Cell Organization:  A cell has only 4 Basic Parts

                1.   cell membrane  - selectively permeable - in/out.
                                                     (a phospholipid bilayer)

                2.   a DNA region      -  (nucleoid or nucleus)  

                3.    - protoplasm:    -  a 19th century term for vital fluids of cells
                       - cytoplasm:     -  the molecular skeleton giving form to a cell
                                                    via cytoskeletal fibrous protein as actins/tubulins,
                                                    and everything within a cell
- cytosol:          -  is the aqueous compartment without organelles
                4.    - organelles:     - 'mini organs' within cells with specific metabolic functions

                          Basic parts of a eukaryotic cell

     So lets take a close look at the structural anatomy of Cells...

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         There are only
2 successful Structural Plans of Cell Organization

                                  Prokaryotes  vs.  Eukaryotes
distinguished by size & internal structure & presence/absence of

Prokaryotes...  Gk πρό- (pro-) "before" + καρυόν (karyon) "kernel = nucleus"
are single-celled organisms without a nucleus or major cell organelles...
  bacteriaarchaea, & 
  [bad puns & jokes] 
          prokaryotes are primitive, simple, yet versatile, and a ubiquitous unicellular life form
          a most successful evolutionary life form-
                 making up about 2.5% of total biomass of planet Earth
                 over 2,500 different species identified 
(easily cultured in lab)
                 500-1,000 species live in out human gut
                 guesstimates: 1% to 3% of 200 lb Human is bacterial [i.e., about 2 to 6 lbs] 


  anim of prokaryote structure    &    characteristic parts
              little to no internal compartmentation (maybe a few organelles, as ribosomes)   
lack complex membrane bound organelles (may have some specialized membranes*)
              genome is "naked DNA*" - i.e., no protein complexes & no real "chromosome?"
              typical size range - 0.1 to 10 µm diameter:    Largest bacteria discovered
size relationships
&   Scale of Life*

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Procaryotes...  includes all the UNICELLULAR organisms of TWO Domains :
                the Archaea (Archaea journal

                the Bacteria (
Eubacteria =   cynaobacteria,   mycoplasma,  & rickettsiae).

Prokaryotes - both archaea/bacteria evolved by solving environmental challenges
                and a versatile cell chemistry,  i.e.,  via novel & new metabolic solutions...
       1. ARCHAEA  - many living prokaryotic archaea are called Extremophiles*
are organisms that thrive in physical or geochemical extreme conditions which seem
                detrimental to the majority of life on Earth...
Extremophile origanisms records*:
                    NASA found that after almost 20 years of continuous human presence, the
                     International Space Station has developed a core microbiome of 55 different
                     microorganisms. As part of a project called the Biology and Mars Experiment,
                     researchers found that bacteria, algae, lichens and fungi survived on the exterior
                     of the Space Station for 533 days. 
                    ...they seem to be highly conserved - "living forms evolved for many environments" 

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EUBACTERIA...  [ images ]     "True bacteria...  modern day microbes"
          includes all living bacterial species and cyanobacteria    [excluding the archaea].

There are a number of ways microbiologists have categorized Eubacteria:

    1-  most exhibit 3 common bacterial shapes:   COCCI,   BACILLUS,   SPIROCHETES 

                  shapes of bacteria*
      (pics of bacteria 
on pin  &  syringe  &  staph aureus infections
    2-  many microorganisms possess a flagella for motility  fig of flagella
 can also be distinguished by their cell wall components via  Gram Staining*,  
                  which can
determine what type of bacteria is present & a treatment.
    4-  several eubacteria are  pathogens 
nd cause many  human diseases*:
                  several Nobel Prizes have been awarded for research on pathogenic-harmful bacteria
                  yet, of the 2,500 species (? or more) only 170 species are pathogenic in mammals.
                  and many bacterial species also make antibiotics, which kill other species of bacteria.
                       History of Antibiotics  &  timeline of antibiotics 
&  the Discovery of Penicillin

      CYANOBACTERIA (are eubacteria) - also called blue-green algae (but no relationship)...
description - are aquatic photosynthetic unicellular Gram-negative eubacteria  (pics)
                They have cytoplasmic membranes & may catalyze N2 fixation
[ N2 --> NH3, NO2-, NO3- ]   




 EUKARYOTIC  [Gk: eu -true   karyon -nucleus...] cell plan of MULTI-CELLULAR ORGANISMS,
     eukaryotes (eukarya) include the fungi, algae, protozoa, and all plants & animals all contain
     many internal membrane bounded organelles...
organelle - a subcell part that has a distinct metabolic function;
                                                  [akin to a subcontractor on a construction job]
            have a nucleus  - single greatest step in evolution of higher organismal cells
                        genes are in
*  [colored bodies... made of DNA + proteins]
                        contains more DNA (1,000x  more) than prokaryotes:  linear vs. circular.
            presence of less cell "wall" structure with a more flexible extra-cellular matrix
            extensive internal membrane systems
            elaborate cytoskeleton  - provides internal framework; favors larger cells
            presence of organelles  - significant internal compartmentalization of functions
            reproduce sexually
            usually larger   - cell volume 10X > than bacteria  - size 5.0 to 20 µm diameter

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2 major kinds of eukaryotic cells are commonly recognized:  

animal -   metazoan cell*        -   heterotrophic metabolic feeder 

                   plant   -    metaphyta cell*      -   autotrophic producer
contain chloroplasts, large vacuoles, & a cellulosic cell wall
                   Procaryotes vs. Eucaryotes
                                   -  table of similarities & differences*(later)
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How do research biologists study & identify the subcell parts, - the Organelles




    Cells are very small so we need to magnify them...

Light  Optical  Microscopy
                          History of Light Microscope     
                          Nikon's Museum of Microscopy

                            basic parts of student microscope
typical binocular compund microscope
                              & its parts*
  parts of a microscope
2.  Key Functions of Microscopes:
     Optical microscopy involves the diffraction, refraction, or dispersion* of light (electromagnetic   
 interacting with 
live or prepared samples & subsequent collection of scattered radiation
          (light) to build up 
magnified images
 of small objects using optical compound lenses* 

   Magnification  =   objects appear larger in a light microscope = typically about 1,000 fold  

*    =   minimum distance between objects that can still be seen as 2 dots...
                                 resolution of human eye                = 0.2 mm  (200um)
                                 resolution of light microscope        =
0.2 µm  
(200nm)  (1,000x human eye)
resolvable size scale   &   scale of biological parts* ] 
      Killing/Fixing of samples
* :  specimens are preserved from decay and autolysis;
                  ongoing biochemical reactions are stopped, & proteins denatured & 'fixed' in place;

                  formaldehyde  &  glutaraldehyde denature all of a cell's proteins

                  increasing mechanical stability,  but may produce
artifacts* in microscopy. 

       Embedding & sectioning : Cell water is replaced by a more rigid paraffin or plastic material

                  and sectioned by a
* (1 to 10 µm thick tissue sections)  
staining stains (dyes) attach to specific molecules colorizing them (root

   Cyandown.gif (233
                          bytes)         Types of Light Microscopy*












Some advanced LIGHT MICROSCOPY examples
corn root A fluorescence microscope* is a light microscope that views emitted fluorescent  light from a fluorophores* (such as GFP)
bound to an intracellular molecule.

      X-sect stem* Fluorescence microscopy of cross-section of a corn root,
                           showing the monocot vascular systems of xylem and phloem.


Confocal fluorescence microscopy* is a form of fluorescent microscopy that illuminates and detects a single diffraction-limited spot in a specimen, instead of flooding an entire sample with light to excite the fluorophore, which gives a blurred image.
   In CFM , a pinpoint (laser) light source is used to excite the fluorophore resulting in enhanced contrast (images*).  
Confocal Laser Fluorescence microscopy produces stunning images*.

2014 Nobel Prize  brings optical microscopy to nanoscale level
pics*)    enabling study of living cells at single molecular levels.

  Cyandown.gif (233
                         Light microscopy advances since 1986Read @ home   
                          Olympus Bioscapes Microscopy Gallery
                          Nikon Small World photomicrography

                     A cell phone microscope for possible clinical pathology in the field.  

    Material for Exam # 2 ends here






Electron Microscopy...    How electron microscopy allowed identification of subcell parts...
animation on how EM works*   and    a primer on Electron Microscopy 
                  George Palade (NP-1974) - pioneered use of EM for studies of cell structure
    resolution* = 0.2 - 2.0 nm -         (scale of biological parts  &  specimen preparation*) 
        image analysis...
pic of TEM scope        3D restructuring*images*
                                                                            an analogy =
  Mark Light or
Hard Rock
    4 types of Electron Microscopy include:      
         TEM  -  Transmission: 
a TEM micrograph*
(often stained w osmium tetroxide binds to lipid membranes)
         SEM  -  Scanning: 
image from 2ndary e's emitted from electron beam on a metal shadow cast
comparison* - sample is killed/fixed/dried - coated with gold/palladium* for output of 2ndary e's.
                                              the typical resolving power is about 2 nm (1/10 of a ribosome)
                        some examples*   &   lily pollen grain  &   a Tardigrada winner
         FFEM  -  in Freeze Fracture EM samples are frozen & cracked along plane of least resistance,
                        usually along hydrophobic membranes.
  how to prepare* results*, & TEM v. FFEM
         Cryo-EM  -  protein samples are cooled to cryogenic temps (-2000C) in vitreous water to observe
                            via narrow e- TEM beams with multiple images of each electron to reconstructe
                            its  biomolecular structure at near atomic resolution (2nm).  [protocol
* & 3D-fig*].     

    Model Biological Experimental Systems for use with Light & Electron Microscopy include...  
a.  isolation and/or culture of cells:    RBC cells   &   1st Human Cells cultured-HeLa cells*  
Cell Fractionation & differential Centrifugation
*  is used to isolate cell organelles
c.  3D cell imaging*view@home ---> Allen Cell Explorer     
 Cyandown.gif (233 bytes)                                         Summary examples of microscopy images*...            










Microscopy has given us views of the major eukaryotic organelles
    [common ex: epithelial cells]

  NUCLEUS :                                  membrane, pores, 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 :                             cis & trans
sided - 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.

back   next Lec

copyright c2024     Last update -  February 2024
Charles Mallery,    Biology 150, Department of Biology,   U.Miami,  Coral Gables, FL 33124







                      Gram Staining is a  method for the differential staining of bacteria
                                        samples are stained in a solution of
crystal violet, & then treated with
                                        iodine solution, rinsed, and then counter-stained with safranin O;
                                        The staining differences are due to the bacterial cells wall structure

 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 due to a differences in cell wall structure* & is useful
                                    in identification & determining an appropriate treatment for an infection
















 SKIP all of the MATERIAL BELOW this point:
 types* - stained:     creates contrasting images.

  a combination of eukaryote & prokaryote traits occur in the  Archaea  

  table of some key differences between ARCHAEA and BACTERIA 

  Martian analogs - extremophile environments, microbes, & Mars habitats. 



non-cell things with LIFE-LIKE PROPERTIES  (can cause diseases)???

? VIRUSES... [Latin: to poison]  
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* - single infective virus...    common viral forms & shapes 
& bacteriophages*
        VIROID   - RNA molecules w/o capsid consisting of 240-600 np's, that infect plants.
                          some other RNA viri include: EBOLA* [poster] & HIV-type I & Human Rhino Virus-Flu virus
     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 acquired protein
            coats & the ability to transfer to other hosts (and became infective)

 Synthetic (man made) Polio

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


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


SOME TYPES of LIGHT MICROSCOPY living and unstained samples
Brightfield Microscopy:  
   Standard transmission of light through a living cell 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 [iL] is out of phase with transmitted light [tL] and when the phases of the light are synchronized by an interference lens, a new image with good contrast is seen. 
pahse contrast 
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. (trout & melanocytes)
Zeiss Research scope
  inverted microscope


Confocal laser endomicroscope

          Size relationship of eukaryotic organelles   [some fun stuff:   Powers of 10 Images & Scaling] 

                        Some examples of extremophiles living on Earth:  
                     ACIDOPHILES...   Picrophilus oshimae              - acid loving microbes pH < 5,  sulfur springs
                     ALKALIPHILES...   Natranobacterium gregoryi   - pH > 9,   live in soda lakes, Nevada, USA
   Halobacterium salinarum       - salt loving,  live in Dead Sea & Great Salt Lake
Methanobacterium                 - CO2 + H2 --> CH4    make methane
PSYCHROPHILES..  Polaromonas vacuolata         - cold loving - live in antarctic ice
Pyrobus fumarii                    - acid heat loving hot springs, hydrothermals at [YNP]

Artificial Life Forms