CHEMICAL ARCHITECTURE of CELLS...   if 70% is water what's other 30% ?

 INORGANIC Elements in cells...                                            
                          95% of mass of cells is ONLY 6 ELEMENTS

                       - C H O N P S         " C. HOPKIN'S  CaFe  Mg " ?    table 2.1*

                       -  Why only These ?    covalent bond reactivity*      

    Role of inorganics in cells (including many metal ions):  
       1. they make up parts of other... molecules, & bone, exoskeleton, vitamins, etc...
       2. are dissolved in aqueous media of the cell.      
  
            Dissociation of Water =    pH scale             (READ* pgs 52-548/e or 53-567/e)
            1 H+ per 555 million waters = 1 x 10-7                john kyrk's animation of pH scale     
        
           Campbell - Concept Activities - chapter 3.3 - Dissociation*  & Water, Acids, Bases, pH * 

animl35.gif (4368 bytes)


 

 

 

 

 
Metabolome - the complete set of small molecule metabolites
                                                            found in an organism (akin to a genome).
    - estimated to be about 2,500 metabolites, 1,200 drugs, & 3,500 food components in human body
    - metabolome of plants = 50,000 metabolites
    - majority of metabolome components are the...

   
   ORGANIC Molecules...   molecules composed of C and H 
  

            CLASSES                          BIOLOGICAL ROLE
            carbohydrate (CH2O)       structure & energy molecules 
  

            fats (lipids)   (CHO)          structure & energy molecules 
  

            phospholipids (CHO-P)       membrane structure 
  

            steriods/sterols                membrane structure - hormones 
  

            proteins                              structural, enzymatic (catalytic) 
  

 
fish01.gif (295 bytes)    nucleic acids                        informational, genetic role

    

 

 

 

 

 

 

 
 
Some Basic Organic Chemistry...

      
ways to represent molecules graphically...
              Molecular
or Empirical formula   vs.   Structural formula
              ...stick and space filling models             fig 4.2  &  fig 4.3*  &   3D molecular models

         Hydrocarbons - Carbon & hydrogen molecular skeletons : 
              ...some examples  :   chains   vs.  rings                 fig 4.5*
 
         ISOMERS - structural or                                       fig 4.7a*
                                ...have the same empirical formula, but different structure
               
           - optical                                                   fig 4.7c*
                            
   ... bend plane of light is different directions (mirror images)

                           -
geometric                                              fig 4.7b*
                                ... differ in arrangement of groups attached to C=C
 
fish02.gif (331 bytes)         Campbell - Concept Activities - chapters 4.2 - Diversity of Carbon Molecules*  and Isomers*
                           

                              

 

 

 

 

 

 
 
A.
   CARBOHYDRATES.....    have a consistent ratio of [ CH2O
]n     glucose-C6H12O6

     MONOSACCHARIDES...   the simple sugars,
      which are the monomers  that make starch, glycogen, & cellulose
                                (single molecules)                                    (polymers)
       
          2  TYPES of  Monosaccharides:
                        -  aldoses 
[built on an aldehyde    vs.    ketoses  [built on a ketone
                        -  names based on # C's - triosespentoses,  hexoses     fig 5.3*

 

          STRUCTURES:     linear  vs.  ring structure...        example: glucose
                         ring form*,   abbreviated ring*,   α & β isomer forms*,   &   other isomers*  
 
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      DISACCHARIDES...
   

            a glucose "polymer" composed of only 2 monosaccharides

            formed by condensation rx*        ---->        GLYCOSIDIC bond*
                                                                                           -C-O-C-
         
   Concept Activities - chapter 5.1 - Polymer*s, 5.2 - Models of Glucose * &   Carbohydrates*

       
  dissacharide bond             polymer
  maltose*   a-1,4 glu-glu --->   amylose
sucrose*       a-1,2 glu-fruc --->   sugar
cellibiose*   [3D ß-1,4 glu-glu  --->   cellulose

 

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  POLYSACCHARIDES....        the complex sugars.
                                     ... polymeric chains of monosaccharides
                                     ... normally form long repeats in a  helix shape...   (staircases)
 
            STARCH*...  glucose polymer of a-1,4glu units     
                                 also know as...                  AMYLOSE            unbranched
                                                                       AMYLOPECTIN     branched    
            GLYCOGEN*...  very branched  [branching helps solublize it]  

            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
                                                    
   fish15.gif (351 bytes)   TAKE HOME MESSAGE here.....   
             
µ   "Molecular structure is critically important to function, and structure
                      relates to the 'ORIENTATION' of covalent bonds in 3D space"
  end 6

 

 

 

 

 


 
Importance of Molecular Shape to Biological Activity
 
2 UNIQUE properties of BIOMOLECULES gives them special FITNESS for the Living State
             

  Configuration - is the spatial arrangement of atoms in a molecule...
       
    configuration can't be inter-converted without breaking chemical bonds
            often needs an asymmetric Carbon atom...  (carbon w 4 diff. groups attached*)
   
    examples: STEREOISOMERS    &   CHIRAL molecules    (animation)
                   
     also called  enantiomers*  =  mirror images
                             isomers with identical chemical structures, but which
                             rotate plane of polarized light at different angles...
     
          levorotatory      [ L ]  or  [R]     =    left handed    -  counter clockwise     
               dextrorotatory  [ D]   or [S]     =    right handed   -  clockwise       figure*
    

    medical ex: 1.Parkinson's Disease  & 
dihydroxyphenylalanine   L-DOPA      figure* 
                             converted to dopamine - reduces symptoms
 [Awakenings]
                 2. Ibuprofen & Albuterol occur as R & S enantiomers
  
fish14.gif (150 bytes)                     each with only one of the two stereoisomer being effective - C8e: fig 4.8*
 
                           

 
 
 
 

 

 

 
 
 

 
        
   Configurations -
        good ex:  isomers that are based upon "covalent bond" configurations
                              especially presence of double covalent bonds C = C
   
              DOUBLE BONDS fix atoms ABOVE & BELOW plane of molecule
              removes ability of groups to free rotate*
      
              ex:  Configuration (structural) Isomers...   cis and trans configurations
  

                        cis                    vs.    trans                      
figure*

      

                        11-cis-retinal   vs.    11-trans-retinal 
    
retinal*   
    
                        estradiol          vs.    testosterone          figure*
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 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*
      µ 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 2.18(C8)* - morphine is an opiate isolated
                              from opium and heroin is made from morphine.    In 1975 endorphins
                             (signal molecules of pituitary that bind to brain receptors relieving pain)
                              and opiates 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 different isomeric forms,
fish03.gif (363 bytes)                 but often, only one isomer may be biologically active
                      
or a simple functional group substitution can be significant...
 

 

 

 

 

 

 

 FATS and LIPIDS...
  
     a  TRIGLYCERIDE or Fat or Triacylglycerol...  
             a triacylglycerol is formed by condensation rx of
                     1 GLYCEROL   and  3 FATTY ACIDs         figure*      figure*
 
      
         Properties
             glycerol end of F.A. is...........HYDROPHILIC     (POLAR)
             hydrocarbon end of F.A. is...HYDROPHOBIC    (NON-POLAR)    figure*
             SATURATED* (solids) vs. UNSATURATED (oils)* fats*           figure*
                                                            fats  vs.  carbs*  as energy sources 
  
     a   PHOSPHOLIPID...
              1 glycerol,  2 fatty acids, PO4,  &  an organic molecule      
figure*
          
Properties           MICELLES      BILAYERS                figure* & figure*
  

      CHOLESTEROLS...  are lipids because they're insoluble in water
           
(13 Nobels)                   anabolic steroids   figure*       in membranes*
 fish07.gif (365 bytes)
                                            Campbell Concept Activities - chapter 5.3 - Lipids*
 

 

 

 

 

 

 

 

 

 

 

 
 
NUCLEOTIDES
...

          are the monomers of the nucleic acids & are composed of 3 parts...   
  

          a nitrogenous base*, a ribose (5C) sugar*, a  phosphate*(-PO4

      polynucleotide building blocks* yield a polymer of single nucleotides [ATCG (U)]
            
made by linking nucleotides together via phosphodiester bond
*
 
  

                  RNA   -    ribose nucleic acid  -
sugar-phosphate backbone
*
                  DNA   -   deoxy ribose nucleic acid

                                        double helix of 2 polynucleotide chains
*  
                                        
  
 fish09.gif (288 bytes)             Campbell Concept Activities - chapter 5.5 - Nucleic acids: Structure*  &  Functions*.
 

 

 

 

 


      FUNCTIONAL GROUPS...  groups of atoms acting as a unit,
        that give organic molecules their physical properties,
        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   AMINE* =    amino acid
-C=Ox CARBONYL* =    aldehyde/ketone
  -COOHx CARBOXYL* =    acid
  -OHx HYDROXYL*  =    alcohol
-CH3 METHYL* =    hydrocarbon
-PO4 PHOSPHATE* =    organic phosphate
-SH SULFHYDRYL* =    disulfide

  fish14.gif (150 bytes)  

                      Campbell Concept Activities - chapter 4.3 - Functional Groups*
                                
                                     
                             
                                     
                                
                               
                  

 
 
 
 

 
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, corrosive liquid with a pungent odor
 
        Ethyl mercaptan   CH3-CH2-SH        "rotten eggs" - the smell of natural gas

    back to outlines                                                              a paradigmkey concepts*

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