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 volume),
 

            found in all eukaryotic's     (except erythrocytes & sieve tubes cells of phloem)
 

            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.
         

 

 

 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*      &    structure nuclear pore complex*  
                      functional diameter of pores - 10 nm      &    NUCLEAR TRANSPORT*
    c. chromatin - the genetic 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*
                                                                                chromatin distribution within a chromosome

    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  animation*  &   DNA supercoil 
            chromosome locales within nucleus*                   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 autoradiography^G to follow movement [pic]   

           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)
                        a likely mechanism* for nuclear protein transport.
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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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 Mitochondria

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

                    gas exchange in cell   -  CO₂ is released   &   O₂ is taken up & reduced
   

                    Krebs cycle   -  metabolic pathway oxidizes PYRUVATE  --->  CO₂  +  H₂O
   

                    Respiratory ETC chain  &  Oxidative Phosphorylation,  which make ATP
 

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

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

   
    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:       has its own DNA - 16,569 nucleotide pairs: about 37 genes
                        has its own ribosomes (prokaryotic size) & protein synthesizing ability
                        holds enzymes for cellular respiration  

                                                                   john kyrk's animation of mitochondria

  
  plastids

        group of double membrane bound plant cell organelles...
            found in all higher plants
            produce all the organics required by metazoan cells [sucrose, etc...],
                         store polymers of carbon & contains various pigments

       PROPLASTID
                 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*]

  

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

        as a plastid -->  site* of autotrophic metabolism = PHTS,  O₂ evolution,  CO₂ 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)      (eucarya 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)
                                            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).
        

 

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 ]

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 - discovered by George Palade in 1940's using TEM

                           ... site of cellular protein synthesis    (artistic concept)

  

            spheroid shape  - 17 to 23 nm dia      
            composed of 2 subunits*  oo      (computer model & Noller model & 2009 Nobel Prize)
                    small subunit and a large subunit, which binds tRNA's  (functional structure*)
                    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*]
end

  
   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)

           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)     
           Functions:
              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 ---> glycoproteins
                                            which will help transport the proteins to specific cell sites
                                        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    Structure -  three 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
protein trafficking through the Golgi & Cis Matauration*

 
     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*)

                       have diverse shapes, mostly spherical*
                       functions in intracellular digestion (phagosomes* & autophagy)
 
                                    Sumanas, Inc. animation - signal sequence & vesicle processing* ^{listen at home}


  
      PROTEASOMES... barrel shaped protein complex responsible for Protein Digestion
            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,
                              first proposed by George Palade in 1940's.     

        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.
  

   Exocytosis: 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.
   Endocytosis: external material is pinched off into a vesicluar endosome,
                 which can fuse with a lysosome for intracellular digestion  -->   vesicular transport

        
  
       Protein Sorting* - proteins bound for different destinations have diff carbohydrate tags
         
 

 cytoskeleton

      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[ F-actin ] of polymerized monomeric globular proteins of G-actin*
                          ... a "conserved" polypeptide of 375aa + 1 ATP molecule

                    3 types of G-actins:

                                alpha actins of muscle cells
                            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

                           Role of cytoskeleton in cell structure*

 
        OTHER  CYTOSKELETAL  ELEMENTS  and/or  ORGANELLES... 
   
                 Centrosome*  :  Centriole: 9 sets of MT triplets...     facilitate spindle fibers
                                                      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 in center,
                         covered by plasma membrane & 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* - a motor protein attaches & releases to MT doublets. video*
          if cross-links are present(blue in fig), the MT's are held in place, then dynein causes
                 MT doublets to "curve (bend)*" the cilia or flagella.
          if no cross-linking proteins  - one foot of dynein arm binds as other releases
                 allowing MT to "walk along" MT as doublets "slide*" past each other. 
                figure of dynein MT walking* 

Cytoskeletal elements  &   Cell Movements -         actin filaments bear the TENSION (wire) forces of the cytoskeleton         microtubules (above) are the COMPRESSION (rod) units [tensegrity]         provoding internal structural support for cell organelles.

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.

  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, i.e.,
                    they prevent leakage of materials between epithelial cells (normal vs. celiac disease*)...
                    made of 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.     
                                                          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. 
 

 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*
  
                           ^*                  cells set to music                    Key Concepts* 
                                                         virtual cell animations*^{-recommended by not required}

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               copyright c2007,   Charles Mallery,

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

               Last Update - October 07, 2009
               [Vaults (?) - cytoplasmic RNP's  [part of a pore? nuclear pore complex (the central plug)]

ignore the material below for Bil 150-pt

          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*


    protein recycling*      Targeting Signals for semi-autonomous oragnelles (mito, chlp, peroxisome)