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What is the difference between a biological and chemical process?
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What types of reactions are favored under oxic and anoxic conditions?
- Oxic: oxidation
- anoxic: reduction
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Explain mineralization:
decomposition of organic matter into simpler inorganic molecules.
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What occurs in nutrient immobilization?
Nutrients are converted into biomass, and are not available for nutrient cycling.
-
Describe Carbon fixation.
- CO2 turned into organic molecules.
- step 1
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Describe oxidation of organic matter
- Organic carbon is burned for energy (glycolysis, fermentation)
- step 2.
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Describe methanogenisis
Coming from oxidation of organic matter, an alternate pathway produces methane.
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Describe lignin degradation:
- Oposite of forming of peat bogs and muck soils.
- Must occure in Aerobic conditions.
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What are the steps in the carbon cycle?
- Carbon fixation
- oxidation of organic molecules
- methanogenesis
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What are the steps in the Nitrogen cycle?
- ammonification
- anammox reaction
- assimilation
- denitrification
- nitrification
- nitrogen fixation
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Describe Nitrogen fixation:
- N2 into NH3
- the nitrogen is now useable
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Describe nitrification:
Taking amonia (NH4) into a nitrite NO3
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Describe denitrification:
taking a nitrite and turning it into N2
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describe ammonification:
taking organic N into ammonia NH4
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describe anammox:
NO2 and NH4 get turned into N2.
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Describe the general features of the Phosphorous cycle:
- No gaseous component.
- Environmental phos is ususally the limiting factor.
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Describe the Iron cycle:
Iron is reduced and oxidized as it changes between anaerobic and aerobic conditions.
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Which form of mercury is less toxic than the other?
- de methylated.
- with a methyl group it is lipid solluble and very toxic.
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Describe the importance of biomagnification in the mercury cycle.
The toxic mercury builds up in the fats of successive levels of predation.
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Describe biodegredation:
- 3 outcomes:
- 1. minor change.
- 2. fragmentation
- 3. mineralization.
- : can produce more toxic products.
- Can degrade things we don't want, like metal
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Describe bioremediation:
- Takes toxic and turns it into non toxic forms.
- Involves many intermediates.
- May need artificial supplimentation of the limiting factor.
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How can oil spills be cleaned?
- Through bioremediation.
- The hydrocarbons are degredated naturally.
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Describe phytoremediation:
- it is a form of bioremediation.
- Using plants and bacteria to degrade and use the toxic materials.
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Describe bioleaching of Copper:
- Copper is pulled off of the minerals, it then undergoes a change in oxidation and is precipitated out.
- Fe2+ is used.
- Bacteria facilitate changes in oxidation.
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Describe bioaugmentation:
- Adding more microbes to microbial communities.
- Has only shown short term increases in degredative activity.
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What is Chemolithotrophy?
Using inorganic molecules as an energy source
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Discuss the general features of chemolithotrophy
litho denotes inorganic molecules as an energy and electron source.
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Identify the major energy sources used by chemolithotrophic bacteria
Hydrogen, reduced nitrogen compounds, reduced sulfur compounds, ferrous Iron.
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Describe the stages of chemolithotrophy in nitrifying bacteria
- 2 different genera needed.
- 1. ammonia to nitrite
- 2. nitrite to nitrate.
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Discuss the adaptability of chemolithotrophs
many can switch between chemolithotrophy to chemoorganotrophy
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What is phototrophy?
- Light energy trapped and converted into chemical energy.
- 2 parts: light and dark reactions.
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Define photosynthesis
- light reaction.
- light absorbing pigments.
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Discuss the requirements and the products from the Light reactions
- Only ATP produced and NaDH.
- H20 not used so no O2 produced.
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Discuss the requirements and the products from the Dark reactions
- Energy from Light reaction (ATP and NADH) used to turn CO2 into organic molecules.
- "Calvin cycle"
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Describe the main features of oxygenic photosynthesis
- H20 is present as final electron acceptor,
- O2 produced.
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Describe the main features of anoxygenic photosynthesis
- Strict anaerobes.
- No H20 or O2.
- Only ATP produced.
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Discuss phototrophy in Archaea and identify the differences with photosynthesisin other phototrophs
- Uses bacteriorhodopsin.
- light driven proton pump.
- NO ETC
- ATP only produced by chemiosomoiss.
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Characterize a Photolithoautotroph
- C source: CO2
- Energy Source: light
- e- source: inorganic e- donor.
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Characterize a Photoorganoheterotroph
- C source: organic carbon
- energy source: light.
- e- source: organic e- donor.
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Characterize a Chemolithoautotroph
- C source: CO2
- energy source: inorganic chemicals
- e- source: inorganic e- donor.
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Characterize a Chemolithoheterotroph
- C source: organic carbon
- energy source: inorganic chemicals
- e- source: inorganic e- donor.
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Characterize a Chemoorganoheterotroph
- C source: organic carbon
- energy source: organic chemicals (often same as C source)
- e- source: organic e- donor.
- (most non photosynthetics)
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Why is Nitrogen required and how do microorganisms obtain it?
- Nucleic and Amino acids.
- Org. mol.
- ammonia.
- N2, nitrate.
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Why is Phosphorous required and how do microorganisms obtain it?
- Phospholipids, nucleic acids.
- inorganic phosphate.
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Why is Sulfur required and how do microorganisms obtain it?
- Amino Acids, vitamins.
- Sulfate.
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What are micronutrients, and how are they obtained?
Trace elements, needed in very small amounts.
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What are growth factors and how are they obtained?
- Essential cell component precursers that the cell cannot synthesise.
- Amino Acids,
- Purines, pyrimidines
- vitamins.
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Describe passive diffusion
- High Conc. to Low.
- H2O, O2, CO2.
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Describe Facilitate diffusion
- From High to Low, via "facultative" pores.
- Sugar transport.
- More promenant in Eukariotic cells.
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Describe active transport
- ATP dependent. Against conc. gradient.
- Concentrates molecules.
- involves carrier proteins.
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Describe group translocation
- Chemically modified molecule is brought into cell.
- PEP is an example.
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describe iron uptake
- Ferric iron is very insolluble.
- Siderphore complex used to pick it up and then transport into cell.
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With respect to the chemical composition, describe Defined culture media:
We know exactly what is in the medi.
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With respect to the chemical composition, describe complex culture media:
we don't know everything exactly about the media
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What is mean by a supportive (general purpose) media?
supports growth of many microorganisms.
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What is mean by an Enriched media?
- general purpose media augmented with something special
- blood, special nutient.
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Describe a selective media:
Favors growth of some, inhibits growth of others.
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What is mean by a differential media?
distinguishes between different groups of microorganisms.
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Describe the 3 methods of isolating pure cultures:
- 1. Streak Plate
- 2. Spread Plate
- 3. Pour Plate.
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How do colonies develop in solid culture media?
From a single cell
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Describe the events in the bacteria cell cycle.
- replicates chromosome,
- divides, septum forms
- grow and repeat.
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In bacteria, how are chromosomes replicated and partitioned?
- through an origin of replication and terminus.
- Only 1 point of replication per cycle.
- Multiple repication going on at same time because of rapid division.
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Describe the chromosomal sites involved in bacterial DNA replication
- Origin of replication.
- Terminus.
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What is a replisome?
Group of proteins needed for DNA synthesis.
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What roles to MreB and FtsZ play in cytokinesis?
- MreB: Determining cell shape, and moving chromosomes to opposing ends of the cell.
- FtsZ: Z ring formation to form cross wall.
-
 Describe a typical growth curve:
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What events occur during the lag phase?
- The cell is synthesizing new components.
- time frame depends.
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What is happening during the exponential phase?
- Constant growth rate.
- Population most uniform.
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What is going on during the stationary phase?
- Constant viable number of cells.
- reproduction may stop, or
- reproductive rate=death rate.
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Why do cultures enter a stationary phase?
- This phase is entered because of:
- Nutrient limitations,
- O2 available,
- waste accumulation,
- population density critical.
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How do bacterial cells respond to starvation?
- Endospore formation,
- Decrease in size: protoplast shrinks, nucleoid condenses.
- Produces starvation proteins.
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Describe the Death phase:
- 2 ideas:
- 1. viable, but not culturable. (VBNC)
- 2. Part of population undergoes programmed cell death.
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What is the generation time?
- The doubling time.
- ranges from 10min to several days by species and environmental conditions.
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How would you calculate the number of cells from exponential growth?
- P1 (origional population)
- n (number of cycles)
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Define direct cell count:
- counting chambers
- electronic counters
- membrane filters
- counting actual cell bodies.
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Describe counting chambers:
- Like a net, just count what is in the square.
- Cheap and easy.
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Describe electron counters:
- cells move through and disturb current.
- Disturbances counted.
- Usefull for large cells.
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describe direct count on membrane filters:
- Dark membrane & fluorescent stained cells.
- can distinguish living and dead.
- good for bacteria.
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Define viable cell count:
- Expressed in CFU's colony forming units.
- dilute, let grow, count colonies.
- count=colonies x dilution factor.
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How can one use a measurement of cell mass to estimate the cell numbers?
- By dry weight,
- By how much of particular component.
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Characterize continuous culture:
Chemostat or turbidostat.
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Characterize chemostat
- Limiting nutrient.
- inflowing media=outflowing media.
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characterize turbidostat
- No limiting nutrient.
- flow rate determined by cell density or turbidity.
- Operates best at high dilutions.
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What is water activity?
- aw
- amount of water available to organisms.
- reduced by solute molecules.
- ex: pure water vs. blood vs. dried fruits.
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Identify specific microbe adaptations to maintain tonicity:
- compatible solutes to increase osmotic concentrations
- proteins and membranes require high concentrations for stability and activity.
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What are compatible solutes?
- they keep plasma firmly pressed against cell wall.
- they do not interfere with metabolism or growth at high concentrations.
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What are:
Halophiles
Extreme halophiles
osmotolerants
- Halophiles: optimal growth @ 0.2M
- Extreme Halophiles: og@ 2M
- osmotolerants: can grow over wide ranges of water activity.
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What are:
Acidophiles
neutrophiles
alkalophiles
- acidophile: og between pH 0-5.5
- neutrophile: og between 5.5-8
- alkalophiles: og between 8-11.5
- producing a "buffer" waste.
- protection proteins
- proton impermiable membrane.
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What are the 3 cardinal tempuratures?
- Minimum, optimum, maximum.
- On a graph they show the relation between growth and temp.
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What are
psychrophiles
psychrotrophs
mesophiles
thermphiles
hyperthermophile
- psychrophiles: og -5-15
- psychrotrophs: og 0-35
- mesophiles: 15-40
- thermophiles: 50-75
- Hyperthermophile: 80-100
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describe superoxide dismutase
2 O2 +2H into peroxide and O2
-
Describe catalase
peroxide into water and O2
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Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for obligate aerobe:
- Only grows in O2 presence.
- SOD+Catalase
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Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for falcultative anaerobe:
- Can do without O2, but does best in it's presence.
- SOD Catalase
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Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for aerotolerant anaerobe:
- Ignores O2 alltogether.
- Has SOD, but no catalase.
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Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for strict anaerobe:
- Only grows away from O2.
- No SOD, No Catalase.
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Describe the need for/response to oxygen, applicable enzymes, & type of metabolism for microaerophile:
- Can only live in certain concentrations of O2.
- Has SOD, and maybe Catalase.
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What is required to culture anaerobes?
Paladium pellets, sillica gel, sealed container and an o2 indicator.
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what distinguishes barotolerant and barophilic microbes?
- barotolerant: hurt by pressure, just not as bad as others.
- barophilic: require, or grow more rapidly at 400atm or higher.
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What effect does ionizing radiation have on microbes?
- disrupts chemical structure.
- DNA etc.
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What effect does UV radiation have on microbes?
formation of thymine dimers through forbidden diels-alder reactions.
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what is the effect of visible light radiation on microbes?
- at high intensities generates singlet oxygen.
- caroteniods protect many light exposed microorganisms from photooxidation.
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What are biofilms and how do they form?
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what is quorum sensing and how does it work?
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Describe oligotrophic conditions in nature. How do microorganisms respond to these conditions?
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Energy source: chemoorganotroph, chemolithotroph, and phototroph
- Organic molecules
- inorganic molecules
- light
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Carbon source: autotroph and heterotroph
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Electron source: organotroph and lithotroph
- organic molecules,
- inorganic molecules.
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describe fermentation
- Uses endogenous electron acceptor like pyruvate.
- No etc or pmf.
- ATP only produced by substrate level phosphorylation.
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What is respiration? How does it differ between aerobic and anaerobic microorganisms?
- Glycolytic pathways,
- transition step,
- tricarboxylic acid cycle
- oxidative phosphorylation in ETC.
- They vary in final electron acceptor.
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Describe the Embden-Meyerhof pathway:
- Breaking down sugar.
- occurs in cytoplasm of both prokaryotes and eukariotes.
- most common.
-
Describe the pentose phosphate pathway
- can operate same time as other pathways.
- can be aerobic or anaerobic.
- Is amphibolic.
- Produces NaDPH, and Sugars.
- ATP can be made from intermediates.
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Describe the Entner-Doudoroff pathway
produces 1 of everything vs 2 of glycolyses.
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Describe the reactants and products of the Tricarboxylic Acid Cycle
- Common in aerobic microorganisms.
- Piruvate in CO2 and NADH and ACoA.
- Each ACoA:
- 2 CO2
- 3 NADH
- 1 FAD2
- 1 GTP
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Describe the reaction involved in the formation of acetyl CoA from pyruvate.
- TAC,
- Each pyruvate: 1 CO2, 1 NADH, 1 ACoA
-
Identify the differences between the mitochondrial ETC and the prokaryotic ETC
- Location, mitochondria vs. cell membrane.
- Different electron carriers.
- May have branches or be shorter.
- May have lower P/O ratio.
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Explain the chemiosmotic hypothesis and function of the Electron transport chain.
Pumps protons out to churn atp synthase on the way back in via PMF.
-
Explain the chemiosmotic hypothesis and function of ATP synthase
Proton diffusion through protein results in atp being formed.
-
Summarize ATP production during aerobic respiration.
- Glucose is oxidized and ETC creates most ATP
- Oxygen is final e- acceptor.
- 36-38 ATP.
- actual closer to 30.
-
What are some uses of the Proton motive force in the cell?
- ATP Production
- flagellar rotation
- active transport.
-
Discuss the differences anaerobic respiration and aerobic respiration
- Inorganic Ions act as e- acceptor.
- Organic receptors also work.
- Less effective than aerobic.
-
Identify the major electron acceptors used in anaerobic respiration
-
Describe overall processes of anaerobic respiration that occur in Paracoccus denitrificans
- reduction of nitrate to nitrogen gas inavailabile.
-
Describe overall processes of anaerobic respiration that occur in Methanogens
CO2 or CO3 2- is reduce to methane CH4
-
Describe overall processes of anaerobic respiration that occur in Desulfovibrio
SO4 2- is reduced to H2S
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Compare and contrasts the processes of respiration and fermentation.
- NADH Produced, but is then oxidized.
- Pyruvate is electron acceptor.
- No oxidative phosphorylation.
-
Describe the two stages in the process of fermentation
- NADH Produced, but is then oxidized.
- Pyruvate is electron acceptor
-
Describe alcoholic fermentation
Alcohol and Co2 are produced as pyruvate degrades.
-
Describe homolactic fermentation
Only NADH is given off as pyruvate degrades to lactate.
-
Describe heterolactic fermentation
Lactic acid, ethanol and CO2 produced.
-
Describe mixed acid fermentation
Ethanol and other acids produced.
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How are monosaccharides catabolized?
converted into glucose 6 phosphate to enter glycolysis.
-
How are disaccharides catabolized?
cleaved into monosacharides
-
How are Glycogen and Starch catabolized?
subunits cleaved by phosphorylases.
-
How is PHB (poly-beta-hydroxybutyrate) catabolized?
it is turned into ACoA for the TCA cycle.
-
Describe the stages in the catabolysis of lipids
- Turned into glycerol for glycolysis
- or fatty acids, Then ACoA for TCA
-
Describe deamination
removal of amino group from AA,
-
In the simplest way possible describe:
Symbiosis
Ectosymbiosis
Endosymbiosis
Consortium
- symbiosis: simple relationship between two or more.
- Ectosymbiosis: one on top of another
- Endosymbiosis: on inside another
- Consortium: having more than one symbiont
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In the simplest way possible describe:
Mutualism
Cooperation
Commensualism
Predation
Parasitism
Amensalism
Competition
- Mutualism: Obligatory ++
- Cooperation: not obligatory ++
- Commensualism: 0+
- predation: x+
- Parasitism: -+
- Amensalism: 0-
- Competition: --
-
Describe Staph Food poisoning:
- Staphylococcus aureus
- GI probs, 6-36h
- Contaminated Food.
- Keep food hot or cold, in doubt throw out.
- All people susceptible
-
Describe Syphilis
- The great pretender
- Treponema pallidum - gramneg spirochete
- Hypcrates and tuskegee
- Human reservoir 21 day ave. (10-90)
- infectus until latent stage
- rashes and lesions
-
Describe Listeriosis
- Listeria monocytogenes grm+ rod. flagella
- pigs, rodents, undercooked pork. melons
- most asymptomatic
- can penetrate epithelial lining.
-
Describe Gonorrhea
- Neisseria gonorrhoeae diplococci
- 5 phase. human reservoir. Many asymptomatic carriers.
- Lots of african americans 20-24.
- 2-5d. men up to 1month.
- Dysuria. or painfull discharge.
- 2nd to chlymidia as bacterial STD.
-
Describe Typhoid Fever
- Salmonella enterica serovar Typhi Rod grm-
- Falcultative anerobe, peritrichous flgella.
- bile resistant, found only in humans.
- Asymptomatic typhoid mary.
-
Describe Botulism
- Clostridium Botulinum. grm+ rod. anaerobic. endospore forming.
- 7 neurotoxins. 3 types. food, infant, wound.
- paralysis.
- people and animals.
- food, ingesting endospores.
- infant, honey or airborn particles.
- Wound, like tetanus.
-
Describe Cholera
- Vibrio cholerae 16 strains. grm- flgellum.
- contaminated water or food.
- LOTS of diarrhea
-
Describe Pertussis
- Bordetella pertussis. grm- aerobic coccobacillus.
- binds to cillia in resp. sys.
- Whooping cough.
- person-person , dtap.tdap
-
Describe Lyme disease:
- Borelia burgdorferi. spirochete.
- mice, ticks (lxodes scapularis), deer.
- bruise with halo.
- no more vaccine.
-
What are macronutrients?
Nitrogen, Phosphorous, Sulfur.
-
Based off the following graph, what type of metabolism do the following microorganisms exhibit?
- Obligate aerobe
- facultative anaerobe
- aerotolerant anaerobe
- obligate anaerobe
- microaerophile
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