MICB 3301 - Exam 2

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55 Terms

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nutrients

substances used in biosynthesis and energy release

required for microbial growth

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microbial cell dry weight

macronutrients: C, O, H, N, S, P, Fe

micronutrients: cobalt, copper, zinc, manganese

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sources of nitrogen

ammonia (NH3)

nitrate (NO3)

some use nitrogen gas (N2)

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nitrogen fixation

N2 reduced to ammonia 

  • Rhizobium: in symbiosis with plants, lives in soil, forms root nodules

  • Azotobacter: free living in soil

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acquiring nutrients

food must enter:

  • at high rates 

  • across membranes

  • selective fashion

  • often against a concentration gradient

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passive transport

  • no energy required

  • high → low gradient

  • passive diffusion: only small molecules and certain gases

  • facilitated diffusion: uses membrane carrier proteins, still requires gradient

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active transport

  • energy dependent

  • moves against gradient

  • uses ATP or proton motive force

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primary active transport: ABC transporters

  1. binding of nutrient and protein

  2. conformational change caused by complex

  3. 2 ATP used to drive movement of nutrient into cytoplasm through ABC transporter

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ABC transporter types

Uptake ABC: move nutrients in

Export ABC: Multidrug Efflux, move substances out

  • in bacterial cells move antibiotics out, bacteria becomes resistant to antibiotics 

  • in cancer cells move anitcancer drugs out, tumor becomes resistant

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Secondary Active Transport

  • uses potential energy of ion gradients

  • e- transport across a membrane generates H+ gradient

  • can be used to move another nutrient

    • ex. Lac Permease, moves lactose powered by proton moving in

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Group Translocation

nutrient is chemically altered

ex. phosphate group is added

energy from phosphoenolpyruvate attaches P to sugars, glucose → pyruvate 

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Iron Uptake

all microbes require Fe, little free Fe available

solution: microbes release siderophores to acquire Fe, siderophore-iron complex then transported into cell often using ABC transporter

ex. Enterobactin, E. coli siderophore 

<p>all microbes require Fe, little free Fe available</p><p>solution: microbes release <strong>siderophores&nbsp;</strong>to acquire Fe, siderophore-iron complex then transported into cell often using ABC transporter</p><p>ex. Enterobactin, E. coli siderophore&nbsp;</p>
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Metabolism

all chemical reactions in a cell

catabolism: breakdown of complex molecules into smaller ones with release of energy

anabolism: reactions that build cells

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Adenosine Triphosphate

ATP

  • phosphate group

  • ribose sugar

  • Adenine base

P removal (hydrolysis): large negative standard free energy change

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Energy generating systems

Oxidative phosphorylation: aerobic respiration, anaerobic respiration

Substrate level phosphorylation: fermentation

Photophosphorylation: photosynthesis

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ribozymes

catalytic RNAs

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lowering activation energy

  • enzymes increase local concentration of substrates

  • orient substrates properly for reactions to proceed

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redox reactions

oxidation: removal of electrons

reduction: gain of electrons

donor: substance oxidized

acceptor: substance reduced

  • uses electrons and protons, ex. NAD+/NADH

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reduction potential

equilibrium constant for redox reactions

measures tendency of donor to lose electrons 

  • more negative Eo better donor

  • more positive Eo better acceptor

greater difference in potential → more energy released

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Classes of e- carriers in redox

  • freely diffusible (in cytoplasm)

    • NAD+, NADP+

    • reducing forms (NADH, NADPH) are “reducing power” of cell → biosynthesis

  • membrane-bound

    • flavoproteins, cytochromes, quinones

    • important components of ETC

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Microbe transfer of energy

reduced food molecules (glucose) → diffusible carriers in cytoplasm → membrane-bound carriers → O2, metals or oxidized forms of N/S

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autotrophs

  • use CO2 as C source

  • synthesize organic compounds used by hetertrophs

  • primary producers

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heterotrophs

  • reduced, preformed organic compounds as C source

  • convert large amounts of C to CO2

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sources of energy for growth

phototrophs: light

chemotrophs: oxidize chemical compounds (often same as C source)

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source of electrons

lithotrophs: inorganic molecules as electron donors, unique to few Bacteria and Archaea (prokaryotes)

organotrophs: organic molecules as donors, ex. glucose

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Eukarya

  • photoautotrophs (plants and algae)

  • heterotrophs (animals, protozoa, fungi)

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Photoorganoheterotroph (table 11.1)

energy: photo-light

electrons: organo-organic compounds

carbon: hetero-organic compoundsn

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aerobic respiration

  • completely catabolizes organic energy source to CO2 using glycolysis, TCA cycle, ETC

  • produces ATP indirectly via e- transport

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Glycolysis

  • Embden-Meyerhof

  • most common form of glucose breakdown

  • occurs in cytoplasm

  • functions in presence and absence (fermentation) of O2

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TCA Cycle

  • pyruvate completely oxidized

  • occurs in mitochondria of eukaryotes, cytoplasm of prokaryotes

  • generates: CO2, NADH and FADH2, precursors for biosynthesis

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Electron Transport and Ox Phos

  • net yield 2 ATP from oxidation of glucose

  • most ATP from NADH and FADH2 oxidation in ETC

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Electron Transport Chain

  • electrons from NADH and FADH2 generated by oxidation of organic substrates transferred through series of membrane bound electron carriers to a final electron acceptor

  • e- flow from carriers with more negative E0 to more positive E0 - energy released used to make ATP by ox phos

  • 3 ATP per NADH

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Where does ETC occur?

Eukarya: mitochondrial membrane

Bacteria + archaea: plasma membrane 

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Chemiosmotic Hypothesis

energy released during e- transport used to establish proton gradient and charge difference across membrane

  • proton motive force

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Proton Motive Force (PMF)

e- flow causes protons to move outward across membrane, ATP made when they move back in through F1F0ATP Synthase

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Electron acceptors

Organic e- donor

  • fermentation: endogenous organic electron acceptors

  • aerobic respiration: O2

  • anaerobic respiration acceptors: NO3-, SO4(2-), CO2, fumarate

Inorganic e- donor

  • chemolithotrophy acceptors: O2, SO4(2-), NO3-

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Anaerobic Respiration Example

Denitrification NO3- → N2

  • nitrate is e- acceptor, reduces to N gas

  • Paracoccus denitrificans: facultative anaerobe in soil 

  • depletes soil N, lower crop yield

Escherichia coli

  • uses nitrate as e- acceptor, reduces first to nitrite

  • basis of nitrite strip test for UTI diagnosis

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Fermentation

catabolism without the electron transport system and terminal acceptor

  • in cytoplasm

  • electrons from NADH → pyruvate

  • generates: NAD+, ATP, lactic acid, ethanol 

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Electron donors

organic: glucose

inorganic: chemolithotrophs - H2, NO2, Fe(2+)

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Iron-oxidizing bacteria

oxidizes iron compounds as e- source using O2 as e- acceptor, yields little energy?

ex. Acidithiobacillus ferrooxidans

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Nitrifying Bacteria

nitrification: oxidation of ammonia to nitrate

  • Nitrosomonas: ammonia to nitrite

  • Nitrobacter: nitrite to nitrate

  • used to remove ammonia in wastewater

often followed by denitrification

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Photosynthesis - phototrophs 

  1. light reactions: light energy trapped, converted to chemical

  2. dark reactions: chemical used to reduce CO2 and synthesize cell material

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Photosynthetic production

oxygenic: oxidize H2O for e-, forms oxygen

  • eukaryotes and cyanobacteria

anoxygenic: e- from other source

  • all other prokaryotes

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light absorbing pigments

eukaryotes and cyanobacteria: chlorophyll

purple, green bacteria: bacteriochlorophylls

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Asccessory pigments

  • transfer light energy to chlorophylls

  • absorb different wavelengths than chlorophylls

  • quench toxic forms of oxygen (photoprotectants, antioxidants)

  • ex. carotenoids, phycobiliproteins

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Photosystems

chlorophylls and accessory pigments that are assembled into light-harvesting arrays, embedded in thylakoid membranes

  • PSI and PSII

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Plants and cyanobacteria light reactions

  • in thylakoids

  • use chlorophyll

  • oxygenic

  • PSI and PSII

  • cyclic and noncyclic photophosphorylation 

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Green and purple bacteria light reactions

  • in plasma membrane

  • bacteriochlorophyll

  • anoxygenic

  • only PSI

  • only cyclic phosphorylation

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Archaea (photosynthetic?)

some are but they use a pigment protein called Rhodopsin instead

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Microbial rhodopsin

  • pigment protein

  • located in plasma membrane

  • found in human retina, enables vision in low light

  • absorbs light that causes conformational change in rhodopsin

  • pumps H+ our across membrane

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Anabolism

uses ATP and reducing power often in the form of NADPH synthesis

NADH used to power e- transport chains

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Calvin cycle

  • anabolic pathway for fixing CO2 into carbs

  • dark reactions

  • chloroplasts → plants

  • cytoplasm → bacteria

  • provides organic matter for heterotrophs

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Carboxylation (CC)

enzyme RuBisCo adds CO2 to Ribulose 1,5 bisphosphate generating 2 3-phosphoglycerate

  • occurs in carboxysomes

  • 18 ATP to make 1 glucose

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Reduction (CC)

3 phosphoglycerate reduced to glyceraldehyde-3-phosphate

  • requires reducing power from NADPH

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Regeneration (CC)

numerous carbs are generated

Ribulose 1,5 bisphosphate regenerated