INTRODUCTORY  CHEMISTRY  of  LIFE
   
  The chemical conditions of primitive Earth may have lead to the Origin of Life?
  To know how simple molecules in the early oceans & atmosphere become cells?
       
What are the Chemical Properties of the Biomolecules of Life?
  
  We hypothesized that "Cells might be be called... Chemical Machines"...
  
            
for cells are made of MOLECULES   &    molecules are made of MATTER  
  
                  
matter    --->    molecules    --->    cells
                  
   
 
   MATTER
:  physics defines it as anything that occupies space & has Mass   
                     the mass of an object is the 
number of atoms the object has in it.
       Mass is often equated to weight, but weight & mass are not equal:
                     weight is due to pull of gravity;   mass is amount of matter in an object
                     (150 lb person on moon weighs 25 lb, and on a neutron star = 21 trillion lb)
     
         Matter is composed of the  ELEMENTS  of the Periodic Table.
 
next pagenext panel


 

 

 

 

 

     

 

  
 
  


I. 
ELEMENT
- is a pure substance that contains only one type of ATOM...
 
           Atoms of each element has an identical number of PROTONs in their nucleus.
           Atoms CAN NOT be reduced to simpler substances by normal chemical means.
                There are 92 naturally occurring elements and
112
IUPAC recognized
                elements all arranged in a Periodic Table
*              Periodic Table of Elephants

   
an ATOM - is a unit of matter that has a particular structure...
     
         -
it's the smallest unit of an element, having all the
           characteristics of that element & consisting of a dense,
           central, positively charged nucleus surrounded by
           a system of negative electrons. The entire structure has
           an approximate diameter of 10-8 cm and characteristically
           remains undivided in chemical reactions except for
           limited removal, transfer, or exchange of certain e's.








      click on image
  atom1a.gif (405
                            bytes) next panel














 

 

 

 

 

 

 

 

 

 

     

     

     

    


2.  Structure of an Atom:   at the center of an ATOM is its NUCLEUS,
                                                                
which has 2 fundamental sub-atomic particles
:  

PROTON         [mass - in grams   =   1.673 x 10-27grams]
     + charged particle
     # protons present defines the ATOMIC NUMBER   6C
     helps define the chemical properties of that element

                  

carbon atom
  click on image           

NEUTRON
                    has equal mass [
1.7 x 10-27grams] as a proton,
                    but has a NEUTRAL electrical charge
           an atom's   NUCLEUS  in the  Niels Bohr Model    animation*
  moleculeball.gif (483
                      bytes)next panel

 

 

 

  

 

 

 

 

   
  the 3rd fundamental particle is the  ELECTRON
       
hypothesized in 1892 by Dutch physicist Hendrik Antoon Lorentz.
             In 1897, J. J. Thomson proposed the neutrality of atoms when he proposed a model
             of the atom with negative electrons scattered throughout a sphere of positive charge.


   Fundamental Properties of Electrons:

        1.  has a much smaller mass  [
1/1,836th of proton

        2. 
is NEGATIVELY charged - 
in non-ionized atom # of electrons = # of protons
        3.  obey the Law of Charge Conservation and do not spontaneously decay (live forever)
        4.  has intrinsic Spin  (and may provide a sense of compass direction*)
        5.  surrounds an atom's nucleus in an 
Orbital Cloud
*
                            
cloud:   area where electron is likely to be found
                            
space:  if e- were size of an apple, then shell's orbit = a 1 mile diameter 

             
Helium atom
- animation*  
  

  
Orbital Stability...  is  achieved when all the Subshells are filled with electrons resulting in                               
                                in the stable electron arrangements of 2, 10 (2+8), 18 (2,+8+8), etc... 

        
Na with atomic # of 11 = 2, 8, 1 electrons in Outer Subshells
&  subshells of Al & Cr

    Valence Subshell...  the OUTER ORBITAL containing  Valence Electrons*...  
              
valency is the number of electrons required to complete an atom's 

               outermost (valance) subshell by forming chemcial bonds with another element.
          An element chemical reactivity
* depends upon the degree to which outer shells is filled.
 
molecule2.gif (447
                      bytes)   next panel       

                                                                                                                                          

 

 

 

 

 

 

   

CHEMICAL REACTIVITY comes about mainly because some electrons are easily
       attracted 
 AWAY FROM    or attracted   TO   the outer orbitals of other elements
;
       electrons are directly involved in chemical reactions to form chemical bonds...

      • LOSS of e-   =   OXIDATION
      • GAIN of e-   =   REDUCTION

ION...  an atom or a group of atoms that has acquired a net electric charge
            by gaining or losing one or more electrons.
         
 
Sodium (Na - from Latin natrium
    has an atomic # of 11 & mass # of 22
          (11 protons & 11 electrons).
    easier to lose 1e 
  (2,8,1)  (= Na+ ion)

A stable isotope is Na 23 with 11 protons
    and 11 electrons, but 12 neutrons.
   
     
  ions   cartoon  
next panel      



                   

 

 

 

 

 

 

   
 
ISOTOPE... atoms with same # of protons but MORE neutrons  (it has a greater mass)
  atomic #          =   number of protons in an atom
  atomic mass   =   number of protons + neutrons  (often called atomic weight)
             comparison of how heavy one atom is to another is expressed
             as AMU, atomic mass units, also called  DALTONs (Da).
                  all atoms were originally compared to hydrogen = 1.0079amu
                  but now,  1 amu  =  1/12
th of mass of carbon  =  1.660 x 10-27gm 
         among all naturally occurring Carbon atoms...
                     99%    <  carbon-12    atomic number   6C12   atomic mass  6p + 6n
        <  1%    <  carbon-13    atomic number   6C13   atomic mass  6p + 7n
        <  1%    <  carbon-14    atomic number   6C14   atomic mass  6p + 8n
   
         Unstable isotopes undergo spontaneous radioactive decay* of the atomic nucleus giving
         off subatomic particles, energy & leaving 1 more proton... with a constant 
half-life decay*
                     Sr 90 =  28.6y                            Cs 137  =   30.2y                     H3   =   12.3y
                     C 14  =  5,730y  [C14dating*]     U 238    =   4.5 billion y [ U238 decay ]
     

        Uses of ISOTOPES:   an example of tracing a biomolecule during a metabolic process*
experiment0b.gif
                        (419 bytes)
next panel 


 

 

 

 

 

 

 


  

II. Molecules... Life is definable by the forces (chemical bonds) that make Molecules:

         Chemistry boils down to changes in the electronic structure of atoms and then molecules, i.e.,
         the processes by which changes occur in electronic structure of atoms that form compounds
         with new emergent properties i.e., groups of ATOMS [
2 or more
] held together by
        
"energy" in form of a "chemical bond"

   
         Electronegativity* - atoms ability to attract electrons to itself when bonded to another atom.
    
   Types of Chemical Bonds:    
     
Make a List*
   Ionic bond...  an attraction between atoms of opposite electrical charge   +/-
      • Na   with 11 e's it has 1 outer unpaired electron     11 Na (2,8,1)
      • needs a full orbital of  e-  to be stable..., could gain 7 more  e- 
      • thermodynamically easier to lose its 1  e-  to achieve electronic stability
      • leaves + charge  (1 extra proton) in the atom...  thus -->   CATION (+)
                      
        . 
      • Cl   has 7 outer e-'s    17 Cl (2,8,7)
      • needs only to gain one  e-  to become stable, so favored energetically,
      • giving an extra  -   charge (extra electron) in the atom...
      • thus --->  ANION  (-)
testtube.gif (476 bytes)      animation on ions*        Iionic bond image*          NaCl ionization*
                Na
+ & Cl-  is a good example of molecules with emergent properties* 

                                          

     











     

 
 
 
 
 
    a Covalent Bond*... 
         thermodynamic stability is achieved via atomic orbitals merge into
         one "molecular orbital" that extends over more than one atom; i.e.,

         by sharing electrons between 2 atoms...
     

             American chemist Linus Pauling (1939) first proposed that a covalent
         bond forms when the the electronic area of different atoms overlap in space.
         Robert Mulliken & Frederick Hunds (1966) hypothesized "molecular orbitals". 

      • two atoms share atomic nuclei via their outer e- orbitals
      • results in orbital stability for each, thus energetically favored
      • a much stronger attraction than ionic bond  [100x stronger]
      • is a dynamic entity with all components constantly in motion,
            not a static one as seen in textbook figures     
      • shared electrons can form  covalent bond (animation)*

                     1H (1)   +   1H (1)      --->         H-H   or  H ..
           
         
                     C-bonds  
                     
         Single,   Double,  Triple bonds  in  H,  O, &  N* 

      atom1a.gif (405 bytes)next panel                                                                                                                                

  


 

 
 
 
 
       
                                          
                
 
 
 
 

 

 

 

 

    
 
  Molecular Architecture of Cells

        the Structure of Cells in Chemical Terms                   the Key Concepts*

                     Some Salient Features of Chemical Nature of Cells:

                                         70% of mass of a cell is water  (H2O),
   
                                                                   i.e., 30% is non-water

                                         extremes...  dry plant seeds < 1% water
                                                             ctenophores & coelenterates
> 95% water


              
"chemistry of life is often described as the chemistry of water"...
    
                                           - or  solution chemistry.

   

 

 

 

 
 
 
 
 
 
 
 

 

 

 

 

 
  
Role of water & its location in cells...
  

           
1.  the cytosol is described as SOLUBLE PHASE of the cell - but, where is the water?

 
 
                we assume cell is full of water, but...   Look at some EMs*   &   the cytoskeleton* 
                 classical paradigm --> a living cell is an
aqueous membrane sac with stuff 
                                                     floating in a water based compartment.

                                           
"a molasses filled balloon with floating ping-pong balls"
  

               BULK* vs. VICINAL interfacial water,  i.e., solutions vs. water at an interface*

                                              interfacial water has different chemical & physical properties,
                     but, we will continue to assume that cells function on the bulk properties of water.

  
            2.  thus, water is solvent for chemical reactions in a test tube & supposedly in cells...
  

                                                     water is the oxide of hydrogen    
H-O-H
  

            3.  thus, water is SUBSTRATE for and PRODUCT of many enzymatic reactions...

  

                                         
            6 CO2 + 6 H20 <-----> C6H12O6 + 6 O2  
        
            4.  and water plays a structural role, especially with large macromolecules...
                                                    ...
it hydrates DNA, RNA, proteins & enzymes

 
experiment0b.gif (419 bytes)next panel                                 ... it adds form & dimension to many molecules     HOW?
 

            

                        

 
 
 
 
 
 
 
 
 
 
 
 
          

 

 

       
  
Emergent Properties of water favoring Life:

      
 
Water exits in 3 forms*:    gas    liquid    solid     due to its molecular arrangements

      -  it is a liquid at ambient [room] temperature       (not alot of molecules are)
      -
 has high surface tension...  a measure of cohesiveness
* of water for itself.
                      how does water get to the top of tall trees?      -->   
transpiration
             only metal Hg has a greater surface tension     -->   water bugs
      -  has high specific heat...   is the amount of energy  [heat being absorbed]
                      needed to raise 1 gm water 10C                                1 cal =  4.186 joule/gm
                      water's specific heat is as high as many oils/alcohols, higher than some metals
                      provides good thermal insulation...                            pics ( Gulf stream - temps )
      -  has high heat of vaporization amount of heat energy to convert LIQUID to GAS.
             for water it's  540 cal/gm - greater than ether or ammonia    
             evaporation of sweat... releases 540 cal of heat per gram [ml*] of vapor/sweat
    - heat of fusion is 79.7 cal/gm... freezing water converts molecular motion of liquid water
                      into solid & releases heat energy during the phase transition, and vice versus
                        
solid --->
liquid  =  + 80 cal/mol          liquid ---> solid = - 80 cal/mol   (graph)  
                      ice melts in scotch rocks when heat is absorbed from the surroundings.
 
       -  on freezing...  as a solid water is LESS DENSE*   increases its volume.
                      liquid water is 10% more dense that ice  
          
       -   Water is Weirdanim - why is it such a strange molecule? 
*

   flasks.gif
                        (452 bytes)
   

 

 

 

 

 

 

 

 

 

 

  
 
Structure of Water
            
...defines the physical properties of water and of many biological molecules.   
 
   
Oxygen     =   8O  [2,6]         i.e., needs to gain 2 e-  to be more stable...
    Hydrogen  =   1H   &   1H     i.e., each need to gain 1 e-  to be more stable...

             
so, let's put them together:
                  
atoms
one Oxygen & two Hydrogens  each share 1 e-
                   forms 2 covalent bonds 
[ H-O-H ]
                   bonds that form  a 
tetrahedral shape*        -
              

     Tetrahederal shape of water 
bonds makes water a Polar Molecule
                
properties of water - anim*    &   non-polar  vs.  polar covalent bonds animation
                        
i.e., water shows an unequal distribution of internal charge -->  polar bonds
 

       Water is Molecular Dipole (magnet-like) with two opposite charged ends in the same molecule.
                  slightly + on one side &  -
  on other side ;  binds to NaCl*  &  protein*
                      
the dipole of water makes water a great Solvent...
                        
hydrogen bonds provide structure to biomolecules* 

raindrop.gif (18903 bytes)    weird factoid: 1 cubic mile of ocean water holds 400 lb of gold (but not really extractable)             

 

 









 
 
        Learning the pH Scale
 

       Hydronium ion anim*
 

       Dissociation of Water


         
pH scale of [H+]
* ----->

 
            (READ pgs 51-5312/e
)

 
    Pure water contains equal
             amounts of ions

    pH 7 has  =  #'s of OH- & H+ ions
             1 x 10
-7   moles per liter   
 
    
 


raindrop.gif (18903 bytes)  acids, bases, & pH animationview@home

 

 

 
 
    


 
 
 
 
 

 

 

   
     Often molecular structure in cells depends upon...
          

     Hydrogen Bonds
... which is responsible for the structure of water.

                   H-bonds are weak electrostatic attractions between water molecules
                       and/or any molecule containing a dipole (such as COOH & NH3)...
                       electropositive end of one H2O is electrostatically attracted to
             
         electronegative end of another H2O or another dipole.

                       not really a "bond"* at all, but rather a weak electrostatic attraction
                               

                  
Thus: All the properties of water stem from its H-bonds --> properties*
  

                       
There is no life without water:  and  water's properties may be
                        one reason that the molecules of life formed in the first place.

         

   
                      a paradigmkey concepts*          Ray guns         

                                  Material for Exam #1 Summer 2024 ends here...                                           
   
  
                 back        next lec      copyright c2024    
               Charles Mallery,    Biology 150, Department of Biology,   U. of Miami,  Coral Gables, FL 33124
                   

 

 

 

 

 

 

 

 

 

 

 










 

 

 


 

 

 

 

 






          (secret of water walking)
                   Home |About |News |Syllabus |Lecture-outlines |Links |FAQ |Sitemap |Contact