the Shapes of the Biomolecules...         
         determines how molecules interact with other molecules.
 
        It is the weak molecular forces that shape molecules and build

 
            Molecular Complexity   &   Biological Activity 
   &   Life.
    
  Biological work entails mechanical functions, biosynthesis, transport, electrophysiology,
        homeostasis, etc...    all of which depend upon the SHAPE of MOLECULES.  
     
  
  Structural Chemistry
:         3D-molecular shape is dependent upon the
                                            
orientation of covalent bonds in space.
     

  Molecular Configuration
:   
results in specific bond angles & molecular geometry
                 methane             CH4        109.5o  - a tetrahedron with free rotation
                 formaldehyde    
H2C=O   120o     - same plane  with no free rotation

  orientations*

   
  One key to understanding molecular shapes is seen in the ASYMMETRIC  [chiral]  CARBON ATOM...
                a carbon atom bound to 4 dissimilar atoms in a nonplanar configuration often
                forms molecules based upon a
tetrathedron* shape    [ water + other examples*]...
                
           

 

 

  
  

 

       

 

 



 
 
 Asymetic carbons result in molecules that differ in 3D-orientations in space i.e.,

           STEREOISOMERS...  or optical isomers*,                      
                 molecules, which have identical composition, but are not equivalent, as they  
                 have different molecular orientations in space or are MIRROR IMAGES...

                such chiral molecules are not superimposable on its mirror image...
                 as with human hands. They are
also called ENANTIOMERS*.
 
       
              Stereoisomers may have mostly
identical chemical properties, but do show an 
              unusual optical property: the isomers rotate plane of
polarized light at different angles.
                       
LEVOROTARY
  (L or S) - rotates light left    (- negative optical rotation)
          
   DEXTROROTATORY  (D or R) - rotates light
right  (+ positive optical rotation)
      

       Stereoisomers can often have different BIOLOGICAL ACTIVITY:   some examples... 
          a.
  dihydroxyphenylalanine [L-DOPA fig* -->  Encephalitis lethargia & "awakenings"
          b.   sedative thalidomide* =  severe birth defects due to L (or S isomer); D or R helps nausea
                                                           
Gruenenthal Pharmaceutical Group apology - statue.
                 ???
  Which do you think would be more thermodynamically stable and why?
                                       a homochrial polymer  (made of same enantiomer isomer - say all D)
                               vs.   a
heterochiral polymer (made of a mix of enantiomer isomers - D & L)
?

  

    
 

 

     

 

 

 

 

 


 

 

 

 

 
     
Biological activity
...
is the catalytic ability of molecules to do work. 
      
There are 2 structural properties of biomoleculeswhich contribute to a 
        molecule's
unique Fitness for Biological Activity & the Living State                      Text description -
                      Shape and Form of Biomolecules*

1st.   CONFIGURATION:  the permanent geometry that results from the spatial arrangement
                         of a molecules bond's, i.e., the spatial arrangement of atoms via bonds
in the
                         molecule
that may not be
inter-converted without those breaking bonds.


          Some example of covalent bond molecular configurations
...              
                  ISOMERS...
 
based upon covalent bond orientations [glucose vs. galactose]*
                                      
and each has different chemical & biological properties.
      

                 
ISOMERS... built upon planar covalent double bonds*    -C=C-               
                                       fix atoms above & below plane of molecule (planar) &
                                       restricts free rotation, thereby fixing a 3D shape
in space.
                                                         
  Cis   vs. Trans*
                                            maleic (cis)      vs.     fumaric (trans
                    11-cis-retinal   vs.     11- trans-retinal* 

 

 

        

 

 

 

 

 

 

 

 

 
  
Biological Activity  
& the   Shape of Biomolecules   continued...

2nd. CONFORMATION  [or shape] - is the surface outline or contour of molecules
      - is 3D orientation of all chemical groups in molecules free to
             assume different positions in space without breaking any bonds 

      - do primarily to...
      
    
FREE ROTATION of atoms about a single chemical bond &
           WEAK NON-COVALENT FORCES hold atoms in spatial arrays
3D-conformation
      - consequence of conformations...
            different conformational shapes (forms) of molecules can exist,
           
only one of which may be biologically active  (the other conforms aren't) 

  
    
ENZYMES can distinguish between
biologically active forms (CONFORMS*
                       based upon the "
SHAPE" of that molecule.
      
             
 

 

 

 

 

 

 

 

 

 

 

  
Molecular Conformations are due to the  Weak Molecular Forces* of a cell's environs...
    IONIC bonds* attraction between cation (+) & anion (-); no fixed geometry for electrostatic
                             
field-uniform in all directions; readily soluble with polar water
[Na+,K+,Ca+2,Mg+2,Cl-]
    DIPOLES*        attractions via asymmetrical, internal distribution of charges in a neutral, 
                              molecule,
one which has no net charge (opposite poles +/- attract weakly)
    DISPERSION* (van der Waal’s) Forces- electrostatic interaction between orbitals of 2 atoms...
                               generates transient dipoles that attract/repel; results in cohesion between non-
                               polar molecules
that don't form H-bonds 
 mcb fig 2.10  important in 3-D shapes
    HYDROPHOBIC Interactions* - repulsion of electrostatic dipoles of water by non-polars-
                                                      "fatty-hydrocarbon" groups can self assembly -
"
like dissolves like
"  
    HYDROPHILIC Interactions* - substances that dissolve readily in water (ions & polar molecules) 
                                                     water, as a dipole, surrounds & solubilizes a solute molecule
    HYDROGEN bonds*  electrostatic attraction between H of one atom & pair of non-bonded e-’s
  
                                    on an acceptor group; linear directionality  OH  &  N-H  with   O-  &  N-  
   Non-covalent Electrostatic forces in action*...    (all are in the 1-10 kcal/mol range)

   
 
 
 
 
 
 
 
 
 

 

 

 

 

 
 
Covalent vs. Weak Molecular Forces of Life
 ...                

TYPE of BOND   ENERGY (kC/mol) TYPE of INTERACTIONS   ENERGY (kC/mol)
 
SINGLE COVALENT BONDS NON-COVALENT BONDS (in water) Tbl 2-1
O - H 110    IONIC BONDS 2.5 - 3.5
H - H 104    HYDROGEN BONDS 0.5 - 1.5
C - H 99    HYDROPHOBIC 1.0 - 2.0
C - O 84    VAN DER WAALS 0.1 - 0.5
C - C 83
S - H 81
C - N 70
C - S 62
DOUBLE BONDS
C = O 170
C = N 147
C = C 146

                   bond
                  energies

                    








 











   
A fundamental question of the living condition has always been (???)
...

    How do Weak Molecular Forces & Molecular Shape build biological design & form? 
    How do individual groups of molecules assemble into living organisms?
 
        
 
Is there a Fundamental Principle that guides form in biological organization ?
          
Some common universal/principle or rule of molecular assembly?
           One often sees recurring patterns of spirals, triangulated forms, & pentagons in
          
everything from
molecules to viruses to
plant flowers - biological forms & shapes*.   
 

           How do molecules join to form larger & more stable structures, often with new & 
     
      emergent properties…
   macromolecules -> organelles -> cells -> organs ->
organism 
   

Maybe an answer lies in well known an architectural principle known as  TENSEGRITY...  
   
Tensegrity (tensional integrity) is when a structure maintains stability under tension;

    Tensegrity defines mechanical rules of how structures are stabilized        
          by balancing forces of internal tension and compression [tensional integrity].

          It may be
a architectural rule that contributes to biological form and shape.


    Can we apply this general architectural principle to biomolecules & living systems?

    
7











 

 

 

 

 

 

 

 

 
 
TENSEGRITY
  
occurs in an architectural pattern where push/pull forces balance, 
                           & are mechanically stable, yet dynamic, and the forces of

                           of tension and compression are compliments to each other.
                          

 
      "tension & compression are eternally complementary elements in any structure"
 

 Geodesic Domes...   Buckminster Fuller --> a Bucky Ball* is a fullerene.
     
     Fuller coined term "geodesic" and patented it in 1954. 
               A dome distributes its mechanical stresses across an entire structure. 
  
             Frames of rigid struts connected into triangles, squares, pentagons,
         
     or heptagons, each of which balances compression & tension...
               while tensioned wires delineate them spatially.

geodome

     Examples: Tensegrity Structures (Ken Snelson - pic1* - Tree I 1981)
     have struts that bear
compression are distinct from wires bearing tension.
 
   Compression members can provide rigidity while remaining separate,
 
    not touching one another, held in stasis only by means of tensed wires.


           
     In both of the structures above tension is continuously transmitted across
     all the structural parts of the structural members.

             Some examples  -
    toy models*    and     suspension bridges* 
     




                                 

 

 

 

 

 

          
 
   but, can we apply Architectural Tensegrity
to Biological Systems ???    
  
         
   at the Organismal Level...   (a crude biological analogies...)  
                  
bones* are the compression struts and     [do it again]
                  
muscles, tendons, & ligaments* are the tension bearing wires
  
 
  
Cell (early view)...    
membrane bounded viscous gel (a molasses filled balloon)
          (
today's view)...
cytoskeletal*  microtubules awash in a viscous gel,
                                                           tensed by microfilaments, surrounded by membrane

     

                                                       
role of cytoskeletonas in  suspension bridges    
              
cytoskeletal elements, as the microtubules...   might act as compression "girders";
              
while microfilaments may exert tension, providing rigidity while remaining separate.

               Cytoskeleton animation
*.
    
  
      ►     the Cytoskeleton then may be a hard-wired molecular system that stabilizes
               cell form & shape, according to the architectural principles of
tensegrity
?
9                                               

    

 

 

 

 

 


 

 

 

    



               
   


 
Biological Tensegrity suggests - 
       that the structure of cell's cytoskeleton can be changed by altering the balance
       of physical forces transmitted across the cell’s surfaces and this might result
       in changes in shape and form.  
           for examplecultured cells nuclei on glass
[are flat]   vs.   a flexible surface [are round]

                     
Donald Ingber’s Tensegrity Model of a Cell*  [Architecture of Life by Don Ingber]
                                                                   
 
Tensegrity & Mechanotransduction further suggests
 
     
Since many enzymes and other substances that control protein synthesis, energy
      conversion, & growth in the cell may be physically
immobilized upon the cytoskeleton,
   
  changing the cytoskeletal geometry may affect biochemical reactions and even 
      alter the genes, which may be activated & thus proteins may be made.
 
 
  

   
   Binding a signal molecule (or mechanical stress) to a receptor, which traverses a cell
      membrane into a cell, may cause conformational changes at the opposite end of
      the receptor, which may then trigger a cascade of molecular restructuring inside
      a cell, including
reorientation of the cytoskeleton...  some examples

      
cell movement* & morphogenesis* cyclosis &  mechanotransduction*  [Ingber 2006],  

7

 


  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 


 

    

 
   
  SELF-ASSEMBLY
of molecules into organelles and/or cells into tissue 
             is
not much different from self-assembly of atoms into compounds. 
                        The shape a molecule assumes is characteristic of the way 
                        the structure as a whole will behave in 3-D space, and maybe  
                        cells respond in a similar way according to rules of
Tensegrity

    Fully triangulated tensegrity structures, once self assembled, 
          may have been
selected for through evolution,
because of their
     
                  their structural efficiency,
                        their high mechanical strength
               
        their minimal use of materials. and
                       
their ability to stabilize structures in a changing environment.

    
  Tensegrity may be a most economical and efficient way to build cell form and structure
                     and therefore was molecularly selected for during cellular evolution
???

 


     7                      




 

 

 

 

 

 

 

 

 


 

 

 


      

 
   
a brief SUMMARY of...  shape of molecules & biological activity:
   

      
a few fundamental principles of chemistry are essential for understanding
       cellular processes at the molecular level:
  

            
1. small molecules are the building blocks of larger molecules...
                         
monomers make polymers, make supramolecular complexes, make organelles
...
                          figure
*
            
2.  covalent & non-covalent electrostatic forces control MOLECULAR form and shape...
                          forces of
configuration & conformation result in biologically active molecules

                          figure
*
             3.  architectural tensegrity may balance the force of tension and compression
                          foster the establishing and ability to change shape and form with cells.  

                          figure*

     
 more of the details of Biological Activity will be covered under section on METABOLISM (later).
            
4.
chemical reactions are reversible depending on rate constants & the [P] & [R]
                          figure
            
5. the source of cellular chemical energy is the hydrolysis of ATP, as high energy
                          phospho-anhydride bonds are broken by addition of water (hydrolysis).

                          figure

      
       
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