Major Eukaroytic Cell Organelles:                             
                                         subcell parts with special catalytic functions
    1st described & named by Robert Brown 1831 - stamens of Tradescantia virginiana
   1st localization of DNA in cells was by Frederich  Meischer 1869 -
white blood cells and the sperm of trout
    Largest organelle   (picture)*        Concept Activity - 6.1 - Metric System Review
                                                                                                          6.1 -
Size and Scale of Our World
            maximum dia 10 um,     volume up to 40 um3    (10% of cell),
            found in all eukaryotic's     (except erythrocytes & sieve tubes cells)
            evolutionary origin... not well known, possibly via  mesosome like process, i.e.,? 
                       simple infoldings of the plasma membranes in bacteria during EM prep;
                       ...may have "surrounded" a primitive nucleoid (genophore) of early prokaryotes.
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 Components*  of the nucleus  -   fig 6.9 (8e-overview of cell)  
    a. nuclear envelope* -  nucleus is a double membrane bound organelle -   pic*
    b. nuclear pore complexes*   &    EM of pores*    &    structure nuclear pore complex*  
                      functional diameter of pores - 10 nm      &    NUCLEAR TRANSPORT*
    c. chromatin - the stuff 'inside of' the nucleus is...
                DNA (5x10-12gm)  complexed with  histone proteins  &  acidic nuclear proteins
                          heterochromatin    (condensed & inactive - dark in EM's)
                          euchromatin          (less dense & active - greyish in EM's)       TEM*
    d. nucleolus - site of rDNA genes which make rRNA
    e. nucleoplasm - soluble (aqueous) phase of the nucleus that contains...
                                        enzymes, RNA's, solutes, chromatin, etc.
       Role of Nucleus - site of genetic information, control of cell divisions
                                     Concept Activity
 - chapter 6.3 - Role of Nucleus-Ribosomes in Protein Synthesis
                Chromosome Structure*   =     nucleosomes  &  DNA supercoil 
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john kyrk's animation of chromosomes





 Nuclear Transport Experiments to Determine Transport & Pore Sizes

    1960's - Carl Feldherr injects gold particles in unicellular amoeba's
                          TEM's showed particles congregating at nuclear pores within a minute;
                           within 10 min, gold particles were in nucleoplasm        see a micrograph* 
    1970's - used fluorescent tagged proteins - showed proteins of less than 60,000 MW passed
    1980's - How do large proteins get in/out?     (such as ribosomal proteins & rRNA of ribosome)
                 Ron Laskey - studied a nuclear protein... nucleoplasmin   (a chromosomal protein)
                 he radioactively tagged nucleoplasmin & used autoradiographyG to follow movement
            see experiment*      panel a - shows nucleoplasmin (head & tail regions) enters nucleus
                                                    and suggests protein has an aa sequence that helps mobility
                                         panel b - where is signal in head or tail? - they split & tagged
                                                    tail entered nucleus, thus it holds aa sequence
                                         panel c- where in the tail? cut tail into pieces & spliced to a
                                                    non-nuclear cytoplasmic protein -
   µ result:  nucleoplasmin holds a 17 amino acid sequence that targets transport into nucleus
                          it is known as the  NUCLEAR LOCALIZATION SIGNAL (NLS)
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- Current Model of Nuclear Pore Transport includes as many as 6 different molecules including:

        the molecules                       an analogy to a moving company
        Importins                            the delivery truck proteins
        ATP & ADP                          the gas
        GTP & GDP                          the unloading crew
        and a protein called Ran       the moving supervisor

                               an importin binds to cytoplasmic protein with an NLS (requires ATP)
              figure *      Ran + bound GDP complexes with importin-cyto-protein & diffuses into nucleus
                               in nucleus GDP is phosphorylated & cytoplasmic protein is released,
                               Ran escorts importin back to cytoplasm.

       Exportins - proteins found in nucleus that are counterpoints of importins
                         RAN & GTP are also required, and a Nuclear Export Signal may be involved

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     site ofcellular respiration   -  redox rx's...       oxidation of CH2O --> CO2 +  H2O

                    gas exchange in cell   -  CO2 is released   &   O2 is taken up & reduced
                    Krebs cycle              -  oxidizes PYRUVATE  --->  CO2  +  H2O
                    Respiratory ETC chain  &  Oxidative Phosphorylation,  which makes ATP

     role of :  site of conversion of covalent bond energy of food molecules --> into ATP...

                    it couples redox transfer of e- & H+ protons...   to   ATP-synthase --> ATP

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    1st described 1900's - Vital stains  (req living cells)   as Janus Green B    (pic)
            today: best seen via TEM*  &  with fluorescent dyes, false color scanning EM's*

    double membrane bound organelle*
            outer membrane - contains transport protein porin (passes molecules up to 5K)
            inner membrane - very selectively permeable (i.e., impermeant to most molecules)
            peri-mitochondrial space - (in between)  area where H+ accumulate            
            cristae* - inner membranes that hold the respiratory assemblies of ETC
            mitoplasm* - "matrix" aqueous compartment - DNA, ribosomes, KC, etc 
    structure :    elongate cylinders to oblate spheroids*  
                         3-5 um long by 0.5-1.0 um dia,
                        "shape-shifters", mobile
    number :       20 to 1,000 per cell ;     the more active a cell  = the greater their #'s 
                        can make-up as much as 20% of cell's volume
    contents:       its own DNA - 16,569 nucleotide pairs: about 37 genes
 its own ribosomes (prokaryotic size) & protein synthesizing ability
                        enzymes for cellular respiration  
 downball.gif (177 bytes)                                                                  john kyrk's animation of mitochondria





        group of double membrane bound plant cell organelles...
            found in all higher plants
            produce all the organics required by metazoan cells [sucrose, etc...]

                 precursor plastid to all the other plant plastids...
                 found in  apical meristems - dividing cells of root/shoot tips 

         local cell environment defines Type of Plastids to be made from proplastids 
           ETIOPLASTS ... chloroplasts developed in dark, have an interior array of cystalline-
                             membranes & yellow-chlorophyll precursor-like molecules  [pic1 + pic2]
LEUCOPLASTS ... non-pigmentous, 2x5 µm, variable shaped plastids for storage
                             3 types:  AMYLOPLASTS (starch),   ALEUROPLAST (protein),   ELAIOPLASTS (oils)   
CHROMOPLASTS ... plastids with water soluble pigments, flower color, etc... [fig*]

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  CHLOROPLAST.....   develops in the light from proplastids,

        as a plastid -->  site* of autotrophic metabolism = PHTSO2 evolutionCO2 reduction

        shape* - oblate spheroid = shape variable (stellate, reticulate)    
                                                                                Scanning E.M. of chloroplast* 

        size:  2-3 um dia  by 5-10 um long   &   number:   15/20 - 100's/cell

        contents = aqueous stroma (CHLOROPLASM) holds within itself...  
                1)  internal membrane system  made of   THYLAKOID membranes*
                                GRANA Stacks   and   INTERGRANAL membranes*
                2)  70s ribosomes (bacterial size)      (eukarya have different size ribosomes [80s])
                3)  lipid droplets
                4)  naked DNA pieces (highly supercoiled & repetitive)
                5)  starch granules & pyrenoids
                6)  enzymes of CO2 fixation (reduction)
downball.gif (177 bytes)                                            Concept Activity - chapter 6.5 - Build a Chloroplast and a Mitochondrion






endosymbionts ?  by Lynn Margulis - 1981

                           "Mitochondria  &  Chloroplasts  are derived from prokaryotes,
                             which were once free living, but joined into a symbiotic
                             relationship with eukaryotic aerobes during cellular evolution

    Preliminary support includes:
            many of today's single celled eukaryotes live in oxygen
            poor places (gut), lack mitochondria, & function anaerobically.

                                Pelomyxa palustris
is a eukaryotic amoeba,
                                that lacks mitochondria, yet holds aerobic bacteria
                                within its cytoplasm (in a symbiotic relationship).

            Chloroplasts share a common molecular ancestry [DNA sequences are similar]
            with the cyanobacteria (the 1st photosynthetic prokaryotes).
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Number striking similarities of  Bacteria  &   Mitochondria/Chloroplasts
      both organelles are double membrane bound.... 
                      possibly the result of.....  a phagocytotic engulfment
                      mitochondria?      chloroplasts?     eukaryotic evolution*
        both are semiautonomous
                     derived from themselves, by divisional fission...
                     i.e., replicate independently from their cell hosts
       both have their own DNA (a circular molecule like DNA of prokaryotes)
                  & protein biosynthetic systems
(can make some of own proteins)
      DNA sequence homology....  each has similar DNA sequences
                        mitochondria DNA related   to   aerobic bacterial DNA
                        chloroplast DNA related     to   cyanobacterial DNA
    › ribosomes are same size as bacterial ribosomes (70s)    (in eukaryotes  =  80s)
[ s = Svedberg unitsg ]
downball.gif (177 bytes)                                           Sumanas, Inc. animation - Evolution of cell organelles*






  Ribosome...             (a non-membrane bound organelle)

        RIBOSOME ... is a subcell ribonucleo-protein particle    (RNP)
a complex of RNA & Proteins
                           ... site of cellular protein synthesis    (artistic concept)
            spheroid shape  - 17 to 23 nm dia      
            composed of 2 subunits*  oo      (a computer model)       models of ribosome shape 
                    small subunit and a large subunit, which binds tRNA's
                    prokaryotic vs. eukaryotic composition  =   35% protein   and   65% rRNA
            found in 3 different places in cells...
               1.  free in cytoplasm, as individual subunits or dimers,  
               2.  membrane bound* on outer surface of Endoplasmic Reticulum membranes,
               3.  attached to mRNA molecule  in a   POLYSOME   [or  polyribosome*]
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ENDOPLASMIC RETICULUM...     (just membranes)
           is found in all eukaryotic cells with a nucleus
           has structural continuity with the nucleus (i.e., it's contiguous)    [ fig 7.7a & fig]
           makes up 50% of all membranes of a cell
           composed* of flattened sheets-sacs  &  tubes of membranes.
                 convoluted 3-D membrane network enclosing internal spaces
                 LUMEN - is internal compartment of cisternae  [makes up to 10% of cell's volume]
           2 Types:              Smooth E.R.   (SER - tubular membranes without ribsosomes) &
                                      Rough E.R.*   (RER - surface of cisternae with ribosomes)     
              SER: lipid & bile biosynthesis and drug detoxification
              RER: makes, transports, & packages proteins into membrane vesicles
                  SIGNAL SEQUENCE* :   aa's @ N-term, bind, release into lumen...    Gunter Blobel
                  glycosylation*  - adding carbohydrate groups to ER proteins
                                            which will help transport the proteins to specific cell sites
downball.gif (177 bytes)                                        proteins have many sorting signals - table of signals                            




Golgi Bodies
: a part of the ENDOCYTOTIC Pathway...
         the cell's internal membrane system for                             
              1.   endocytosis - packaging of extracellular molecules for internal digestion
              2.   exocytosis (secretion) - packaging & delivery of newly synthesized
                                                       proteins/carbo's for extra-cellular secretion
   Size* - 1 to 3 µm diameter  by  4 to 7 membranes stacks high
   Number* - up to 100 per cell
   Structurethree parts   (or sides)... 
      CIS side [entry side]... faces R.E.R
             proteins made on R.E.R. 
             pass from E.R. lumen --> vesicles --> cis Golgi
      MEDIAL cisternae elements...
             proteins are modified by adding sulfates, carbohydrates & lipids
             these modifications --> "address" membrane vesicles to a destination
      TRANS side [exit]... Golgi side          modified vesicles leave as...
                  export vesicles,   lysosomes,  other membrane bound vesicles
downball.gif (177 bytes)              Sumanas, Inc. animation - signal sequence & vesicle processing* listen at home






     LYSOSOME ...
 a  cytoplasmic single membrane bound vesicle 
                                      containing hydrolytic enzymes with acid pH optima (pH 5.0).
                                      lysosomal membrane has ATP driven membrane H+pump
G (faces in*)

       a sample of lysosomal enzymes

acid phosphatase removes phosphates
acid nucleases digest nucleic acids              
proteases digest proteins
glucosidase digest polysaccharides
phospholipase phospholipids & membranes
                       have diverse shapes, mostly spherical*
            functions in intracellular digestion (phagosomes* & autophagy)

      PROTEASOMES... barrel shaped protein complex responsible for Protein Digestion
downball.gif (177 bytes)          ubiquitin binds to protein & transports it into a proteasome  fig 19.12*   (Structure)





 Endocytotic Pathways -                     Concept Activity - Chapter 6.4 - The Endomembrane System
        migration path through the various organelles of the endomembrane system.   
        The endomembrane system is a complex part of the cell's compartmental organization.
        Nuclear envelope is connected to the rough ER & smooth ER.
                vesicles made by the ER flow... as transport vesicles to the Golgi.
        Golgi modifies the molecular composition and metabolic function
                 of the endomembranes as they flow from ER through the Golgi.
        Golgi, in turn, pinches off vesicles that give rise to lysosomes and vacuoles.        c8 fig 6.16*
        Plasma membrane can fuse with vesicles born in the ER and Golgi...
                 results in release of proteins -  Secretory protein pathway*  and
                 other products to the outside of the cell in exocytosis.
       Protein Sorting* - proteins bound for different destinations have diff carbohydrate tags
                                          Targeting Signals for semi-autonomous oragnelles (mito, chlp, peroxisome)
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      network of protein fibers running throughout the cytoplasm
      that give a cell its shape & provide a basis for movement (cytoplasmic streaming)

      stained cytoskeleton*,   TEM's*,    an SEM*  &    fluorescent microscopy pic1* & pic2* 

       Cytoskeletal proteins include... 

            1.  microfilaments (actin*) ..... 7 to 8nm dia & of indefinite lengths   
                    actin* is a universal (from protists to verts) eukaryotic protein
                    5% of total cell protein
                    linear filaments of polymerized monomeric globular proteins...  G-actin
                          ... a "conserved" polypeptide of 375aa + 1 ATP molecule

                    3 types of G-actins:
                                alpha actins of muscle cells
downball.gif (177 bytes)                            beta & gamma actins of non-muscle cells  (microvilli of epithelia*)
           2.  intermediate filaments...  (10nm dia -   ex:  keratin, vimentin & lamin)
                     protein fibers [rope-like] with an intermediate diameter
                     spans cytoplasm providing framework for mechanical strength
                     made from a heterogeneous family of filamentous proteins

           3.  microtubules...  25nm dia tubulin proteins (highly conserved evolutionarily)
                    21-25 nm dia, up to several um long
                    make long fibrillar protein complexes that form spontaneously
                    repeating globular units: 2 different proteins:  alpha & beta tubulin  
   summary of   types of proteins*  &  location & pics of proteins with cells*     
                                                          which are universal in eucaryotic cells 


                 Centrosome*  :  Centriole: 9 sets of MT triplets... forms spindle fibers
  downball.gif (177 bytes)                                                     Concept Activity - Chapter 6.6 - Cilia and Flagella*  







Cilia and Flagella and cell movements: 
   Flagellum   are microtubule (MT) extensions projecting from cells for
                    propulsions via an undulating-like motion* (ex: sperms & algae)
   Cillum      are MT extensions held in place in tissues that move fluids over the tissues
                  like oars, via alternating power/recovery stroke cycles*  (ex: lining of windpipe & mucus)
        structure*: both have same structure -  9 MT doublets surrounding 2 singlet MT's is center,
                         covered by plasma membrane 7 often held by cross-linking proteins (blue)

   Basal Body*  anchor of cilia & flagella:  a centriole* found at the base of flagella or cilia

   Bending Motion is via Dynein arms* - motor proteins attached to MT doublets
          if no cross-linking proteins (blue in fig) - one foot of dynein arm binds as other releases
                  allowing MT to "walk along" MT as doublets "slide*" past each other. 
          if cross-links are present, the MT's are held in place, so the doublets "curve (bend)*"
                  the cilia or flagella.
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 Microfilaments   &   Cell Movements -
        actin filaments bear the TENSION (wire) forces of the cytoskeleton
        microtubules (above) are the COMPRESSION (rod) units.

B-Tree sculpture by Ken Snelson at NIH
     contractile force of muscles*:   myosin & actin (microfilament) are motor proteins
          that via repeated cycles of binding and release  = a walking like movement (CONTARCTION)

     amoeba's crawl
*: along a surface via psuedopodia due to the assembly/disassembly of
          individual actin subunits on microfilaments

     cytoplasmic streaming
*: in plant cells occurs via actin/myosin interactions and sol/gel
      transformations which results in a circular flow of cytoplasm around the cell.

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  Intercellular junctions...
                    Cell surface regions specialized for intercellular contact = multicellularity
                    especially prominent in epithelial cells
   3 Major Functions
      1. impermeabilize areas     2.  adhereing junctions     3.  communication
      Tight Junctions* -  they impermeabilize regions
                    prevents leakage of materials between epithelial cells
                    a fibrillar protein network at apical end of epithelial cells
                                    "SIX-PACK MODEL"
     Desmosome - an adhering junction -   (anchors cells together)
                    spot desmosome - spot weld with tonofilaments (a microfilament)
belt desmosome (zona adherens) - wide band of desmosomes
     Gap Junctions -   intercellular channels for communication    [dia= 0.2nm]
                    allows ions, electric impulses, etc... to pass between
     Plasmodesma* - cytoplasmic strands between plant cell walls [dia= 70nm]
                    makes these plant cells a syncytium*...  cells not separated
                    from one another by cell walls or membranes.     
downball.gif (177 bytes)                                                          Concept Activity -  chapter 6.7 - Cell Junctions*






 the plant VACUOLE          (animal cells also have small vacuoles)

    is a membrane-bound [tonoplast] sac that plays roles in intracellular digestion
                                                          and the release of cellular waste products.

    In animal cells, vacuoles are generally small.

    In plant cells, vacuoles tend to be large and play a role in maintaining turgor (pressure).
            When a plant is well-watered, water collects in cell vacuoles producing rigidity.
            With insufficient water, pressure in the vacuole is reduced and the plant wilts.

    Vacuoles accumulate toxic wastes:  phenolics, acids, and a range of nitrogenous wastes and
            water-soluble pigments, especially anthocyanins - responsible for red-pink-blue-purple
            coloration in many (but not all) flowers and fruits.

    the tonoplast (vacuole membrane) holds transport proteins, mostly active-transport carriers
            for one way accumulation of toxics into the vacuolar spaces. 

    As plant cells age.. onset of death is usually associated with tonoplast leakage & breakdown. 
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 ENDODERMIS and CASPARIAN STRIP...    [in plant roots]

    endodermis is an innermost layer of cells in the cortex of a plant roots
            forms a cylinder of tissue* - one cell layer thick -
            that separates the outer root cortex from the inner vascular stele

    endodermis contains a waterproof Casparian Strip* made a wax-like insoluble molecules 
            that runs completely around each cell, making the cells impermeable to exterior flow,
                   thus all materials must move into and through the endodermis cells to reach the
                   transport cells of the inner cortex of the root...  
                              SYMPLASTIC  ROUTE - internal via plasmosdesma
                              APOLPLASTIC ROUTE - external via intercellular space     figure*
                  downball.gif (177 bytes)         
       a paradigmKey Concepts*      

         U of Miami Home Page | Biology Home Page | Dr. Mallery's Home Page | On-Line Testing Center
               copyright c2007,   Charles Mallery,
               Department of Biology, University of Miami, Coral Gables, FL 33124
               Last Update - May 29, 2008
               [Vaults (?) - cytoplasmic RNP's  [part of a pore? nuclear pore complex (the central plug)]



















          expanded table of differences between Prokaryotes & Eukaryotes

           Chaperones - proteins that help fold other proteins into proper shape
                               (Sumanas protein folding & degradation animation*)

Sumanas animation-vesicle processing*