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                                                                                                                                          *                                     So lets take a close look at the structural anatomy of Cells...                                     There are only 2 successful Structural Plans of Cell Organization                                       Prokaryotes  vs.  Eukaryotes              distinguished by size & internal structure & presence/absence of organelles     Prokaryotes...  Gk πρό- (pro-) "before" + καρυόν (karyon) "kernel = nucleus"            are single-celled organisms without a nucleus or major cell organelles...                includes:  bacteria,  archaea, & cyanobacteria,                  [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*                                                                                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"                       2. 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     3-  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  and 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]        Some common CHARACTERISTIC of EUCARYOTES:             have a nucleus  - single greatest step in evolution of higher organismal cells                         genes are in "chromosomes*"   [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                                      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)                                                                                                                                  How do research biologists study & identify the subcell parts, - the Organelles                                            Cells are very small so we need to magnify them... 1. Light  Optical  Microscopy                           History of Light Microscope                                Nikon's Museum of Microscopy                             basic parts of student microscope *   parts of a microscope 2.  Key Functions of Microscopes:           Optical microscopy involves the diffraction, refraction, or dispersion* of light (electromagnetic              radiation) 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        Resolution*    =   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 microtome* (1 to 10 µm thick tissue sections)          Selective staining:  stains (dyes) attach to specific molecules colorizing them (root*)            Types of Light Microscopy*                                       Some advanced LIGHT MICROSCOPY examples 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.                            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                  2. 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*           b.  Cell Fractionation & differential Centrifugation*  is used to isolate cell organelles           c.  3D cell imaging*view@home ---> Allen Cell Explorer                                                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) 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 due to a differences in cell wall structure* & is useful                                     in identification & determining an appropriate treatment for an infection.                                  back

  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  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).	Nanobes
? 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

     

   

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.    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
                     HALOPHILES...    Halobacterium salinarum       - salt loving,  live in Dead Sea & Great Salt Lake
                     METHANOGENS..  Methanobacterium                 - CO₂ + H₂ --> CH₄    make methane
             PSYCHROPHILES..  Polaromonas vacuolata         - cold loving - live in antarctic ice
                    THERMOPHILES...  Pyrobus fumarii                    - acid heat loving hot springs, hydrothermals at [YNP]

 END SKIPPED MATERIAL

Artificial Life Forms