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Week 1 –  9/2 – 9/3 – NOTES

 – Summer Institute and Summer Assignment Connections:
Today in class I will be connecting many of the concepts that you initially learned this summer with a discussion that will contain the following:
Many of you came from AP Biology last year and I know a few had Regents Chemistry last year but the year before you had Living Environment.  So from AP Biology and Living Environment we can think that Biology essentially can be broken down into really one concept:
                                                                                                                    Proteins !!!
                                                          Yes DNA is important but it codes for the proteins that gives us our ALLELES or our traits!! 
                                                                                   I always say that proteins are the soldiers of the DNA!
Proteins catalyze chemical reactions that produce everything that life requires!!  
                  without chemical reactions there is no life!
Proteins help cells identify the world around them as they act as receptors.  Without these receptors our immune system would not work and we would all die from the “common cold”! 
Proteins are important chemical messengers (hormones like insulin). Without our cell would not be able to transport glucose into our cells and we would not have the free energy to live and survive.
Proteins are help in transporting materials like hemoglobin that transports oxygen (O2) in our blood and transport proteins that help NAD+  or FAD reach the mitochondria.  NAD+  or FAD transports electrons to the electron transport chain (in oxidative phosphorylation) in aerobic respiration!
Proteins are used as a nutrient and can feed cellular respiration to provide free energy to living organisms.
Proteins are made from 20 different amino acids that arrange the elements oxygen (O), nitrogen (N), carbon (C), and hydrogen (H) 20 in different 3 – D shapes.  The ability of proteins to do their biological job depend on the number and arrangement of these 4 elements!  Why these elements?  The details of biology are in the chemistry!

  Proteins are polymers that are made of monomers called amino acids.  Amino acids have a unique   group of Carbon,  Hydrogen, Oxygen, and Nitrogen elements that give the molecule the properties   that make it an amino acid.

 The atoms of  C, H, O, and N arranged in this fashion create amino acids that create proteins.  Atoms and  the chemistry behind them ARE the microscopic details of Biology!
      The details of Biology are in the chemistry!!!!  Why do we require Oxygen in cellular respiration?
If you remember Oxygen pulls electrons electrons through electron transport chain. Once the chain is complete it eventually accepts electrons and 2 H+‘s to become water. 
So oxygen is needed to force our cells to produce the most ATP possible by the transport of high energy electrons from glucose using FAD and NAD+ into the matrix of the mitochondria.  Without this system there are no complex forms of life!  (See Figure 1)
So even though biology macroscopically (large picture) is really about proteins, life’s most important process, cellular respiration boils down microscopically (small picture) to electrons that drive chemical reactions that give cells free energy and the electrons that keep protein’s elements together in chemical bonds.
So chemistry principles are the details of Biology (and electrons are the details of chemistry)!

Figure 1: Oxidative Phosphorylation (electron transport chain of cellular respiration):
So we have learned FROM THE SUMMER INSTITUTE or the SUMMER ASSIGNMENT that Redox reactions are chemical reactions that pass electrons around (which is exactly what happens .  Redox reactions are the most abundant chemical reactions that exist.  If you ever have any doubt what kind of chemical reaction that is occurring the BEST guess is that it is a redox reaction. 
The reason why REDOX is the most abundant is that we naturally have a large number of available elements that have a great ability
                                                                        to lose electrons = Oxidation 
*2/3 of all naturally occurring elements are LARGE ELEMENTS 
                                     example from figure 1:                      NADH —> NAD+ + e-
NADH delivers an electron to the chain and thus is oxidized in the process.
This oxidation cause high energy electrons to pump H+ into the inter membrane space in high concentration. The high H+ concentration diffuses through ATP synthase and makes the protein move to ADD Phosphate ion onto an ADP to make ATP!  That is why they call it Oxidation Phosphorylation!!!
and the reason why REDOX is the most abundant is that we naturally have a large number of available elements that have a great ability 
                                                                        to gain electrons = Reduction
*1/3 of all naturally occurring elements are SMALL ELEMENTS but because some these are in high abundance in nature like oxygen in our atmosphere these types of elements are in constant contact.
So because we have these 2 main type of elements (Big and Small) this sets the stage for Redox (transfer of electrons) reactions.  How does the size of atoms lead to REDOX or even oxidation phosphorylation in cellular respiration?
                                                                This lead us to the one concept that Chemistry is all about!
Like Biology (which is about proteins) Chemistry is about electrons or better yet how electrons are attracted to the positive nucleus.
                                                                                         The details of Biology is Chemistry!
                                                    The details of the Chemistry are the Physics 
or the physical laws that govern all matter (atoms), specifically how electrons (that are negatively charged are attracted to the positive nucleus (made of protons).
                                                    The physical law that governs all of chemistry is Coulombs Law!
                                                      Coulombs Law =   F  =  K  q1 q2
                                                    F = Force of Electrostatic Attraction 
                                                    K = proportionality constant ( I will explain this later)
                                                    q1 = size of negative charge
                                                    q2 = size of the positive charge
                                                    d2 = distance between the 2 opposite charges squared      
The Force (F) of attraction between 2 point points charges of opposite charge (q1 & q2) is directly proportional to the size of the charges and inversely related to the square of the distance between these charges.  
Directly proportional to the size of the charges – 
-IF the size of the opposing point charge increases then the Force of Attraction will be greater proportionally.  We will see this in insoluble salts (ionic compounds) that cannot dissolve in a couple of weeks.  
Example:                                          NaCl  (s)      —>      Na(aq)    +   Cl– (aq)
sodium chloride can break into its ions in water because the Coulombic force between positive and negative ions in the crystal of NaCl are weak compared to the ions attracted to water.  Water which we will learn has a positive and negative area (its polar) and so its positive area can attract the  Na+ (aq)  ion enough to pull it away from the Cl (aq) ion that it is attracted to to make the compound. When this happens we say it is soluble (meaning water can break the electrostatic attraction between the negative part of the salt and the positive part of the salt.
We say they are soluble since water will break apart the ionic solid – which is called dissolving
Please watch this animation to see what I am talking about:
This is an example of spontaneous physical reaction. 
Now MgO is not soluble and does not dissolve in water because the coulombic force between the to ions of different charges are too large!  If I made an animation of water trying to dissolve MgO it would be boring as no salt would dissolve.
This would be an example of a non-spontaneous physical reaction.
                                                             MgO (s)  —>  does not break apart into its ions in water 
This is because the Mg+2  and O-2 ions have HIGHER point charges THUS the Force (F) between the ions is TOO LARGE for water to break apart thus it is insoluble and remains as solid in water.
Inversely related to the square of the distance between these charges- 
– IF the distance increases between the 2 point charges then the F decreases (inverse square relation).  We will look at this inverse square in our atomic structure discussion later in the course. But in terms of the outermost negative electrons ( Q1) and their Proximity (d) to the positive nucleus (Q2) the farther away the electrons the lower the Coulombic attractive force that these electrons feel, thus these elements generally lose electrons (oxidize).  We see this in the sodium metal demo in water.   
                                                                        WATER easily pulls an electron away from the sodium metal
                                                                       What I am showing you is a half reaction because Na is oxidized
                                                                    while the water is reduced. I am only showing you half of the redox as
                                                                      I am omitting the reduction.
                         Oxidation :                    Na              —>           Na+1   +    1 e–   +  Energy 
The reason Na can lose electrons (LEO) and oxidize in water is because the size of the Na atom is so big that is outermost electron (valence) feels the positive nucleus less and can be removed.
The electrostatic forces are weaker between the negative electron and the positive nucleus.  Larger the atom the weaker the electrons are held!
Notice the lowered Force is amplified because of the squaring of the larger distance that metals have between their nucleus and outermost (valance electrons). Increasing the size of the denominator will always Increase the entire value of the formula.
Here is my demonstration of adding sodium metal atoms into water:
This is an example of a spontaneous reaction.


IF the distance decreases between the 2 point charges then the Electrostatic Force (F) increases .  In terms of the outermost negative electrons (Q1) and the Proximity (d) to the positive nucleus (Q2) the CLOSER the electrons are to the nucleus, the greater the coulombic attractive force that these electrons feel, thus these elements generally gain electrons (reduce).  We see this every time you see a combustion reaction where oxygen grabs electrons from metals causing them to corrode or change into a new compound or in combustion when oxygen grabs electrons from carbon (bigger nonmetal)
Here are 2 examples of combustion reactions:
Combustions reactions are guess what??
REDOX reactions that use oxygen (a small atom) that is able to attract electrons so well because of its small size (d2) and it large number of protons (q2).
Making the proton number larger (numerator) and the denominator smaller leads to a LARGE F  or electrostatic force!
This is why oxygen is the earths most important oxidizer!!
It cause other atoms, molecules, or ions to lose electrons.  Oxygen causes oxidation! 
Why don’t you think they call the losing of electron Oxidation

Here are 2 examples of combustion (or REDOX reaction that uses Oxygen as the oxidizer): 

                                                 2Fe    +     O2      —>       2FeO        +     Energy 
                                               Pure Iron                                             RUST 
                                                C6H10O5     +     6O2     —>      6CO2       +          5H2O   + Energy
This second reaction is cellular respiration!! Why do we need to breath oxygen??  To get the high energy electrons out of glucose to make ATP and those high energy electrons that was put their by photosynthesis!!  Everything is connected!
                                                       Reduction half reaction for both:               O    +     2e      —>        O-2  

 In both cases Oxygen became reduced or pulled the electrons because of its higher coulombic attraction due to electrons Closer to the nucleus (smaller d) in part due to the atomic radius being smaller.  In the case of the combustion reaction of the cotton ball oxygen has both smaller d and greater (Q2) due to having a greater nuclear charge (more protons) than carbon. That is how Oxygen (a nonmetal) can pull an electron from another nonmetals (carbon)!!!!!!!

Now lets get back to size of atoms and how we can predict their type of chemical reactivity.  We now know why oxygen takes electrons from things like metals based on Coulombs Law( to make rust ) but we have not figured out why oxygen is so small in the first place.  We saw that Na is large and due to Coulombs law it tends to lose electrons (oxidize) unlike Oxygen which is small and tends to gain electrons (reduce).
If we look at periodic chart of elements and use their relative atomic radii (size compared to each other) we can see a trend:
 The elements are arranged according to their the number of their number of protons (q2) and the electron shells (row number) they have. 
Protons increase left to right and then start a new row. 
Example: H has 1 proton, while He has 2 and Li has 3 and so forth…
The proton number changes the numerator in Coulombs Law!
Every additional shell is farther away (d2)from the nucleus that contains protons.  
Example: Na has electrons in 3 shells while K has electron in 4 shells .
The proton number changes the numerator in Coulombs Law!
Notice as you move across the Periodic Table the atomic radius generally decreases because you are adding more electrons in the same electron shell.  Notice F (fluorine) is smaller than oxygen because it has more protons.  This causes F to reduce better than O.  If we breathed in F instead of oxygen the electron would not move through the electron transport chain. They would immediately be sucked up by F.  This is one of the reasons that F2 gas is toxic!!!
Notice are you move down the Periodic Table (in the same column) the atomic radius generally increases as you are adding additional shells of electrons. Shells are determined by the row number.  Na (sodium) is in row 3 and thus has 3 shells of electrons while K (potassium) is in row 4 and thus has one more shell of electrons that is father away from the nucleus than Na.  This explains why K loses electrons or oxidizes more than Na.
The larger elements like Na are bottom left and the smaller elements light oxygen are top right.
    The elements that oxidize are bottom left and the element that reduce are top right.
                     The larger elements are metals and the smaller elements are nonmetals.
                                                 Metals oxidize and Nonmetals reduce.
                            Metals are reducing agents and Nonmetals are oxidizing agents
Elvira the outermost electron: (start at 6:20)

So lets put this all together in a chemical reaction that represents a great example of a Redox reaction that features a metal and a nonmetal.
                            2 Na (s)    +    2 Cl2 (g)      —>     2NaCl (s)
                                         Metal                    Nonmetal                        Ionic Compound (salt)
                                        Large atom             Small atom
                                  Loosely held electrons                Tightly held electrons
                                     Loses electrons         Gains electrons
                                        Gets oxidized          Gets Reduced    
                      acts as the reducing agent     acts as a the oxidizing agent  
Here is the chemical reaction (demo):
                   oxidation half reaction:                                    2Na0   —>   2Na+  +  2e-
               reduction half reaction:        Cl2    +       2e-    —>    2Cl
                                                 2 Na (s)    +    2 Cl2 (g)      —>     2NaCl (s)
*notice the 2 half reactions are written so that the electrons are cancelled out.
  Electrons lost = Electrons gained.

*notice that the electrons on each side cancelled out!

How many different modules did I interconnect today?? Could you have understood any of this if you did complete the Summer Institute?
Today’s Lecture that you can use instead of reading above: