Bios313 11/22/2011

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Bios313 11/22/2011
2011-12-06 14:03:56

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  1. Grame Postive Bacteria Low G:C
    • Mollicutes
    • clostridia
    • bacilli
  2. phylum: Firmicutes
    • 3 classes:
    • Mollicutes
    • Clostridia
    • Bacilli
  3. Mollicutes
    • The mycoplasmas
    • lack cell walls and are pleomorphic
    • canno synthesize peptidoglycan precursors
    • penicillin resitant
    • lysozyme resistant
    • smallest bacteria capable of self-reproduction
  4. Mycoplasma
    • pathogens
    • Mycoplasma mycoides: bovine respiratory disease in cattle
    • Mycoplasma hypnuemoniae: pneumonia in swine and primary atypical pneumonia in humans
    • genomes: less than 1000 genes and one of the smalles prok.
  5. Class: Clostridia
    • genus: Clostridium
    • fermentative metabolism
    • ferment amino acids using stickland rxn
    • oxidation of one amino acid using another ass an electron acceptor
    • the fermentations produces responsible for unpleasant odors associated with putrefaction
  6. Impotanta species of Clostridium
    • C. botulinum: food spoilage (canned foods) botulism
    • C. tetani: tetanus
    • C. perfringens: gas gangrene
    • C. acetobutylicum: manufacture of butanol
  7. Class Bacilli
    • gram positive
    • 2 orders: Bacillales and Lactobacillales
  8. Bacillus subtilis
    • model organism for cellular differentiation, divison and other processes
    • varies species produce antibiotics
  9. Important species of Bacillus
    • B. anthracis: anthrax
    • B. thuringiensis and B. sphaericus: parasporal body and have solid protein crystals that contains toxin
  10. Famly: Staphlyococcaceae
    • facultatively anaerobic
    • nonmotile
    • gram-positive cocci
    • usually form irregular clusters
    • normally assoicated with warm blooded animals in skin, skin glands, and mucous membranes
  11. Staphylococcus aureus
    • produces virulence factor: coagulase which cause blood plasma to clot
    • produces alpha hemolysin which is a toxin which lyses cells
    • Major cause of food posioning
    • found in nasal membranes and sking and GI and urinary tracts
  12. Order Lactibacillales
    • largest genus
    • lactic acid bacteria
    • grow optimally in slightly acidic conditions pH= 4.5- 6.4
    • lactic fermentation
    • ferment sugars for energy
  13. Genus Lactobacillus
    • widely distributed in natures
    • on plants surfaces
    • in dairy products, meat, water, sewage, beer, fruits
    • normal flora of mouth , intestinal tract and vagina
  14. Streptococci
    • non motile
    • facultative and strict anaerobes
    • homolactic fermentation
    • alpha hemolysis: incomplete lysis of RBC seen as greenish zone around colony in blood agar
    • beta hemolysis: complete lysis of RBC seen as clear zone around the colony in blood agar
  15. Gram Postive High G:C content
    • Actinomycetes
    • Corynbacterium
  16. Actinomycetes
    • source of most currently used antibiotics
    • also produce metabolites that are anticancer, antihelminthic and immunosupressive ex Steptomyces
    • complex life cycle
  17. Life cycle of Actinomycetes
    • involves developments of filamentous cells (hyphae) and spores
    • hyphae can form brancing network
    • can grow on the surface of substrate or into it to produce substrate mycelium
    • some hyphae differeniate and form aerial mycelium which extends above the substatum and form exospores which are called sporangiospores
    • at this stage forms seconadry metabolites
  18. ecological significance of Actinomycetes
    • in soil
    • important role in mineralization of organic matter
    • most free living and few are pathogens
  19. Corynebacterium
    • Family: Corynebacteriacae
    • harmless soil and water saprophytes
    • many are animal and human pathogens
    • C. diphtheria: diptheria
  20. Genus : Mycobaterium
    • Family: Mycobateriaceae
    • M. bovis: tuberculosis in catter and other ruminants
    • M tuberculosis: tuberculosis in humans
    • M. leprae: leprosy
  21. Order: Bifidobateriales
    • nonsporing rods
    • founds in mouth and intenstinal tract of warm blooded animals in sewege and in insects
  22. Protobacteria
    • largest phylogenetically cohereant baterical group
    • over 2000 species assinged to more than 500 genera
  23. Purple Non-Sulfur bacteria
    • metabolically flexible
    • normall grow anaerobically as anoxygenix photo-ogranoheterotrophs
    • posses bateriaochlorohphylls a or b
    • if there is no light some carry out fermentations and can grow anaerobically
    • found in mud and water of lakes and ponds with abundant organic matter and low sulfide levels
    • some marine species
  24. cysts
    • resting cells: resitant to desiccation but less tolerant of heat and UV than bacterial endospores
    • made is response to nutrient limitation
    • have thick outer coat and store polyhydroxybutyrate
  25. Genus: Rickettsia
    • class : Alphaproteobacteria
    • order: Rickettsiales
    • family: Rickettsiaceae
  26. genus: Coxiella
    • similar to rickettsia
    • Class: Gammaproteobacteria
    • order; Legionellales
    • family: Coxiellacae
  27. common features of Coxiella and Rickettsia
    • gram-neg cell walls
    • no flagella
    • very small
    • parasite or mutualistic
    • parasite species grow in vertebrate erthrocytes, macrophages, and vascular endotheial cells
    • also live in blood-sucking arthropods which serve as vectors or primary hosts.
  28. Rickettsia rickettsii
    causitive agent of Rocky Mtn Spotten Fever
  29. Rickettsia prowazekii and Rickettsia typhi
    typhus fever
  30. Coxiella burnetti
    Q fever
  31. Caulobacteraceae and Hyphomicrobiaceae
    • have at 1 of 3 distinguishing features
    • 1. prostheca: extension of cell. including plasma mem, that is narrower than a mature cell
    • 2. stalk: nonliving appendage produced by the cell and extending from it
    • 3. reproduction by budding, the progeny cell is a bud that first appears as a small protrusion on a parent cell and enlarges to form a mature cell
  32. Genus: Hyphomicrobium
    • Class: Hyphomicrobiaceae
    • prosthecate, budding bateria
    • aerobic chmoheterotrophs
    • grow in ethanol, acetat, and one-carbon molecules ( faculative methyltroph)
    • frequently attached to solid objects in aquatic and terrestrial env.
  33. life cycle of Hyphomicrobium
    • 1. hypha forms
    • 2. new nucleoid moving into hypha
    • 3. young bud
    • 4. Hypha lengthens more and produces another bud
    • 5. swarmer cell with subpolar to lateral flagellum (1 to 3)
  34. Genus: Rhizobium
    • gram neg motile rods
    • contain poly-beta-hydroxybutrate granules
    • grow symbiotically as nitrogen-fixing bacteroids within root nodule cells of legumes
    • bacteria induce formation of and live in nodules on the roots of legumes
  35. genus: Agrobacterium
    • do not stimulate nodule formation or fix nitrogen
    • invade crown, roots, and stems of many plants
    • transform infected plants cells into autonomously proliferating tumors
  36. Agrobacterium tumefaciens
    causes crown fall disease by means of tumor-inducing (Ti) plasmid
  37. Nitrification
    • ammonia to nitrite to nitrate
    • happens by action 2 genera
    • 1. Nitrosomonas (beta)- ammonia to nitrite
    • 2.Nitrobacter (alpha): nitrite to nitrate
    • nitrate is easliy used by plants
  38. Genus: Neisseria
    • nonmotile
    • gram neg cocci
    • have capsules and fimbrae
    • some human pathogens:
    • Neisseria gonorrhoeae: gonorrhea
    • Neisseria menigitidis: meningitis
  39. Burkholderia and Ralsonia
    • nitrogen fixiation
    • both genera form symbiotic associations with legumes silimlar to rhizobia
  40. genus: Bordetella
    • mammalian parasites that multiply in respiratory epithelial cells
    • Bordetella pertussis: non motile encapsulated species
    • causes whooping caugh
  41. order Pseudomonadales
    • family: Pseudomonadaceae: has 15 genera
    • psuedomonas most important genus
    • gram neg straight or slightly curved rods
    • motile by one or several polar flagella
  42. importance of Pseudomonads
    • metabolically versatile
    • degrade alot of organic molecules
    • mineralization
    • microbial breakdown of organic materials to inorganic substrates
    • important in experiemtns
    • major animal and plant pathogens
    • some cause spoilage of refrig. food
    • can grow at 4 c
  43. order: Vibrionales
    • one family: Vibrionaceae that has 8 genera
    • most are aquatic
    • most free-living
    • important pathogens
    • symbiotic in luminous organs of fish and other aniamsl
    • closley related to 2 other orders Enterobacteriales and Pasteurellales
  44. Vibrio cholerae
    • causes cholera
    • 2 circular chromosomes
    • copies of some genes present on both chromosomes
  45. Vibrio fischeri
    • capable of bioluminescence
    • emession of ligth catalyzed by luciferase
    • 2 species
    • free-living
  46. order: Enterocateriales
    Escherichia coli

    • inhabits most intenstinal tracts of animals
    • idicators organisms for testing water for fecal contamination
    • some strains are pathogenic
    • gastroenteritis
    • UTI
  47. important pathogenic enteric bacteria
    • Salmonella: typhoid fever and gastroenteritis
    • Shigella: bacillary dysentery
    • Klebsiella: pneumonia
    • Yersinia: Plague (black dead)
    • Erwinia: blights, wilts, crop plants
  48. order: Pasteurellacae
    • important pathogens
    • Pasteurella multiocida: fowl cholera
    • Pasteurella haemolytica: pneumonia in cattle sheep and goats
    • Haemophilus: meningitis in children
  49. order: Bdellovidbrionales
    • family: Bdellovidbrionaceae
    • which has 4 familys Bdellovibrio:
    • predatory bacteria
  50. Class Delata Proteo Bacteria
    • Desulfuromondales
    • Myxococcales
    • Desulfomonile
    • Syntrophobacteraceae
    • Desulfobactereae
    • Desulfobubbasceae
    • Desulfovibrionales
  51. Class: Epsilon Proteo Bacteria
    • smallest proteobacteria class
    • one order: Campylobacteriales with 3 families
  52. Genus: Campylobacter
    pathogenic and nonpathogenic
  53. Campylobacter fetus
    • reproductive disease and abortions in cattle and sheep
    • septicemia (pathogens or their toxins in blood)and enteritis in (inflammation of intestinal tract) humans
  54. Campylobacter jejuni
    • abortions in sheep
    • enteritis diarrhea in humans
  55. Genus Helicobacter
    • Helicobacter pylori
    • cuases gastritis and peptic ulcer disease
    • produce large quantaties or urease
    • urea hydrolysis apears to be associated with birulence
  56. Aquificae and Thermotogae
    • all thermophillic prok
    • optimum growth at temps above 85 C Arachea
    • Bacteria: Aquificae and Thermotogae
  57. phylum Aquificae
    • deepest and oldest branch of bacteria
    • 1 clas, 1 order and 5 genera
    • Aquifex and Hydrogenobacter
  58. Phylum Themotgae
    • second deepest branch of Bacteria
    • 1 class, 1 order, and 6 genera
    • Thermotoga
  59. Thermotoga
    • gram neg rods
    • optimum growth at 80 C maz at 90 C
    • grow in active geothermal areas
    • marine hydrothermal vents and terrestrial solfataric springs
  60. Deinococcus Thermus
    • class: Deinococci
    • order: Deincoccales and Thermales
  61. Deinococcus
    • spherical or rod-shaped
    • pars or tetrads
    • mesophilic
    • aerobic
    • catalas pos
    • produce acid from only a few sugars
    • genome: 2 ciruclar chromosomes, a megaplasmid, and small plasmid
    • radiation resistant due to the ability to repair the genome which is damaged
    • DNA system repair
    • resistant to desiccation and radiaiton
    • isolated from gound meat, feces, air, fresh water,
  62. photosynthetic bacteria
    • 3 groups of gram neg photo. bact
    • purple bacteria
    • green bacteria
    • cyanobactiria
  63. cyanobacteria
    • carry out oxygenic photosynthesis
    • have 2 photosystems
    • use water as electrom donor and geneate oxygen during photosyntheis
    • obligate photolithoautotrophs
    • can grow slowly in the dark as chemoheterotorpsh
  64. hormogonia
    small motile fragments of filamentous cyanobactiera
  65. akinetes
    • specialized, dormant, thick-walled resistant cells that are resistnat to desiccation
    • oftner germentate to from new filaments
  66. baeocytes
    • produced by multiple fission
    • small, spherical cells, escape when the outer wall ruptures
    • some motules by gliding motiltiy
  67. heterocysts
    • specialized cells used for nitrogen fixiation
    • produced by an organism is nitrogen deprived
    • differentiate from individual cells in fimalent
    • reorganization of photosynthetic mem
    • thick heterocyst wall prevents oxygens diffusion into heterocyst which would inactivate nitrogenase which is the enzyme responsible for nitrogen fixiation
  68. ecology of cyanobacteria
    • tolerant env. extreme
    • grow up to 75 C
    • often primary colonizater
    • caused bloo,s in nutreint rich ponds and lakes produce toxin
  69. symbiotic relationships of cyanobacteria
    • phototrophic partner to most lichens
    • symbionts with protozoa and fungi
    • nitrogen-fixing species for associations with plants
  70. Phylum Chlamydia
    • gram neg
    • obligate intracellular parasites
    • cause diease
    • can grow within hosts , protist and vertebrate and invertebrate cell with out adverse effects
  71. genus Chlamydia
    • nonmotile coccoid gram neg bacteria
    • cell walls lack muramic acid and peptidoglycan
    • small genomes
    • obligate intracellular parasites
    • forms elementatry body and reticulate body
  72. C. trachomatis
    • infects humans and mice
    • causes trachoman, nongonococcal urethritis, and other disease in humans
  73. C. psittaci
    • infects humans and many other animals
    • causes psittacosis in hums
  74. C. pneumoniae
    cause human pneumonia
  75. phylum Spirochaetes
    • gram neg bacter
    • slender long flexible helical shape
    • creeping and crawl;ing molitlity due to axial fialment
    • chemoheterotrophs
  76. spirochete motility
    axial fibrils rotate and cause a corck-screw shape outer sheath to roated and move throughout the liquid
  77. Bacteroides
    • gram neg rods
    • anaerobic chemoheterotropsh
    • fermentatives
    • oral cavity and intestinal tract
  78. Microorganisms
    • Beneficial: provide vitamins, decompose, and
    • produce antibiotics
    • Harmful: responsible for infections
  79. Louis Pasteur
    • Disprove spontaneous generation with swan flask
    • experiment.
    • Would be full of organisms if spontaneous
    • generation was true. No organisms
    • Organisms grow from dust contacting sterile
    • liquid
  80. Prokaryotic:
    • Arachea
    • bacteria
  81. Eukaryotic:
    • Plant (macro)
    • Animals (macro)
    • Algae
    • Fungi
    • Protozoa
  82. Examples of microorganism’s
    • Agriculture: N2 fixation, nutrient
    • cycling, and animal husbandry
    • Food: food preservation, fermented
    • foods, food additives
    • Disease: indentifying new diseases,
    • treatment and cure, and disease prevention
    • Plant disease:
    • great potato blight of Ireland caused by oomycetes bacteria another example
    • anthrax, Bacillus anthracis. Bacteria
    • Energy/environment: biofuels (methane
    • and ethanol), bioremediation, and microbial mining
    • Biotechnology: genetically modified organisms, production of
    • pharmaceuticals, gene therapy for certain disease
  83. Coccus:
  84. Bacillus
    • elongated
    • or rod shaped
  85. Spirochetes
  86. Actinomycetes
    chains of rod shape and produce antibiotics.
  87. To test pathogen
    • Step 1: isolate blood samples from and
    • healthy animal and diseased animal
    • Step 2: grown suspected organism in a
    • pure culture
    • Step 3: give organism to healthy
    • animal, should cause disease
    • Step 4: reisolate organism from second
    • animal and compare it to the first pure culture. Should be the same.
  88. Fermentation
    creates biofuels (ethanol) by fermenting sugar with the activities for specific microorganisms
  89. Microbial ecology
    • Involved in
    • carbon, nitrogen, and sulfur cycles

    • Oxidation of
    • iron, sulfur, and ammonia obtain energy
  90. Self-feeding:
    • uptake
    • chemicals from the environment and eliminate waste into the environment. Open
    • system
  91. Self-replication:
    • chemicals from
    • the environment are turned into new cells under the direction of pre-existing
    • cells
  92. Differentiation:
    • forming a new cell structure is
    • part of the life cycle (example: producing a spore)
  93. Chemical signaling
    • cells communicate and interact through chemicals that are
    • released or absorbed
  94. Evolution
    • evolve to display new biological properties. Short, rapid
    • generation time leads to evolution
  95. 1 nm
    200 µm
  96. 1 µm
    • micrometer
    • = 10-6 m
  97. 1 nm
    10-9 m
  98. 1 angstrom
    Å= 10-10 m
  99. light
    refracted (bent) when passed through a medium
  100. refractive index
    a measure of the amount a substance slows the velocity of light
  101. Lenses
    strength related to focal length. the short the focal length= greater magnification
  102. focal point
    where the light rays focus
  103. focal length
    • distance between the center of the
    • lens and the focal point
  104. working distance
    • distance
    • between the objective and the slide with the specimen
  105. Microscope resolution
    • ability of the lens to separate or
    • distinguish small objects that are close together.
  106. Wave length of light effects resolution
    Shorter wavelength = greater resolution
  107. Light microscope
    • bright-field microscope,
    • dark-field microscope, phase-contrast microscope, fluorescence micro scope, and
    • confocal microscope. Compound
    • microscopes (2 lenses).
  108. bright-field microscope
    • produces dark image against a
    • bright background

    Many objective lenses.

    Living organisms
  109. Parfocal microscope
    • remain in focus when the
    • objectives are changed.

    • Total magnification: product of
    • the magnifications of the ocular lenses and the objective lenses.

    • Too see objects really small,
    • replace water with immersion oil. The different medium caused the light rays to
    • refract and reflect different. Oil = 100x
  110. dark-field microscope
    • image is formed by light reflected
    • or refracted by the specimen and produces a bright image of the object against
    • a dark background

    • see living, unstained
    • preparations

    • observe internal structures in
    • eukaryotic cells

    identify bacteria

    gives more contrast
  111. phase-contrast microscope
    • converts slight differences in
    • refractive index and cell density into easily detected variations in light
    • intensity

    • light rays from the hallow cone
    • of light passes through the unstained cell and dark compared to background

    living cells


    internal structures

    detect endospores
  112. The differential interference contrast

    The differential interference contrast
    • DIC. Creates image by detecting
    • differences in refractive index and thickness of different parts of the
    • specimen

    Living cells, unstained

    Appear brightly- colored and 3-D

    • Cell walls, endospores, granules,
    • vacuoles, nuclei are clearly visible
  113. fluorescence micro scope
    • exposes specimen to ultraviolet,
    • violet, or blue light

    • Specimens usually stained by
    • fluorochromes (make fluorescent).

    • Shows bright image of the object
    • that results from the fluorescent light that is emitted by the specimen

    Light generated by laser

    • Used to indentify unknown
    • pathogens (fluorochrome-labeled probes: antibodies or tags.

    • Can localized specific proteins
    • in cells
  114. confocal microscope
    • confocal scanning laser microscopy
    • (CLSM) creates a sharp, composite 3-D image by using laser beams, an aperture
    • to eliminate stray light and computer interface

    study of biofilms

    rotate in space on computer

    can also use for florescence
  115. staining and preparation:
    increase visibility of specimen

    • accentuates specific morphological
    • features

    preserve specimen

    increase contrast
  116. dyes:
    • make internal and external
    • structures of the cell more visible by increasing the contrast with the
    • background 2 common features
  117. Chromophore groups
    • chemical
    • groups with conjugated double bounds. Gives the dye its color
  118. ionizable dyes
    have charged groups

    basic dyes: positive charges

    acid dyes: negative charges
  119. simple stain
    single stained used

    • determines size, shape and
    • arrangement of bacteria
  120. differential staining
    • divides microorganisms into groups
    • based on their staining properties
  121. gram staining
    • two groups, color based on
    • difference in the structure of the cell wall.

    gram positive: purple

    gram negative: pink/red
  122. acid-fast staining
    • used to detect the presence or
    • absence of structures (endospores, flagella, capsules)
  123. endospores staining
    • heated, and double staining technique. The endospore turns one
    • color while the vegetative cell is a different color.
  124. Capsule staining
    • used
    • to visualize capsules around bacteria. Negative
    • staining makes the capsules colorless against the background
  125. Flagella staining
    • mordant
    • applied to increase the thickness of the flagella
  126. fixation
    • preserves internal and external
    • structures

    • usually killed and firmly attached
    • to slide
  127. Heat fixation
    • used with bacteria and archaea.
    • Preserves the overall morphology but not internal structures
  128. Chemical fixation
    • larger
    • more delicate organisms. Protects fine cellular substructure and morphology
  129. Electron microscopy
    • Electrons replace light with a
    • illuminating beam

    • Wavelength is shorter than light
    • and results in a higher resolution

    Morphology in great detail

  130. Acid-fast staining: Mycobaterium
    • High
    • lipid content in the cell walls helps stain
  131. Transmission electron microscope (TEM):
    • electrons scatter as they pass
    • through the sections of the specimen

    Under vacuum

    • Denser regions in a specimen
    • scatter more electrons and appear darker.


    Black and white
  132. Specimen preparation for TEM
    • must be cut very thin, After cut, they are chemically
    • fixed and stained with electron dense materials (heavy metals) that will
    • scatter electrons

    Negative stain: heavy metals create a dark background

    • Shadowing: coating specimen with a thin film of heavy metal on one
    • side only (morphology, flagella, and DNA). 3-D image

    • Freeze etching: freeze the specimen and fracture it along the lines
    • of greatest weakness. Allows 3-D observation of shapes of intracellular
    • structures and reduces artifacts
  133. Scanning electron microscope
    • use electrons reflected from the
    • surface of the specimen to create a detailed image. 3-D image of the specimen’s
    • surface. Black and white. Replace water with carbon dioxide
  134. Electron cryotomography
    • freezing
    • technique 3-D. extremely high resolution. Can see cytoskeletal elements,
    • magnetosomes, inclusion bodies, flagellar motors, and viral structures.
  135. Scanning probe microscopy
    • Scanning tunneling microscope: 100 millionX. Atoms on the surface
    • of a solid. Use of a steady current through a tunnel that is maintaining
    • between the microscope probe and the specimen. The up and down movement of the
    • probe and it maintains current produces an image of the surface of the
    • specimen. DNA

    • Atomic force microscope: no current. Sharp probe moves over the
    • surface of a specimen at a constant distance and the up and down probe detects
    • the distance and creates an image
  136. Prokaryotic Cells
    • Complex cell walls/ membranes
    • Simpler interior
    • Much smaller than Eukaryotes
    • Range from 7,000 nm to 27 nm
  137. Selective permeable barrier
    • allow
    • components/ molecules to go in and out.
  138. uniporter
    • one
    • component transported in one direction
  139. symporter:
    • 2
    • components transported at the same time in the same direction
  140. antiporter
    • 2
    • components transported at the same time if opposite directions
  141. Nutrient and water
    • interchange
    • or nutrient exchange
  142. PM Detection of environmental
    • proteins
    • are sensors of the environment source of nutrients or toxic compound, PH, temp
    • and react to adapt and survive
  143. PM Involved in movement
    • react
    • depending on environment
  144. PM difference between prok. and euk.
    • Cholesterol (steroid) gives stability in PM to
    • Eukaryotic cells and bateriohopantetrol (hopanoid) gives stability plasma
    • membrane to Prokaryotic cells
  145. integral protein:
    goes all the way through the PM
  146. peripheral protein
    only stick to one side
  147. PM of prok
    • phospholipid bilayer with glycolipids, sugars,
    • and proteins.

    Inner membrane differ depending on amino acids
  148. Internal membranes of prok
    • in
    • cyanobacteria the membrane system is involved in photosynthesis and contain
    • inclusions
  149. Mesosomes
    • false
    • results, artifacts
  150. Phospholipid bilayer
    • Hydrophobic: fatty acid tail,
    • H-C bonds with –COOH (carboxylic acid)

    Hydrophilic: glycerol head

    Dynamic structure

    • Proteins can move through
    • membrane help with nutrient and waste transport through PM
  151. Gram-positive cell wall

    • Thick
    • peptidoglycan layer in cell wall

    Plasma membrane

    Teichoic Acid anchors PM to peptidoglycan

    Negative charge
  152. Gram-negative cell wall

    Cell wall has a thin peptidoglycan layer and outer membrane

    Plasma membrane

    Outer membrane contains porin (transport proteins)
  153. LPS (lipopolysaccharide) Mono phospholipid layer:
    • causes negative charge
    • Outer lipid layer is LPS and the inner
    • lipid layer is a phospholipid layer (not phospholipid bilayer)

    which is a toxic component

    has O side of the chain which is an antigen

    • differences in O chains determine what kind of
    • antibodies or how to fight the infection

    • Lipid A (glucosamine and fatty acid, P) + core
    • polysaccharide + O side chain (antigen)
  154. Braun’s lipoprotein
    • anchors
    • the outer membrane to the peptidoglycan layer
  155. Porin
    • hallow
    • and form complex that allows the pass of molecules.
  156. Periplasmic space
    • space in cell wall between the peptidoglycan and
    • the plasma membrane

    • Differences in colors due to structure of cell
    • wall
  157. Peptidoglyca
    • : formed
    • by simple monimers and becomes repeated molecules in a long chain that are
    • parallel to each other and linked together by peptides to form a thick layer.
    • (Gly-Peptide interbridge)
    • .
    • Peptidoglycan is not stained put is permeable to the crystal violet and it goes
    • into the periplasmic space
  158. Osmotic
    Protection of the cell wall
    • The cell wall protects the cell from the
    • environment and osmotic stress.
  159. Penicillin
    • inhibits
    • call wall synthesis (formation) and forms protoplast.
  160. protoplast
    • cell without a cell wall and needs same osmotic
    • pressure on the outside of the cell as on the inside of the cell in order to
    • survive.

    • When a protoplast is
    • transferred into a dilute medium (water into cell) the cell swells due to water
    • influx and causes it to lysis (break)
  161. Capsule
    • in pathogenic cells
    • resistant to phagocytosis
    • ex: Streptococcus
    • pneumoniae causes strep throat
    • have 3 layers
    • slime layer
    • Glycocalyx
    • S-layer: contributes to fool the immune system.
    • Sticks to the surface to produce biofilm.
  162. Biofilm
    • hard to treat, more resistant to chemicals.
    • Water contamination.
    • Functions:
    • Adhesion to surfaces
    • Protection against environmental conditions (PH,
    • temperature)
    • Protected against the immune system because
    • cells will a capsule cannot be detected by the immune system
    • Produced when the cell experiences environmental
    • stresses.
  163. Fimbraie
    • thinner
    • than flagella and are not involved in motility
  164. Pili
    • less abundant than Fimbriae and Larger and are
    • required for bacterial mating. They interchange DNA by horizontal transfer.
  165. Patterns of Flagellum
    • Monotrichous: one
    • flagellum

    • Amphitrichous: two
    • flagellum, one at each pole

    • Lophotrichous: two
    • flagellum clusters, one at each pole

    Peritrichous: flagellum evenly spread over the surface
  166. Flagellum
    • Gram-Positive: less
    • complex than negative.
    • M ring in PM about 22 nm
    • S ring in Periplasmic Space
    • Rod goes connected to the S
    • ring and goes through periplasmic space and peptidoglycan layer
    • Hook inside of rod
    • Filament inside of the hook

    • Gram-Negative:
    • More complex than positive
    • All positive components plus
    • the following
    • P ring in peptidoglycan layer
    • L ring in outer membrane
  167. Self assembly of flaglellum
    pushed through hallow base.

    One globular protein

    • Ribosome to mRNA flagellin
    • (filament) synthesized through hook

    • Once formed they are rigid like
    • a propeller
  168. Flagellum movement
    • Movement depends on how many
    • flagellum and where they are located
    • Mechanical portions are
    • proteins
    • Rotation driven by proteins or
    • sodium gradients and force direction in one direction or another
    • Motor proteins near PM and is
    • connected to a sensing mechanism that responds to the gradient of sodium ions
    • and caused it to move
    • Mot B and Mot A integral
    • proteins in PM
    • Fli G, M , N compose the C ring
  169. Chemotaxis
    • movement towards or away from
    • chemicals.

    Have chemoreceptors

    Positive: towards

    Negative: away
  170. Interior
    of Prokaryotic Cell
    • Inclusion bodies
    • organic or inorganic and are
    • used for storage of glycogen and glucose
    • With or without a single
    • membrane
    • Organic example: poly-β-hydroxybutric
    • acid (PHB) which is used for bacteria to store polymers of glycogen (glucose =
    • monomer)
    • Inorganic example:
    • polyphosphate, sulfur, iron (magnetosomes)
  171. Interior
    of Prokaryotic Cell
    Gas vesicles
    • makes
    • bacteria float close to the surface in aquatic environments
  172. Interior
    of Prokaryotic Cell
    • protein synthesis
    • in the cytoplasmic matrix and are smaller than Eukaryotic ribosomes
  173. Interior
    of Prokaryotic Cell
    • where DNA is located and used
    • to classify organisms. Has NO nuclear membrane
  174. Interior
    of Prokaryotic Cell
    • resistant structure that is
    • produced when the organism experiences a harmful environment.

    Gram-positive bacteria: Bacillus

    a lot of layers

    position of endospore varies
  175. cell division
    • axial filament formation: the PM invaginates and starts
    • to separate the DNA (cell wall around PM remains unchanged)
    • septum formation:of the PM to completelyseparate into 2 sections inside the cell wall each surrounded by PM, Smallsection is the endospore
    • Engulfment of the endospore by other part of the cell
    • DNA not located inside of the endospore starts to degrade because of the harmful environment
    • Cortex formation around the endospore by adding a lot of layers around it
    • Coat synthesis begins and a exosporium surrounds the spore coat which surrounds the cortex which surround the endospore and protects the DNA
    • After the completion of coat synthesis there is an increase in refractility and heat resistance
    • Lysis of sporangium causes the spore to be released and is then a free spore
  176. Euk and prok differences
    Membrane-delimited nuclei

    Nucleus has double membrane

    • Membrane-bound organelles that
    • perform specific functions

    • More structurally complex
    • (internal) than Prok.

    All fungi have cell walls
  177. Plasma
    Membrane and Membrane Structure of Euk cells
    • Fluidmosaic model: fluid and flexible
    • Allows proteins to move
    • Majormembrane Lipids: phospholipids
    • Phosphoglyceride
    • Sphingolipids: greater in number in PM because they are related to sensing and signaling
    • Cholesterol (no cholesterol in
    • Prok.)
    • Lipid rafts: micro-domains that are enriched for certain lipids (sphingolipid)
  178. Cell movement in Euk Cells
    • cell movement- shape and
    • direction

    • transduction- signaling that
    • causes a cascade to a genetic response
  179. Cytoplasmic
    Matrix and Cytoskeleton
    in Euk Cells
    cytoplasmic matrix: (CM) internal network where many organelles are located

    • cytoskeleton: formed
    • from filaments and plays a role in cell shape and cell movement
  180. microfilaments in Euk
    one type of protein: actin

    4 to 7 nm in diameter

    • Scattered within the CM or
    • organized into networks and parallel arrays

    • Involved in cell motion and
    • shape changes
  181. microtubules in Euk
    • more than 1 type of protein:
    • tubuline (2 types: α-subunit and β-subunit) and is constantly being synthesized
    • and desynthesized

    • shaped like thin cylinders
    • about 25 nm in diameter

    helps maintain cell shape

    • involved with microfilaments in
    • cell movement

    • participate in intracellular
    • transport processes because it creates “high ways” for motor proteins to move
    • along that transport molecules and requires energy
  182. intermediate
    filaments in Euk
    only in cytoskeleton

    10 nm in diameter

    Role unclear

    • Helps cells connect together to
    • form tissues
  183. Endoplasmic
    reticulum (ER) in Euk
    • Irregular network of branching
    • and fusing membranous tubules (cisternae, cistern) and flattened sacs
    • Group of cisternae creates ER

    • Functions
    • Transport:proteins, lipids, and other materials in cell
    • Cellsynthesis
    • Proteins (rough ER)
    • Lipids (smooth ER)
    • Lysosomes.
  184. Rough
    ER in Euk
    Ribosomes attached

    • Synthesis of secreted proteins associated
    • with ribosomes in vesicles
  185. Smooth
    ER in Euk
    No ribosomes

    • Synthesis of lipids of
    • associated enzymes
  186. Golgi
    Apparatus in Euk
    • Membranous organelle made of dictyosomes: cisternae stacked on each
    • other

    • Involved in modification,
    • packaging, and secretion of materials

    • Receives vesicles from the ER
    • and they fuse with the Golgi and then modification takes place

    • Peripheral
    • tubules

    • Cis/forming
    • face: associated with ER and receive secretary vesicles

    • Trans/maturing
    • face: where molecules exit
  187. Lysosomes in Euk
    Single Membrane-bound vesicle

    • Involved in intracellular
    • digestion

    Contains hydrolases, enzymes which hydrolyze molecules

    • Enzymes process nutrients or
    • help degrade damaged or unused cells

    • Function best under slightly
    • acidic environment which is maintained
    • by pumping protons into their interior

    Formed in ER
  188. Biosynthetic
    Secretory Pathway in Euk
    • Proteins synthesized by
    • ribosomes on the rough ER and a released small vesicles cis face of Golgi trans
    • faces of Golgi and released
    • After vesicles released from trans they
    • deliver their contents to lysosomes or cell membrane
    • Membrane of vesicle because part of the
    • cytoplasm after it exits the Golgi
  189. Quality
    assurance mechanism
    in Euk
    • Ubiquitin
    • polypeptides: target unfolded or misfolded proteins that are
    • secreted by the cystol to destroy

    • Proteasomes:
    • destroy target proteins that are damaged and need to be destroyed

    Requires activation by enzyme

    Requires ATP
  190. Steps of degradation of
    protein in Euk
    • Ubiquitin
    • protein ligation: needs
    • ATP and 3 enzymes: Ubiquitin-activating, Ubiquitin-conjugating, and Ubiquitin-ligase.
    • Protein attached to polyubiquitin chain

    • Recognition
    • of Ubiquitin-conjugated protein: labeling. recogniczed by
    • proteasome

    • Degradation
    • of Ubiquitin-conjugate protein: by proteasome into degraded
    • peptides (was damaged protein). Need ATP

    • Release
    • and recycling of Ubiquitin: regeneration
  191. Endocytic
    in Euk
    • Endocytosis: bring
    • materials inside of cell

    • Solutes or particles are taken
    • up by extensions of the cytoplasm and are enclosed in vesicles that are pinched
    • from the PM, the PM fuses and the vesicle is engulfed

    • Most cases delivered to
    • lysosomes and destroyed
  192. Phagocytosis in Euk
    • Endocytosis.
    • Uses the cell surface protrusions to surround and engulf a particle when a
    • substrate is detected by receptors in the membrane
  193. Phagosomes in Euk
    • resulting vesicles which are
    • formed by subunits and once inside of the cell it will disassemble
  194. Receptor-mediated
    Endocytosis (Clathrin-dependent Endocytosis):
    • involves membrane regions
    • called coated pits (coated by clathrin protein on the cytoplasmic side)

    • Coated pits have external
    • receptors that specifically bind to macromolecules

    • The coated pits are pinched of
    • to form coated vesicles
  195. Caveolae-dependent
    Endocytosis in Euk
    • Molecules enriched in
    • cholesterol and the membrane protein Caveolae

    • Do not deliver their contents
    • to lysosomes

    • Play a role in signal
    • transduction

    • Transport of small molecules
    • and macromolecules
  196. Autophagy in Euk
    digestion without Endocytosis

    • Digestion and recycling of
    • cytoplasmic components (internal parts: damage cell part, organelles, or
    • mitochondria)

    • Autophagosome: double
    • membrane the surround the cell component

    Double membrane is possibly from ER

    • Autophagosome fuses with late
    • endosome which forms a lysosomes
  197. Ribosomes in Euk
    80S in size

    • Maybe attached to ER or free in
    • cytoplasmic matrix

    • Proteins made on ribosomes of
    • RER are often secreted or inserted into the ER membrane to create integral
    • proteins. Attached ribosomes synthesize secretory or membrane proteins

    • Free ribosomes synthesize
    • nonsecretory and non membrane proteins and some are inserted into organelles
  198. Mitochondria in Euk
    • site of tricarboxylic acid
    • cycle activity (TCA cycle)

    where ATP is generated

    • electron transport and
    • oxidative phosphorylation

    double membrane
  199. inner membrane of mt.
    • a lot of folding structures and
    • are attached to ATP-ase which is present on the membrane and is a
    • enzyme/protein

    • cristae: crista
    • folded structures inside of IM increase surface area and production of ATP

    • location of enzymes and
    • electron carriers for electron transport and oxidative phosphorylation

  200. outer membrane of mt
    • contains
    • porin
  201. mitochondrial matrix in Euk
    inside space of inner membrane

    • contains ribosomes,
    • mitochondrial DNA, and large phosphate granules

    • contains enzymes of the TCA
    • cycle and enzymes involved in catabolism of fatty acids

    carboxylic acid
  202. Chloroplasts in Euk
    • pigment-containing organelles
    • in plants and algae

    • site of photosynthetic
    • reactions

    double membrane
  203. stroma in euk
    • matrix in the Inner Membrane of
    • the chloroplast

    contains DNA


    lipid droplets

    starch granules
  204. thylakoids in euk
    • flattened,
    • membrane-delimited sacs and is the site of light reactions. Traps light energy
    • to generate ATP, NADPH, and Oxygen\
    • grana:
    • granum, stacks of thylakoids
    • pigment necessary for
    • photosynthesis
    • site of dark reactions: formation for carbohydrates from water and carbon
    • dioxide
  205. nucleus in Euk
    • membrane-bound structure that
    • houses genetic material or Euk. Cell has

    double membrane
  206. chromatin in Euk
    • dense fibrous material in
    • nucleus

    gives stability

    contains DNA

    • condenses to form chromosomes
    • during cell division

    double membrane with pores

    • transfer to cytoplasm through
    • meditative transport
  207. nuclear envelope in euk
    • double membrane structure that
    • delimits the nucleus

    • nuclear pores that allow
    • materials to be transported into or out of the nucleus that are regulated by
    • proteins
  208. nucleolus in euk
    not membrane enclosed

    important ribosome synthesis

    • directs synthesis and
    • processing of rRNA

    • directs assembly of rRNA and
    • ribosomal proteins to form ribosomes
  209. mitosis in Euk
    one component of cell cycle

    distributes DNA to 2 nuclei

    • ploidy: number
    • of chromosomes

    • ploidy of parent and progeny
    • cells are the same

    • diploid organism remains
    • diploid
  210. meiosis in euk
    • two stage process of nuclear
    • division

    • hapliod
    • ploidy

    haploid gametes
  211. Cell Wall

    Algae: cellulose and protein

    Diatoms: silica

    • Fungi: chitin, cellulose,
    • glucan

    • Oomycytes (not true fungi):
    • cellulose
  212. Pellicle
    • rigid
    • layer of components just beneath plasma membrane
  213. Protozoa pellicle
    • Not as strong or rigid as cell
    • wall

    Provides shape and protection

    Rich in proteins

    Helps with Endocytosis
  214. Cilia
    • 50
    • to 200 micrometers long
  215. Flagella
    • 100-200
    • micrometers long

    Axoneme: set of microtubules (9+2) arrangement

    • Basal body: at
    • base of flagellum or cilia and directs synthesis of flagella and cilia and
    • anchors
    • membrane bound
  216. Prokaryotic and Eukaryotic
    • Basic chemical composition:
    • same molecules and polymers

    Genetic code

    Basic metabolic processes
  217. Metabolism
    • the
    • total of all chemical reactions in the cell
  218. Catabolism
    the energy-conserving rxns
  219. Anabolism
    • the synthesis of complex organic molecules
    • from simpler ones

    Requires energy. ATP

    • Requires a source of electrons that are stored
    • in the form of reducing power
  220. Energy
    sources (ATP) Chemoorganotroph
    • energy
    • from organic molecules
  221. Energy
    sources (ATP) Chemolithotroph
    • energy
    • from inorganic molecules
  222. Energy
    sources (ATP)Prototroph
    • energy from
    • light
  223. Carbon
    source (makes precursor metabolites)

  224. Carbon
    source (makes precursor metabolites)
    • organic
    • molecules
  225. Electron
    source (energy) Organotroph:
    organic molecules
  226. Electron
    source (energy) Lithotroph
    • organic
    • molecules
  227. Precursor metabolite + energy
    • = monomers/building blocks to make macromolecules
    • The processes organisms use to obtain energy
    • and do chemical work are the basis of functioning ecosystems
  228. Energy
    • capacity
    • to do work or cause a particular change
  229. Chemical work
    • synthesis
    • of complex molecules
  230. Transport work
    • take up of
    • nutrients, elimination of wastes, and maintenance of ion balances
  231. Mechanical work
    • cell motility
    • and movement of structures with in cells
  232. Thermodynamics
    • a science that analyzes energy changes in a
    • collection of matter called a system. ( all other matter in universe besides
    • the system is call its surroundings)
  233. Energy units
    • Calorie
    • (cal): amount of heat energy needed to raise 1 gram of water from 14.5 to 15.5 °C

    Joules (J): units of work capable of being done by a unit of energy

    1 cal = 4.184 J
  234. 1st law of thermodynamics
    energy cannot be created or destroyed

    • The total energy in the universe remains
    • constant
  235. 2nd law of thermodynamics
    • physicl and
    • chemical processes lean towards the most possible disorder/chaos
  236. Entropy
    • the
    • amount of disorder in a system
  237. Free energy
    • the change in energy that can occur in
    • chemical reactions and other processes

    • used to decide if rxn will spontaneously
    • occur
  238. ∆G = ∆H- T * ∆S
    • ∆G = change in
    • free energy and is the amount of energy available to do work.

    • ∆H= the change
    • in enthalpy (heat)

    • T= temperature
    • in Kelvin

    • ∆S= change in
    • entropy

    • Free energy is always defined at standard
    • conditions
  239. Equilibrium
    • Keq=
    • equilibrium constant: the equilibrium concentrations
    • of products and reactants (products/reactants)

    • When the forward and reverse reaction rates
    • are equal
  240. Exergonic

    Keq> 1

    ∆ is G negative

    Thermodynamically favorable, spontaneous rxn

    Products favored
  241. Endergonic
    • Keq = 1
    • ∆G is positive
    • non spontaneous
  242. ATP
    • adenosine
    • 5-triphosphate and is the energy currency of the cell

    • in Exergonic rxns the breakdown of ATP is
    • couple with and Endergonic rxn to make the Endergonic rxns more favorable
  243. rxn that
    make ATP (ADP +P )
    aerobic respiration

    anaerobic respiration


  244. rxns that require ATP
    chemical work

    transport work

    mechanical work
  245. oxidation-reduction rxn
    • electron
    • transfers
  246. Electron carriers
    • used to transfer electrons from an electron
    • donor to an electron acceptor.

    • When electrons are transferred, it can result
    • in a release of energy which can be conserved or used as ATP.

    • Electron Carriers
    • NAD:nicotinamide adenine dinucleotide
    • NADP: nicotinamide adenine dinucleotide phosphate
    • FAD: flavin adenine dinucleotide
    • FMN: flavin mononucleotide
    • CoQ: coenzyme Q
    • Quinone
    • Ubiquinone
    • Cyctochromes: use iron to transfer electrons Iron is part of heme group
    • Nonheme: iron proteins
    • Ferrodoxin :Use iron to transport electrons and iron is
    • not part of the heme group
  247. Standard
    reduction potential (E0):
    equilibrium constant for redox rxn

    • The measure of the tendency of the reducing
    • agent to lose electrons

    • More negative E0 : better
    • electron donor

    • More positive E0 better
    • electron acceptor

    • The more negative ∆G, the greater difference
    • between the of the acceptor and the of the donor. (Exergonic rxns)
  248. Electron Transport Systems (ETS)
    • Electron carriers organized so that the first
    • electron carrier has the most negative E0

    • This causes the potential energy stored in the
    • first redox couple is released and used to form ATP
  249. Protein catalysts
    • have
    • great specificity for the rxn catalyzed and the molecules acted on
  250. Catalyst
    • substance that increases the rate of the rxn
    • without being permanently altered
  251. Substrates
    • reacting
    • molecules
  252. Product
    • substances
    • formed by the rxn
  253. Enzyme structure
    • Some
    • composed only of polypeptides

    • Some have 1 or more than one polypeptide with
    • a non-protein component
  254. Apoenzyme
    • protein
    • component of an enzyme
  255. Cofactor
    non-protein component of an enzyme

    • Prosthetic
    • group:
    • firmly attached

    • Coenzyme: loosely
    • attached
  256. Haloenzyme
    • apoenzyme
    • + cofactor
  257. Coenzyme
    • act as carriers and transport substances
    • around the cell

    • Small organic non-protein molecules that
    • carry chemical groups

    Also known as co-substrates

    • An enzyme with a coenzyme position to react with
    • 2 substrates

    • Coenzyme picks up the chemical group from
    • substrate 1

    • Coenzyme readies the chemical group for
    • transfer to substrate 2

    • Final action is when group is bound to
    • substrate 2 and altered substrates are released from the enzyme
  258. Oxidoreductase
    • redox
    • rxn
  259. Transferase
    • rxns involving
    • transfer of groups between molecules
  260. Hydrolase:
    hydrolysis of molecules
  261. Lyase
    • removal of groups to form a double bond or
    • addition of groups to a double bond
  262. Isomerase
    • rxn
    • involving isomeraztions
  263. Ligase
    • joining
    • of 2 molecules using ATP energy
  264. Transition state
    resembles both the substrate and the products
  265. Activation energy
    • the
    • energy required to form a transition- state complex Enzyme speeds up rxn by lowering the Ea

    • Increasing the concentrations of the
    • substrate at the active site of the enzyme

    • By orienting substrates close to each other
    • in the right orientation to form the transition-state complex
  266. Substrate
    • Rate increase as the substrate concentration
    • increases

    • Not further increase if rate after all the
    • enzyme molecules are saturated (all active sites filled) with the substrate

    • Vmax: the rate
    • of product formation when the enzyme is saturated with the substrate and is
    • acting as fast as possible

    • Km= the
    • substrate concentration required by the enzyme to operate at half its max
    • velocity
  267. Denaturation:
    • loss of enzyme’s structure and activation
    • when the temp and pH rise too much above optima
    • pH and
    • temperature
    • each enzyme
    • has a specific temp and pH optima
  268. Competitive inhibitor
    • directly competes with binding of substrate
    • to an active site
  269. Non-competitive inhibitor
    • : binds
    • enzyme at allosteric site (site other than the active site)

    • Changes the enzyme’s shape so it becomes less
    • active
  270. Metabolic
    Conservation of energy and materials

    • Maintenance of metabolic balance even when
    • there are changes in the environment
  271. 4 regulatory mechanisms
    • Metabolic channeling: can generate marked variation in metabolite concentrations
    • different localizations of enzymes and
    • metabolites

    • compartmentation:
    • differential distribution of enzymes and metabolites among separate cell
    • structures and organelles

    • regulation of amount of synthesis of a
    • particular enzyme

    • reversible
    • control

    • allosteric regulation: effector binds and alters
    • the shape of the active site and the enzyme is inactive because it cannot bind
    • to the enzyme that catalyzed the rxn

    • covalent
    • modification: regulation of glutamine synthetase requires ATP which creates 12
    • adenyl groups covalently bound

    • feedback
    • inhibition: post-transcriptional regulation and is also called end product
    • inhibition

    • inhibition of one or more critical enzyme in
    • a pathway regulates the entire pathway

    • pacemaker
    • enzyme:
    • catalyzes the slowest or rate-limiting rxn in the pathway

    transcriptional regulation

    • chemotaxis: regulated
    • by enzyme activity

    • system involves a number of enzymes and other
    • proteins that a regulated by covalent modification

    • phosphorelay system which has a sensor kinase
    • and a response regulator

    • modulation of the activity of the
    • phosphorelay system determines the rotational direction of the flagella and
    • where the cell will run or tumble
  272. aerobic respiration
    oxygen is the final electron acceptor
  273. anaerobic respiration
    • final
    • electron acceptor is exogenous

    • NO 3-, SO4
    • 2-, CO2, Fe3+, SeO4 2-

    • Organic
    • acceptors may also be used
  274. PMF (proton motive force):
    • is generated
    • as the electrons move through the ETC to the final electron acceptor

    • used to make
    • ATP

    • carbon atoms
    • can also be used as a electron/energy source

    • substrate
    • level P

    requires ADP

    • makes ATP
    • and CO2
  275. fermentation
    uses an endogenous electron acceptor

    • usually and
    • intermediate of a pathway that is used to oxidize organic energy



    does NOT use ETC or PMF
  276. substrate level
    • only way ATP
    • is synthesize in fermentation

    • How ATP is
    • made in glycolysis (ADP +P = ATP)
  277. Aerobic catabolism
    3 stage process

    • ATP primary
    • made by oxidative P

    Stage 1

    • Polymers
    • (large molecules) are degraded to monomers (small molecules)

    • Polysaccharides
    • to monosaccharides

    • Sucrose to
    • fructose +glucose

    • Proteins to
    • amino acids

    • Lipids to
    • glycerol and FA

    Stage 2

    • Initial
    • oxidation and degradation of pyruvate


    • monosaccharide
    • to pyruvate

    • pyruvate to
    • Acetyl CoA

    • glucose to
    • pyruvate produces NADH and ATP

    • pyruvate to
    • acetyl CoA produces NADH

    • Amino acids
    • to NH2 and other intermediates that can then go through glycolysis

    • Glycerol +
    • FA convert to acetyl CoA and produce NADH and FADH2

    Stage 3

    • Oxidation
    • and degradation of pyruvate by TCA cycle

    • Produces
    • ATP, NADH, FADH2, and CO2

    • Acetyl CoA
    • from pyruvate

    • Intermediates
    • from amino acids go through the TCA cycle
  278. ETC
    • NADH and
    • FADH2 transferred to CoQ

    • NADH AND
    • FADH2 are produced from glycolysis, glycerol +FA, and the TCA cycle

    • CoQ
    • transfers to Cyctochromes

    • Cyctochromes
    • to oxygen

    Produces ATP
  279. Amphibolic Pathways
    • Function as
    • both catabolic and anabolic pathways

  280. Embden-Meyerhof
    • Occurs in
    • the cytoplasm (P and E)

    • Most common
    • pathway for glucose to pyruvate

    • Stage 2 of
    • aerobic respiration

    • Broken into
    • 3 carbon and 6 carbon phases

    One 6C molecule (glucose to F1,6-BP)

    • Only G6-P to
    • F6-P is reversible

    Two 3C molecules ( rest of cycle) 2x all rxn

    • All rxn
    • except pyruvate to PEP is reversible

    Pathway: ( enzyme and produced or consumed)

    • Glucose + P
    • +ATP +hexokinase Glucose 6-P
    • +ADP

    • G6-P is the
    • precursor metabolite and starting molecule for the pentose phosphate pathway

    • ATP in, ADP
    • out

    • G6-P + phosphoglucose
    • isomerase Fructose 6-P

    • G 6-P is an
    • aldehyde

    • F 6-P is a
    • ketone an precursor metabolite

    • F6-P + phosphofructokinase + ATP Fructose
    • 1,6-biphosphate + ADP

    • ATP in ADP
    • out

    • F1,6-BP + aldose dihydroxyacetone phosphate and glyceraldehye
    • 3-P

    • Produces two
    • 3 carbon molecules

    • Only G3-P is
    • a precursor

    DHP + Triphosphate isomerase G3-P

    • Now both 3
    • carbon molecules are precursor metabolites

    (2x) G3-P + gylceraldehyde 3-P dehydrogenase + NAD+ (2x) 1,3-bisphosphate + NADH

    • Phosphorylation
    • oxidizes G3-P

    • The
    • electrons released reduce NAD+ to NADH

    (2x) 1,3BP + phosphogylcerate kinase + ADP 3-phosphogylcerate +ATP

    • (2x) ADP in
    • ATP out

    • ATP produced
    • by substrate level P

    (2x) 3-PG + phosphogylcerate mutase 2-phosphogylcerate

    (2x) 2-PG + enolase phosphoenolpyruvate

    • loss of
    • water

    (2x) PEP + pyruvate kinase + ADP pyruvate + ATP

    • Pyruvate is
    • one the most important precursor metabolite

    • (2x) ADP in
    • ATP out

    • important
    • info for pathway

    • adding P
    • primes the pump

    • oxidation
    • step (dehydrogenase) generates NADH

    • NADH are
    • high energy molecules used to synthesize ATP by substrate level P
  281. Pentose Phosphate Pathway
    • Also called
    • hexose monophosphate pathway

    • Operates at
    • the same time as Glycolytic pathway

    • Can operate
    • both aerobically and anaerobically


    • Produces
    • NADPH which is needed for biosynthesis
  282. Oxidation
    • G6-P to
    • 6-phosphogluconate

    • G6-P is
    • oxidized that reduces NADP+ to NADPH

    • 3 H2O and 3
    • NADP + in

    3 NADPH and 3 H+ out

    6-PG to 3 ribulose 5-P

    • 6-PG is
    • oxidized and decarboxylated

    3 NADP+ in

    • 3 CO2, 3
    • NADPH, and 3 H+ out

    • Sugar
    • transformation rxns

    • Catakyzed by
    • transalsolase and transketolase

    • Some further
    • degraded and catabolized into pyruvate

    • Some
    • regenerate more G6-P

    • The sugars
    • necessary for biosynthesis are produced
  283. Transketolase rxns
    • Two 5-carbon
    • molecules react ( 10 c total)

    • Produce one
    • 7-carbon molecule and a 3-c molecule

    • A 5- carbon
    • molecule and a 4-c molecule (9 carbons total)

    • Produce a
    • 6-carbon mole and a 3-carbon molecule
  284. Transadolase rxn
    • a 7-C and a
    • 3-C react (10 C total)

    • Produce a 6C
    • and 4C
  285. Entner-Doudoroff Pathway
    • Glucose goes
    • through the rxns of the pentose P pathway and then goes through the rxns of the
    • Glycolytic pathway

    Yeiled per glucose

    1 ATP

    1 NADPH

    1 NADH
  286. TCA cycle (tricarboxylic acid)
    • Also called
    • the citric acid or Kreb’s cycle

    • Common in
    • aerobic bacteria, free living protozoa, most algae and funi

    • Major roles
    • is the source of carbon skeletons that are used from biosynthesis

    • For each
    • acetyl-CoA that is oxidized, the TCA cycle procuces:

    2 CO2

    3 NADH

    1 FADH2

    1 GTP
  287. Prok. ETC
    • In plasma
    • membrane

    • Moves H+
    • into the periplasmic space

    • Different
    • electron carries

    • May be
    • branched

    • May be
    • shorter

    • May have a
    • lower P:O ratio: the number of
    • molecules of ATP generated per atom of oxygen consumed in the ETC
  288. ETC of E.Coli
    • Branched
    • pathway

    Upper branch: stationary phase and low aeration

    Lower branch: log phase and high aeration
  289. Oxidatitive Phosphorylation (OP)
    • How ATP is
    • made from the ETC that is driven by the oxidation of a chemical energy source

    • Diffusion of
    • H+ back across the membrane (down the gradient) drives formation of ATP
  290. ATP synthase
    • : enzyme that
    • uses the H+ down gradient to catalyze ATP synthesis

    • is located
    • in the Matrix and has a tail attached to the IM in Euk.
  291. ATP yield from aerobic respiration
    from glycolysis

    2 NADH

    8 ATP total

    • 6 ATP from
    • OP

    • 2 ATP from
    • SLP

    • Pyruvate
    • oxidation

    • 6 ATP from
    • OP

    TCA cycle

    5 NADH

    2 FADH2

    24 ATP total

    • 18 ATP from
    • OP of NADH

    • 4 ATP from
    • OP of FADH2

    • 2 GTP from
    • SLP

    Total aerobic yield = 36-38 ATP

    • NADH
    • produces 3 ATP

    • FADH2
    • produces 2 ATP
  292. fermentation of pyruvate
    • Pyruvate or
    • derivative used as an endogenous electron acceptor

    • Substrate
    • only partially oxidized

    • Oxygen is
    • not needed

    • Pyruvate
    • fermentation produces lactate and recycled molecules

    • Uses NADH
    • and NAD+ is recycled

    • Ethanol:
    • alcohol fermentation

    • Lactate:
    • homolactic fermenters and heterolactic fermentors

    • Used for
    • food spoilage
  293. Fermentation of amino acids
    • Stickland rxn: the
    • oxidation of one amino acid with the use of a second amino acid as an electron
    • acceptor

    • Carried out
    • by some Clostridium

    • Alanine to
    • pyruvate to acetyl CoA to acetyl P to acetate

    • 2 glycine to
    • acetate
  294. Catabolism of carbohydrates
    • Carbohydrates
    • = energy source

    • Can be
    • supplied externally or internally (internal reserves)


    • Converted to
    • other sugars that enter the glycoltic pathway

    Disaccharides and polysaccharides:

    • Cleaved by
    • hydrolases or phosphorylases

    • Maltose: 2
    • glucose (maltase)

    • Sucrose:
    • glucose + fructose (sucrase)

    • Lactose:
    • galactose + glucose

    • Cellobiose:
    • 2 glucose

    Reserved polymers

    • Used as
    • energy sources in the absence of external nutrients

    • Glycogen and
    • starch

    • Cleaved by
    • phosphorylases

    • Glucose 1-P
    • goes to Glycolytic pathway



    • PHB to
    • acetyl CoA

    • Acetyl CoA
    • enters the TCA cycle
  295. Lipid catabolism
    • Trigylcerides
    • are common energy sources

    • Hydrolyzed
    • glycerol and FA by lipases

    • The glycerol
    • is degraded via gly. Pathway

    • FA oxidized
    • via β oxidation pathway

    • FA chain is
    • shortened by 2 C atoms

    • Produces
    • FADH2 and NADH
  296. Protease:
    • hydrolyzes
    • protein to amino acids
  297. Deamination
    removal of an amino group from an amino acid

    • Results in
    • organic acids that are converted to pyruvate, acetyl-CoA, or other TCA cycle
    • intermediates

    • Occurs
    • through transamination: transfer
    • amino group

    • Alanine + α-ketoglutarate
    • which is made into pyruvate and glutamate
  298. Chemolithotrophy
    • Electrons
    • released from an energy source (inorganic molecule)

    • Transferred
    • to the terminal electron (O2) in the ETC

    • ATP
    • synthesized by OP

    • Calvin cycle
    • requires NADH as the electron source for fixing CO2

    • Use reverse
    • electron flow to generate NADH

    • Can switch
    • from chemolithotrophic metabolism to chemoorganotrophic metabolism

    • Can switch
    • from autotropich metabolism (calvic cycle) to heterotrophic metabolism

    • Nitrifying bacteria: Oxidizes
    • ammonia to nitrate
  299. Sulfur-oxidizing
    ATP by OP and SLP
  300. Phototrophy
    • energy from
    • light is trapped and converted to chemical energy

    • 2 part
    • process

    • Light rxn: light
    • energy is trapped and converted to chemical energy

    • Dark rxn: uses the light energy produces to reduce CO2
    • and synthesize cell constituents
  301. Oxygenic
    • euk. And
    • cyanobacteria

    • In the light
    • rxn

    • chlorophylls are major
    • absorbing pigment

    • accessory pigments:
    • transfer energy to the chlorophylls through carotenoids and phycobiliproteins

    • absorb
    • different wavelengths of light than chlorophylls

    • different
    • chlorophylls have different absorption peaks
  302. Anoxygenic
    • all other
    • bacteria

    • H20 not used
    • as electron source and o2 is NOT produced

    • Only 1
    • phosphostem involved

    • Uses different
    • pigments and mechanism to generate reducing power

    • Carried out
    • by phototrophic green and purple bacteria, and heliobacteria
  303. Anabolism
    • From carbon source and inorganic molecules,
    • microbes can synthesize new organelles and cells

    A lot of energy require for biosynthesis
  304. Turnover
    • continual degradation and resynthesis of
    • cellular constituents by non-growing cells

    • Rate of turnover is balanced by the rate of
    • biosynthesis

    Metabolism carefully regulated
  305. DNA
    • stores
    • genetic info

    • Info is
    • duplicated by replication and passed on
    • to the next generation
  306. Flow of genetic info within a single cell
    • Process
    • called gene expression

    • Expression
    • of DNA determines structure and function of the cell

    • DNA divided
    • into genes

    Transcription: yields RNA

    • RNA: ribonucleic acid, copy of
    • specific gene

    • Translation: use mRNA to
    • synthesize polypeptide
  307. Nucleic Acids
    • DNA and RNA
    • are nucleic acids

    • Polymers of
    • nucleotides that linked by phosphodiester bonds
  308. Nucleoside
    n base and sugar
  309. Nucleotide
    • n base,
    • sugar, phosphate group
  310. Base pairing
    • Two
    • complimentary strands

    • Adenine and
    • thyamine A:T = 2 H bonds

    • Guanine and
    • cystine G:C = 3 H bonds

    • Purine
    • paired with a pyrimindine A:T
  311. Nucleosome
    combination of DNA and proteins
  312. Semi-conservative
    • 2 strands
    • separate and each serve as a template for a synthesis of a complimentary strand

    • : each
    • daughter cell has one ole and one new strand
  313. DnaA protein
    • iniation of replication and binds origin of
    • replication
  314. DnaB protein
    • helicase 5
    • to 3 breaks the h bonds of the double helix

    promotes DNA primase activity

    • Involved in
    • primosome assembly