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Q2 – Week 9 – 1/17 – 1/21

                                                                                                                                Jump to:  Tuesday,   Wednesday,  Thursday,  Friday                                                                                                                                   ___________________________________________________________

1/17 – Monday.        Martin Luther King Jr Day – 

I have a dream that one day this nation will rise up and live out the true meaning of its creed: “We hold these truths to be self-evident, that all men are created equal.”

I have a dream that one day on the red hills of Georgia, the sons of former slaves and the sons of former slave owners will be able to sit down together at the table of brotherhood.

I have a dream that one day even the state of Mississippi, a state sweltering with the heat of injustice, sweltering with the heat of oppression, will be transformed into an oasis of freedom and justice.

I have a dream that my four little children will one day live in a nation where they will not be judged by the color of their skin but by the content of their character.

I have a dream today!

I have a dream that one day, down in Alabama, with its vicious racists, with its governor having his lips dripping with the words of “interposition” and “nullification” — one day right there in Alabama little black boys and black girls will be able to join hands with little white boys and white girls as sisters and brothers.

I have a dream today!



1/18 – Tuesday –  A Day – 

Main focus –                                                                                                                                                          
a)  To Complete part 2 of the Genetics Test in first period.
                                                                                                                                                                                     1.  Part 2 of the genetics test will be given.                                                                                                                                                                                                                                                                                                                                                                                                                                                          


1/18 – Tuesday’s Homework: –

 Begin Metabolism and Energy – Thermodynamics and Spontaneity 

*Connections –
 We are beginning are Energy Unit but we are really just picking up where we left off in genetics.  We left off in genetics where we observed anabolic (Trp Operon) and catabolic  (Lac Operon) pathways in E. Coli regulated by repressor allosteric proteins from upstream “switches” or regulatory genes.  Gene regulation that controls the transcription and thus the expression of the genes is often regulated by Inducers or Repressors that are tied to the concentration of compounds that obtained from our environment.  That is our genes interact with our environment!!!  Through Natural Selection we have adapted to become very efficient in our use of energy and resources available.  All life requires a constant supply of energy and it is absolutely advantageous for all organisms from simple prokaryotes like bacteria (E. Coli) or eukaryotes (US!) to use available energy efficiently.  In the case of the Lac Operon in the E. Coli it would not be efficient use of energy and resources to transcribe and translate enzymes that breakdown lactose if there is no lactose in our cells.  That energy and resources are available for other life sustaining processes if there is no lactose present and thus there is a clear selective pressure for organisms to maximize efficient use of Energy.  Without our adaption to harness Energy and use it efficiently there can not be DNA duplication in the S phase of Interphase of meiosis or mitosis which we started talking about this summer.
1:  Please read the Text 142 – 149. Concept 8.1 – 8.2
2: Read my passage ABOVE AND BELOW when directed to in the form.
*For question 3 – Please read The Second Law of Thermodynamics section and the first paragraph of the Biological Order and Disorder section on page 144 – 145 in the text. Then read my contribution below: (the book is a little vague but I am extremely specific!!!)
3: Complete the form below.
OK You should understand the Second Law of Thermodynamics describes that processes that occur without an input of energy are spontaneous and spontaneous processes are those that are “favored” on the universe because they increase the entropy (∆S) of the entire universe. Entropy is a measure of randomness but it can also be considered the dispersion or energy from concentrated sources to less concentrated sources. The dispersion of  energy from concentrated (ordered ) sources to less concentrated (more random) sources is the best way to explain entropy.  
For example, heat flows from Hot to Cold because of the 2nd Law of Thermodynamics. When Heat is released the surrounding gas molecules in the air move away faster with this energy (And Disperse the Energy).  COLD does not flow!!!  The universe favors the processes that disperse energy or increase randomness (of energy).  When the universe favors a certain pathway or process it is said to be spontaneous.  Do not confuse this with something that occurs without any input of energy (AS THE BOOK STATES INCORRECTLY!!) All chemical reactions require an input of energy (which is called activation energy) to start the reaction.  Even the most volatile explosives require a detonator or gasoline needs a match. Spontaneous processes or chemical reactions are favored because they are self-sustainable. When you light propane for your stove or BBQ do you need to have a continuous supply of energy to keep the propane lit?  When you start the BBQ don’t you just spark it once?  Does a rock the rolls down a hill need to be pushed down the hill continuously?   Both of these are spontaneous processes because they are sustainable on their own AND increase the entropy of the universe (disperse the energy).  
                                                                                  REACTANTS                                PRODUCTS
In terms of the chemical reaction of propane:  C3H8  +  5 O2   –>   3 CO2  +  4 H2O  +  HEAT

1 Propane molecule (C3H8reacts with 5 oxygen molecules (O2) ——> to make 3 carbon dioxide                                                                                                                                    molecules (CO2) and 4                                                                                                                                          water molecules (H2O) 

                                                                        Thus 6 molecules        ——->      become 7 molecules
This reaction gives off HEAT (which makes surrounding gas molecules in the atmosphere move faster) AND creates more degrees of freedom of movement by increasing the total number of individual molecules that can move!  This disperses energy OR increases randomness. 
Thus there are 2 ways entropy (randomness or energy dispersion) can change:
1. Heat flowing into a system or out of a system (In the case of the combustion of propane above, Heat produced from the chemical reaction and moved toward surrounding gas molecules that causes them to move faster and thus disperse the energy from the concentrated source (propane tank) outward to the rest of the universe.
2. The change of the number of free particles (molecules) that can move independently.  Large molecules like propane have many atoms (like Carbon and Hydrogen) that are bonded to each other and although they do wiggle and vibrate when bonded together they are not as “free” to move as much as smaller molecules who have less atoms bonded to them. These smaller molecules with less atoms have more degrees of freedom and thus can disperse the movement energy outward into the universe if the products of reaction have more molecules than the reactants.  Also having more products in the gas or liquid phase in the products side of a reaction also contributes to an increase in Entropy, randomness, or dispersion of energy. 
This is a spontaneous process or direction that follows the second law of the thermodynamics!!!  Which means the reverse process must be non-spontaneous!!  Do you ever see propane reforming from carbon dioxide and water?  If the forward is spontaneous then that means the pathway is favored by the universe and thus the reverse is NOT FAVORED and must be spontaneous.
Now in terms of cells, they must be able to make complex molecules from simper ones (anabolic). 
Life creates amazing amount or order!
Examples:  Translation of polypeptides from amino acids, Replication of DNA by combining nucleotides into double helix, and plants creating starch (many glucose molecule bonded together) from individual glucose molecules.  How is this possible if we are LOWERING the degrees of freedom so that the less molecules can disperse energy?  Remember that there are 2 factors, Heat Flow and the number of free particles!  So if the chemical reaction is creating less dispersed molecules which is not favored by the Second Law of Thermodynamics then, THEN there must BE A LARGE AMOUNT OF HEAT RELEASED to compensate for the Lack of “free molecules”.  THUS the Entropy of the universe (∆S) still increases and these anabolic processes are spontaneous!!  If heat was not released in these processes then processes would not occur.  
Why are we warm?   
Not all chemical reactions that build the order that life requires release energy so there must be another mechanism that increases entropy even though we are not compensating by releasing heat!  This is explained by COUPLING!  We are heterotrophs that require ENERGY to live.  This is why we must eat to live.  We ingest and  break down food (break bigger molecules into smaller ones!) to gain energy (energy is released) and this process is clearly spontaneous because we are releasing heat and increasing the degrees of freedom of molecules. THIS ENERGY that we get from eating and digesting food (breaking down glucose) from a spontaneous process DRIVES the non-spontaneous process of building more complex molecules from simpler one.  So the order that life creates requires a continuos supply of energy to move in pathways that GO AGAINST THE 2nd LAW OF THERMODYNAMICS!!  Eventually the Universe wins!! 🙁
We say that spontaneous processes ( that increase the entropy ∆S of the universe because they disperse energy either by the heat released or by increasing the degrees of freedom by producing smaller molecules from larger ones) are self sustainable because they do not need a constant supply of energy to keep them going forward.  Non-spontaneous processes need a constant supply of energy to move them forward.  Because spontaneous processes are self-sustainable THEY PRODUCE FREE ENERGY ∆G) for use to use to accomplish non-spontaneous processes.  We obtain FREE ENERGY ∆G from our food! We obtain electricity on Long Island mostly by burning fuel oil (diesel) to boil water that creates steam and pressure to turn turbines (generators).  This process utilizes the spontaneous burning or combustion of diesel fuel to provide FREE ENERGY ∆G  to create electricity.  The electricity we do have to pay for….
Is a riding a pony spontaneous?  What do you think Abigal??  Is Entropy increasing in the universe?  Is it energetically favorable?  Does it create Free Energy?   Yes because I use the free energy of the pony to move me.  Because I am using the Free energy we say that ∆G (free energy is decreasing!!) or negative for spontaneous processes.  ∆S of the universe is positive and increasing for spontaneous processes. 
3:  Metabolism Form 1::

End of Tuesday!


1/19 – Wednesday –  B Day 

Main focus –                                                                                                                                                          
a) To Complete Part 2 of the test.  

                                                                                                                                                                                      b) To define spontaneity, free energy, entropy in thermodynamics.

1.  Complete Part 2 of the test. If you need more time please come after school.

2.  Thermodynamics (in class) begins!


 Thermodynamics Notes:

Burning paper spontaneous??? 
    From today’s class discussion with the burning of paper:

        Spontaneous = dispersion (spreading out) of energy 
                                    = Increase in entropy
    concentrated source of energy —-> less concentrated source
       example:  paper burning
Wood has concentrated source                ———>     Less concentrated source of energy because
of energy because it was once living                            energy was released AND smaller particles of 
and living things collect energy by                               matter (CO2 gas and water gas) are moving
building more cells, proteins, DNA, etc                     away from reaction.
Simplified chemical reaction:


*Notice there are 2 C6H12O6  + 2 Ca +  13 O2    = 17 individual molecules that we started in paper
*Notice there are CaCO3  + 10 CO2 + 10 H2O = 22 individual molecules produced in burning it!
17 particles  and some of these are large  ——-> 22 particles and most of these particles are particles that are slow moving solids.                                                 fast moving gases).
        Solids have lower absolute entropy            ——–>   gases have greater absolute entropy
Energy is being dispersed by the increase of individual molecules (increase of the degrees of freedom) and their ability move faster as gases.
Energy was ALSO dispersed because energy ( Energy is written on the product side of the reaction to show that it is produced ) is RELEASED into the surroundings
The heat released by the reaction can make the surrounding molecules move faster (increase their kinetic energy) and DISPERSE!!  This leads to and increase in Entropy.
Spontaneous Process – The universe allows things to occur IF ENERGY is dispersed through Energy (heat) being released and increasing the number of free molecules = increase in Entropy!
Why do we care????
If a process is Spontaneous it gives us FREE ENERGY to do things! Cells need a constant supply to live!!!!!
NOW if a process is spontaneous the reverse process process MUST be non- spontaneous, which means energy is being organized and concentrated AND THAT REQUIRES A CONSTANT INPUT OF ENERGY.  THink about it !!  Is the reverse of burning spontaneous?  Have you ever seen CO2 and water vapor come together to make paper??  ONLY IN PHOTOSYNTHESIS!!!! Which requires a constant energy (LIGHT!) and thus the making of wood (or a tree growing) from photosynthesis is Non-spontaneous because energy is being concentrated.


1/18 – Wednesday’s Homework: –

1. Make one more submission form this Tuesday’s form (Metabolism 1)  if needed-
    I will grade it and send it to you so you can review and use today’s discussion / lesson to help  
   learn (relearn) these concepts .
2.  Read the my notes above regarding the burning of paper AND Connections below:
      It might be helpful to re-read the notes I posted Under Monday.
3.  Watch the lecture.  
      a) watch the whoosh demonstration.
            Read the notes for the demonstration
      b) gummi bear demo.
             Read the notes for the demonstration
4.  Complete the form using information below and the Vsauce Video:                                                                          You have three submissions to this form!
Most of the all the organisms on the earth including plants and animals require glucose,  C6H12O6 (s) for Free Energy.  
                      C6H12O6 (s)  +   6 O2 (g)     ——>     6 CO(g)   +    6 H2O (g)  + Energy
                                    7 molecules           ——>               12 molecules
 A concentrated source of energy         ——>       To a less concentrated source
We use this spontaneous reaction to provide the Free Energy to Force non-spontaneous reactions of life (building complex organized structures).
Spontaneous Reaction = Exergonic Reaction = an increase in Entropy = favorable pathway
Lecture – I did have some problems with one demo (lol) it wound up being non-spontaneous due to the alcohol have too much water mixed with it. Good times!!
Today’s demo:  Whoosh bottle – this one better
Whoosh bottle Demo Notes:
Once the I have the alcohol in the gas phase, which has now mixed with the oxygen in the air inside the container I ignite the flammable mixture by providing a spark and the combustion reaction begins. This is an example of an spontaneous reaction that releases energy exothermically, (exergonic reaction).   Here is the chemical change that takes place:

                        2CH3OH(l)   +  3O2(g)  . 2CO2(g) +   4H2O(g)  + Energy                                                                                                   Alcohol                Oxygen          carbon dioxide       water                  


                                                                          (l) = liquid, (g) = gas


Notice the Coefficients that balance the reaction due to the Law of Conservation of Mass.  We have the same number of Carbon (C), Hydrogen (H), and Oxygen (O) atoms on both sides. This is chemical change due to the fact that there are new substances (compounds) produced which means bond have been broken and reformed.


Notice that initially 3 gas molecules (3O2(g)) are used with 2 liquid molecules .

These are called Reactants as they on the left side of the chemical reaction and this is what we start with before the chemical reaction begins.

The products (2CO2(g) +   4H2O(g) ) are the chemicals that are on the right side and they include 6 gases. So 3 gas molecules and 2 liquid molecules become 6 gas molecules .  

The entropy is increasing and the chemical reaction is spontaneous

Gummy Bear Demo Notes:
In this demonstration potassium chlorate – K2ClO3 was heated to a liquid demonstrating an endothermic phase change and then decomposed into O2 and KCl.  The oxygen reacted with the sugar in the Gummi Bear exothermically. 

1. melting the white solid:                  KClO3(s)  +  heat   —> KClO3(l)

2. hot liquid reacts:                           2KClO3(l)  +  heat    —>   2 KCl(s) +   3 O2(g)


3.  Sucrose (table sugar in gummi bear reacts with oxygen:

                               C12H22O11  +   35/2 O2   —>   12CO2  +   11H2O   +   heat (5635 kJ)                                                             sucrose

Vsauce video:
GIVE THIS VIDEO A CHANCE!! It appears initially that it has nothing to do with what we are learning but THEN IT WILL HAPPEN!!

The form below:
I know that some may be really lost BUT I promise it will be crystal clear after tomorrow when I redo these demo’s and Teach this topic in class.  I will look like a hero because you will have struggled a bit at home and I will (hopefully) make sense of all of this in class.

3:  Vsauce and the Entropy Demos form::

End of Wednesday!


1/20 – Thursday –  A Day 

Main focus –                                                                                                                                                          
a)  To view Chemical and physical reactions and determine the spontaneity of the process
b)  Label a potential energy diagram                                                                                                                                                                                               

1. Review the class notes.

Gibbs free Energy and Entropy Classwork and Notes.pdf
View Download
2. Review Metabolism 1 form.
3: Completed 1st page class worksheet – Gibbs free Energy and Entropy.pdf
4: Demos (Dancing Gummy Bears)  – Note-taking 
Gibbs free Energy and Entropy.pdf

View Download

Reviewed the Free Energy Diagrams – 
-focused on the energy barrier/ activated complex / How enzymes lower the energy barrier
Every chemical reaction requires collision that are effective = Effective Collisions
effective collisions require 2 things:
                 1. Energy to overcome repulsive forces of electrons (that are on the outside of the molecules) . ELECTRONS FROM ONE REACTANT REPELS THE ELECTRONS FROM THE OTHER SINCE  ELECTRONS ARE NEGATIVE AND LIKE CHARGES REPEL.  
Thus as two reacting molecules start to collide they start to repel until they reach a maximum energy of repulsion = peak energy = Activated Complex.  The energy needed to overcome the activated complex peak is called Activation Energy (Ea).  Every chemical reaction exergonic or endergonic must overcome the energy barrier with Ea.
                  2.  Molecules have to collide in areas that can bond and not in area that it cannot.  Thus molecules must collide with the correct orientation ALONG with Ea.
A couple of points to keep straight.
– A reaction that is non-spontaneous by itself can be made spontaneous with respect to the entire universe IF IT IS coupled with a spontaneous process.
– Free energy is based on Heat coming or going AND the entropy of the system (the particles).
– You can have the entropy of the surrounding (usually gas molecules moving ) and you can have entropy of the system (particle changes).                                                                                                                                           


1/20 -Thursday’s Homework: –

1.  Complete side one with me that we started in class with the video with me below. It will start RIGHT at the spot I need you follow at!
 Take notes on your worksheet as I go through it.   Please watch till the end!
2 . Please read today’s notes below the form.
                                                  KClO3 (s)  +  FREE ENERGY  —->  KClO3 (l)
The chemical reaction by itself is endergonic but when combined with the chemical reaction in the torch (coupling) the above reaction with the reaction in the torch IS SPONTANEOUS!!
SOME of the Free Energy of the Torch reaction went into the above reaction but MOST OF IT went into the surrounding this the entropy of the universe increased and the entire coupled process is Spontaneous!  Look at the Review of the Gummy Bear demonstration – diagram below.
3: Please complete the following form based on Chapter 8.  You will need to read parts 

      of Chapter 8  in the text, and review the notes  below to answer the form below.                           

Today’s Notes:

Exergonic    = Spontaneous =        self sustaining reactions/process     = entropy of universe increases  
Creates (releases) Free Energy from a concentrated energy source that can be used to do work.
ΔG = negative (Free energy is decreasing as the reaction/process proceeds).  Riding the pony! 
Endergonic Nonspontaneous = requires a constant input of energy = entropy of the universe decreases
Uses (absorbs) Free Energy to make a concentrated energy source.
ΔG = positive  (Free energy is increasing as the reaction/process proceeds).   Carrying the pony! 
                Entropy (ΔS )=  measure of the amount of dispersed energy.
     And according the 2nd Law of Thermodynamics the ΔSuniverse must increase if there is a             
                      pathway for the process to proceed = spontaneous reactions.
                                     The ΔSuniverse is measured by ΔG (Free Energy).
The Entropy  ΔSuniverse  is affected by two factors    
There are two ways that energy can be “dispersed” or released.
            1.  Heat or thermal energy is released into the surroundings. ΔH = heat of reaction
                    This thermal energy will increase the temperature of the surroundings and increase the motion of
                    surrounding molecules. This increased motion will make these surrounding molecules “move away”
                    and disperse their motion energy “away” from the system.
                    ΔH = negative if HEAT energy is released – (increases  ΔSuniverse )
                   ΔH = positive if HEAT energy is absorbed – (decreases  ΔSuniverse )
            2.  The degrees of freedom of the particles or molecules increases. ΔS = entropy of particles
                   The chemical reaction or physical process increases the number of moving “parts” so that motion
                    energy is dispersed as the chemical or physical process proceeds.
                    ΔS  = positive if degree of freedom increases for molecules as process proceeds.
                   ΔS  =  negative if degree of freedom decreases for molecules as process proceeds.
To measure a if the Entropy ΔSuniverse is decreasing or increasing we use Gibbs Free Energy Formula:
                                                                                            ΔG =  ΔH – TΔS
                         IF ΔG = negative then the Entropy ΔSuniverse  is increasing = Spontaneous
                         IF ΔG = positive  then the Entropy ΔSuniverse  is decreasing = Non – Spontaneous

Review of the Gummy Bear demonstration – 
1: AP Biology THermo Review:

3:  Metabolism Form 2 quiz

End of THursday!

  – -___________________________________________________________________________________________________________________

1/21 – Friday – B Day

Main focus –                                                                                                                                                          
a)  To determine the spontaneity of a reaction by using the values of ΔS, ΔG, and ΔH.
b)  To Introduce the concept of equilibrium and relate it to ΔG.


1. A review of the Coupled Gummi Bear Demo Diagram to review the flow of Free Energy from a spontaneous process to DRIVE a non-spontaneous process. Notice the loss of energy in every step!

IF  the spontaneous process IS SPONTANEOUS ENOUGH TO OVERCOME THE non-spontaneous process then overall process will occur DUE TO AN OVERALL POSITIVE change in entropy of the universe.  

Another way to say this is, “Is the Spontaneous Process enough OR is ΔG a large enough negative value to overcome the positive ΔG of the non-spontaneous process??

2. We will start by determining the values of ΔS, ΔG, and ΔH values from the whoosh bottle                            demonstration that I will do live.   Also plot a potential energy diagram! catalyst effect!

3.  Demonstrate how ΔS of a system and ΔS of the surroundings will contribute to the value of ΔG.          
4.  A very cool balloon demo! 

                                                                                                                                                                                                5.  A cool uplifting Reaction demo:  Started the Back side of last nights homework.                                                                                                                                                                                                                                          Gibbs free Energy and Entropy.pdf                                                                                                               View Download


Today’s Notes:

To measure a if the Entropy ΔSuniverse is decreasing or increasing we use Gibbs Free Energy Formula: 
                                                                                                                                                                                                                                                                              ΔG =  ΔH – TΔS.   
      ΔG = Free Energy Change due to the change of the Entropy of the entire Universe! 
                        IF ΔG = negative then the Entropy ΔSuniverse  is increasing = Spontaneous
                         IF ΔG = positive  then the Entropy ΔSuniverse  is decreasing = Non – Spontaneous


The Entropy  ΔSuniverse  is affected by two factors    
There are two ways that energy can be “dispersed” or released.   
            1.  Heat or thermal energy is released into the surroundings. ΔH = heat of reaction
                    This thermal energy will increase the temperature of the surroundings and increase the motion of
                    surrounding molecules. This increased motion will make these surrounding molecules “move away”
                    and disperse their motion energy “away” from the system.
                    ΔH = negative if HEAT energy is released – (increases  ΔSuniverse )
                   ΔH = positive if HEAT energy is absorbed – (decreases  ΔSuniverse )                                             
                                                                                                                                                                                                                                    2.  The degrees of freedom of the particles or molecules increases. ΔS = entropy of particles
                   The chemical reaction or physical process increases the number of moving “parts” so that motion
                    energy is dispersed as the chemical or physical process proceeds.
                    ΔS  = positive if degree of freedom increases for molecules as process proceeds.
                   ΔS  =  negative if degree of freedom decreases for molecules as process proceeds.

Today’s lesson:

Spontaneity of a balloon with liquid nitrogen: (anyone have a large bill?)

The Cool and “up lifting demo!!”:


1/21 -Weekend’s Homework: –

1. Please complete the backside of last nights worksheet which is based on today’s Cool Uplifting demo.  Please review with the key below, Especially the diagrams!

Gibbs free Energy and Entropy.pdf

View Download

Gibbs free Energy and Entropy – Cool Reaction Key.pdf

View Download

2. Please view the Thermodynamic signs lecture below.

3.  Complete the Thermodynamic Signs Form below: ( You can have 3 submissions)

aminoacyl-trna link:  for next week (this id for Mr. Grodski only <iframe width=”560″ height=”315″ src=”” title=”YouTube video player” frameborder=”0″ allow=”accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture” allowfullscreen></iframe>

2:  Thermodynamics Signs Form Lecture

3:  Thermodynamic Signs Form – 

End of week 9!