Results of Microscopy Investigations of Cells...  
 
                     - helped define some of the major EUKARYOTIC ORGANELLES

      The light microscope, so called because it employs visible light to detect small objects,
      is probably the most well-known and well-used research tool in biology. Live cells lack
      sufficient contrast and internal cell structures are colorless and transparent. Contrast
      is increased by staining with selective dyes (plant section), which involves killing and fixing
      the sample, which can introduce artifacts.

      The electron microscopy uses a focused electron beam on fixed sectioned of cells, which
      are static (fig 1.7a) to describe organelles, mostly by presence or absence of membranes...

                       The material below on CELL ORGANELLES* is a general review of your
                       freshman biology cell structure. Please REVIEW this material ON YOUR OWN.
                       Pay close attention to new material highlighted with a red arrow  ►
                       At end of this review are Practice Question's on this material.  
  

 

 

 

 

 

 

 

 

  

 

    
REVIEW OF MAJOR EUKARYOTIC ORGANELLES...  [review on your own]
  
Double Membrane Bound Organelles:                                     
     
 1. nucleus...  largest; double membrane bound* - outer membrane contiguous with ER membranes.
         synthesizes DNA, rRNA, tRNA, primary transcript (mRNA preccursor)    
         peri-nuclear space (2-5nm) is contiguous with lumen of ER                 nucleus em*
         pores of protein nucleoporins (ecb 8.15*) regulates nucleoplasm-cytoplasm exchange
                via NLS of 7 aa sequence @ C-terminus (N-pro-pro-lys-lys-lys-arg-lys-val-C)
         nucleolus - regions of rDNA that makes rRNA (but, ribsosomal proteins made in cytoplasm)
         nucleoplasm - the 'cytoplasm' of the nucleus
                heterochromatin - condensed (darker EM color) = inactive DNA -    figure*
                euchromatin - non-condensed (lighter EM color) = active DNA
                lamins - fibrous proteins adjacent to inner nuclear membrane = frame for nuclear shape
  
 
 2. mitochondria... conducts ATP production of cell via oxidative metabolism of glucose & fatty acids
        outer membrane (50:50 lipid/protein) contains porins (fig*) that  transports most ligands < 10K
        inner membrane (25:75 lipid/protein) strictly regulates most transport into mitoplasm
                 cristae - infoldings of inner membrane (ecb14.8* &  figure*    pic1* & pic2*) 

          ► a new discovery of antimicrobial role* of mitochondria in killing bacteria
       
      
    
 

 

 

 

 

 

 

 
 3. chloroplast...
      largest green plant cell organelle (0.5-2.0 µm by 10 µm) has
      double membrane with extensive inner membrane-limited sacks called thylakoids (ecb14.28*)
      absorbs light energy via chlorophyllous pigments & makes ATP & NADPH (chemiosmosis)
      reduces CO₂ into CH₂O
          Similarities of Mitochondria & chloroplasts...
             1.  make ATP/NAD(P)H via similar mechanisms
                      - chemiosmosis: oxidative creation of H+ gradient coupled to ATP synthase
             2.  show mobility throughout cell
             3. divide by fission independent of whole cell's division
             4. autonomously replicate their own DNA [mito: 16,569 nucleotide pairs: about 37 genes,
                          while chlp has about 120 genes - highly supercoiled & repetitive-up to 6 copies]
             5. both contain 70s - bacterial size ribosomes  [eukaryotes have 80s ribosomes]
             6. synthesize their own proteins on their own protein synthesizing machinery
   
             

 

 

 

 

 

 

 

 

 
  Membrane Complexes...   as Organelles: 

  4. endoplasmic reticulum... network of closed-flattened membrane sacks called cisternae
         found in all nucleated cells; involved in protein/lipid biosynthesis
         2 types:  SER (smooth) - lacks ribosomes                                                        ecb 1.21*
                                            - makes FA & phospholipds (esp. in hepatocytes)
                                            - detoxifies hydrophobic chemicals including carcinogens & pesticides
                        RER (rough)  - membranes bound with ribosomes                              ecb 15.12*
                                            - makes plasma membrane proteins & exportable proteins of ECM
                                            - abundant in cells making  -  antibody proteins (plasma cells)
                                                                                    - pancreas (digestive enzymes & hormones)

 5. Golgi Complex... series flattened membrane sacks (cisternae) that take up ER transport vesicles
         and process contents via glycosylation (addition of carbohydrate residues).
         3 divisions:  cis - where ER vesicles enter                                                         ecb 15.2*
                           medial - where modifications (glycosylations) occur
                           trans - vesicle packages & budded off here for secretion               mcb9.6* 
                         
 
 

 

 

 

 

 

 

 

  
  
Single Membrane Bound Organelles: (Digestive)
  
6. endosomes... membrane bound vesicles of extra-cellular milieu internalized by ENDOCYTOSIS
        a.  endocytosis - cathrin protein "coated" membrane pits - pinch off endosome vesicles
        b. phagocytosis - whole cells engulfed & passed to lysosomes for digestion
        c. autophagy - worn-out organelles fuse with lysosome   ecb 1.24 &  endosomes & lysosomes*

 
7. lysosomes... hundreds single membrane bound vesicles* (exclusive to animals- plants use vacuoles)
        have acid pH environment to help denature proteins (H⁺ATPases* & Cl transporters --> HCl)
        contains hydrolytic enzymes (nucleases, proteases, phosphatases, glycosylases) for digestion.
                         Tay-Sachs (tt): defective lysosomal enzyme which degrades ganglosides,
                                                glysolipids buildup in neurons ≈ dementia, blindness, and death
 
        nuclear & some cytosolic proteins aren't digested within lysosomes, rather by proteasomes,
        which are large protein complexes inside all eukaryotes, archaea & some bacteria.
        In eukaryotes: located in nucleus & cytoplasm their main function is to degrade unneeded or
        damaged proteins by proteolysis.

    

 

 

 

 

 

 

 

  
  Other Single Membrane Organelles:
  
  8. plant vacuole...  membrane limited interior space (up to 80% cell volume) containing
            membrane transport proteins accumulate ions, nutrients, & wastes.                 ecb 12.17*
            lumen holds digestive enzymes (has acid pH optima [H-pump]- acts like lysosomes).
            tonoplast membrane permeable to water influx, helps establish turgor pressure (5-20 ATM)


  9. peroxisomes... spherical (0.2-1.0 µm) organelle containing oxidases (catalase) that use O₂
                           to oxidize (remove e^-'s from) molecules as H₂O₂ (& other toxins).  mcb9.4*
           degrades FA's to acetyl groups - used to make cholesterols (esp. impt in liver/kidney cells).
                                  X-linked adrenoleukodystrophy (ADL): no FA digestion occurs,
                                  leads to several neuro-linked defects and death.                 
                                                                                                            
           plants contain glyoxysomes which oxidize stored lipids (very similar to peroxisomes).

  

    

 

►  Membrane-less Organelles:  eukaryotic Biomolecular Condensates (organelles without membranes).

In addition to membrane-encased organelles - as the nucleus, mitochondria, and Golgi apparatus, eukaryotic cells harbor a variety of condensate compartments that lack a casing (2017). These protein based liquid globules (membrane-less organelles) form by Phase Separations selectively permit entry of proteins, enzymes and substrates to carry out various cellular functions that would be less efficient or not possible at all in the cytoplasm. Membrane-less organelles allow cells to compartmentalize compounds and reaction rates and cordon off interfering molecules.  figure*       These structures are highly dynamic, and range in size from 0.1–3.0 uM in diameter, often far bigger than just a few molecules clustered together or than multi-component molecular machines such as ribosomes (20 nm).     The NUCLEOLUS, the largest and most prominent nuclear compartment lacks a membrane, and is a globular structure known to play critical roles in ribosome biogenesis.

The emerging picture of the inside of the cell is that the cytoplasm and nucloplasm are complex fluids that can stably segregate, like a cruet of oil and vinegar [ liquid-liquid phase separation ].

other ex:   in slow-growing E.coli,  the RNA polymarase is not uniformly distributed,                                                       but is clustered in liquid droplets in fast-growing E.coli.                  Cajal body  -  in nucleus,  snRNP maturation  and  regulation and packaging of Splicesomes                  P-body        -  in cytoplasm,  is a mRNA processing and decay entity

biomolecular condensate-mutations-diseases -  prevention of condensation formation = diseases ?

         

  

   

    

 

 

 

 

 

 

   

► Prokaryotic "Geometric" Organelles:  geometric compartments of reactivity in prokaryotes

Prokaryotes are defined as lacking organelles... In 2009 Egbert Hoiczyk observed 32 nm-wide structures resembling 12-sided dice, about the size of typical bacteriophages. These microcompartments have been found in a range of bacterial phyla, suggesting that the prokaryotic cytoplasm is highly organized. These microcompartments structures create a specialized microenvironment for metabolic processes ("organelles").

*

Microcompartments are composed of protein coats akin to virus capsids, but with a different assembly into hexagonal tiles forming 12 faces and pores. Bacterial microcompartment shells are built out of thousands of protein subunits of 3 basic structural motifs:  BMC-H, BMC-T, & BMV (fig*).  Searching microbial gene databases for these gene protein sequences turned up 23 types of microcompartments spread across 28 bacterial phyla.

Prokayotic microcompartments can maximize the turnover of metabolites by keeping reaction intermediates close and interfering chemicals at a distance.

Some ex:  carboxysome     - carbon fixation in cyanobacteria (via RuBisCo & carbonic anhydrase)                  metabolosomes - enzymes that degrade metabolites & sequester toxic aldehydes

    

   

  

 

 

 

 

 

  
 
 
 

                "The Inner Life of a Cell " - a movie animation by David Liebler & Harvard U.
 

                a figure labeling quiz?:    animal*  (ans)    &    plant*  (ans)

                an electron micrograph labeling quiz.    the EM* (ans)

                 Download Power Point  practice questions...   (ans)

  

    next - molecular chemistry of cells      

 

 

 

 

 

 

 

 

Please skip all the material below this point...