Cell Types Prokaryotes  vs.  Eukaryotes
Definition of a cell ....                  Concept Activity - Chapter 1.1 (6.2) - Comparing Prokaryotes & Eukaryotes
A living CELL is a .....
      self contained,
      self assembling,
      self adjusting,
      self perpetuating,
      isothermal mix of biomolecules,
        held in a 3-D conformation by weak non-covalent forces,
      which extract raw materials (precursors) & free energy from surroundings,
      that catalyzes reactions with specific biocatalysts (enzymes), that it makes,
      and which shows great efficiency & economy of metabolic regulation,
      and that maintains a dynamic steady state far from equilibrium,
Cyandown.gif (233 bytes)  and which can self-replicate using the informational molecule DNA. 






... remember, there are 3 Biological Domains of life...  
,     Eubacteria,    and    Eukarya
                         domains are based upon difference in nucleotide sequences in rRNA    [Phylogeny]

...Cell Organization [structure]     3 Basic Parts of a Cell
                1.   membrane (selectively permeable - in/out)
                2.   a DNA region (nucleoid or nucleus)
                3.   the cytoplasm & its subcell parts:  organelles

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...but, all cells are divisible into only 2 successful Cellular Plans of Organization
distinguished primarily by size & type of internal structure (organelles)

Procaryotes...  "before nucleus"                             
                     today's prokaryotes includes:   blue green algae   &   bacteria...         [bad puns & jokes]       
                    primitive, simple, versatile, ubiquitous, unicellular life form
                    a most successful life form-
                                          80% to 90% of total biomass of planet
                                          2,500 different species known   
(easily cultured in lab)
                    some characteristic parts
*   &   an E.M. pic of E. coli* 
                           lack complex membrane bound organelles (some have specialized membranes
                           genes are "naked DNA" - i.e., no real "chromosome?"
                           little to no internal compartmentation (organelles)    figure*
                           size range - 0.1 to 10 m diameter           size relationships*

                    current paradigm is that eukaryotes evolved from simpler prokaryotes
Cyandown.gif (233 bytes)                                                                         Chapter 6.2 - Prokaryotic Cell Structure & Function.    





Procaryotes...  includes all the unicellular forms from the TWO Domains :
                the Archaea (
Archaeabacteria) & 
                the bacteria (
Eubacteria   =   cynaobacteria,   mycoplasma, &   rickettsiae).
    the procaryotes - archaeans/eubacteria evolved to solve environmental challenges (problems) 
                              via their versatile chemistry - they evolved new metabolic solutions...
                              ...they are are highly conserved - "living fossil forms"

    ARCHAEABACTERIA  - many living archaebacteria are called Extremophiles:
  Sulfolobus acidocaldaries - acid loving microbes pH < 5,  sulfur springs
 Natranobacterium gregoryi - pH > 9,   live in soda lakes
    Halferax volcanii - salt loving,  live in Dead Sea & Great Salt Lake
methanobacterium       CO2 + H2 --> CH4    [Oregon culture collection]
PSYCHROPHILES.. Polaromonas vacuolata - cold loving - live in antarctic seas
           THERMOPHILES...  heat loving,   in acid hot springs, deep ocean geysers [YNP]

Cyandown.gif (233 bytes)                               there is a mix of eukaryote & prokaryote traits in Archaea  
differences between ARCHAEA and BACTERIA*     fig-1   &   fig-2






EUBACTERIA...    [ images ]
                includes all the other living bacteria [except the archae]- i.e., "the modern forms"
                human gut holds about 1,000 different bacterial species & some 10 trillion bacterial cells
                most exhibit 3 common shapes bacterial shapes: cocci,   bacillus,   spirochetes 
                                                           -  shapes of bacteria*  (pics
on pin   &   syringe   &   staph)
               often possess flagella for motility  a picture
 distinguished by  Gram Staining* of wall components
               several eubacteria are pathogenic a
nd may cause diseases:  [table] including:
                         Bacillis anthracis            =   anthrax   (spores EM pics)
                         Clostridium botulinum     =    botulism
                         Staphylococcus aureus    =    sepsis, endocarditis, & nosocomial infections
Salmonella                     =    food poisoning & typhoid
               many make antibiotics: (history of antibiotics)
                         Streptomyces                 =   streptomycin (1943)
Penicillus*                      =   penicillin (1928 - pics)   [resistance]

               also includes CYANOBACTERIA  
[description]  - are photosynthetic eubacteria  (pics)
                 with cytoplasmic membranes; may catalyze N2 fixation [N2 --> NH3] for aa's & N's 
    Cyandown.gif (233 bytes)           Martian analogs - extremophile environments, microbes, & Mars habitats. 






 EUKARYOTIC   [eu -true   karyon -nucleus...]   cell plan of multi-cellular organisms,
     eukaryotes (eukarya) include the fungi, algae, protozoa, slime molds, & all plants & animals,
     contain many internal membrane bounded organelles...
                                          organelle - a subcell part that has a distinct metabolic function
            have a nucleus  - single greatest step in evolution of higher animals
                          genes in "chromosomes"   [colored bodies... made of DNA + protein]
                          contains more DNA (1,000x  more) than procaryotes
            presence of organelles  - significant internal compartmentalization of function
            presence of flexible cell "walls" (extra-cellular matrix)  - allows phagocytosis
            presence of cytoskeleton  - provides internal framework; favors larger cells
            extensive internal membranes
            reproduce sexually
            usually larger   - cell volume 10X > than bacteria  - size 5.0 to 20 m diameter

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     2 major kinds of eukaryotic cells  
                animal -   metazoan cell*        -   heterotrophic feeder 
                plant   -  metaphytian cell*    -   autotrophic producer
contain chloroplasts, large vacuoles, cellulosic cell wall
Concept Activity  - 6.2  - Build an Animal Cell and a Plant Cell
                                                        Concept Activity  - 6.7  - Review of Animal Cell structure & function
                                                        Concept Activity  - 6.7  - Review of Plant  cell structure and function
      Procaryotes vs. Eucaryotes
              table of similarities & differences*(later)

                                        Concept Activity - 6.2 - Comparing Prokaryotes & Eukaryotes.

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? VIRUSES...    
pathogens, smaller than bacteria...       (TMV - 1935 - Wendell Stanley)
     obligatory intracellular parasites...  not capable of metabolism or self-replication  
C7-fig 18.5*
     pathogens made of a protein
capsid (a surrounding protein capsule)
genetic material...  ss or ds RNA or DNA... (animal viruses & viral ultrastructure)
      VIRION* - a virus outside of host   viral forms & shapes 
& bacteriophages*
      VIROID   - plant RNA virus w/o capsid consisting of 240-600 np's, that infect plants.
                      some other RNA viri include:  EBOLA  &  HIV-type I
      EXTREME VIRUSES - maybe life's early precursors?
      Viruses (like extremophiles) can live in Earth's most extreme environments.   
          Origin of Viri(?)...  small fragments of cellular chromosomes, that maintained an
         autonomous existence within cells. Overtime these genetic elements acquired protein
         coats & the ability to transfer to other hosts (and became infective)

  Synthetic (man made) Polio virus
 synthetic poliovirus

? Nanobes  are tiny filamental structures found in some rocks and sediments;
      smallest are just 20nm long. May be crystal growth, but they're purported to hold DNA;
           look similar to the life-like structures found in meteorite ALH84001 (pic). 

PRIONS - protein infectious pathogens....   biological activity without RNA or DNA ???...
                      cause diseases as:
encephalopathies... scrapie,  Creutzfeldt-Jacob, mad-cow  
          Cyandown.gif (233 bytes)          not infective virus/microbe, but rather --> misfolded proteins?   NOVA prion debate






  Identification of subcell parts    

1. Light Microscopy
                          History of Light  Microscope     
                          Nikon's Museum of Microscopy

                                basic parts of student microscope
typical binocular compund microscope & its parts*
           magnification     =   how much larger objects appear  - typically 1000 fold
           resolution          =   distance between objects: allows one to distinguish 2 dots = 0.2 m

           killing/fixing of samples :  formaldehyde  &  glutaraldehyde denature all proteins

           embedding & sectioning : by a microtome (1 to 10 m thick tissue sections)

           selective staining stains (dyes) attach to specific molecules colorizing them  (picture)

Cyandown.gif (233 bytes)        types - unstained:  bright field,  phase-contrast,  Nomarski,  &  dark-field
             types - stained:     creates contrasting images.



                 Identification of subcell parts continued........

   2.  Electron Microscopy      A primer on Electron Microscopy    (pic of TEM scope 4.1)*

            resolution = 0.1 nm         specimen preparation* 
            image analysis...             3D restructuring of images* ? analogy  =   Orange Bowl* 

         three types of electron microscopy:   
            TEM  -  Transmission:   a TEM picture*
            SEM  -  Scanning:         prep*  &   TEM vs. SEM pic's   &  
see some examples
            FEM  -  Freeze Fracture:   how to prepare* results*,   &    FEM picture


  Cell Isolation & Tissue Culture...  Model Experimental Systems.
                         RBC cells   
&    HeLa cells    &    how to culture HeLa cells
   4.  Cell Fractionation*  &  Differential Centrifugation*   leads to organelle separations
   5.  Size relationships - see text figures*   [fun stuff:  Powers of 10  and Images & Scaling]
 Case Studies - Process of Science - Chapter 7 - Size Relationships


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    The major eucaryotic organelles:

  NUCLEUS :    envelope, pore, chromatin, nucleolus, nucleoplasm
MITOCHONDRIA :    peri-mitochondrial space, cristae, mitoplasm (matrix)
CHLOROPLAST :    peri-chloroplast space, thylakoids, chloroplasm (stroma)
RIBOSOME :    small subunit, large subunit, polysome
ENDOPLASMIC RETICULUM :    smooth & rough
GOLGI BODY :    sided:  cis & trans;  endomembrane pathway
LYSOSOME :    hydrolytic enzymes
MICROBODIES :    peroxisome & glyoxysome
CYTOSKELETON :    microfilaments, microtubules, intermediate filaments
CENTROSOME :    centriole, basal body, flagella, cilia
INTERCELLULAR JUNCTIONS : tight junctions, desmosomes, gap junctions, plasmodesma
PLANT CELL VACUOLE :  tonoplast, cellular waste, and osmoregulation
CELL MEMBRANE :  selective transport barrier.

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 GRAM Stain...    a method for differential staining of bacteria
        smears are fixed, stained in a solution of crystal violet and treated with
        iodine solution, rinsed, decolorized, and then counterstained with safranin O;

 Gram-positive bacteria stain purple-black
    walls* contain peptidoglycans - protein + carbohydrates


Streptococcus Bacillus
 and Gram-negative bacteria stain pink;
    thinner walls* more membrane-like -lipopolysaccharides  


Coccus E. coli

                           Gram staining is useful in bacterial taxonomy and identification,
   back                and also in indicating fundamental differences in cell wall structure.