CHEMICAL ARCHITECTURE of CELLS
... 

             
if 70% of a cell is water what's other 30% ?

          it's the Elements and Molecules within CELLS...

   96% of mass  of cells
(i.e., the other 30%) is ONLY 4 ELEMENTS   tbl 2.1*
     -  C H O N + P S
 
[ old mnemonic---> "C. HOPKIN'S  CaFe  Mg" ]

     -  Why only these lelements ?
  
their valances favor covalent bond reactivity
*
   - they readily form molecules due to their electronegativity.
               
-  these elements make up the inorganic and organic molecules of cells:

   Cellular elements, plus many METAL IONS, responsible for many reactions:
 
           1.  make up parts of organisms as bone, exoskeletoms, and vitamins.
                some examples: Mg in chlorophyll, Fe in heme, & nickel in enzymes.

           2.  are dissolved in aqueous media of the cell and serve
                as catalysts for many chemical reactions.

    

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Metabolome    is the complete set of small molecule metabolites
                           occurring in an organism (akin to the term 'genome'). .
   - metabolome of plants =  50,000 components
   - estimates in Human    =  40,000+, & some 2,080 enzymes, & 115 pathways
                                                 the human metabolome database
   - the vast majority of all metabolome components are:   

   
   ORGANIC Molecules...   molecules composed primarily of elements of C & H,
                                            are the building blocks
* of polymeric biological molecules.
                                            the macrolmolecules that make up cells & Life

 

            MOLECULES
*                      BIOLOGICAL ROLE
            carbohydrate (CH2O)            structure & energy molecules
               
            proteins (CHONS)                 structural, enzymatic (catalytic)          
            nucleic acids (CHONP)         informational, genetic role 
  
 
            fats (lipids)   (CHO)               structure & energy molecules          
               
     phospholipids (CHO-P)         membrane structure    
            steriods/sterols (CHO)          membrane structure - hormones
 
  

 
fish01.gif (295 bytes)      Why is it that organic life is based upon Carbon and not SiliconThought Question             es 6

    
 
 
 
 
 


 

 

 

 

 

   
Some Basic Bio-Organic Chemistry...

      
including the ways to represent molecules graphicallyin texts and figures...
 

      Molecular
(or Empirical) Formula   vs
.   Structural Formula
              ...stick and space filling models                           fig 4.3*  &   3D molecular models

      Hydrocarbons - molecules made of Carbon & Hydrogen & have molecular skeletons*
              ...some examples  :   chains   vs.  rings               fig 4.5*
 
      ISOMERS    - structural or                                           fig 4.7a*
                                ...have the same empirical formula, but different structure
                           - geometric - cis-trans isomerism            fig 4.7b
                                ... differ in arrangement of groups attached to planar C=C

               
           - optical                                                   fig 4.7c*
                            
   ... bend plane of light is different directions (mirror images)


         
                                                summary of all isomers =   fig 4.7

 
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A.  CARBOHYDRATES... are polymers of simple sugar molecules, which
         have a consistent ratio of [
CH2O]
n  glucose -  C6H12O  or galactose C6H12O6
                                amylose
                              (starch)                              

       1.  MONOSACCHARIDES...   or the simple sugar monomers,
               are the monomers  that make polymers as starch, glycogen, & cellulose
                     (single molecules)                                                                       (polymers)
       
            Chemical CLASSES of  Monosaccharide monomers
                        -  built upon the chemical groups of an aldehyde or a ketone
                        -  aldoses 
[built on an aldehyde    vs.    ketoses  [built on a ketone
                        -  names based on # C's - triosespentoseshexoses     fig 5.3*
  
            Structures of Monosaccharide Glucose  C6H12O6
                Glucose    -  straight chain vs. ring structures*,   [glu images*]     
                       
         
            abbreviated ring*, optical isomers*, other isomers*,   α & β isomer forms*
  
  
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      DISACCHARIDES...
   

            are composed of only 2 monosaccharides...

            formed by condensation rx       ---->      polymers*A             

           
videos:      disaccharides*A       ---->      GLYCOSIDIC bond*   -C-O-C-
                     
                                   

       
  dissacharide bond           polymer
  maltose*   α-1,4 glu-glu --->   amylose

sucrose*       α-1,2 glu-fruc --->   sugar

cellobiose*   [3D ß-1,4 glu-glu  --->   cellulose

                                                        [animation - descriptions of carbs] View@home       

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  POLYSACCHARIDES...  the complex sugar macromolecules are  
                                     ...  polymeric chains of many monosaccharides linked together.
                                     ...  forms long repeats in helical shapes...  (like a staircase)
 
            STARCH...  a polymer of glucose monomers in the  α-1,4glu  configuration:    
                                also know as...       AMYLOSE             is an unbranched polymer
                                                               AMYLOPECTIN     is a branched polymer   

            GLYCOGEN
*...  multi-branched polymer [helps solublize it in human & animals] 


  
            CELLULOSE
*
... unbranched glucose polymer of ß-glu (for ex: in leaves*   
                                         
animals lack cellulase but symbiotic bacteria can digest cellulose
   
            CHITIN*... exoskeleton  of insects & crusteceans,    adds +NH2 group 
    

            Review of Carbohydrate StructuresView@home &  tutorial on carbohydratesView@home
                                                    

 
the take home message here is ...  
       
   "MOLECULAR STRUCTURE is CRITICALLY IMPORTANT to FUNCTION, &
                STRUCTURE relates to the 'ORIENTATION' of covalent bonds in 3D space"
 
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Importance of Molecular Shape to Biological Activity


2
unique PROPERTIES of BIOMOLECULES gives them special FITNESS for Living State...

             

  1.
Configuration -
is the PERMANENT GEOMETRY of a molecule that results from the
                              spatial arrangements of its COVALENT BONDS in space:

       
     Configurations can't be inter-converted without breaking chemical bonds &
             often involves an
asymmetric Carbon
atom...  (carbon w 4 diff. groups attached*)
  
   
  exSTEREOISOMERS,  also called  enantiomers have same molecular formula
             but differ in 3D orientation of atoms in space and are mirror images, which are
            
not superimposable upon each other thus they exhibit property called CHIRALITY.

                  a unique property of amino acid stereoisomers with identical chemical structures,
                  is that they rotate plane of polarized light at different angles...
          
  levorotatory        [ L ]  or  [S]   =   left handed    -  counter clockwise     
            
dextrorotatory     [ D]  or  [R]   =   right handed  -  clockwise

 
         molecular examples:  
amino acids   &  
glucose   &   limonene*

         medical ex:  Parkinson's disease
and an L-DOPA treatment -[Animation* & Awakenings]
                           (L-DOPA* -DihydrOxyPhenylAlanine) is converted to neurotransmiiters
                             as dopamine, which reduces the symptoms of Parkinson's


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 Configurations - permanent geometry due to spatial arrangement of bonds:
                examples: are Structural Isomers, as pentane and isopentane.
                     but often the
best examples are seen with cis-trams isomerization,
isomers that
                     are based upon the presence of "
covalent bonds",
especially carbon-carbon
                     double bonds  
C = C   
   
              Double bonds fix atoms in one plane =   above  &  below plane of molecule
                     removes ability of groups attached to C-C bond to  freely
* rotate

                    the C=C bond
makes the molecule Planar C=C*    3D*     no free rotation
      
              examples:  Configuration (geometric) Isomers...  &    cis and trans configurations
  
    
                                           cis                   vs.      trans                    
figure*


                                 a biological example of Cis & Trans isomerizations:
      
                                       11-cis-retinal   vs.      11-trans-retinal     retinal*   
 
                                 other example of configuration differences  =  functional differences: 
                                           estradiol          vs.    testosterone          figure* 
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2.
Conformation[3D-shape]...    the surface outline or contours...
             3-D orientation of a molecule, which results without breaking any covalent bonds
             due to free rotation [360o] of atoms about a single chemical bond
             & the weak electrostatic forces holding molecules together...
figure
*

 
    STRUCTURE, SHAPE and FORM   and   BIOLOGICAL ACTIVITY... 
           Molecular shape is CRUCIAL in biology, because it determines how
           biological molecules recognize & respond to one another with Specificity.
 

           Molecules with complimentary shapes can form weak bonds with each other:
          
       ex: endorphins - include a group of nervous system & brain hormones
               (dopamine, serotinin, oxytocin) that bind to analgesic receptors promoting
                    positive feelings & reduce the perception of pain.

     
        thought question* : how do opiates like morphine & fentanyl work on the brain?  
 
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B. FATS and LIPIDS...          (another macromolecue)
  
  
        a  TRIGLYCERIDE or Fat or Triacylglycerol...       animation of fat structure* 
                     a triacylglycerol is formed by condensation reaction of
                     1 GLYCEROL   and  3 FATTY ACIDs         figure*     
 
      
        PROPERTIES...   structural figure*      

             glycerol end of fat is............
HYDROPHILIC     (POLAR - attracts water)
             hydrocarbon end of fat is....
HYDROPHOBIC    (NON-POLAR - repels water)
   
           
Saturated* (solids) vs. Unsaturated (oils)*  
cis-trans fats* - properties*          
                                 fats  vs.  carbs*  as energy sources   

    

  a   PHOSPHOLIPID...   (basis of membranes)
              1 glycerol,  2 fatty acids, PO4,  &  an organic molecule       
P-lipid*
              
                Properties         MICELLES      BILAYERS       amphipathic* 
    

        CHOLESTEROLS...  classified as lipids because they're insoluble in water
           
(13 Nobels)           cholesterol & anabolic steroids  figure*  &  in membranes*

  
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                                                 [animation describing all types of lipids] View@home           
 

 

 

 

 

 

 

 

 

 

 

 
 
C. NUCLEOTIDES... 

          the organic monomers [ATGC & U] of the nucleic acids
          are composed of 3 parts...
   
                     
a nitrogenous base*a ribose (5C) sugar* phosphate (-PO4)
    

          they are part of the cell's energy nucleotide - adenosine triphosphate - ATP
*       

           and form a part of polymer* of single nucleotides [ATCG (U)] made by
                 
linking the nucleotides together via phosphodiester backbone
*
                               

                  RNA   -    ribose nucleic acid          -   (single stranded)
  
                  DNA   -   deoxy-ribose nucleic acid - 

                                  polynucleotide building blocks of DNA & RNA*
    

                                 
DNA double helix of 2 polynucleotide chains
*  animation
*View@home
                                        
  
 fish09.gif (288 bytes)               bonds we have learned  to date* 
                                       
 

 

 

 

 

  

 

 

 
      FUNCTIONAL GROUPS...  (key to understanding the chemistry of biological reactions):
             ...  groups of atoms acting as a unit,
             ...  give organic molecules their physical properties,
                  and their chemical reactivity,  &  solubility in aqueous solutions. 
                             most possess electronegative atoms (N, P, O, S...  EASILY ATTRACT PROTONS)
                             key bonds are :    ester  (C-O-C=O)  
&   amide   (O=C-N-)
                           are ionizable at physiological pH.

   

-NH2   AMINO* =    amino acid - weak base

-C=Ox CARBONYL* =    aldehyde/ketone
  -COOHx CARBOXYL* =    weak acid
  -OHx HYDROXYL*  =    alcohol

-CH3 METHYL* =    hydrocarbon

-PO4 PHOSPHATE* =    organic phosphate

-SH SULFHYDRYL* =    disulfide
 



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       Campbell Biology - Chapter 4 - figure 4.9*   animation*view@home
                                
                                     
                             
                                     
                                
   
 
 
 
 
 
 
 
                            
                  

 
 
 
 
 
 
Consequences of Substitution of a  H  with a Functional Group
  
...Linking STRUCTURE,  EMERGENT PROPERTIES, and  BIOLOGICAL ACTIVITY ?

       
      
   Ethane                CH3-CH3                 toxic, flammable gas
 
   Ethanol               CH3-CH2-OH          ethyl alcohol, a potable drink
 
   Propionic acid     CH3-CH2-COOH     colorless liquid with a sweet odor; preservative
 
   Ethyl mercaptan  CH3-CH2-SH          "rotten eggs" - the smell of natural gas

                                Chemical building blocks* &  Biomolecules summary table*
  

       back   next lecture          
a paradigmkey concepts*                  
 
       copyright c2021    
 
         Charles Mallery,    Biology 150, Department of Biology,   University of Miami,  Coral Gables, FL 33124
  
        

 






















                                                                                                                 
            
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    SKIP ALL THE MATERIAL BELOW...



 
 
Conformation[3D-shape]...    the surface outline or contours...
      3-D orientation of a molecule, which results without breaking any covalent bonds
             due to free rotation [360o] of atoms about a single chemical bond
             & the weak electrostatic forces holding molecules together...
figure
*

 
    STRUCTURE, SHAPE and FORM   and   BIOLOGICAL ACTIVITY... 
           Molecular shape is CRUCIAL in biology, because it determines how
           biological molecules recognize & respond to one another with Specificity.
 

   
           Only molecules with complimentary shapes can form weak bonds with each other:
                 ex: opiates & endorphins -
fig 2.16* - morphine is an opiate isolated
                       from opium and heroin, from which it is made.    In 1975 endorphins
                      (signal molecules of pituitary that bind to brain receptors relieving pain)
                       & opiates, as morphine, were shown to have molecular shapes similar to
                       each other, and they can mimic them by
binding to endorphin receptors.

   

 
 

        Molecules may have many shapes or forms...
                         but How does shape influence biological activity?
       

beta-2 adrenergic receptor
       adrenergic   receptor
When one of the vast numbers of molecules milling around
in our cells
(adrenaline) is of precisely the correct shape and
decorated with the right charges, it
binds to a receptor where
it can produce a vital reaction as making a heart beat faster.
      
Beta-1 receptors are found in the myocardium
(heart muscle) & leads to cardiac stimulation.

Beta-2 receptors are found in smooth muscle,
skeletal muscle, and the liver. They are involved
in bronchodilation and vasodilation.
adrenaline
adrenaline
(epinephrine)
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           The 3-dimensonal shape of a receptor protein
          
(<-- as the beta-2 adrenergic receptor) within a cell
           allows the specific binding of signal molecules,
           here adrenaline
(adrenaline/adrenergic receptors)

 

 

          Leptin* - the fat hormone

 

         polymers

 

                                  2. Ibuprofen & Albuterol occur as R & S enantiomers, which characterize
                          the configuration of the whole molecule, not a specific stereocenter (NH2).

                       
Only one of two stereoisomers, R or S, is effective - fig 4.8*