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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ELEMENT - 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
NEUTRON                     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 3^rd 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*

   
   
       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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  ISOTOPE ...  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  =  1/12^th of carbon  =  1.6605 x 10^-24gm

  

                      99%    <  carbon-12    _{atomic number   6}C^{12   atomic mass}

                     <  1%    <  carbon-13    _{atomic number   6}C^{13   atomic mass}

                     <  1%    <  carbon-14    _{atomic number   6}C^{14   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 ]
 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  (-)

 

 

 

 

 
    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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  CHEMICAL ARCHITECTURE of CELLS

        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
 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* (fig^cm 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
  
      -  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:
                   atoms [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*

       Campbell - Concept Activities - chapter 3 -
                          3.1 - Polarity of Water*, 3.2 Cohesion of Water*, 3.3 - Dissociation*  & Water, Acids, Bases, pH *

   
   HYDROGEN BONDS...

                     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.
                                                             key concepts*
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                              Last Update - 16 September, 2008