Micro Test 3

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Micro Test 3
2015-11-09 09:10:25
lecture 21-29
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  1. oxidation reduction reactions
    • 1.electrons move from an electron donor to an electron acceptor
    • 2. carried by many enzymes
    • 3. (O2 + 2H2 -> 2H2O)
    • 2H2 -> 4e-'s + 4H+
    • 4 e-s from above + O2 -> 2O2-
    • 4H+ + 2O2- -> 2H2O
    • 4.
  2. reducing agents (reductants)
    Electron donors
  3. oxidizing agents
    electron acceptors
  4. Reduction potential Eo
    • 1. a measure of the tendency of the reducing agent to lose electrons
    • 2. Positive E = has negative change of G, gain of electrons is yield of energy
    • 3. Negative E = energy is yielded by reverse reaction, in oxidative state
    • 4. If a redox couple has a more negative reduction potential than a second couple, the reductant of the first couple will donate electrons to the oxidant of the second couple.
  5. Change in Eo
    • 1.the difference in the reduction potential between a donor and an acceptor
    • 2. proportional to the free energy of the reaction
  6. Aerobic Respiration
    use of O2 as termial electron acceptor in an electron transport system. a proton gradient is generated and used to drive ATP synthesis
  7. aerobic respiration vs. photosynthesis
    when O2 is present, much more energy can be used than when it is absent and NO3 is used
  8. energy carriers
    • 1. are molecules that gain or release small amounts of energy in reversible reactions
    • 2. some energy carriers transport e-'s
    • 3.enzymes can couple oxidation reduction rxns together for greater efficiency by cycling electron transfer with the enzyme
  9. mechanisms of ATP synthesis
    • 1. substrate level phosphorylation
    • 2. chemical gradient
    • 3. oxidative phosphorylation
  10. substrate level phosphorylation
    • 1. a type of ATP synthesis mechanism
    • 2. converts ATP from ADP by coupling rxn with ADP to an exergonic reaction
    • 3. phosphoenol pyruvate ADP -> ATP + pyruvate
  11. chemical gradient
    • 1. type of ATP synthesis mechanism
    • 2. ATP via an ATP synthase
    • 3. moves H+ from outside to inside
  12. oxidative phosphorylation
    • 1. mechanism of ATP synthesis
    • 2. use energy from electron transport to synthesize ATP production
  13. NADH
    • 1. Nicotinamide adenine dinucleotide 
    • 2.it carries two or three times as much energy as ATP.  It also donates and accepts electrons.
  14. three stages of catabolism
    • 1. polymers are converted   to monomers 
    • a.Not much energy is released 
    • b.Usually occurs outside of cells
    • 2. monomers are converted to simpler molecules
    • (ex. Pyruvate, acetyl CoA)
    • a. some energy is generated in the form   of ATP, NADH and   FADH2
    • 3. simpler molecules are degraded for   further energy generation
  15. ex of stage 1 and 2 of catabolic rxn
    • Proteins + extracellular proteases -> amino acids 
    • amino acids + deamination -> organic acids
  16. stage 1 products of catabolism
    • polysaccharides + (extracellular enzymes) --> smaller mono saccharides -> glucose
    • 2. monosaccharides brought into cell by a p
    • 3. amino acids brought in by symporters
    • 4. with protein reactant, goes to amino acids
    • with polysaccharides, goes to monosaccharides
    • lipids go to fatty acids and glycerol
  17. 3 pathways for catabolism of glucose to pyruvate
    • 1. glycolysis
    • 2. entner -dourdoroff (ED)
    • 3. pentose phosphate shunt (PPS)
  18. Glycolysis
    • 1. 1 pathway for glucose to pyruvate
    • 2. Input: 2 atp 
    • 3. Output: 4 ATP & 2 NADH 
    • 4. NET: 2 ATP & 2NADH
    • 5. other name: embder meyerhof pathway
    • 7.eukaryotes only have this pathway
  19. entner doudoroff pathway
    • 1. in some bacteria, in presence w/ glycolysis
    • 2. can start w/ sugars other than glucose
    • 3. Input: 1 atp
    • 4. 2 atp, 1 nadph, 1 nadh
    • 5. NET: 1 atp, 1 nadph, 1 nadh
    • 6. compared to glycolysis: 
    • a. get 1 less atp
    • b. gets pyruvate only 4 steps instead of 9 
    • c. provides nadph quickly
    • d. used in BIOSYNTHETIC rxns rather than catabolic
    • e. pathway found only in prokaryotes
  20. Pentose phosphate shunt
    • 1. may be used simultaneously w/other pathways
    • 2. important for biosynthesis, especially 6C and 5C sugars (for nucleic acids) 
    • 3. leads to variable C length chains + NADPH
    • 4. found in ALL euk's and prok's
  21. Pyruvate
    • 1. aerobic respiration (O2)
    • 2. Anaerobic respiration (no O2)
    • a. electrons transported to compounds other than O2
    • 3. Fermentation: no electron transport
  22. Aerobic respiration
    • 1. type of pyruvate process
    • 2. uses TCA cycle , then electrons transported to O2
    • 3. invest 3 atp -> to 1 pyruvate -> acetylCoA + 3 nadh + 1 fadh2 + 1 atp
  23. oxidative phosphorylation
    • 1. process by which energy from electron transport, which is stored in the form of proton motive force, is used to make ATP
    • 2. proton motive force: for of storage ,
    • kicks a lot of electrons out, will be available for when start ATP
    • 3. for euks , 3 atp produced per nadh & 2 atp per fadh2
  24. electron transport chain
    • 1. series of membrane-bound electron (and proton ) carriers; it establishes proton motive force during the transport of electrons from a primary electron donor to a terminal electron acceptor
    • 2. in the cytoplasm membrane of prokaryote
    • 3. in the innermembrane of mitochondria in euks
  25. catabolism
    process in which nutrients are broken down to release energy
  26. catabolic rxn stage 2 w/ lipid
    B-oxidation pathway, extremely energy yielding process
  27. TCA Cycle
    • 1. occurs in all euks and aerobic proks
    • 2. occurs in mitochondria of euks
    • 3. occurs in cytoplasm in proks
    • 4. uses ETC in stage 3, which leads to ATP production
  28. Reaction centers for electron transport
    • 1. often present as cofactors associated with proteins 
    • 2. amino acids hold metal ions in place
    • 3. iron can have oxidation states -2 to +6
    • 4. reaction centers include: metal ions, such as iron and copper, which are readily converted between many oxidation states AND heavily conjugated heteromatic rings, which allow electrons to be mobile due to electron sharing in interconnected p-orbitals
    • 5.side chains alter tendency to accept electrons (reduction potential)
    • 6. many types of hemes
  29. electron transport system components
    • 1. oxidoreductase: proteins that oxidize one substrate 
    • 2. quinone: organic compounds that function as mobile electron carriers
    • 3. cytochrome: proteins that function as electron carriers (red or brown due to association w/ heme) they may function as mobile electron carriers or be a component of an oxidoreductase protein complex
  30. electron transport system has:
    • 1. initial substrate oxidoreductase (designated a dehydrogenase) 
    • ex/ NADH dehydrogenase
    • 2. mobile electron carrier:=
    • 3. terminal oxidoreductase: 
    • A. if O2, is oxidase
    • B. if something other than O2, it is reductase
  31. Electron transport system: stage 1
    1. initial donation of electrons from NADH
  32. step 2 of electron transport donation
    transfer of electron by a mobile electron carrier (a quinone) from the NADH dehydrogenase to a terminal oxidase
  33. step 3 of electron transport system
    donation of electrons to O2
  34. a complete electron transport chain for aerobic NADH oxidation
    8 protons produced out of cell for each NADH
  35. PMF (proton motive force)
    • 1. charge (electrical ) differential
    • 2. pH (H+ concentration) defferential . either or both can be used to do work.
    • drives ATP synthase and other cell processes
    • 3. either OR both can be used to do work
    • 4. drives ATP synthase and other cell processes
  36. F1Fo ATP Synthase
    • highly conserved
    • two parts:
    • 1. Fo: embedded in membrane. forms a proton channel
    • 2. F1: cytoplasmic: generates ATP 
    • entry of 3 protons drives synthesis
    • F1 is the 2 hemispheres in visual and generates ALL ATP
  37. chemiostatic theory
    in oxidative metabolism products store their energy in an electrochemical gradient used to make ATP (Energy is stored as potential energy or PMF)
  38. ETS summary
    • 1. substrate dehydrogenase receives a pair of electrons from an organic substrate, such as NADH, or an inorganic substrate, such as H2.
    • 2. donates electrons ultimately to electron carrier, such as quinone
    • A. quinone picks up 2H+ from solution and is thus reduced to quinol
    • B. there are many quinones, each w/ a different side chain; so for simplicity theyre collectively referred to as Q and QH2
    • 3. oxidation of NADH and reduction of Q is coupled to pumping 4H+ across a membrane
    • donation of electrons to O2 happens in this step
    • 4.a. a terminal oxidase complex, which typically includes a cytochrome, receives 2 electrons from quinol (QH2)
    • b. 2H+ are translocated outside of membrane
    • c. transfer of 2 electrons through terminal oxidase complex is coupled to the pumping of 2H+
    • 5. a. terminal oxidase complex transfers electrons to a terminal electron acceptor such as O2
    • b. each oxygen atom receives 2 electrons and and combines w/ 2 protons from the cytoplasm to form one molecule of H2
    • c.E. coli ex/: ETS of e. coli can pump up to 8H+ for each NADH molecule, and up to 6H+ for each FADH2 molecule
  39. mitochondrial respiration
    • 1. in contrast to bacteria, mitochondria only have a single ETS
    • 2. while mitochondrial ETS has homologs of bacterial ETS components, it does differ from that of E.Coli by:
    • a. an intermediate cytochrome oxidase complex transfers electrons 
    • b. mitochondrial ETS pumps more protons per NADH
    • c. homologous complexes have numerous extra subunits
    • 3. ATP must be kept in outer bag,
    • 4. musts have membrane to secure those protons so it doesnt acidify
  40. anaerobic respiration
    • 1. reductases are specialized
    • 2. cells will use strongest electron donor (most negative E) and strongest electron acceptor
    • 3. in sediments: as each successive compound is used up, one w/ next most positive reduction potential will be used, usually by a different organism
    • 4. not as efficient in ATP synthase as aerobic respiration 
    • 5. small change in E between NADH and SO4 2- or NO3- , which means lower amount of proton motive force & less energy to make ATP
  41. denitrifiers
    • 1. nitrate can be successively reduced to N2: 
    • nitrate -> nitrite -> nitric oxide -> nitrous oxide -> nitrogen gas
    • 2. whole process is dissimilatory denitrification 
    • 3. using nitrite as a terminal electron acceptor does NOT generate a lot of free energy and nitrite is toxic; therefore reduction past nitrite occurs 
    • 4. any given species can only carry out 1 or 2 transformations in the series : denitrification occurs in communities
    • 5. occurs in plants, occurs w/ bacteroids
    • 6. -waterlogged soils are important source of greenhouse gases (N2O) and cause for loss of N from waterlogged soil
  42. sulfur reducers
    • 1. sulfate can be reduced to H2S (4 rxns, 5 states)
    • 2. H2S makes manure storage tanks smell
    • 3. sulfate common in ocean, common terminal electron acceptor there
  43. metal reducer
    • 1. any metal w/ multpile redox states can be reduced: Fe3+ -> Fe 2+ and Mn4+ -> Mn 2+ very common
    • 2. Fe3+ important to atmosphere before atmosphere became oxygenated
    • 3. metals like uranium and gold form precipitates when they are reduced
  44. insoluble metals
    1. may be used by bacteria that have cytochromes in their outer -membranes or in "nanowires" , which are pili -like protein structures that conduct electrons
  45. bacteria make different oxidoreductase that vary in
    • 1. substrate (electron donor)
    • 2. terminal electron acceptor
    • 3. ability to pump protons across the membrane
    • 4. affinity for terminal electron acceptor
    • a. altered by presence or absence of O2
  46. mitochondrial ets vs. bacterial ets
    • 1. mitochondria have only 1 electron transport system 
    • a. multiple electron transfer complexes 
    • 2. in bacteria, electrons can enter transport system via hydrogenase, quinones, or cytochromes
  47. chemiosmotic theory
    1. in oxidative metabolism, products store their energy in an electrochemical gradient used to make ATP (energy is stored as potential energy in PMF)
  48. Chemolithotrophs
    • 1. organisms that can derive energy from inorganic substrates
    • 2. most common electron donors are H2, reduced N compounds, reduced S compounds, and ferrous iron 
    • 3. most common electron acceptor: OXYGEN
  49. lithotroph facts:
    • 1. need a LARGE amount of inorganic materials to get enough energy to survive
    • 2. allowed to do above bc have little competition for those chemicals, can deal w/ metabolic inefficiency of lithotrophy
  50. nitrification
    • 1. ex/ of lithotrophs
    • 2. need both nitrosomes and nirtobacter in same environment
  51. sulfur oxidizing bacteria
    • 1. can cause severe environmental acidification 
    • 2. erosion of stone and concrete structures
    • 3. toxification of streams, lakes, rivers, due to formation of SULFURIC ACID
  52. methanogens
    • 1.use CO2 as a terminal electron acceptor & H2 as a donor + lithotrophy
    • 2. produce methane
    • 3. carried out by archaebacteria
    • 4. chemolithotrophs that use H2 as energy source
  53. phototrophy
    • process of harnessing photoexcited electrons to power cell growth
    • 2. light energy is used to boost electrons to high energy levels, this energy used to generate proton gradient
  54. bacteria may have 3 types of phototrophy:
    • 1. convert light directly into energy for pumping H+ using bacteriorhodopsin 
    • 2. convert light energy indirectly into energy pumping H+ by cycling electrons thru electron transport system w/
    • A. single photocycle system : bacteriochlorophyll is used
    • B. double photocycle system used: using chlorophyll 
    • both A & B require pigments to absorb light, a lot of pigment
  55. bacteriorhodopsin
    • 1. light driven protein pump
    • 2. membrane embedded protein: directly couples electron photoexcitation to driving a proton pump
    • 3. discovered in halophilic archaea
    • 4. takes LOT of bacteriorhodopsin to make H+ gradient, 1 photon moves 1 proton
    • 5. bacteriorhodopsin can cover 50% of cell
    • 6. absorbs green light , red and blue light reflected
    • 7. retinol cofactor is the thing that is excited by light
  56. photosynthesis
    • 1.use of light
    • 2. light reactions: light energy trapped and converted to chemical energy
    • ex:/ atp, nadh, and nadph
    • 3. dark reactions: chemical energy used to reduce CO2 and synthesize cell constituents 
    • ex/: calvin cycle, (6 CO2 -> glucose)
  57. photolysis
    light driven separation of an electron from a donor molecule such as H2O or H2S
  58. light absorbing molecules in photosynthesis
    • 1. chlorophyll, bacteriochlorophyll, and accessory proteins
    • 2. c and bc slightly differ in their substituent grp around ring, lead to different abosrption spectrum
    • a. chlorophyll: found in plants, algae, cyanobacteria
    •  absorbs at 430-660
    • b. form of chlorophyll found in all photosynthetic prokaryotes that are NOT cyanobacteria. absorb far red wavelengths
  59. acessory pigments
    • 1. transfer energy to chlorophylls,
    • 2. absorb light energy beyond those absorbed by reaction center pigment.
    • 3. carotenoid: abosrb blue-green to yellow pigments (470-630)
    • 4. phycobiliproteins: accessory pigments in cyanobacteria
  60. antenna complex
    highly ordered array of chlorophylls and accessory pigments that absorb light and funnel energy to a reaction center chlorophyll
  61. reaction center
    1. chorophyll that donates its excited electron to an electron transport system
  62. 3 types of photosystems:
    • 1. p I: found in some green sulfur bacteria like chlorobia
    • b. does NOT generate O2
    • 2. p II: found in variety of bacteria, including purple sulfur 
    • 3. oxygenic pathway: (z pathway)
    • a. found in cyanobacteria and chloroplasts 
    • b. includes variants of both photosystems I and II
  63. photophosphorylation
    • 1. process in which ATP is generated from a PMF that is formed by light energy
    • 2. p 1 and z pathway are non cyclic photophosphorylation
    • 3. p 2 is cyclic photophosphorylation
  64. photophosphorylation, cyclic
    • 1. p II
    • 2. NADPH is generated:
    • A. using external reductants that can directly reduce NADP+
    • B. using energy to reverse flow of electron in an electron transport chain
  65. microbial phylogeny
    relatedness of bacteria
  66. speciation, diversity
    both discuss how different things are
  67. dna sequence alignment
    allows for better alignment, icresed number of sequence matches, and increase in % identity
  68. species
    • a group of interbreeding or potentially interbreeding natural population that is redproductively isolated from other groups
    • ex/ species: cow and buffalo
    • subspecies 1: cow
    • subspecies 2: buffalo
  69. bacterial species
    collection of strains that share many stable phenotypic and genotypic characteristics
  70. criteria in determining if 2 strains are in same bacterial species
    • 1. dna hybridization: if > 70% of genomic sequences hybridize
    • 2. 16s rRNA sequence similiarity: if 16s rRNA sequence share 97% or more sequence similarity 
    • 3. average nucleotide identity: if orthologous genes share > 95 % match
  71. strain
    population of organisms that have descended from a single organism
  72. biofilm
    surface associated assemblage of cells in a polymeric (mostly polysaccharide) matrix
  73. symbiosis
    includes both positive and negative relationships
  74. ectosymbiotic mutualism
    in which symbiont remains outside of the cell of a host, such as symbionts in the rumen
  75. endosymbiotic
    symbiont lives inside of host, leads to fairly complex set of interactions
  76. fermentation of major plant carbohydrates in rumen
    cellulose, starch, sugars -> VFA, volatile fatty acids
  77. ectomycorrhizae
    colonize only the root surface
  78. endomycorrizae
    • colonize and penetrate the root cell
    • can form arbuscle , a tree like sturcture for nutrient exchange w/in a root cell
    • often called VAM, vesicular arbuscular mycorrhizae
  79. rhizobium-legume symbiosis
    • 1. flavanoid from plant bind nod protein of rhizobium, attracting bacteria to plant
    • 2. rhizobium cell binds to root hair
    • 3. root hair is induced to curl around rhizobium
    • 4. plant cell turns inward as infection thread
    • 5. bacteria travels more into infection thread
    • 6. bacteria makes bacteroids
    • 7. leghemoglobin: oxygen scavenger that binds O2 and keeps it away from nitrogenase
  80. endosymbiotic wolbachia
    • 1. obligate endosymbiont
    • 2. secrete hormone like molecules increasing its fertility in host worms
    • 3. not able to do virus/parasite transmission
    • 4. are in cytoplasm of insect cell, triggers immune response of insect