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,   and which can self-replicate using the informational molecule DNA.

   
... remember, there are 3 Biological Domains of life...  
          Archaea (extremophiles),     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

 

 

 

 

 

 

      

...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 µm diameter           size relationships*

                    current paradigm is that eukaryotes evolved from simpler prokaryotes
                                                                         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).
  
  µ  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:
           ACIDOPHILES...   Sulfolobus acidocaldaries - acid loving microbes pH < 5,  sulfur springs
           ALKALIPHILES...  Natranobacterium gregoryi - pH > 9,   live in soda lakes
           HALOPHILES...     Halferax volcanii - salt loving,  live in Dead Sea & Great Salt Lake
           METHANOGENS.. 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]  
       

                               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 and 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 eubacteria 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 
                    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
 

     7 Major CHARACTERISTIC of EUCARYOTES:
            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 µm diameter

     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.

                                                           
 

OTHER THINGS with LIFE-LIKE PROPERTIES ??? ? 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 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                      not an 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

*

           magnification     =   how much larger objects appear  - typically 1,000 fold

 

           resolution          =   distance between objects: allows one to distinguish 2 dots = 0.2 µm

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

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

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

             types* - stained:     creates contrasting images.

TYPES of LIGHT MICROSCOPY:  unstained and living

Brightfield Microscopy:      Standard transmission of light through the cell, which has very little contrast. A cell is 70% water, thus most of the cell is basically colorless and translucent, i.e., invisible to the eye. Phase Contrast Microscopy: Incident light [Io] is out of phase with transmitted light [I] and when the phases of the light are synchronized by an interference lens, a new image with good contrast is seen.  Nomarski (phase-contrast):   is also known as differential interference contrast microscopy. The different phases of incident and transmitted light are synced by a set of special condenser lens mounted below the stage of a microscope. Dark Field Microscopy:   Here the illuminating rays of light are directed from the side so that only scattered light enters the microscope lenses, consequently the cell appears as an illuminated object against the view.

TYPES of LIGHT MICROSCOPY:  killed, fixed, and stained
	a thin section of human pancreas stained with a mixture of Eosin and Hematoxylin viewed with a didymium filter inserted into the light path.
	A fluorescence microscope is a light microscope that views emitted fluorescent light from a fluorophore (as GFP) bound to a cellular molecule. Fluorescence microscopy of endothelial cells using three labels. Red lables the mitochondria, green lables the F-actin cytoskeleton and blue lables the nucleus. Image by Steve Karl - Olympus BX Fluorescence Microscopy. Taken with the Meade Deep Sky Imager.
	Confocal microscopy is a form of fluorescent microscopy, but instead of flooding an entire cell sample with light to excite the fluorophore, which results a blurred image, a pinpoint (laser) light source is used to excite the fluorophore resulting in enhanced contrast (images*).  By Dr. Sonja Pyott, U. North Carolina, Wilmington,  specimen: Cochlea and Hair Cells.  Laser confocal microscopy has produced some stunning images*.

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

   2.  Electron Microscopy   A primer on Electron Microscopy    (pic of TEM scope 4.1)*
                                               George Palade - pioneered use of EM for cells structure studies             resolution = 0.1 nm        specimen preparation* 
            image analysis...            3D restructuring of images*? analogy =  Orange Bowl*- Dolphins

          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*
  
   3.  Cell Isolation & Tissue Culture...  Model Experimental Systems.
                         RBC cells    &    HeLa cells (G.Gey)   &    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
 
   

    The major eucaryotic organelles    [ex: epithelial cells*]

  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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       Charles Mallery, Department of Biology, University of Miami, Coral Gables, FL 33124

       Last Update - 11/14/2008
           Artificial Life Forms ?

 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
		Bacillus Staphylococcus Streptococcus Mycoplasma
and Gram-negative bacteria stain pink;     thinner walls* more membrane-like -lipopolysaccharides
		E. coli Salmonella Heliobacter Legionella Cyanobacteria

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