microbiology exam 3 Flashcards
what is the most common starting pathway for the breakdown of sugar
the most common pathway is glucose
What three general products of the central metabolic pathways does a cell require to carry out biosynthesis
ATP
NADPH
precursor metabolites
What is the purpose of the transition step
the transition step links glycosis to the TCA cycle
how do enzymes speed up their reactions
By lowering the activation energy
what are anabolic reactions
Anabolic reactions are biosynthetic reactions that require energy for the conversion of molecular subunits to larger molecules
what is the purpose of the proton motive force
the proton force is used to syntesize ATP
Form of energy generated as an electron transport chain moves protons across a membrane to create a chemiosmotic gradient.
why would fermentation lead to a slow movement of food spoilage
Fermentation will lead to production of acidic by-products, dropping the pH of the food below a level that bacteria can tolerate.
why would a cell ferment than respire
There is no oxygen present and it cannot use anaerobic respiration OR it lacks the ability to respire (i.e., no electron transport chain).
How can glycosis occur
Glycosis may occur under aneorobic or aerobic conditions
which of the following processes generates the greatest amount of energy ?
Anaerobic respiration generates 34 ATP
Where does oxygen generate from in the photorophic production of energy
oxygen generates from water
the term precuror metabolites refers to molecules
they are used in biosynthesis
the electron transport system referred to
requires a membrane AND generates a concentration gradient of protons
what is the sum of all chemical reactions
metabolism
what is the difference between anabolism and catabolism
annabolism or biosynthesis is the set of chemical reactions that helps cells syntesize and assemble the subunits of macromocules using ATP
catabolism is the set of chemical reactions that degrade compounds releasing their energy
how do chemoorganotrophs obtain energy
chemoorganotrophs obtain energy by degrading organic compounds or oxidizing organic compounds
tell me the difference between endergonic and exergonic
endergonic requires a net input of energy and the products have more free energy than the starting compounds
on the other hand exergonic releases energy because the starting compounds have more energy than the products
define enzyme
subtrate
and activation energy
enzyme is a protein that functions as a biological catalyst speeding up the conversion of one substance
the substrate is the substance on which the enzyme acts on
activation energy is the initial energy required to break a bond
explain ATP
ATP is the main energy currency of cells made up of ribosomes, adenine, and 3 phosphate groups
how is ADP made
ADP isa Molecule that accepts an inorganic phosphate (Pi ) generating ATP
what two processes do chemoorganotrophs use
substrate-level phosphorylation
Synthesis of ATP using the energy released in an exergonic chemical reaction during the breakdown of the energy source.
oxidative phosphorylation
Synthesis of ATP using the energy of a proton motive force created by harvesting chemical energy; the synthesis is catalyzed by ATP synthase
what is photophosphorylation
photophosphorylation
Synthesis of ATP using the energy of a proton motive force created by harvesting radiant energy.
what is the purpose of glycolysis
the purpose of glycoses is to split glucose with 6 carbons into two pyruvate molecules with 3 carbons each
what is the purpose of the pentose phosphate pathway
the primary role of the pentose phosphate pathway is for the production of precursor metabolites NADPH
What is the role of the TCA cycle
the role of the TCA cycle is to generate reducing power, precursor metabolites, ATP
And with the transition step it oxidizes the pyruvate releasing CO2.
what is the role of cellular respiration
Cellular respiration transfers electrons from glucose to the electron transport chain to the terminal electron acceptor
why does fermentation recycle electrons
fermentation recycles electron carriers in a cell that cannot respire so that it can continue to make ATP
explain the process of metabolic processes
aerobic respiration uses the electron transport chain and oxygen as the terminal electron acceptor. the atp generated by the substrate level phosphorylation is 2 in glycosis and 2 in the tca cycle and oxidative phosphorylation is 34 giving off 38 maximum.
anerobic respiration uses an electron transport chain and the terminal electron acceptor for molecules other than oxygen such as nitrite and sulfate
fermentation doesn’t use the electron transport chain. organic molecule or pyruvate derative is the terminal electron acceptor .2 glycosis total from subtrate level and 0 from oxidative phosphorylation and in total 2 atp
describe the characteristics of enzyme inhibitors.
competitive inhibition is when the inhibitor binds to the active site on the enzyme blocks the substrate and example is a sulfa drug
Unnoncompetitive inhibition is when the inhibitor changes the shape of the enzyme so that subunits cant bind to the active site
noncompetitive inhibition is when the enzyme shape is changed making the enzyme no longer functional.
what do central metabolic pathways generate
they generate ATP
precursor metabolites
reducing power nadh, fadh2, and nadph
describe the products of glycolysis
Converts 1 glucose to 2 pyruvate molecules; net yield = 2 ATP, 2 NADH
Investment phase:
2 ATP consumed
2 phosphate groups added
Glucose split to two 3-carbon molecules
Pay-off phase:
3-carbon molecules converted to pyruvate
Generates 4 ATP, 2 NADH
products of the pentose phosphate pathway
Breaks down glucose
Important in biosynthesis for precursor metabolites
Ribose 5-phosphate, erythrose 4-phosphate
Also generates variable amount of NADPH
Product glyceraldehyde-3-phosphate can enter glycolysis
describes what happens in the transition step
CO2 is removed from pyriuvate and the electron transfer reduces nad plus to nadh plus
2 acetylcoa
links previous pathway to tca cycle
describe the tca cycle
Completes oxidation of glucose
Produces
2 CO2
2 ATP
6 NADH
2 FADH2
Precursor metabolites
describe the importance of the electron transport chain
Accepts electrons from NADH, FADH2
Energy released as electrons are passed from one carrier to the next
Energy pumps protons across membrane
Prokaryotes: cytoplasmic membrane
Eukaryotes: inner mitochondrial membrane
Creates electrochemical
gradient called proton motive force
describe the components of the electron transport chain
Quinones
Lipid-soluble; move freely in membrane
Can transfer electrons between complexes
Cytochromes
Contain heme, molecule with iron atom at center
used to distinguish bacteria
Flavoproteins
Proteins to which a flavin is attached
FAD, other flavins synthesized from riboflavi
describe the electron transport chain of mitochondria
Complex I (NADH dehydrogenase complex)
Accepts electrons from NADH, transfers to ubiquinone
Pumps 4 protons
Complex II (succinate dehydrogenase complex)
Accepts electrons FADH2, “downstream” of those carried by NADH
Transfers electrons to ubiquinone
Complex III (cytochrome bc1 complex)
Accepts electrons from ubiquinone from Complex I or II
4 protons pumped; electrons transferred to cytochrome c
Complex IV (cytochrome c oxidase complex)
Accepts electrons from cytochrome c, pumps 2 protons
Transfers electrons to terminal electron acceptor (O2
how does atp sunthase use the proton motive force
Energy required to establish gradient; energy is released when gradient is removed or reduced
ATP synthase allows protons to flow down gradient in controlled manner
Uses energy to add phosphate group to ADP
1 ATP formed from
describe nucleotide synthesis
DNA, RNA initially synthesized as ribonucleotides which can be converted to deoxyribonucleotides
Purines: atoms added to ribose 5-phosphate to form ring
Pyrimidines: ring made, then attached to ribose 5-phosphate
describe aromatic amino acids
Amino acids are feedback inhibitors of enzymes that directs branch to its own synthesis
Amino acids also inhibit formation of original 7-carbon compound
Result is that cell does not make amino acids that are already present
what is the role of glutamate in amino acid synthesis
Glutamate provides bacteria a mechanism for incorporation of nitrogen into organic material
Glutamate is synthesized in a single-step reaction that adds ammonia to α-ketoglutarate
Transamination can then generate other amino acids
describe lipid synthesis
Requires fatty acids and glycerol
Fatty acids: 2-carbon units added to acetyl group from acetyl-CoA
Usually 14, 16, or 18 carbon atoms
Glycerol: synthesized from dihydroxyacetone phosphate generated during glycolysis
describe the calvin cycle
Three essential stages of Calvin cycle
Incorporation of CO2 into organic compounds
Reduction of resulting molecule
Regeneration of starting compound
Six “turns” of cycle incorporate 6 CO2 molecules into one molecule of fructose-6-phosphate
Consumes 18 ATP, 12 NADPH per fructose molecule
describe carbon fixation
Incorporation of CO2 into organic compounds by chemolithoautotrophs and photoautotrophs
Consumes a great deal of ATP, reducing power
cyclic versus noncyclic phosphorylation
Cyclic photophosphorylation – used to synthesize ATP, but not reducing power
Photosystem I produces ATP
Reaction-center chlorophyll emit high-energy electrons
Transferred to electron transport chain (ETC) to pump protons across membrane
returned to same reaction-center chlorophylls
Non-cyclic photophosphorylation – produce both ATP and reducing power
Electrons from photosystem II establish proton motive force and are then donated to photosystem I
Photosystem II replenishes electrons by reducing NADP+ to NADPH and generates oxygen (process is oxygenic)
Electrons from photosystem I reduce
subtrate level phosphorylation versus oxidative phosphorylation
Substrate-level phosphorylation:
2 ATP (from glycolysis; net gain)
2 ATP (from the TCA cycle)
4 ATP (total)
Oxidative phosphorylation:
6 ATP (from reducing power gained in glycolysis)
6 ATP (from reducing power gained in transition step)
22 ATP (from reducing power gained in TCA cycle)
34 (total)
Total ATP gain (theoretical maximum) = 38
groups of chemolithotrophs
Chemolithotrophs fall into four general groups:
Hydrogen bacteria oxidize hydrogen gas.
Sulfur bacteria oxidize hydrogen sulfide.
Iron bacteria oxidize reduced forms of iron.
Nitrifying bacteria include two groups:
one oxidizes ammonia forming nitrite
another oxidizes nitrite producing nitrate
describe the role of photosystems
Reaction-center pigments donate excited electrons to electron transport chain
T
he energy of the electrons is used to pump protons across the membrane to generate a proton motive force
An ATPase uses that energy to synthesize ATP
The process called photophosphorylation to reflect its dependence on radiant energy.
describe the first stage of photosynthesis
Photosynthetic processes are considered in two stages.
The first stage, the light-dependent reactions, captures radiant energy and uses it to generate the following compounds needed to synthesize organic compounds from CO2:
ATP
Reducing power (NADPH or NADH)
chapter 11
what are the characteristics regarding anoxygenic phototrophs
may be motile
contian bacteriachlorophyll
harvest energy from sunlight
contain chlorosomes
may use inorganic or organoc compounds to generate reducing power like hydrogen sulfide
C6H12O6 +12S +6H2O
name the genera that can form a resting stage that allows them to survive the dry periods that occur in many soil.
Endospores—Bacillus and Clostridium
Conidia—Streptomyces-
Microcysts —myxobacteria
give the description of each aneorobic chemotrophs
Propionibacterium species
Lactic acid bacteria
Methanogens
Sulfur and sulfate-reducing bacteria
Clostridium species
Archaea, live in anaerobic environments with H2 and CO2. methanogens
Found in mud with organic material and oxidized sulfur compounds is sulfur and sulfate reducing bacteria
Generally in endospore form in soil, but will germinate to vegetative form when anaerobic conditions arise. Gram-positive rods. clostridium species
Gram-positive, catalase-negative, grow in aerobic environments but only ferment, producing acidic conditions. lactic acid bacteria
Gram-positive pleomorphic (irregular shaped) rods, fermenters, often used in Swiss cheese production.
review all the differences between archaea and bacteria
archaea are prokaryotic organisms and belong to their own domain.
the ribosomal and protein sequences of archaea are related to eukarya than bacteria.
the domain archaea are closely related to the domain eukarya.
Characteristics that define archaea include unique membrane lipids, cell wall construction and composition, and metabolic pathways.
Adaptations to metabolic pathways allow archaea to live in extreme environments, such as areas with high levels of salt (halophiles) or high temperatures (thermophiles)
why are nitrogen fixing bacteria important
can go into an organic matieral by incoroporating N2
help limit CO2 build up in the atmosphere
incoroporate CO2 into organic matieral
what can oxygenic photrophs do
include the cyanonbacteria
generate o2
are primary producers
play a role in nitrogen fixation
what is a method that cyanobacteria do not use
cyanobacteria do not use this method of isolating nitrogenase into endospores only germinate at night to protect their nitrogenase from oxygen
what are the characteristics of nitrifying bacteria, sulfur oxidizing bacteria, and hydrogen oxidizing bacteria
nitrifying bacteria is gram negative oxidizes inorganic matieral like ammonia
hydrogen oxidizing bacteria use H2 as an energy with O2 as tea and negative obligate chemolitirophs
sulfur oxidizing bacteria negative rods/spirals may filaments, oxidizes hydrogen sulfide with o2 as tea
describe mycobacterium thermus deinococcus micrococcus pseudomonas species
micrococcus species gram positive cocci found in soil dust particles and obligate aerobes pigment colonies slaty conditions
mycobacterium plemorphic rods bad stain. human diseases.resist destaining
Acid fast
pseudomonas species negative polar flagella
pigments harmless but can be pathogens of humans
thermus speices negagtive stain unusual cell wall and survive well in high heat
deinococcus species gram positive odd multicelluar cell wall resist gamma radiation
what are the characteristics of coliforms
facultative anaerobes
gram positive and negative
facultative anaerobes
indicators at fecal pollution
ferment lactose
entobacteriaceacea
Entobacterria are what
Gram-negative rods
Facultative aneorobes
Coliforms that ferment lactose
Names from intenstinal tracks of human animals
Form microbiota
Match members of chemoorganotrophs with the disease they cause
Mycovacterium liprae Leprosy Hanson disease
Yersinia pestis bubonic and pneumonic plague
Vibrio vulfinificus systemic illness, especially with liver disease
Pseudomonas aerguinosa opportuniistic disease in hospitalized patients
Vibrio parahemolyticus gastrointestinal disease
Describe conidia cysts microcysts and endospores
Endpospores formed by gram positive bacillus and clostridium species highly heat resistant
Cysts can resist drying and if radiation and negative azotoboctar species
Mocrocysts gram negative myoxybacterial fruiting bodies and moderately resistant to heat /radiation
Conidia positive streptomyces and resistant to drying and tips of hyphae
Describe argobacterium and rhizobiu
Obtain nutrients from plants
Are terrestrial microbes
Grab negative bacilli
Rhizobia: Gram-negative rods that often fix nitrogen and form relationships with legumes
Live as endosymbionts in nodules on roots of legumes
Agrobacterium: Gram-negative rods
Can genetically alter plants for their own benefit
Ti plasmid of A. tumefaciens is transferred through wounded plant tissue
ability to synthesize plant growth hormone; results in plant tumor
Agrobacterium use opine as nutrient
Description for each method of nutrient retention for aquatic bacteria
Unusual movement magneto using a special type of flagellum housed with periplasm to move through thick mud
Formation of store granules accumulated sulfur nitrate phosphate with cytoplasm of cell
Prosthecate bacteria extension of cell wall increase cell surface area. distinct method of bacteria
-Caulobacter is model for cellular differentiation
Predator of organisms bacteria prey upon other cells directly
Sheathed bacteria self form, change and taste within a tube. The rule allows cells to talk to solid object. chains of cells
Include Gram-negative rods Sphaerotilus, Leptothrix
Motile swarmer cells exit open end of sheath, move to new surface, attach
Match obtaining nutrients from legionella species
Bdellovibrio species
Epulopiscum species
Photobsacterium species and vibrio
Bdelllovibrio species gram-negative curved rod that prey on e.coli highly motile
Parasite attaches secretes digestive enzymes; forms hole in cell wall of prey
Parasite divides while attached; daughter cells released when host cell lyses
Legionella species reside in protozoa. negative obligate aerobes utilize immuno acids
Photo bacterium/ vibrio species Forman Endo symbiotic relationship relationship with certain types of fish and squid and bioluminescence
Epulopiscum species gram positive cigar shaped bacteria reside in the intensity Al tract of surgeonfish
What is true about mycoplasma
Lack a peptiodglycan cell wall
Difficult to filter growth media
Penicillins no affect
Describe the thermophe nanoarchae
Sulfur oxidizers
Thermophillic extreme acidophiles
Sulfur reducing hyperthermophiles
Methane generating hyperthermophiles
nanoarchae grow as 400 mm attached to the surface Ignononcoccus
Sulfur oxidizers obligate Aerobes that use oxygen as a terminal electron acceptor ph 1 and 6 oxidize sulfurcompounds
Thermophillic extreme acidophiles Members grow optimally below ph 2. Original isolated from a coal waste pile
Sulfur reducing hyperthermophiles use sulfur was tea generating H2s obligate anaerobes hot sulgur environments /hydrothermal vents
Methane generating hyperthermophiles oxidize H2 using CO2 as tea to yield gas. 97 C growth methanothermus
methanoyprus grows 122 C
describic thermophilic extreme acidophiles
Thermoplasma, Picrophilus growing in extremely acidic, hot environments
Thermoplasma grow optimally at pH 2, lyses at neutral pH
Picrophilus tolerate even more acidic conditions, grow optimally at pH below 1
describe extreme halophiles
Most can grow in saturated salt solutions
Aerobic or facultatively anaerobic chemoheterotrophs
Phylum eucharyarchetoa
Variety of shapes: rods, cocci, discs, triangles
Includes Halobacterium, Halorubrum, Natrono-bacterium, Natronococcus
describe methanongens
Methanogens are group of methane-producing archaea
Oxidize H2 gas to generate ATP
Alternatives energy sources include formate, methanol, acetate
CO2 as terminal electron acceptor
Anaerobic Chemoorganotrophs Anaerobic Respiration
Chemoorganotrophs oxidize organic compounds (for example glucose) to obtain energy
Anaerobes often use sulfur, sulfate as electron acceptor
Sulfur and Sulfate Reducing Bacteria
Produce hydrogen sulfide
co2 plus H2s
fermentation
glucose plus pyruvate is lactic acid
The genera Clostridium and Clostridioides are common fermenters
clostridia
Gram-positive rods that can form endospores
Common soil inhabitants that live in the anaerobic microenvironments
Endospores tolerate O2, heat, drying, chemicals, and irradiation
Germinate and multiply when conditions become favorable
lactic acid bacteria
Gram-positive bacteria that produce lactic acid as a product of fermentation
Most can grow in aerobic environments; lack catalase so they only ferment
Streptococcus inhabit oral cavity; normal microbiota
Lactococcus species used to make cheese
Enterococcus inhabit human, animal intestinal tract
Lactobacillus rod-shaped, common in mouth, vagina
purple bacteria
Gram-negative; appear red, orange, or purple
Photosynthetic apparatus in cytoplasmic membrane
purple sulfur bactera
Large cells; some motile
May have gas vesicles to control depth
Most store sulfur in intracellular granules
use H2S to generate reducing power
wolbachia
Wolbachia: W. pipientis is only known species
Infects arthropods and parasitic worms
Parasite kills male embryos or embryos resulting from mating
resides in filarial worms causing river blindness and elephantiasis; debilitating inflammation results from immune response to Wolbachia
Obligate Intracellular Parasites Chlamydia, Chlamydophila
infectious elementary bodies
Released when cell ruptures
Chlamydia trachomatis causes eye
infections and STI similar to gonorrhea
Chlamydophila species cause types of pneumonia
obligate intracellular parasites
Coxiella: C. burnetii is only characterized species
Obligate intracellular bacterium; can survive outside host cell as spore-like structures called small-cell variants (SCVs) formed during intracellular growth
C. burnetii causes Q fever
Obligate Intracellular Parasites Rickettsia, Orientia, Ehrlichia
arthropod-transmitted human diseases
R. rickettsii (Rocky Mountain spotted fever)
R. prowazekii (epidemic typhus)
O. tsutsugamushi (scrub typhus)
E. chaffeensis (human ehrlichiosis)
obligate intracellular parasites
Obligate Intracellular Parasites cannot reproduce outside a host cell: host cells supply compounds need to synthesize
Bacteria That Inhabit Mucous Membranes Treponema and Borrelia
Treponema and Borrelia: Gram-negative spirochetes
Treponema are obligate anaerobes or microaerophiles; often inhabit mouth, genital tract
T. pallidum causes syphilis,
Borrelia includes three pathogens, transmitted by arthropods such as ticks and lice
B. recurrentis and B. hermsii cause relapsing fever
B. burgdorferi causes Lyme disease
Borrelia genome is linear chromosome
Bacteria That Inhabit Mucous Membranes Neisseria
: Gram-negative,kidney bean-shaped cocci found in pairs
; grow on mucous membranes
Typically strict aerobes; some grow anaerobically
N. gonorrhoeae (gonorrhea), N. meningitidis (meningitis)
Nutritionally fastidious
Bacteria That Inhabit Mucous Membranes Mycoplasma
Mycoplasma: lack cell wall
Most have sterols for added strength and rigidity
Colony growth produces characteristic “fried egg” appearance
M. pneumoniae causes walking pneumonia;” antibiotics target peptidoglycan synthesis not effective
Bacteria That Inhabit Mucous Membranes Haemophilus
Gram-negative coccobacilli
“Blood-loving”: require hematin and/or NAD,
common microbiota of respiratory tract
H. influenzae causes ear infections, respiratory infections, meningitis
H. ducreyi causes the STI chancroid
Bacteria That Inhabit Mucous Membranes Campylobacter and Helicobacter
Campylobacter and Helicobacter: microaerophilic Gram-negative curved rods
C. jejuni typically lives in intestinal tract of poultry
Causes diarrhea in humans
H. pylori causes ulcers
Produces urease, which breaks down urea to ammonia
Bacteria That Inhabit Mucous Membranes Bordetella
Gram-negative coccobacilli
Aerobic
Nutritionally fastidious
B. pertussis causes whooping cough in humans
B. bronchiseptica causes “kennel cough” in dogs
Bacteria That Inhabit Mucous Membranes Bifidobacterium
Gram-positive irregular rods
Anaerobes; reside primarily in intestinal tract of humans and other animals
Bacteria That Inhabit Mucous Membranes Bacteroides
Gram-negative rods and coccobacilli
Small; strict anaerobes that inhabit mouth, intestinal tract, genital tract of humans and other animals
Important in digestion
Animals as Habitats Bacteria That Inhabit Mucous Membranes
Respiratory system
Streptococcus, Corynebacterium
Genitourinary system
Lactobacillus (vagina)
Intestinal tract
Clostridium, Enterobacteriaceae
Animals as Habitats Bacteria That Inhabit the Skin
Staphylococcus species inhabit the skin
Skin typically dry, salty; inhospitable
Staphylococcus are Gram-positive cocci
Facultative anaerobes; catalase-positive
S. epidermidis
S. aureus (skin and wound infections; food poisoning)
S. saprophyticus (urinary tract infections)
The Genera Thioplaca and Thiomargarita
Sulfur (energy source) and nitrate (terminal electronacceptor
Thioploca species form long sheaths; cells shuttle betweensulfur-rich sediments and nitrate-rich water
Thiomargarita namibiensis cells can reach 0.75 millimeter
Cells have a nitrate storage vacuolesurrounded by cytoplasm containing globules of s
genus spirullum
Gram-negative spiral-shaped microaerophilic bacteria
S. volutans stores phosphate as volutin granules
Metachromatic granules
bacteria that store compounds
Some bacteria form nutrient storage granules
Anoxygenic phototrophs often store sulfur granules as electron source
Some bacteria store phosphate
Some store compounds that can be used to generate ATP
Magnetotactic Bacteria
Magnetotactic bacteria contain a string of magnetic crystals that align cells with Earth’s magnetism
Allows movement up or down in water or sediments
Magnetospirillum are Gram-negative; spiral-shaped
spirochetes
Gram-negatives with spiral shape and flexible cell wall
Endoflagella or axial filament contained within periplasm at each end of the cell allow corkscrew-like motion
Spirochaeta live in muds, anaerobic waters
Leptospira are aerobes; some free-living, others inhabit animals
L. interrogans causes leptospirosis
bioluminescent bacteria
Symbiotic relationships with certain fish, squid
Help with camouflage,
Luminescence catalyzed by enzyme luciferase
Luciferase controlled by quorum sensing
Gram-negative straight or curved rods, facultative anaerobes, marine environments
Thriving in Terrestrial Environments Myxobacteria -
Streptomyces
Aerobic Gram-negative rods with unique developmental stage and resting form
Favorable conditions: secrete slime layer, form swarm
Nutrients depleted: cells congregate into fruiting body
mycoxy bacteria the thing from spongebob red flower
Streptomycrs of aerobic Gram- positive bacteria
Growth resembles fungi: form mass of branching hyphae called mycelium
Chains of spores (conidia)
Conidia resistant to drying; easily spread by air currents
Produce extracellular enzymes, geosmins
genus azobacter
Gram-negative pleomorphic rods
Form resting cell called a cyst
Withstand drying and UV radiation
Fix nitrogen in aerobic conditions
High respiratory rate maintains low O2 in a cell
Protein binds nitrogenase, protects from O2 damage
endospore formeers
Gram-positive rods
Clostridium species are obligate anaerobes
Bacillus include obligate and facultative anaerobes
Both can cause disease:
C. tetani causes tetanus
B. anthracis causes anthrax
epcophysiology diversity
Ecophysiology: Study of the adaptations of physiological mechanisms that prokaryotes use to live in terrestrial and aquatic environments
descroibe the family entobacteriaccdes and the genus vibrio
Found in marine environments, require some Na+ for growth
Gram-negative straight or slightly curved rods
Pathogens include V. cholerae, which causes cholera
Some are bioluminescent
Gram-negative rods found in intestinal tract of humans, other animals; some thrive in soil
Faculatatuve aneorobes
Use aneorobic respiration but can ferment if o2 is not available
Cyanobacteria gram positive phlemorpjic rods
Wide spread
Coryneforms or diphtheroids
C diphtheria causes diphtheria
Aerobic chemoorganotrophs
Oxidized organic compounds for energy
Use oxygen as tea
Organic compounds plus o2 (tea) co2+h2o
Aquifex have maximum growth at 95 degrees , Hydrogenobactera among few hydrogen-oxidizing bacteria that are obligate chemolithotrophs
Thermophilic; typically live in hot springs
O2 requirements low; possibly available in certain niches due to photochemical processes that split water
h2 energy source + 1/2 O2 terminal electron acceptor = h2O
nitrifieers
Nitrifiers are a diverse group of Gram-negatives
Oxidize inorganic nitrogen compounds for energy
Can deplete water of O2 if wastes high in ammonium
Ammonium oxidizers: Nitrosomonas, Nitrosococcus
nh4+ 1/2 o2 terminal electron acceptor — no2- +H2O+ 2h+
Nitrite oxidizers: Nitrobacter, Nitrococcus
NO2- (energy source)+1/2 O2 terminal electron accpetor —-> NO3-
filamentous sulfur oxidizers
Beggiatoa, Thiothrix: sulfur springs
Store sulfur as intracellular granules
Beggiatoa filaments move by gliding motility
Thiothrix filaments immobile; progeny cells detach, move via gliding motility
unicelluat sulfur oxidizers
Acidithiobacillus: terrestrial and aquatic habitats
Unicellular sulfur oxidizers
Oxidize metal sulfides; oxidation of gold sulfide produces sulfuric acid; lower pH converts metal to soluble form
Can oxidize sulfur in fuels to sulfate
aerobic chemolithotrophs
gain energy by oxidizing reduced inorganic chemicals
Sulfur-oxidizing bacteria:
Gram-negative rods, spirals
oxygen is terminal electron acceptor; generates sulfuric acid
sulfur (energy source)=1/2 o2 as tea —. h2o-h2so4
purple non sulfur bacteria
use organic molecules instead of H_2 S as source of electrons
Lack gas vesicles
May store sulfur; granules form outside cell
Most can grow aerobically in absence of light using chemotrophic metabolism
Representatives include Rhodobacter, Rhodopseudomonas
green bacteria
Gram-negative;
Use H2S; form sulfur granules outside of cell
lack flagella
Strict anaerobes
Representatives include Chlorobium, Pelodictyon
Filamentous Anoxygenic Phototrophic Bacteria
Form multicellular arrangements
Exhibit gliding motility
Many have chlorosomes
Metabolically diverse
Some preferentially use organic compounds to generate reducing power, can grow in dark aerobically using chemotrophic metabolism
Chloroflexus best studied, especially thermophilic strains found in hot springs
oxygenic photrophs
Cyanobacteria
Earliest oxygenic phototrophs
Use water as source of electrons for reducing power
harvest sunlight to convert CO2 into organic compounds
Diverse group of Gram-negative bacteria
6CO2 carbon source + 6H2O electron bacteria —> C6H12O6+ 6O2
cyanobacteria
Morphologically diverse
Unicellular: cocci, rods, spirals
Multicellular: filamentous associations: trichomes
motile trichomodes
Also have phycobiliproteins
what are primary producers
consumer
decomposers
primary producers Autotrophs that convert CO2 into organic materials; serve as a food source for other ecosystem members
consumer- Heterotrophs that eat other organisms; several together can create a food chain, while multiple chains create a food web.
decomposers Heterotrophs that digest the remains of the other two groups in ecosystems; specialize in digesting complex molecules such as cellulosse
define ammonification
Denitrification
Nitrogen fixation
Nitrification
Deamination of organic compounds yielding NH4 is ammomnification
dentrification Reduces nitrate through a series of steps to nitrogen gas
nitrogen fixation Removes N2 from the air with the primary product of NH4+
nitrification The oxidation of NH4+ to NO2− and NO3−
Which of the following factors can influence the ability of an organism to compete successfully for a habitat?
The rate at which the organism multiplies.
The ability of the organism to withstand adverse environmental conditions.
e ability of the organism to inhibit other microbes by producing antimicrobial compounds
Place the layers that would exist in a microbial mat in the correct order from top to bottom layer
A green layer filled with photosynthetic cyanobacteria.
A reddish-pink layer consisting of purple sulfur bacteria.
A black layer filled with sulfate-reducing obligate anaerobes.
define metagenomics
dna microarrays
flouorescent in situ hybridization
metagenomics
Using microbial DNA sequence information to observe commonly conserved genes for particular traits.
flourecent in situ Using fluorescent probes to look for specific microbes in an area/community.
Comparing microbial populations by studying gene expression.
dna microarrays
the effect of environmental pH on population composition.
Lactococcus lactis right behind 4.0
Lactobacillus species most acidic 3.0
Yeasts and molds ph 5.5
Putrefying bacteria is ph 6.8
idenntify the steps that can lead to “dead zone” formation in bodies of water such as Lake Erie and the Gulf of Mexico.
Algae/cyanobacteria grow, using photosynthesis to produce organic compounds
organic compounds
Aerobic decomposition of organic compounds by heterotrophs depletes oxygen
Animals flee hypoxic environment or die
define
Microenvironment Population
Community
Biosphere
Ecosystem
Ecology
Ecological niche
Study of the interaction of organisms with each other and their environment, Ecology
Organisms of the same type in a given environment, Population
All of the different organisms in a location is a Community
Community of organisms and the non-living environment with which they interact , Ecosystem
All of the ecosystems on Earth Biosphere
Role of an organism in a particular ecosystem , Ecological nichet
Environment immediately surrounding an individual microbe. microenvironment
Select the factors that play a role in microbial competition
Ability to produce antimicrobial compounds.
Ability to multiply faster than other microbes in the environment.
Ability to withstand adverse environmental conditions.
ways in which microbes are identified and classified in the laboratory.
16S rRNA sequencing
18S rRNA sequencing
Deducing amino acid sequences in ribosomal proteins
what researchers can learn about a microbial community using metagenomics.
They can identify the genes that are present in a microbial community.
Knowing what genes are present in a community may facilitate identification of microbes.
They may learn what role a particular microbe has in the environment.
Steps involved in creating an aquatic dead zone into the correct sequence.
River water carrying nutrients acquired from urban, agricultural and industrial areas flows into the sea
Algae and cyanobacteria (primary producers) use excess phosphates and nitrates for growth, multiplying rapidly.
heterotrophic microbes metabolize the organic compounds made by primary producers, and consume dissolved O2.
Depletion of dissolved O2 results in large hypoxic zone, causing animals to flee or die.
TRUE statements regarding microbes in soil.
Dry soils favor the formation of bacterial endospores.
Acidic soil suppresses bacterial growth, allowing fungi to flourish.
Algae and protozoa tend to grow near the soil surface rather than at deeper levels.
Soil organisms with their characteristics.
Bacillus species
Azospirillum species
Streptomyces specie
Produce antibiotics Streptomyces species
Form endospores Bacillus species
Fix nitrogen azospirillum species
Sulfur oxidation
Nitrification
Methanogenesis Ammonification Denitrification
Anammox
Carbon fixation
Nitrogen fixation
Process in which NH4+ is oxidized to NO3−2 Nitrification
Process that reduces NO3−, converting it to gaseous forms such as N2O and N2 Denitrification
Process that converts CO2 to an organic form by living organisms Carbon fixation
Anaerobic oxidation of NH4+ as an energy source Anammox
Oxidation of H2S and SO as energy sources sulfur oxidation
Oxidation of hydrogen gas, using CO2 as a terminal electron acceptor, and generating CH43, Methanogenesis
Reduction of N2 to form NH3 for incorporation into cellular material8Nitrogen fixation
Decomposition process that converts organic nitrogen into NH3 ammonification
list the types of symbiotic relationships
Living organisms interact with each other in symbiotic relationships
Mutualistic: both organisms benefit from relationship
Commensalistic: one benefits; other unaffected
Parasitic: one benefits; other is harmed
microbial competition
Ability to compete related to rate of multiplication, also
ability to withstand adverse environmental conditions
describe microbial communities
Microbial communities
Often grow as biofilms attached to solid substrates or at air-water interfaces
Microbial mat is a specific type: thick, dense, highly organized structure composed of distinct layers
Photosynthetic cyanobacteria (green)
Anoxygenic phototrophic purple sulfur bacteria (pink)
Obligate anaerobic sulfate-reducers (black)
what is metagenomics
Metagenomics is cultivation-independent study of communities or their members by analyzing genetic material taken from an environment
descripe the aquatic habitats
Oligotrophic (nutrient poor) waters limit growth of autotrophs due to lack of inorganic nutrients
Eutrophic (nutrient rich) waters encourage growth of autotrophs, which produce organic compounds that foster growth of heterotrophs in lower layers
what are the characteristics of soil
Soil forms as rock weathers
Water, temperature changes cause rock to crack, break
Bacteria, fungi use as carbon sources, produce acids, other chemicals that gradually decompose the rocks
As soil slowly forms, plants begin to grow
When these die and decay, accumulated organic materials form humus
Soil environment can change abruptly
Clay soils more likely to be anaerobic; sandy soils more likely to be aerobic
describe the microorganism rhizobacteria in soil
Rhizosphere: zone of soil adhering to plant roots
Root cells secrete organic molecules used by microbes
Higher concentrations of Gram-negatives
microorganisms in soil
Most are aerobes, grow in top 10 centimeters of soil, degrade complex
Some are free-living, others live symbiotically
Mycorrhizas are fungi growing in symbiotic relationship with plant roots
Assist individual plants AND create hyphal networks that link various plants
Algae, protozoa also found in most soils
Algae depend on sunlight for energy, so mostly live on or near soil surface
biogchemical cycling
Biogeochemical cycles are paths elements take as they flow through biotic and abiotic components of ecosystems
Important in recycling limited amounts of elements
Carbon, nitrogen cycles particularly important
Involve stable gaseous forms with global impact
Elements continually cycle, but energy does not
Must be continually added to ecosystem to fuel life
human activites have major impact
Conversion of N2 into ammonia-containing fertilizers has increased food production,
Increased amount of fixed nitrogen available leads to pollution of lakes,
Burning fossil fuels releases CO2 along with other carbon containing gases which raise global temperature the greenhouse effect
three puposes in metabolism
Elements have three purposes in metabolism
Biosynthesis (biomass
production)
Required for all organisms; many different pathways
Energy source
Reduced carbon compounds such as sugars, lipids, amino acids used by chemoorganotrophs
Terminal electron acceptor
In aerobic conditions, O2 is used
In anaerobic conditions, prokaryotes may use nitrate, nitrite, sulfate, or carbon dioxide
methane oxidation and methagonesis
anaerobic environments, CO2 used by methanogens
These archaea obtain energy by oxidating hydrogen gas, using CO2 as terminal electron acceptor
Generate methane CH4
Methane enters atmosphere, is oxidized by ultraviolet light and chemical ions, forms carbon monoxide (CO) and CO2
nitrogen fixation cycle
N2 is reduced to ammonia
Can be incorporated into cellular material
Enzyme complex nitrogenase catalyzes
Requires tremendous energy since N2 has very stable triple bond
azobacter diatrophs form relationships with higher order organisms
Heterotrophic, aerobic, Gram-negative rods; may be main suppliers of fixed nitrogen in ecosystems that lack plants with nitrogen-fixing symbionts (for example, grasslands)
Dominant free-living anaerobic soil diazotrophs are members of genus Clostridium
sulfur cycle
microbes assimilate as sulfatereducing and the incorporating into biomass
Decomposition of sulfur-containing amino acids releases hydrogen sulfide gas
phosphorous and other cycles
Phosphorus is component of nucleic acids, phospholipids, ATP
Most plants, microbes take up as orthophosphate
relatiobnship between microrganisms and eukaryotes
Microorganisms and herbivores
Microbes inhabit specialized compartment, digest cellulose and hemicellulose of plant material
nitrogen fixers and planters
Plant-bacterial communication - Plant root secretions attract appropriate rhizobial species that colonize roots
Root hairs curl - Bacteria produce Nod factors (NFs) that induce root hair to curl, trapping the bacterial cells
Bacteria pass through infection thread - Rhizobia travel through infection threads into plant cells where they become a specialized nitrogen-fixing cell called a bacteroid
Nitrogen-fixing nodule forms - Relationship not obligate, but offers competitive advantage to both partners
what is a type of symbiotic nitrogen fixer and planter
Rhizobia include members of diverse group of genera
Most agriculturally important symbiotic nitrogen-fixing bacteria
Grow within nodules on roots of legumes, including alfalfa, clover, peas, beans, peanuts
mutualistic relationshipas between microorganisms and eukaryotes
Mycorrhizas are fungi in symbiotic relationships with plant roots
Fungi help plants take up phosphorus, other nutrients; they gain nutrients from root secretions
Endomycorrhizas: fungi penetrate root cells, grow within them
Ectomycorrhizas: fungi grow around plant cells, form sheath around root; associate with certain trees
whar are energy sources for ecosystems
bacteria archea oxidize H2S use energy to fix CO2
hydrothermal vents release h2s
Chemotrophs harvest energy trapped in chemical bonds
