What chemical conditions of primitive Earth lead to Origin of Life?
    How did simple molecules in the ocean & atmosphere become cells?                

What are the CHEMICAL PROPERTIES of the MOLECULES of Life?
                  "Cells might better be called... Chemical Machines"
     Cells are made of MOLECULES  &  molecules are made of MATTER  
matter    --->    molecules    --->    cells
     MATTER : is anything that occupies space & has mass    (often equated to weight)
                  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 only 25 lb, but on neutron star = 21 trillion lb
     Matter is composed of the  ELEMENTs  of the Periodic Table
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- A pure substance that contains only one type of ATOM...
                       each element has an identical number of protons in their nucleus
                       which CAN NOT be reduced to simpler substances by normal chemical                              means. there are 117 elements are arranged in a Periodic Table*
                                                                                                                Periodic Table of Elephants
   ATOM - is a unit of matter that has a particular structure...
     - 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 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.
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  at center of an ATOM is   NUCLEUS  which has 2 fundamental particles

PROTON         [mass in grams   =   1.7 x 10-24 grams]
                + charged particle
                # present equals  ATOMIC NUMBER   6C
     defines the chemical properties of that element
     PERIODIC TABLE - from 1 to 94 protons = 94 natural Earth elements






Bohr Model

                    has same mass [
1.7 x 10-24 grams] as a proton,
                    but neutral electrical charge
                                                      Campbell - Concept Activities - chapter 2 & 3 -
                                                           2.2 - Structure of Atomic Nucleus
* and Build an Atom*,
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the 3rd fundamental particle is the  ELECTRON

         electrons surround nucleus in an ORBITAL SUBSHELL CLOUD*
                                cloud = area where electron is likely to be found
                                 space:  if e- were size of an apple, then orbit = a 1 mile dimension
         has small mass  [1/1836th of proton]
         is negatively charged
         & there is one electron per proton                         Helium atom*
Orbital Stability...  achieved when Subshells are electron filled 2, 8, 8, 16, etc...
                Na with atomic # of 11 = 2, 8, 1  electrons in  Outer Subshells*
     Valence Subshell...  the OUTER ORBITAL containing  Valence Electrons*...
                         valency is the number of bonds that an element can form with another element   
                                                                         Student Media Activity - Chapter 2d - Build an Atom*
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       Some electrons are easily attracted  AWAY FROM  or attracted  TO  outer orbitals


      • 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.


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...  an atom with same # of protons but MORE neutrons  (greater mass)
                     atomic #       =   number of protons in an atom
                     atomic mass   =   number of protons + neutrons  (atomic weight)
                                 allows comparison of how heavy one atom is to another
                                 expressed as AMU, atomic mass units, also called  DALTONs (Da)
                                 all atoms were originally compared to hydrogen = 1.0079amu
                                 but now,  1 amu  =  1/12th of carbon  =  1.6605 x 10-24gm
                          99%    <  carbon-12    atomic number   6C12   atomic mass
                         <  1%    <  carbon-13    atomic number   6C13   atomic mass
                         <  1%    <  carbon-14    atomic number   6C14   atomic mass
       Unstable isotopes undergo spontaneous radioactive decay*... with 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 ]
 experiment0b.gif (419 bytes)
next panel        use of isotopes an example of tracing a biomolecule during a metabolic process*





II.   MOLECULES...  group  of ATOMS [2 or more]  held
                                                                  together by energy in form of a CHEMICAL BOND
     TYPES of Chemical BONDS
make a list
   IONIC bond...    an attraction of atoms via electrical charge   +/-
      • Na   has 1 outer unpaired electron     11 Na (2,8,1)
      • wants to form a shared  e-  pair to be stable, but can not,
      • easier to lose its   e-  to achieve electronic stability
      • leaves + charge  (extra proton) in the atom...  thus -->   CATION (+)
      • Cl   has 7 outer e-'s    17 Cl (2,8,7)
      • wants to gain one e-  to become stable, so it does
      • giving an extra  -   charge (extra electron) in the atom...
      • thus --->  ANION  (-)
testtube.gif (476 bytes)    IONIC Bond*...  Na+Cl-  [aggregates into salt crystals*   figure*]      


    COVALENT bond*...  stability is achieved by sharing electrons between 2 atoms
      • two atoms share atomic nuclei via their outer e- orbitals
      • results in orbital stability, thus energetically favored
      • a much stronger attraction than ionic bond
      • shared electrons can form a single, double, or triple bond*

                 1H (1)   +   1H (1)      --->         H-H    

                                               --->         H .. H
      -C-C-C-               C=C             C=C
           Campbell - Concept Activities - chapter 2
           2.3 - Covalent Bonds* , Non-Polar & Polar Bonds *, Ionic Bonds* , and Hydrogen Bonds*

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        structure of cells in chemical terms                                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 the chemistry of water"...
                                - solution chemistry









Role of water & its location in cells...

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


                        we assume cell is full of water, but...   Look at EM*  &   cytoskeleton* 
                        classical paradigm --> a cell is an aqueous membrane sac with stuff floating in it.

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

            2.  water is solvent for chemical reactions in cells

                                                     water is the oxide of hydrogen     H-O-H

            3.  water is SUBSTRATE for & PRODUCT of many enzymatic reactions


                                                            6CO2 + 6 H 20 <-----> C 6H 12O 6 + 6O2      
                   4.  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






Physical Properties of water

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

             -  is a liquid at ambient [room] temperature       (very few molecules are)
 has high surface tension ... a measure of COHESIVENESS of water
              only Hg is greater...  water bugs* (figcm secret of water walking) & transpiration*
has high specific heat...   amount of energy [heat absorbed] needed
                                                        to raise 1 gm water 1C
                             water's specific heat is as high as many oils or alcohols, higher than some metal
                             provides THERMAL INSULATION...    Gulf Stream temps
high heat of vaporization amount of energy to convert LIQUID to GAS
                for water it's  540 cal/gm   - greater than ether or ammonia
                sweat evaporation... releases 540 cal of heat per gram (ml) sweat
         - heat of fusion
is 79.7 cal/gm ..... heat lost as  SOLID ---> LIQUID, as ice melts

 flasks.gif (452 bytes)     -  on freezing...  as a solid it is LESS DENSE* increases its volume   figure*




STRUCTURE of WATER...        
defines the physical properties of water

Oxygen    =   8O  [2,6]       i.e., needs to gain 2 e-  to be more stable...
     Hydrogen =   1H   &   1H      i.e., needs to gain 1 e-  to be more stable...
    so, let's put them together:
[one Oxygen & two Hydrogen] each share 1 e-
                   forms 2 covalent bonds 
                   orbitals form  a  tetrahedron shape*       [geometry of water, methane, ammonia]

                   tetrahederal shape of water & structure of its bonds makes water a POLAR molecule
                             i.e., water shows an uneven DISTRIBUTION of internal charge  H-O-H*

              Water is MOLECULAR DIPOLE (magnet-like)  =  makeing water a great solvent...
                    slightly + on one side &  -  on other side ;  binds to NaCl*  &  protein*

raindrop.gif (18903 bytes)        Campbell - Concept Activities - chapter 3 -
3.1 - Polarity of Water*, 3.2 Cohesion of Water*, 3.3 - Dissociation*  & Water, Acids, Bases, pH *




                     weak electrostatic attraction between water molecules
                                or any molecule containing a dipole (such as NH2) ...
                                    electropositive end of one H2O is electrostatically attracted
                        to electronegative end of another H2O

          not really a "bond"* at all, but rather a weak electrostatic attraction
thus: properties of water stem from its H-bonds - ice vs. liquid*
[john kyrk's animation of water]  

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*
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                              copyright c2008, Charles Mallery, Department of Biology, University of Miami, Coral Gables, FL 33124  
                              Last Update - 16 September, 2008