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2013-12-10 19:00:51

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  1. What is the important role in ecology?
    • It uses biochemistry cycle 
    • -Carbon, sulfate, nitrogen 
    • - marine, soil, symbionts (tubeworms, mussels, clams, snails)
  2. Neuston
    Air/water (10 um)
  3. Euphotic
    photosynthetic zone (200 um)
  4. Aphotic
    No light (heterotrophs (Cannot fix carbon) and litotrophs(uses inorganic)
  5. Benthos
    Floor + Sediments
  6. Coastal regions have a lot of
  7. In the coastal regions it has a lot of
    Contamination, less light to penetrate meaning a lot of bacteria
  8. Oceans are generally ..
    • Oligotrophic 
    • (it has few nutrients--> less bacterial cell)
  9. what is the function of Biochemical oxygen demand (BOD)
    it is the amount of oxygen is being removed from water by AEROBIC RESPIRATION 
  10. Between 200-1000 meters of depth
    • Oxygen minimum zone (OMZ) 
    • (no atmospheric exchange)
  11. Marine biology is mainly
    Planktonic (free floating)
  12. Microplankton
    Large cilated protists/algae
  13. Nanoplankton
    • Smaller algae
    • flagellated protists
    • filamentous cyanobacteria
  14. Picoplankton
    Phototrophs, heterotrophs, lithotrophs
  15. Femtoplankton
    Marine phage (viruses)
  16. Picoplankton can be measured in what way?
    DAPI Staining
  17. Aphotic Zone
    is supported by detrital (rocks falling) material (marine snow)
  18. Which oxidized or reduction molecule will be found in OMZ?
    Sulfate and nitrate
  19. The Benthos (sediments)
    • Low temp
    • heterotrophs/lithotrophs (Fe, Mn oxidizer)
    • Sediment redox gradients
  20. Soil
    mixture of mineral and decaying organic
  21. The primary producer in soil is
    Plants, grass, vegetation
  22. Soil horizons are
    • Organic 
    • Aerated 
    • Eluviated 
    • B. horizon 
    • Water table
  23. Organic Horizon
    Organic matter undergo decomposition
  24. Aerated horizon
    decomposed organic particles and minerals
  25. Eluviated horizon
    Insoluble particles by rain water
  26. B horizon
    clay and minerals
  27. O and A horizon (Soil particles)
    • Collection of organic and inorganic particles 
    • it has colonies, biofilms, bacteria and fungi
  28. Plant Roots (Rhizosphere)
    The region of soil surrounding roots
  29. Plant Roots (Rhizoplane)
    The root surface (it fuel microbial communities)
  30. Enhancing the root capabilities by forming symbiotic association with fungi
    Mycorrhizae (80% plants)
  31. Ectomycorrhizae
    • Colonize the rhizoplane (outside) 
    • - Ascomycota (truffles)
    • - Basidiomycota (mushrooms)

    * does not penetrate cells
  32. Endomycorrhizae
    Hyphae penetrates the plant cells deep within the cortex
  33. Plant symbionts (Endophytes)
    • Bacteria or fungi living within the transport vessels of plants (Pholoem vs. xylem) 
    • - plants pathogens are not
  34. N2 fixation in root nodules
    Oxygen is needed by bacteroid for respiration
  35. Mutualism
    Two organism grow in which both benefits or cannot grow independently
  36. Synergism
    both species benefits through growth or can grow independently
  37. Commensalism
    One species benefits or the partner doesn't and isn't harmed
  38. Amensalism
    one species benefits by harming the partner
  39. Parasitism
    One species (parasite) benefits at the expense of the other (host)
  40. Where can we find bacteria on the skin and description?
    • Epidermis: 10^12 organism 
    • dry, salty, acidic, protective oil
    • moist area (ear, armpit genital scalp)
  41. Mouth
    • Different environments (numerous niches) 
    • - Cheeks, gums, hard/soT palate, tongue, teeth
    • - Many bacteria produce ADHESINS
  42. Lymphoids Organs (Primary Organs)
    Immature Lymphocytes mature into antigen B cells/T cells
  43. Lymphoid Organs (Secondary Organs)
    • Lymphocytes encounters antigens . 
    • any molecules that causes the synthesis of antibodies that specifically binds to antigens.
  44. Secondary Organs (Antibodies)
    • Antibodies (immunoglobins) 
    • glycoproteins made by the body in the response to an antigen
  45. There are two types of Adaptive Immunity
    Humoral and Mediated immunity 
  46. Humoral Immunity
    Antigen that triggers the B cells to differentiate into antibodies which circulate in the bloodstream
  47. Mediated immunity
    T cells get activated by antigens presented outside of phagocytic cells (Macrophages and dendritic cells)
  48. Antigens
    • it can elicit an immune response (antibodies) which is usually made up of many different EPITOPES which binds to a different (multiple) specific antibodies
    • it can recognize 3D shapes (protein/poly)
    • Immunogenicity an antigen elicits and immune response
  49. Immune Response
    • it is an innate response- phagocytosis 
    • some are antigen presenting cites (APC)
    • B cells bind to free antigen 
    • T cells bind to same antigen presented by APC
  50. B cells bind to free antigens
    • differentiate into plasma cells and memory B cells 
    • the plasma produce the antibodies, memory cells and remembers the booster shot
  51. T cells bind to same antigen presented by APC
    Presented on major histocompatibility complex (MHC) 
  52. Immunological Specificity
    Antibodies made for one epitope generally will not bind to other epitopes
  53. ABO blood group (immunological specificity)
    • type O no antigen 
    • both antibodies 
    • universal donor
  54. Type AB (immunological specificity)
    • No antibodies 
    • universal recipients 
    • both are antigens
  55. Antibody (immunoglobins) structure
    • Y-shaped made up of FOUR POLYPEPTIDES 
    • two large heavy chain and two smaller light chains connected by disulfide bonds 
  56. Antibody (immunoglobins) structure cont.
    • two antigen binding sites 
    • there are 5 heavy chains and two light chains 
    • there are five classes of antibodies
  57. What are the five classes of antibodies?
    • it is defined by the heavy chains 
    • IgG, IgM, IgA, IgD, IgE
  58. Antibody Differences
    • Isotype
    • allotypes 
    • idiotypes
  59. Isotypes
    Different classes of antibodies IgA IgM etc.
  60. Allotype
    Difference in constant region of light chain
  61. Idiotype
    Changes in variable region within isotype of an individual
  62. IgG
    • A monomer with four subclasses 
    • Opsonin can cross placenta activate complement
  63. IgA
    • A dimer 
    • secreted across mucosa 
    • secretion such as tears and breast milk
  64. IgM
    • monomer on B cells or pentamer 
    • first antibodies detected during an immune response
  65. Primary antibody response
    • 1. antibodies appears in SERUM several days after exposure to antigen (lag period)
    • 2. B cells bind to antigen differentiate into PLASMA CELLS --> produce and release antibodies/ B memory cells
  66. Secondary antibody response (shorter lag time)
    • Response to exposure at a later time 
    • B memory cells rapidly differentiate to plasma cells
  67. Antibody Response
    • 1. Billions of different B cells 
    • 2. Clonal Selection 
    • 3. Second antigen exposure
  68. Billions of different B cells
    • Antibodies attached to membrane 
    • each cell binds different antigens
  69. Clonal selection
    • Cells that bind antigen replicate 
    • differentiate to plasma cells 
    • it will then secrete antibodies and memory cells
  70. B cells differentiate by
    • Colonal selection 
    • when B cells makes contact with antigen --> it differentiate into plasma cells (secreted antibodies)/ memory cells
  71. Genetic of antibody production
    • Genes undergo DNA SPLICING (deletion)
    • different selected regions 
    • V,D,J-regions
  72. V and J is what region
    Light chain
  73. High point mutation
    rate increases diversity (rearrangements)
  74. T cells are linked between
    Humoral and cell mediated response
  75. what are the two broad categories of T-cells?
    • Helper T cells (Th cells) 
    • Cytotoxic T cells (TCells)
  76. Helper T cells (Th cells)
    • there are 3 types 
    • 1. Th0 cells 
    • 2. Th1
    • 3. Th
    • It is triggered by CYTOKINES (which is a signaling molecule) 
    • it will determine if the immune response will be (Th1 or Th2) 
  77. Th0
    it can differentiate into Th1 or Th2
  78. Th1
    • help activate the Tc cells 
    • it responds to the antigens from the infected cells and activate Tc cells
  79. Th2
    • stimulate B-Cells into plasma cells 
    • responds to antigens in blood stream
  80. Cytotoxic T cells (Tc cells)
    • Destroy membrane of host cell (which is infected by bacteria or viruses) 
    • destroy cancer cells
  81. what does Cytotoxic T cells (Tc cells) secrete?
    • Secrete PERFORIN 
    • it forms pores in the target cells membrane to allow GRANZYMES into target
  82. what is the function of Granzymes?
    Destroy host cells
  83. Major Hostocompatibility Complex (MHC)
    Determines whether a given antigen is recognized as self or non-self
  84. What is the function of Major Hostocompatibility Complex (MHC)?
    To bind antigens and present them
  85. What are the two classes of Major Hostocompatibility Complex (MHC)?
    • the two classes found on cell surface 
    • 1. Class I MHC
    • 2. Class II MHC
  86. Class I MHC
    On all nucleated cells
  87. Class II MHC
    On antigen-presenting cells (APC)
  88. Which cell only recognizes the antigen when presented on MHC?
    • T cells 
    • which then becomes activated if bound
  89. Major Hostocompatibility Complex (MHC) consists of?
    Membrane proteins with different region it can bind antigens
  90. If antigen is presented with Class I or II depends on ?
    How the antigen entered to infect the cell
  91. What are the two category that an antigen enter and infects the cell?
    • Endogenous antigens 
    • Exogenous antigens
  92. Endogenous Antigens
    • Made inside of the cell by viruses or 
    • intracellular pathogens attach to class I MHC
  93. Exogenous Antigens
    • Made outside of the cell and enter by phagocytosis 
    • It attaches to class II MHC
  94. T- Cells Receptors
    • It will interact with antigen (T-cell receptors (TCR)) 
    • It will only bind antigens presented on MHC of APC
  95. The immune system
    consists of both innate and adaptive mechanisms that recognize and eliminate pathogens.
  96. Innate immunity
    • Neutrophils 
    • monocytes- macrophage and dendritic cells (APC, MHC)
  97. Adaptive Immunity
    • Lymphocytes 
    • - b cells- bone marrow produces antibodies
    • - T cells- thymus (TcR)
  98. Neutrophils and Monocytes phagocytize invaders
    produce free antigens and antigens presented by monocytes on MHC
  99. B cells detects free antigens via antibodies
    • antibodies bind antigens in VARIABLE REGIONS of heavy and light chains 
    • it is mark cells for phagocytosis (OPSONIZATION)
  100. Natural killer cells
    • Destroy infected and cancerous cells 
    • if the infected cell lacks cell surface protein NK-cell will destroy it
  101. Complement
    • 20 proteins released by immune cells 
    • it destroy pore in membrane is formed
  102. Pathogens
    • Microbial agent of disease 
    • Bacterial, viral, Eukaryote
  103. Ectoparasite
    Live on surface of host (fungi)
  104. Endoparasite
    Live inside host (Worms)
  105. Virulence factor
    • Allow pathogen to cause disease 
    • a trait encoded by particular sets of VIRULENCE GENES
  106. What does Virulence factor code for
    • Attachment proteins
    • toxins
    • capsules 
    • other mechanisms to avoid immune response
  107. where can virulence genes be found on
  108. Pathogenicity island
    portion of genomes that contain clusters of virulence genes that encode specific functions
  109. Virulence factor Attachment
    • this is the first step of infection (attachment)
    • ADHESION is what promote attachment 
    • CAPSID protein bind to specific host cell recep
    • PILI(FIMBRIAE) contain receptor for mammalian cell surface structure
  110. Virulence factor: bacterial toxin
    • After attachment bacteria secrete protein toxin called EXOTOXIN 
    • - this will lead to cell death 
    • - there are five broad categories
  111. Five Board Categories for EXOTOXIN
    • 1. cell membrane disruptors 
    • 2. protein synthesis disruptors 
    • 3. second messager pathway disruptors 
    • 4. suerantigens 
    • 5. proteases
  112. Cell Membrane disruptors
    • pore form toxin 
    • causes leakage in/out of cell 
    • Alpha toxin of s. Aureus 
    • causes boil and blood infection 
    • hemolysin
  113. Protein synthesis disruptors
    • targets eukaryotic ribosomes and destroy protein synthesis 
    • bloody diarrhea and kidney failure
  114. Secondary messenger pathway disruptors
    Disrupt cellular pathways resulting in ion imbalance
  115. Superantigens
    • Activates the immune system without being processed by antigen presenting cells 
    • it causes a massive release of cytokines 
    • activates a lot of nonspecific MACROPHAGES 
    • toxic shock syngrome s.aureus
  116. Proteases
    • Enzymes that break peptide bonds (cleaves protein) 
    • cleaves several host protein kinase kinases 
    • affects cell growth
  117. LPS
    • gram negative outer membrane 
    • not a protein 
    • bind to b cells and trigger release of cytokines 
    • it can lead to internal bleeding
  118. Protein (Toxin) secretion
    ATP dependent- ABC transport proteins
  119. How do pathogen survive within a host?
    • if you can't beat them join them 
    • engulfed during phagocyosis 
    • INTRACELLULAR PATHOGENS (good place to hide) 
    • it avoids being killed by phagolysomsome
  120. pathogenes have 3 options to survive in host
    • escape phagosome before fusion 
    • prevent fusion 
    • survive fusion
  121. escape the phagosome
    shigella dysenteriae and Listeria monocyogenes use HEMOLYSINS  to break out of phagosome vacuole
  122. inhibit phagosome lysosome fusion
    • that instruct the phagosome and lysosome to fuse
  123. survive fusion
    • needs a acidic environment to survive and grow 
    • harsh conditions within phagosome lysosome favors growth
  124. Extracellular immune avoidance
    • Thick casules 
    • protein that bind the Fc region of antibodies 
    • host mimicry