glucose-6P)
catabolism
breaking down molecules for energy
anabolism
(biosynthesis) using energy to build cell components; reduces entropy to increase/create order
metabolism
balance between catabolism and anabolism; central biochemical pathways used for both TCA cycle, glycolysis, and pentose phosphate shunt
catabolism - substrates
BIG
catabolism - products
SMALL
catabolism - bonds
BROKEN
catabolism - redox
OXIDIZATION
catabolism - energy
RELEASE (exergonic, favorable)
anabolism - substrates
SMALL
anabolism - products
BIG
anabolism - bonds
FORMED
anabolism - redox
REDUCTION
anabolism - energy
USE (endergonic, unfavorable)
enzymes
biological catalysts critical for life; nearly always PROTEINS; have an ACTIVE SITE that interacts with substrates; COFACTORS: metals and vitamins
enzyme rate of activity
can be changed after enzyme production
ribozyme
catalytic RNA enzymes; include ribosomes
classification of enzymes
oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases
oxidoreductases
enzymes involved in oxidation and reduction
transferases
enzymes that attach atoms/groups
hydrolases
enzymes that split with addition of water to break down polymers
lyases
enzymes that split without addition of water to break down polymers
isomerases
enzymes that invert molecular configuration (change handedness, from D to L or L to D)
ligases
enzymes that join molecules using nucleoside triphosphate (ie ATP)
Gibbs Free Energy
ΔG = ΔH - TΔS (ΔH is change in ENTHALPY and ΔS is change in ENTROPY); ΔG must be negative for reaction to occur spontaneously; ΔG depends on concentrations, where having a low product concentration can drive reactions; useful for determining whether there will be a requirement or production of energy
activation energy
energy that is needed to get a reaction started
exergonic reaction
-ΔG; products have less energy than reactants
endergonic reaction
+ΔG; products have more energy than reactants
biochemical reaction energy
entropy is stronger at higher temperatures where breakdown of a large molecule into small ones (such as release of a gas) is favored to occur; diffusion spreads molecules out, which requires energy to contain them
gradient
stored energy; represent potential energy
enzymes reduce
activation energy
electron transfer
major source of cell energy; passage of electrons releases energy; requires electron donor and electron acceptor; electron transport found in all cells
during electron transport
-OH accumulates on the inside of a cell membrane and H+ accumulates on the outside of membrane
electron energy can be stored by/in
reduced chemicals, concentration gradient, and phosphorylation of chemicals
NAD(H)
NICOTINAMIDE ADENINE DINUCLEOTIDE; temporary acceptor/temporary electron holder – 2 electrons and 1 proton; limited amount in cell; NADP is used for anabolism and NAD is used for catabolism
non-protein electron carriers
FMNH2, quinones, FADH2
phosphorylation energy
LESS ENERGY THAN OXIDOREDUCTION; useful energy level for most cell reactions; no electron donor or acceptor needed; phosphate added via dehydration and released via hydrolysis; ATP IS MOST COMMON
ATP
ADENOSINE TRIPHOSPHATE; components: base (adenine), sugar (ribose), and phosphate (3); HIGH ENERGY PHOSPHATE BONDS
substrate level phosphorylation
ATP can by hydrolyzed to do work in cell, whereas some molecules can be used to form ATP directly
phosphoenolpyruvate (PEP)
able to be used for substrate level phosphorylation
lithotrophy
electron donors are inorganic molecules
organotrophy
electron donors are organic molecules
phototrophy
use light energy to reduce compounds then use those as electron donors
respiration
electron acceptors are inorganic molecules
fermentation
electron acceptors are organic molecules
three pathways of glucose metabolism
glycolysis, entner-doudoroff, and pentose phosphate shunt
glycogen
common energy storage polymer in microorganisms
key intermediates of glycolysis
glucose 6-phosphate, fructose 6-phosphate, triose phosphate, 3-phosphoglycerate, phosphenolpyruvate, pyruvate
key intermediates of krebs cycle (citric acid cycle)
acetyl CoA, α-ketoglutyrate, succinyl CoA, and oxaloacetate
key intermediates of pentose phosphate shunt
ribose 5-phosphate, erythrose 4-phosphate, sedheptulose 7-phosphate
glycolysis stage 1
“energy is spent in front end to get more later”:: Glucose + 1 ATP -> Glucose 6-phosphate -> fructose 6-phosphate + 1 ATP -> fructose 1,6-biphosphate… uses 2 ATP
glycolysis stage 2
“splitting into two molecules double the reactants”:: fructose 1,6-biphosphate -> PGAL + DHAP + 2 NAD -> 2 1,3-biphosphoglycerate
glycolysis stage 3
“break even point using substrate level phosphorylation”:: 2 1,3-biphosphoglycerate -> 3 PGA -> 2 PGA… yields 2 ATP
glycolysis stage 4
“pay off- net yield of 2 ATP by substrate level phosphorylation”:: 2 PGA -> phosphoenolpyruvate -> pyruvate… yields 2 ATP
entner-doudoroff stage 1
“energy is spent in front end to get more later”:: glucose + 1 ATP -> glucose 6-phosphate + NADP+ -> 6-phospho-gluconate -> 2-keto-3-deoxy-6-phosphogluconate… uses 1 ATP
entner-doudoroff stage 2
“splitting into two molecules gives one reactant”:: 2-keto-3-deoxy-6-phosphogluconate -> PGAL and Pyruvate + NAD+ -> 1,3 biphosphoglycerate
entner-doudoroff stage 3
“break even point using substrate level phosphorylation”:: 1,3 biphosphoglycerate -> 3 PGA -> 2 PGA… yields 1 ATP
entner-doudoroff stage 4
“payoff - net yield of ATP by substrate level phosphorylation”:: 2 PGA -> phosphoenolpyruvate -> pyruvate… yields 1 ATP
glycolysis
use glucose; 2 ATP used -> 4 ATP made -> 2 ATP NET; 2 NADH made, 2 pyruvates formed, 6 intermediates formed
entner duodoroff
use glucose; 1 ATP used -> 2 ATP made -> 1 ATP NET; 1 NADH and 1 NADPH made, 2 pyruvates formed, and 5 intermediates formed (DOES NOT MAKE FRUCTOSE 6-PHOSPHATE)
net gain of ATP per molecule fermented
2 ATP
pentose phosphate shunt
generates key intermediates; like entner-doudoroff pathway, it forms 6-phosphogluconate which is then converted to key intermediate RIBULOSE-5-PHOSPHATE which in turn produces a series of sugars (each containing 3-7 carbons); this pathway produces 1 ATP and no NADH, but 2 NADPHs for biosynthesis
pyruvate dehydrogenases
pyruvates + NAD+ + CoA -> acetyl-CoA + CO2 + NADH + H+ ; END PRODUCTS: acetyl-CoA + CO2 + NADH; multiprotein complex; 3 COFACTORS: TPP (oxidative decarboxylation - enzyme 1), LIPOAMIDE (acyl transformation - enzyme 2), FAD (flavin protein); CoA and NAD
TCA - Citric Acid - Krebs Cycle
produces 1 ATP, 3 NADH + H+, and 1 FADH2; can occur counterclockwise, clockwise, or in distinct parts depending on the bacteria; intermediate compounds used in biosynthetic pathways and carbon catabolism: α-ketoglutarate, oxaloacetate, succinyl-CoA
total oxidation of pyruvate
for each pyruvate oxidized: 3 CO2 are produced by decarboxylation, 4 NADH and 1 FADH2 are produced by redox reactions, and 1 ATP is produced by substrate level phosphorylation; OXIDATIVE PHOSPHORYLATION
aromatic catabolism
bacteria can degrade many compounds; aromatic compounds converted to pyruvate allows growth in wide range of environments and is used for BIOREMDIATION (cleaning up oil spills, industrial site and degrading toxic compounds)
regenerating NAD+
glycolysis = 2 NADH; Entner-Doudoroff = 1 NADH and 1 NADPH; Krebs cycle = 4 NADH and 1 FADH2; pentose phosphate also generate reduced NAD(P)H molecules… there is limited amount of NAD in cell, so it must be regenerated for reuse later
fermentation
organic molecules; performed by anaerobic microorganisms; PRIMARY PURPOSE: REGENERATE NAD FOR REUSE (electron acceptor is an organic molecule) and SECONDARY PURPOSE: GENERATE ADDITIONAL ENERGY (energy yields are very small) ; as a consequence, growth rates are slower
lactic acid fermentation
performed by lactobacteria; muscles/yogurt/sourdough bread use this
mixed acid fermentation
performed by E. coli; METABOLIC FLEXIBILITY; dumping electrons vs ATP generation
importance of fermentation for cell
electrons from metabolism are dumped; potential source of ATP for cell
importance of fermentation for humans
means of classifying bacteria; important source of solvents
reduction potential
electrons pass from good donors to good acceptors (ΔG < 0)… NADH + H+ is an excellent electron donor while 1/2 O2 is the strongest electron acceptor… E°’ = 1140 mV corresponding to ΔG°’ = -110 kJ, equivalent to as much energy as 3.6 ATPs… ATP + H2O -> ADP + PO4 (ΔG°’ = -30.5 kJ)… the concentration of the donor or acceptor affects actual ΔE (good acceptor - more electronegative, so oxygen is best acceptor)
redox potential energy
molecules differ in their affinity for electrons; moving down the redox energy list is favorable and releases energy
electron transport systems (ETS)
electron transport occurs on membranes – inner membrane of bacteria and archaea; inner membrane of mitochondria and chloroplasts… electron acceptor usually present outside cell; needed in large quantities for respiration; electron passage energy must be captured by cell cytoplasm
respiratory ETS
electrons form NADH -> O2 release energy (too much energy to capture in one step; requires intermediates; multiple steps)… common features in many ETS pathways (NADH OXIDASE, QUINONES, CYTOCHROMES)
glucose
best electron donor
oxygen
best electron acceptor
flavoproteins
common proteins; flavin cofactor; FAD or FMN; carry two proteins and carry two electrons
quinones
isoprenoid lipids dissolved in membrane (the same lipids in archaea membranes); variant structures are known; UQ, MQ, PG; carry protons and electrons
iron sulfur protein
cellular proteins; contain non-heme iron; acid labile; iron coordinated by Cys; electron carrier only – only accept electrons (not protons)
cytochromes
have heme groups; ELECTRON CARRIERS ONLY (only accept electrons); Heme A, Heme B, Heme C, Heme D (in oxidase), Heme O (in oxidase)
mitochondrial respiratory ETS
use favorable movement of electrons in creating a proton gradient; has 4 complexes
4 complexes of mitochondrial respiratory ETS
I. electrons from NADH to coenzyme Q … II. electrons from FADH2 to coenzyme Q… III. coenzyme Q to cytochrome C… IV. cytochrome C to O2
Complex II of Mitochondrial respiratory ETS
not needed to move electrons from NADH to oxygen in mitochondria
E. Coli respiratory ETS
branched electron pathway; different ETS for different concentrations of oxygen; different NADH dehydrogenases (NDH1 -> pumps 4H+/2e- and NDH2 -> pumps 0) and different terminal oxidases (cytochrome bo -> pumps 1H+/e- and cytochrome bd -> 0)… E. Coli can alter its pumping by choosing which branch it uses, so anywhere between 2 to 8 protons can be pumped out from oxidation of one NADH
maximum pumped H+ in E. Coli Respiratory ETS
NDH1 + cytochrome bo
minimal pumped H+ in E. Coli Respiratory ETS
NDH2 + cytochrome bd
proton motive force (PMF)
electrochemical gradient; driven by differences in charge (of ions) and in pH; PMF = Δψ - 60ΔpH [electrical (Δψ) plus chemical (ΔpH) gradient]
NADH ->
10 H+ -> 3 ATP
FADH2 ->
6 H+ -> 2 ATP
PMF is used directly for cell activities
CREATES ATP (ATP synthase at cell membrane); DRIVES FLAGELLAR ROTATION (motors at base of flagella); PUSHES IONS INTO AND OUT OF CELL USING SYMPORT/ANTIPORT
symport
same direction as proton movement
antiport
opposite direction of proton movement
proton potential creates ATP
the F1F0ATP synthase makes ATP: protons enter F0 subunit and cause it to rotate -> F0 ROTATION DRIVES THE F1 SUBUNIT SHAFT WHICH SYNTHESIZES ATP FROM ADP + Pi
3 H+ ->
1 ATP
3 protons (H+) move through ATPase
to produce 1 ATP
anaerobic respiration
occurs in environments lacking oxygen such as gut, deep soil, and deep ocean; other terminal electrons acceptors are used such as nitrogen, sulfur, and metals
nitrate
NO3-; most oxidized form of nitrogen
anaerobic respiration begins with the most oxidized reactant
so reduction can occur
lithotrophy
many materials donate electrons (get oxidized) if a better electron acceptor is present
methanogenesis
PERFORMED BY EURYARCHAEOTA; hydrogen donates electrons and CO2 accepts electrons; high CO2 concentrations drive reaction; CO2 + 4H2 -> CH4 + 2H2O; important anaerobic reaction
phototrophy - bacteriorhodopsin
absorbs light (membrane protein, purple color); absorbs light -> excites electrons -> electron returns to ground state -> releases energy -> generates proton gradient
phototrophy - chlorophyll
absorbs light (different chlorophylls absorb wavelengths – determines where organism can grow: purple bacteria, green bacteria, cyanobacteria, chloroplasts of plants); complexes collect light energy– carotenoids in purple bacteria and antenna complex LH-11 in cyanobacteria and plants
purple bacteria reactions
ADP + Pi -> ATP in presence of light; free source of Δp; able to make tons of ATP; still need to generate NADH; bacteriochlorophyll is not good enough donor to accomplish this so the bacteria must use reverse electron transport
purple bacteria light harvesting
found in cell membrane; bacteriochlorophyll-protein-carotenoid complex; antennae complex closely associated with reaction center; cell membrane highly invaginated to increase surface area; reverse electron transport makes NADH
green sulfur electron transport
reduce Fe/S centers instead of quinones; do anoxygenic photosynthesis like PSI in plants
green sulfur reactions
no reverse electron transport; use inorganic sulfur; generate ATP and NADH; H2S + NAD + QADP + Pi -> S + NADH + H + ATP
green (sulfur) bacteria light harvesting
bacteriochlorophyll; protein and carotenoid; localized in CHLOROSOMES which perform photosynthesis; better donors and only accept electrons; can make NADH and more power (does not need to use reverse electron transport); uses sulfur instead of oxygen
oxygenic photosynthesis
plant-like photosynthetic apparatus or plants are bacteria like; performed by cyanobacteria (formerly blue green algae, thousands of species, lots of variety); extremely important to life on earth
cyanobacteria
perform oxygenic photosynthesis; stole “ideas” from green and purple bacteria; have thylakoids; uses H2O instead of sulfur
cyanobacteria and algae
found in chloroplast or bacterial membrane; two photosystems (purple and green); non-cyclic electron flow; water is oxidized to O2
generation time
time interval required for formation of two cells from one
microbial contamination
prevented by use of aseptic technique
microscopy
(method to enumerate cells) requires specialized staining to observe non-pigmented bacteria
water activity
ratio of vapor pressure of air in equilibrium with a substance to vapor pressure of pure water
binary fission
process bacteria use to grow/divide; asexual reproduction
binary fission process
elongation -> DNA replication -> FtsZ ring forms -> cytokinesis -> cell wall synthesis
prior to DNA replication
both strands of chromosome are methylated on A residue of sequence GATC
FtsZ ring
most active in divisome complexes
Petroff Hauser chamber
counts cells directly; gives an accurate number – but cannot tell if cells are alive or dead (so a stain must be used to distinguish living cells)
viable counts
counts only cells able to reproduce (form colonies); requires time to form the colonies
spectrophotometer
measure optical density – but cannot tell if cells are alive or dead; solution must be between 10^7 - 10^10 cells/mL
growth cycle
lag phase -> log phase -> stationary phase -> death phase
lag phase
“flat” period of adjustment, enlargement; little growth in bacterial population
log phase
The period of exponential growth of bacterial population.
stationary phase
period of equilibrium; microbial deaths balance production of new cells
death phase
population is decreasing at a logarithmic rate but never reaches zero… optical density and viable cell concentration are least proportional to each other
growth kinetics
X = 2^Y x X0
generation time
time for one doubling to take place; doubling time; g = t/Y or Y = t/g
continuous culture
CHEMOSTAT; Dilution rate F/V; bacteria at steady rate while flow controls growth rate and nutrient conditions control culture density
chemostat
cell density is controlled by concentration of limiting nutrient; keeps bacteria in late log phase/state
biofilms
cells secrete material to hold to a surface; cells act together in a mixed community of bacteria stuck to the surface; cells signal to each other using quorum sensing; protects against dispersion and prevents antibiotics from infiltrating
endospores
protect against bad conditions, disseminates cells, forms inside (“ENDO”) mother cell
cells obtain energy from cannibalizing slow responding cells
to ensure spore formation in harsh nutrient poor environment
endospore structure
exosporum (most outer part); coat; CORTEX (for strength, consists of peptidoglycan); core (most inner part, consists of dipicolnic acid)
endospore formation
Stage 0/1: vegetative cell cycle… polar division… Stage 2: asymmetric cell division… Stage 3: engulfment of prespore… Stage 4: cortex… Stage 5: spore coat… Stage 6/7: maturation/cell lysis… germination of spore back to stage 0/1
first stage of committed endospore formation
stage II
bacterial live birth
related to endospore formation, except it is a live birth of the engulfed offspring
heterocysts
specialized cells that undergo nitrogen fixation; oxygenic photosynthesis in nitrogen cycle
myxospores
form inside fruiting body; multicellular structure
actinomycetes
food runs out -> produce aerial hyphae, which protect against bad conditions -> disseminates (spreads) cells
Caulobacter life cycle
SWARMER CELL - motile, but no division; STALKED CELL - non-motile, but able to undergo cell division (reproduce)
optimal growth temperature of bacteria
is most related to optimal temperature for enzyme function
psychrophile
bacteria that prefer cold, thriving at temperatures between 0 C and 25 C.
mesophile
bacteria that prefers moderate temperature and develops best at temperatures between 25 C and 40 C
thermophile
bacteria that thrive best at high temperatures, between 40 C and 70 C
hyperthermophile
bacteria that grow at very high temperatures between 70°C and 110°C
effect of temperature on growth
increased temperature increases bacterial growth rate and decreased temperature decreases bacterial growth rate… but too hot will cause enzymes to denature and too cold will cause decreases in membrane fluidity and enzymatic activity
acidophiles
bacteria that grow in acidic pH < 7
neutrophiles
bacteria that grow at or near neutral pH = 7
alkaliphiles
bacteria that grow at alkaline pH > 7
adapting to pH variations
in strongly acidic environment, amino acid decarboxylases drain protons form cell… in slightly acidic conditions, cells use K+/H+ antiport system to remove internal protons… under alkaline stress, Na+/H+ antiport systems scavenge protons from environment
cytoplasm pH
is always 7
isotonic
water concentration is equal inside and outside of the cell
hypotonic
net diffusion of water into cell
hypertonic
net diffusion of water out of the cell
high osmotic pressure
will kill bacteria
aerobes
Bacteria that require oxygen to grow
microaerophiles
require oxygen concentration lower than air
anaerobes
Bacteria that grow in the absence of oxygen and are destroyed by oxygen
facultative anaerobes
can live with or without oxygen, but prefers oxygen
aerotolerant
do not utilize oxygen but can survive and grow in its presence
barophiles
organisms that live under extreme pressure
xerophiles
organisms able to grow in very dry environments (low humidity)
nonhalophile
A microorganism that cannot grow in the presence of added sodium chloride
halotolerant
can survive at higher salt concentrations but grow best at low or zero concentrations
halophile
an organism that can grow in, or favors environments that have very high salt concentrations; needs added salt in order to survive
extreme halophile
Organism adapted to life in a highly salty environment
sterilization
kills all vegetative cells and spores
disinfection
reduces number of pathogens on inanimate surface
decontamination
makes contaminated surfaces safe to handle by reducing number of microbes present (sanitation)
antisepsis
killing microbes on living tissue/surface
antibiotic
antimicrobial compound made by one living organism that affects other organisms
bacteriostatic
inhibits bacterial growth but does not kill cells
bactericidal
kills cells (but retains cell “bodies”)
bacteriolytic
kills cells and lyses cell bodies
microbial death rate
decimal reduction time – D-VALUE: time required to kill 90% of cells… affected by temperature, type of microorganism, physiological state, and other substances
thermal death point
lowest possible temperature that will achieve complete killing within ten minutes
thermal death time
minimum time to achieve complete killing in a liquid solution at a given temperature
physical - dry heat
INCINERATION (flaming loops) and baking (at 160 degrees C for 2 hours or 171 degrees C for 1 hour)… advantages: cheap and easy / disadvantage: materials must withstand high temperatures and be dry (not aqueous)
physical - moist heat
boiling (but will not kill endospores), tyndallization (discontinuous boiling), PASTUERIZATION (high heat for a short time), AUTOCLAVING (very high heat)… advantages: cheap and easy / disadvantages: materials must withstand high temperatures
pastuerization
first devised by Louis Pasteur; commonly used with juice/beer/milk/dairy products; BATCH - 63 C for 30 minutes, HTST - 72 C for 15-20 seconds, or UHT - 121 C for <3 seconds
autoclaving
commonly used in laboratory; temperatures higher than boiling, using steam pressure at 121 C for 20 minutes; kills all endospores
physical - cold
FREEZING (ki1lls some cells due to ice crystals formations, but does not kill most bacteria); refrigeration (preservation)… advantages: many products tolerate cold better / disadvantages: very little killing and is expensive
physical - filtration
pass liquid or gas through a FILTER with sufficiently small pore size (smaller than 1 micrometer); HEPA - filter out >0.3 micrometer particles… advantages: no thermal damage / disadvantages: viruses not eliminated and must be either liquid or gas
physical - radiation
ULTRAVIOLET (damages DNA with poor pentration), GAMMA RAYS (very good penetration), XRAYS (less penetration)… advantages: very effective with little product damage / disadvantages: dangerous materials need shielding and lack of public trust
chemical treatments
chemotherapeutics for disease treatment or disinfectants for cleaning surfaces; choice is based upon nature of object, kinds of microbes targeted, and desired effect
chemical - phenolics
denature proteins and disrupt membranes; used by Joseph Lister; examples: PHENOL (carbolic acid), lysol, CHLOROHEXIDINE; effective on surfaces but may be too toxic to apply to tissue
chemicals - alcohols
denature proteins and disrupt membranes; examples: ETHANOL, ISOPROPANOL; most effective at 50-70%; increased plasmolysis after damage; commonly used for antisepsis!
chemical - oxidants
damage proteins and lipids; halogens: CHLORINE (disinfectant), IODINE (antiseptic); HYDROGEN PEROXIDE (H2O2): 3% is a weak antiseptic, with the body and many bacteria breaking this down enzymatically
oligodynamic effect
inhibition by heavy metals: silver, copper, mercury, gold; produce zone of inhibition
chemical - surfactants
amphiphilic compounds; disrupt membranes; quaternary ammonium compounds with charged nitrogen and four hydrophobic groups; examples: CEPACOL, ROCCAL
chemical - alkylators
damage proteins or DNA by adding carbon adducts; examples: FORMALIN, glutaraldehyde, ETHYLENE OXIDE (used to sterilize products via gas); highly noxious
fluorescence microscopy
allows visualization of cytoskeletal proteins and nuclear proteins
opportunistic pathogen
causes disease only in the absence of normal host resistance; example: Pseudomonas aeruginosa
DnaA functions in Caulobacter
initiation of DNA replication, transcriptional regulation
ecosystem
sum of the total of all organisms and abiotic factors in a particular environment
habitat
portion of an ecosystem where a community could reside
species richness
total number of different species present
species abundance
proportion of each species in an ecosystem
guilds
metabolically related microbial populations
niche
habitat shared by a guild; supplies nutrients as well as conditions for growth
communities
sets of guilds that interact with macroorganisms and abiotic factors in ecosystem
allochtonous
chemical that comes from outside the ecosystem
population
all individuals of one species in the same area
community 1
photic zone: oxygenic phototrophs
community 2
oxic zone: aerobes and facultative aerobes
community 3
anoxic sediments: GUILD 1 (denitrifying bacteria and ferric iron-reducing bacteria), GUILD 2 (sulfate reducing bacteria and sulfur reducing bacteria), GUILD 3 (fermentative bacteria), and GUILD 4 (methanogens and acetogens)
bigeochemistry
study of biologically mediated chemical transformations; defines transformations of a key element by biological or chemical agents (which typically proceed by OXIDATION-REDUCTION reactions)
environments and microenvironments
physiochemical conditions in a microenvironment are subject to RAPID CHANGE (spatially and temporally)… resources in natural environments are highly variable and many microbes in nature face a FEAST OR FAMINE existence… growth rates of microbes in nature are lower than the maximums defined in laboratory… COMPETITION and COOPERATION occur between microbes in natural systems (syntropy - metabolic cooperation)
biofilm
mixed community of microbes living on a surface… assemblages of bacterial cells adhered to a surface and enclosed in an ADHESIVE MATRIX excreted by cells and is made of a mixture of polysaccharides… these trap nutrients for microbial growth and help prevent detachment of cells in flowing systems
quorum sensing
intracellular communication that is critical in development and maintenance of a biofilm; the major intracellular signaling molecules are ACYLATED HOMOSERINE LACTONES… both INTRASPECIES SIGNALING and INTERSPECIES SIGNALING used in biofilms… used by pseudomonas aeroginosa
reasons for biofilm formation
SELF DEFENSE (resist physical forces that sweep away unattached cells, phagocytosis by immune cells, and penetration of toxins); allow cells to remain in a FAVORABLE NICHE; allows cells to live in CLOSE ASSOCIATION with one another
soils
loose outer material of earth’s surface; consists of four layers: O, A, B, C horizons
O horizon
at the surface, with undecomposed plant material
A horizon
with most microbial growth, rich in organic material and nutrients
B horizon
subsoil where organic material leached from A horizon gathers, little microbial activity
C horizon
base that is directly above bedrock and forms from bedrock
soils are composed of
INORGANIC MINERAL MATTER (~40% of soil volume); ORGANIC MATTER (~5%); AIR AND WATER (~50%); and LIVING ORGANISMS (~5%)
soils are formed by interdependent physical, chemical, and biological processes
carbon dioxide is formed by respiring organisms that form CARBONIC ACID that breaks down rock…. physical processes such as FREEZING and THAWING break apart rocks, allowing plant roots to penetrate and form an expanded RHIZOSPHERE
rhizosphere
area around plant roots where plants secrete sugars and other compounds, is rich in organic matter and microbial life
terrestrial subsurface
deep soil subsurface can extend for SEVERAL HUNDRED METERS below soil surface… archaea and bacteria are believed to exist in deep subsurface in variable concentrations depending on nutrient availability… subsurface microbial life grows in an extremely nutrient-limited environment so small cells are common… deep subsurface is home to a group of organisms that may be the archaea that are most closely related to eukaryotes: LOKIARCHEOTA
freshwater
highly variable in resources and conditions available for microbial growth; balance between photosynthesis and respiration controls the OXYGEN and CARBON cycles
phytoplankton
oxygenic phototrophs suspended freely in water, including algae and cyanobacteria
benthic species
attached to bottom or sides of a lake or stream
stratified lakes
epilimnion, thermocline, hypolimnion… these layers vary greatly in temperature, oxygen availability, and chemical composition
epilimnion
warmer, less dense surface water
hypolimnion
cooler, denser water at bottom of lake or pond
thermocline
separates the epilimnion and hypolimnion
rivers
may be well mixed because of rapid water flow; can still suffer from oxygen deficiencies because of high inputs of organic matter from sewage and agricultural/industrial pollution
biochemical oxygen demand (BOD)
microbial oxygen-consuming capacity of a body of water; increases with influx of organic material (ex: from sewage) then decreases over time
marine environment
open ocean environment is SALINE, LOW IN NUTRIENTS (especially with respect to nitrogen, iron, and phosphorous), and COOLER… microbial activities taking place in them are major factors in earth’s carbon balance due to the size of oceans
oxygen minimum zones (OMZs)
regions of oxygen depleted waters at intermediate depths; high oxygen demand, nutrient rich areas – high levels of denitrification and anammox
Prochlorococcus (major marine phototroph)
accounts for >40% of BIOMASS of marine phototrophs, ~50% of NET PRIMARY PRODUCTION
open ocean
has a pelagic zone
pelagibacter
most abundant marine heterotroph; contain PROTEORHODOPSIN (form of rhodopsin that allows cells to use light energy to drive ATP synthesis)
oligotroph
an organism that grows best at very low nutrient concentrations
must abundant microorganisms in oceans
viruses
> 75% of all ocean water is
deep sea
organisms that inhabit the deep sea must deal with
LOW TEMPERATURE, HIGH PRESSURE, LOW NUTRIENT LEVELS
deep sea microbes are
PIEZOPHILIC (pressure loving) or piezotolerant; often PSYCHROPHILIC or psychrotolerant (but can also be thermophilic or thermotolerant)
piezotolerant
tolerate elevated pressure but grow best at low atm
piezophile
lives optimally at high pressure
extreme piezophile
an organism requiring extremely high pressure for growth
hydrothermal vents
CHEMOLITHOTROPHIC bacteria predominate at the vent because they can utilize the inorganic materials; THERMOPHILES and HYPERTHERMOPHILES are also present
carbon
cycled through all of Earth’s major carbon reservoirs, including atmosphere, land, oceans, sediments, rocks, and biomass…. life on earth is carbon based
all nutrient cycles are linked to the
CARBON CYCLE
largest carbon reservoir
SEDIMENTS (and rocks) in Earth’s crust – about 99.5% of carbon, but not biologically available
most rapidly transferred carbon reservoir
CO2 in atmosphere
CO2 transfers
removed from atmosphere by PHOTOSYNTHETIC land plants and marine microbes (so a large amount of carbon is found there)… found in HUMUS (DEAD ORGANAIC MATERIAL) than is found in living organisms… CO2 is returned to atmosphere by RESPIRATION and DECOMPOSITION (and by human-related activities)
photosynthesis
reduces inorganic carbon dioxide to organic carbohydrates; CO2 + H2O -> (CH2O) + O2
respiration
oxidizes organic carbohydrates to inorganic carbon dioxide; (CH2O) + O2 -> CO2 + H2O
two major end products of decomposition
methane (CH4) and carbon dioxide (CO2)
methane hydrates
form when high levels of methane are under high pressure and low temperature; fuel deep-sea ecosystems called COLD SEEPS
methanogenesis
central to carbon cycling in anoxic environments: most methanogens use CO2 as a terminal electron acceptor, reducing CO2 to CH4 with H2 as an electron donor while some can reduce other substrates to form CH4
syntrophy
where different microbial taxa (ex: methanogens and other partners) work in cooperation to degrade a compound that neither can perform entirely on their own
nitrogen cycle
four major nitrogen transformations: NITRIFICATION, DENITRIFICATION, ANAMMOX, and NITROGEN FIXATION
nitrogen
key constituent of cells; exists in a NUMBER OF OXIDATION STATES (has the largest number of potential oxidation states of the major biological elements)
N2
most stable form of nitrogen and is a major reservoir (about 70% of earth’s air)… used by prokaryotes that can convert inorganic N2 to organic nitrogen through nitrogen fixation… produced biologically by denitrification (reduction of nitrate to gaseous N2)
nitrogen fixation (or ammonification)
N2 -> NH3… only performed by bacteria
anammox
anaerobic respiration of ammonia to N2 gas
denitrification and anammox
result in losses of organic nitrogen from biosphere
nitrogen fixation
synthesis of amino groups; fully reduced nitrogen is yielded (necessary for amino acid synthesis because fixed nitrogen is often a limiting factor for cell growth)
Haber process
makes an industrially fixed nitrogen (ammonia) fertilizer, but is dependent on natural gas… but the oxidized fertilizer runoff contaminates waterways
nitrogenase
required enzyme used to make atmospheric nitrogen bioavailable through the process of nitrogen fixation [but must stay ANAEROBIC – O2 acts as a competitive inhibitor to be reduced to H2O]
four rounds of reduction per N2
- electron donor (NADH) donates electrons… 2. ATP energy used to bind substrate (in the first round– H+ is bound)… 3. electrons reduce substrate… 4. repeats steps 1-3 three more times for a total of four rounds (4 ATPS, 4 NADH equivalents used)
nitrogen fixation limitations
energy intensive process (40 ATPS CONSUMED for each N2 fixed to make NH3 – very costly for the cell)… enzyme production strictly regulated (only made when O2 and NH4+ levels are low)… aerobic organisms make special cells to fix N2 (aerobic cells make glucose, anaerobic HETEROCYSTS make NH3)
nitrogen
limiting factor in environment
rhizobium
A symbiotic bacterium that lives in the nodules on roots of specific legumes and that incorporates nitrogen gas from the air into a form of nitrogen the plant requires (NH3)
nitrogen assimilation
incorporation of NH4+ into amino acids: α-ketoglutarate + NH4+ -> glutamine [with α-ketoglutarate being a TCA intermediate]
transamination
glutamine donates NH3 to make other amino acids:
pyruvate + glutamine -> alanine + α-ketoglutarate…
oxalacetate + glutamine -> aspartate + α-ketoglutarate
nitrification
NH4+ -> NO2- -> NO3-; oxidation of NH4+ provides electrons/energy
nitrosomas
species oxidizes NH4+ to NO2-
nitrobacter
species oxidizes NO2- to NO3-
eutrophication
pollution of water through excess nitrogen (nitrate), often from excessive fertilizer use causing nitrate runoff
denitrification
NO3 - -> NO2- -> NO -> N2O -> N2; DISSIMILATORY NITRATE REDUCTION (nitrate is anaerobic electron acceptor)… NO3- is reduced
sulfur
the bulk occurs in sediments and rocks as SULFATE or SULFIDE minerals (gypsum, pyrite), with OCEANS representing the most significant reservoir of sulfur (as sulfate) ion biosphere
hydrogen sulfide
major volatile sulfur gas that is produced by bacteria via sulfate reduction or emitted from geochemical sources
sulfide
toxic to many plants and animals and reacts with numerous metals
sulfur dioxide
produced by burning of fossil fuels
dimethyl sulfide (DMS)
MOST ABUNDANT ORGANIC SULFUR COMPOUND IN NATURE; produced primarily in marine environments as a degradation product of dimethylsufoniopropionate (an algal osmolyte; can be transformed via a number of microbial processes
iron and manganese cycle
iron and manganese cycle between oxidized and reduced states with each other in aquatic ecosystems… FERROUS (Fe2+) and Mn2+ are the more soluble and more accessible forms, while FERRIC (Fe3+) and Mn4+ is less soluble and precipitates
phosphorous cycle
organic and inorganic phosphates (PO4 2-); PHOSPHOROUS IS A TYPICAL LIMITING NUTRIENT that limits the growth of aquatic photosynthetic autotrophs; alternate forms such as phosphite and hypophosphate rapidly cycle through aquatic ecosystems
calcium cycle
RESERVOIRS ARE ROCKS AND OCEANS; marine phototrophic microorganisms such as foraminifera use Ca2+ to form exoskeleton
silica cycles
marine silica cycle is controlled by unicellular eukaryotes (DIATOMS, SILICOFLAGELLATES, RADIOLARIANS) that build cell skeletons (shells) called FRUSTULES
phosphorous cycle, calcium cycle, and silica cycle vary from the other nutrient cycles
because there is no gaseous phases
bacteriostatic
inhibit cell growth
bactericidal
kill viable cells
minimum inhibitory concentration (MIC)
the smallest concentration (highest dilution) of drug that VISIBLY inhibits growth
minimum bactericidal concentration (MBC)
The lowest concentration of an antibiotic that truly kills all cells
disk diffusion assays
kirby-bauer; standardized conditions…. zones of inhibition, where a larger zone indicates more susceptible and a smaller zone indicates more resistant
E-test strips
drug gradient used and can determine the MIC
tube dilution assay
the drug is diluted in a series, then inoculated and incubated– where growth stops is the MIC… transfer some of the media after and including the point at which visible growth is stopped to new drug-free media tubes – where growth is no longer visible is the MBC
membrane-active drugs
detergents; bind to phospholipid and lipid A to disrupt membranes… include POLYMYXIN and GIAMICIDIN
DNA replication
few clinical drugs affect polymerization; conserved mechanisms can lead to toxicity; DNA gyrase inhibitous… ex: NALADIXIC ACID, NOVOBIOCIN, and FLUOROQUINOLONES
naladixic acid
A subunit – blocks nicking of DNA strands
novobiocin
B subunit – blocks ATP hydrolysis
transcription of DNA
actinomycin D - intercalating agent with no specificity (toxic) and is used a lab reagent … RIFAMPIN – binds to RNA polymerase, specific for bacteria, prevents elongation of transcript after initiation, and is a useful drug against Mycobacterium tuberculosis
aminoglycosides
BINDS 30S and distorts the ribosome, causing translation errors; examples: STREPTOMYCIN, NEOMYCIN, OXAZOLIDIHONES (prevent formation of 70S ribosome initiation complex)
tetracycline
BLOCKS A SITE; prevents tRNA entry, but is a reversible reaction… bacteriostatic
chloramphenicol
BINDS 50S to prevent peptidyl transfer reaction
erythromycin
BINDS 50S SUBUNIT NEAR P SITE to prevent translocation; Macrolides… Lincosumides
translation of DNA
aminoglycosides; tetracycline; chloramphenicol; erythromycin
metabolic - Sulfa drugs
block THFA formation; TETRAHYDROFOLATE is an important carbon and hydrogen carrier; SULFANILAMIDE; TRIMETHOPRIM
other metabolic inhibitors
ISONIAZID (mycolic acid formation inhibited – main anti-tuberculosis drug); FOSPHOMYCIN (PEP Analog)
peptidoglycan inhibitors
compound found only in bacteria so it serves as a good target for drugs; steps that are blocked: FOSFOMYCIN, CYCLOSERINE, VANCOMYCIN, BACITRACIN, PENICILLIN (blocks cross linking)
D-cycloserine
D-ALANINE ANALOG; blocks pentapeptide formation and blocks cell wall formation; cannot assemble peptidoglycan monomer so cells become fragile and lyse – bacteriolytic antibiotic
lipid carrier inhibitors
VANCOMYCIN (prevents release from lipid carrier) and BACITRACIN (blocks regeneration of carrier after release) – both are very toxic to humans and are not commonly used internally as a result
Beta-Lactam Antibiotics - prevent crossing linking
“cillin” ending drugs: PENICILLIN (PENAM); CEPHEM; OXACEPHEM; CARBAPENAM; CLAVAM; MONOBACTAM… all have a “beta-lactam” characteristic ring
peptidoglycan biosynthesis
structural analog to D-Ala; BLOCKS CROSS LINKING, CELLS POP – influenced by penicillin
anti-fungal drugs
having selective toxicity: NYSTATIN, IMIDAZOLES, AMPHOTERICIN B; other: FLUCYTOSINE, GRISEOFULVON
nystatin
targets fungal membrane
imidazoles
inhibit sterol synthesis (of ergosterol of fungi)
amphotericin B
disrupts cell membrane of fungi
flucytosine
synthetic pyrimidine analog
griseofulvon
effective against ringworms/fungi by preventing cell division
anti viral drugs
AMANTADINE (influenza A virus); ACYCLOVIR (herpes viruses – nucleoside analog); RIBAVIRIN (blocks RNA synthesis)
few antivirals
due to toxicity problems – viruses use host cell components so they are difficult to target without also targeting host cells
anti HIV agents
reverse transcriptase inhibitors – AZT (blocks reverse transcriptase), delavirdine, nevirapine… protease inhibitor – INDINAVIR (prevents proper protein development within viral life cycle), nelfinavir, ritonavir
preventing drug resistance
LIMIT DRUG USE (to decrease selective pressure); PROPER DRUG USE (to ensure elimination of pathogens upon taking complete dose); MULTIPLE DRUG TREATMENTS SO DRUGS CAN WORK SYNGERGISTICALLY (antibiotics can work together more effectively)
selective toxicity of antibiotics
antibiotics must affect target organism but not the host (humans), so they should have minimal toxic side effects to host and target the microbial pathway that which is not present in the host– target peptidoglycan (bacterial cell wall component), 70S ribosomes (bacterial ribosomes vs 80S of eukaryotes), and biochemical pathways missing in humans
broad spectrum
antibiotic is effective against many species
narrow spectrum
antibiotic is effective against few or a single species
source of antibiotics
most discovered as natural products then modified by artificial means to increase efficacy and decrease toxicity to humans
microbial antibiotic biosynthesis
antibiotics are SECONDARY METABOLITES… bacteria SECRETE ANTIBIOTICS but also MAKE ENZYMES TO DISABLE ANTIBIOTICS so that the drugs cannot kill the cells that make them
antibiotic resistance
antibiotics are overused (overprescribed and used in farm animal feed), leading to exerted selective pressure for drug resistant strains
HIV Drug Resistance
reverse transcriptase has a high error rate, and infrequently one of those errors produces a drug-resistant variant that is selected for by drug regimen
antibiotic resistance mechanisms
- MODIFY TARGET SO THAT IT NO LONGER BINDS ANTIBIOTIC (mutations in ribosomal proteins confer resistance to streptomycin)… 2. DESTROY ANTIBIOTIC BEFORE IT GETS TO CELL (beta-lactamase enzyme specifically destroys penicillins)… 3. ADD MODIFYING GROUPS THAT INACTIVATE ANTIBIOTIC (three classes of enzymes are used to modify/inactivate aminoglycoside antibiotics)… 4. PUMP ANTIBIOTIC OUT OF CELL (specific and nonspecific transport proteins)
how drug resistance develops
de novo antibiotic resistance develops through gene duplication and/or mutations… can also be acquired via HORIZONTAL GENE TRANSFER (conjugation, transduction, transformation)… recently, has also been attributed to presence of integrons
future of drug discovery
EVOLUTIONARY PRESSURE IS CONSTANT (so there is a required constant search for new antibiotics)… modern drug discovery: use genomics to identify new targets, design compounds to inhibit targets, alter compound structure to optimize MIC, determine spectrum of compound, and determine pharmaceutical properties
eutrophication implications
increased input of nutrients –> increased concentration of microbes –> decreased levels of oxygen
proteobacteria are the most predominant in
aquatic environments
Pyrite
compounds made with iron and sulfur (FeS2)
microbial leaching
removal of valuable metals (such as copper) from sulfide ores by microbial activities ((first reaction: oxidation of reduced sulfides to sulfate and release of reduced iron))… but can lead to environmental damage due to acidic conditions of nearby areas like rivers
Leptospirillum ferroxidans
used in oxidation ponds for leaching copper in mines
U6+
water soluble uranium
U4+
not water soluble uranium
xenobiotic
synthetic chemicals that are not naturally occurring, manmade compounds not found in nature; can be broken down by COMETABOLISM (microbes will break this down alongside other organic molecules – which serve as their primary source of energy)
reductive dechlorination
breaks down manmade chemicals (xenobiotics) in absence of oxygen; important process because anoxic conditions develop quickly in polluted environments
biodegradable polymer
polyhydroxybuterate (PHB) – made by bacteria
wastewater
DOMESTIC SEWAGE OR LIQUID INDUSTRIAL WASTE… “grey water” is water resulting from washing/bathing/cooking and sewage is water contaminated with fecal material
(treated wastewater) effluent water is suitable for
release into surface waters, release to drinking water purification facilities
wastewater treatment
primary, secondary, tertiary
primary wastewater treatment
REMOVAL OF SOLIDS– uses physical separation methods to separate solid and particulate organic and inorganic materials from wastewater
secondary wastewater treatment
REDUCING BIOLOGICAL OXYGEN DEMAND – uses digestive reactions carried out by microbes under aerobic conditions to treat wastewater with low levels of organic materials to remove organic material… ACTIVATED SLUDE and TRICKLING FILTER (ELIMINATES EXCESS ORGANIC MATERIAL) are most common decomposition processes
tertiary wastewater treatment
REDUCING NUMBER OF PATHOGENS – any physiochemical or biological treatment added for further processing of secondary treatment effluent… additional removal of organic matter and suspended solids… reduces levels of inorganic nutrients (phosphate, nitrate, nitrite)… phosphorous removal through FeCl3 – PRECIPITATES EXCESS PHOSPHATE
new contaminants of wastewater that are biologically active pollutants
pharmaceuticals, personal care products, household products, sunscreens
purification of drinking water involves
SEDIMENTATION to remove particles -> COAGULATION and FLOCCULATION form additional aggregates which settle out -> FILTRATION -> DISINFECTION using CHLORINE GAS or UV radiation
biodeterioriation
loss of structural integrity of stone or concrete caused by microorganisms (Bacteria, Archaea, Fungi, Algae, Cyanobacteria)… causes corrosion of sewer lines (causing sewer lines to fail!)
