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Q3 – Week 1 – 1/31 – 2/4

                                                                                                                                   Jump to:  Tuesday,   Wednesday,  Thursday,  Friday                                                                                                                                   ___________________________________________________________

1/31 – Monday  –   A Day – 

Main focus –                                                                                                                                                        
a)  To Complete our Note-taking of Cell Respiration
b)  To Review Enzyme activity

c)  To review concepts of Redox and electron energy


1.  Let’s Continue with Cell Respiration Note-taking: 

Cellular Respiration Chart.pdf
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Cell respiration Bio Notes pics 4 pages.pdf
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Complete Cellular Respiration Formula:                         
                        C6H12O6 (s)       +       6O2       —–>       6CO2(g)        +       6H2O (l)
      glucose      –>      Electron Carriers (NAD+, FAD)          –>      Electron transport System  (Oxygen bonds with H+ to make H2O)
   High Energy                          oxidize glucose                                     high energy electrons used to pump H+ ions against gradient
       Electrons                                                                                                 these H+ rush out of membrane giving atp synthase energy 
                                          High energy electrons   —–>    Low Energy electrons
                                               e – get oxidized                         oxygen gets reduced
                                                from glucose                         accepting the low energy e-
                                                          C    :    H                                         H    :O
                                       Electrons held loosely    ———>      Electrons held tightly
   Proton motor force from 4 page notes—–> Electron Transport Chain Animation below:
       How does the high energy electrons Pump H+ into the inter membrane space of the Mitichondrion?
                      Glucose ———->   Cellular Respiration ———->  O2   + low energy electron = water                                      high energy electrons                                                                                                  low energy electrons   

 A great computer simulation of of the Electron Transport Chain (Oxidative Phosphorylation): Biovisions



Cellular Respiration – Bioflix video:    

What are FAD and NAD+? Presentation:


1/21 – Monday’s Homework: –                                                                                      


1. Study for the Energy, Enzyme, Cell Respiration Test (4) on Energy and Cell Respiration:

            a) : Vocabulary words that match the definitions below:

Vocabulary definitions on Energy Test tomorrow – 


B –uses the proton motor force to generate ATP

C – Metal ions

D –The gain of electrons

– the protein complex that generates ATP in the Electron  Transport System

– blocks substrates from entering active sites

G – release energy when breaking down complex molecules to simpler molecules

-a measure of randomness or disorder molecular particles or energy

– The loss of electrons

J – the change of the shape of the active site of an enzyme when a substrate encounters it

K– Energy that can be used to do work

L– the complete breakdown of glucose to carbon dioxide

           b)  Parts of an energy diagram:
           c) factors the affect enzyme activity
           d) pH
           e) Today’s Chart on the differences in 3 parts of cellular respiration:
Today’ s Chart:
Cellular respiration Chart we filled in class:
Glycolysis  Krebs (Citric Acid) Cycle  Oxidative Phosphorylation 
 OUTSIDE mitochondria
Inside mitochondria (matrix) Inside mitochondria (inner  and outer membrane )
Anaerobic Aerobic Aerobic
 Net 2 ATP  NET 2 ATP (GTP) NET ~34 ATP
 No CO2 produced CO2 produced No CO2 produced
 No water produced No water produced Water formed
2 NADH produced
high energy electrons and protons captured
8 NADH and 2 FADH2 (2 turns )
high energy electrons and protons captured
NAD+ and FAD recycled
high energy electrons and protons delivered
No proton motor force No proton motor force Proton motor force 
Glucose becomes 2 pyruvate pyruvate becomes Acetyl CoA high energy electrons from reactions of glucose and Acetyl CoA create proton motor force
Requires Enzymes Requires enzymes requires protein complexes (electron transport system)  AND the ENZYME = ATP Synthase. 
Glucose gets oxidized Glucose fragments get oxidized Oxygen gets reduced in water
Free electrons in C-H bond taken Free electrons in C-H bond taken tightly held electrons in water

Overall Spontaneous 
breaking large molecule (glucose) in smaller components and energy released

G = –

Overall Spontaneous
breaking large molecules (Acetyl CoA) in smaller components and energy released

G = –

Spontaneous because of coupling
Free Energy  +  ADP + Pi —> ATP

Energy from electrons oxidized from glucose  create the proton motor force that produces the ATP

G = +

Chemical oxidation:  Losing electrons (LEO)                     LEO the Lion says GER!!!
Chemical reduction: Gaining electrons (GER)
          f) Thermodynamics-
Forms that cover all these topics:
Metabolism Form 2 quiz 2021 – Google Forms Key.pdf
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Energy Concepts Extra Credit Form – Google Forms Key.pdf
THermo Quantities and Sign Form 1920 – Google Forms Key.pdf
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ATP_Enzyme Form 2021 – Google Forms Key.pdf
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Catalase Lab Form 2021 – Google Forms Key.pdf
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Important Form:

Connections FORM! – Google Forms Key.pdf
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Energy and Cellular Respiration Form – Google Forms Key.pdf
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2/1 – Tuesday –  B  Day – 

Main focus –                                                                                                                                                          
a)  To Take the Energy Test (4) in class.

1.  Let’s Review Enzyme activity ( in terms of Temperature and pH)

Acidic R groups have -COOH endings that will become -COO–  (have a negative charge) because the H+ will be taken by the base in a basic solution.  So proteins that have amino acid that have R groups that are acidic will become negatively charged and they will attract other R groups that are positively charged. If the R groups change their attractive partners then THEIR SHAPE and thus THEIR FUNCTION changes. (Basic R – groups will also become charged (+) in the higher pH solutions.)
So R – groups that have ionic attractions will be be affected by slight changes in pH because there will more ions in the solution that these R could attract too.  This means that changes in the pH will cause changes in the amount of H+ and OH- in the cell which will cause the R groups of amino acids to attract the H+ (if the R group is negative) and attracts the OH- (if the R group is positive) AND thus change the shape of the tertiary folded protein. Changing the shape is called denaturing and denaturing changes the function of the protein when the active site is changed.
Form and Function!  


So Arginine, Histidine, Lysine have positive R groups that will be affected by OH (Bases)
Aspartic Acid and Glutamic Acid have negative R groups that will be affected by H+ (acids)
Proteins (enzymes) that have less of these amino acids with these R groups will be more resistant to pH changes and will denature at lower or higher pH’s as compared to enzymes that have more of these amino acids.
Remember the 4 types of attractive forces that occur in folded tertiary proteins:
Remember that tertiary proteins are long chain polypeptides (amino acid linked together) that take an active form (shape) by the R groups attracting each other.  There are 4 types:

    a) Ionic – positives attract negatives

            –H+ and OH compete with these!

    b) H – bonding – electron deficient Hydrogens

            – Strongest attractive force    

    c) Disulphide Bridges – Sulfur bonding to Sulfur

– Strongest force (chemical bond)
that keeps R groups together

    d) Hydrophobic – LDF’s – (non-polar attractions)

– weakest attraction


A permanent change in the shape of the protein is called DENATURING.  A denatured protein or enzyme will have no enzymatic properties as the active site will no longer have the shape to interact with the substrate.
Enzymes can become denatured if the temperature is too high as this high energy state will cause R group attractions to break and unfold the protein. “How did the Boiled enzyme do in our lab?
Remember the Taq polymerase in our PCR – Taster Lab? Taq polymerase is an enzyme that has a higher temperature tolerance that most enzymes do not have .  It is an example of the heat tolerant bacteria (Thermostable)that is in the graph below. They have a lot more disulphide bridges R group connections which are actually chemical bonds, and much less hydrophobic R – attractions in our folded proteins. 
All enzymes have optimum pH ranges and optimum temperatures that they work most effectively:
SO DNA does not just code for the amino acids that make certain shapes they also code for certain amino acid combinations that can make them more or less stable in certain environment.


2. Play some of the Cell respiration animations.

                                                                                                                                                                                  3. Energy, Enzyme, and Cellular Respiration (intro) Test                                                                                                                                                                                           

Cellular Respiration – How Mitochondria produces Energy:    

Cellular Respiration – Powering the cell – Biovisions

1:  Energy / Cellular Respiration (intro) Test

End of Tuesday!


2/1 – Tuesday’s Homework: –


1. Make one more submission to today’s test.
2. Please view the video below and complete the form based on the mitochondria.
  Just one response tonight!   

Mitochandria – Jodi Nunnari (UC Davis) :

1:  Mitochondria Video form:

End of Tuesday!


2/2 – Wednesday –  A Day 

Main focus –                                                                                                                                                          
a) To Review Yesterdays Energy Test and Mitochondria Form


1.  Review Energy test 1.                                                                                                                                                           

2. Review mitochondria form.

Metabolism, Thermo and enzyme Presentation:

Energy and Cellular Respiration Test 2:


2/2- Wednesday’s Homework: –

1. Please make another submission to the mitochondria form.
2. Review your graded Energy Test 2 (once it is emailed back to you)
3: Please watch the following videos on Photosynthesis. Please watch them in the following order:
                                  a) Shedding light on Photosynthesis:    – about 12:00 minutes
                                   b) Photosythesis – MIT 7.01sc :    -about 17:00 minutes
4:  And Complete the Form below 🙂


4: Photosynthesis Form 1 :


2/3 – Thursday –  B Day 

Main focus –                                                                                                                                                          
a)  To Review the Thermodynamics Test and Cellular Respiration Test
b)  To Begin Photosynthesis!                                                                                                                                                                                     

1.  Review of the Thermo cell Respiration Test

2.  Photosynthesis discussion and note-taking
photosynthesis diagrams.pdf
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Photosynthesis diagram overview.pdf
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Photosynthesis diagram worksheet 2.pdf
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Endosymbiosis ——> mitochondria , chloroplast

Electron Micrograph of a chloroplast:     

 [thylakoid disk——-> stack of thylakoid disks——-> granum] = light dependent reactions 


[stroma —–>outside the thylakoid] = light independent reaction OR Dark Reactions 

                                                                                                   Andrew Douch


“we are just using them for their hydrogen..haha…we take the hydrogen off them and chuck the oxygens away.”
12 H2O  —–>  24 H (hydrogen ions/protons) + 24 NADP+  ——-> 24 NADPH——> light independent reaction                                                     
                                                                     18 ATP produced       ————————————–>  light independent reaction                                (no ATP leftover for anything other than the light dependent reaction)
                                                      inside thylakoid                                                             ——–> stroma
                              24 hydrogens ripped of water eventually become 6 H2O (12) and 1 C6H12O6 (12
                                                            6 carbons from 6 CO2 become 1 C6H12O6 (glucose)
                  18 ATP        +       12 H2O (l)     +     6 CO2 (g)   ———>   6 O2 (g)    +     C6H12O6     +      H2O
     made from sunlight      roots uptake     stomata (pores)          waste             concentrated energy
                                                                              ΔG = ?                         ΔSuniv = ?
    Is energy coupling occurring here?
                                                       What did he leave out?   (electrons!)
  Graham Walker, PhD (MIT professor)
Cyclic Photophosphorylation – Preceded Respiration – 3.4 BYA
“sunlight kicks an electron up to higher orbital and when it is in a higher orbital it is easily lost”
“chlorophyll absorbs a particular wavelength from sun but this embedded in a multi-protein structure that has a bunch of other molecules that absorb at different wavelengths and then funnel that energy into the one that chlorophyll comes in.”
“When chlorophyll absorbs energy (the electron) goes up to an excited state ..and now is in a higher energy state (father away from the protons in the nucleus) and is more easily removed. “It is so easily removed that it actually becomes a strong reducing agent – (itself gets oxidized but helps other GAIN electrons).
 In this diagram Dr.Walker is diagraming the thermodynamic pathway of the electrons!

High free energy  ——->   Lower free energy
Excited  electrons                            less energetic

During this free fall Free Energy by excited electrons are used to pump H+ into the thylakoid.  This creates an electron gradient (high concentration of  H+ ) which is another form of Free energy that is used to create 18 ATP!


             So Free Energy of the Sun ——->  Free Energy of the High Hconcentration ———> ATP 
                   (excites electrons)
So Free Energy of one form is being converted to free energy of another. So what must be released in each step?
And this 18 ATP in Cyclic Photophosporlation is used by the prokaryote cell to drive life sustaining reactions.  The low energy electrons are returned to the chlorophyl.
                “there are still bacteria that exist today that still use Cyclic Photophosphorylation” 
“ATP is not enough to take carbon dioxide and make into sugars or carbon compounds.  We need a source of reducing power as well … Remember that CO2 is the most oxidized form of carbon.     


Notice the electrons in double bond of Carbon (C) are being pulled away from the C (carbon) toward the oxygen (O). Because Oxygen is the element that has the one of the greatest attraction for electron (its the reason it is such a small atom) AND this oxygen is BONDED ON BOTH SIDES of the molecule, Carbon “kind of” has its valence electrons removed or lost.  This “kind of” loss is oxidation.
These ancestral organisms used H2S to as a source of reducing power AND NADP+ to gather the reducing power for biosynthesis (making sugars, etc).
                                              H2S   +    NADP+   ———————–>  S  +   NADPH   +  H+
                         “The key is to get CO2 down to a more reduced form of Carbon”
                   It was done by using the reducing power of NADPH and the ATP made.
                        Non- Cyclic Photophosphorylation –  3.0 BYA – (Current Photosynthesis)
In Noncyclic Photophosphorylation the electron  that were excited by chlorophyll are used to generate a proton force in the same way as cyclic BUT these electrons ARE the ones that are the source of reducing power when they combine with NADP+.
Why is it an improvement over the Cyclic?
“it uses the energy of the sun to make ATP (like Cyclic) BUT it also uses energy of the sun to make NADPH!”
“So in other words, this second version gives the cell simply from the energy of the cell everything it needs to take carbon dioxide (CO2) and make it into organic (carbon based compounds).
It gives it the energy to reduce CO2!
The Noncyclic process accomplishes this by using a second photosystem that reenergizes the electrons that were just used to pump H+ into the thylakoid.  Once re-energized by the absorption of energy by the sun ( in the second photosystem, photosystem I) the electron is now at higher energy state that can reduce NADP+. This electron is not returned to Photosystem II.


In this current process, since the electron does return to the original photosystem it must get another electron from another source.  That of course is water. 
Photosynthesis diagram  – Cyclic vs Noncyclic Photo phosphorylation , Diagram photosynthesis diagrams.pdf


2/3 -Thursday’s Homework: –




2/4 – Friday – A Day

Main focus –                                                                                                                                                          
a)  To Review Cyclic Photophosphorylation and Non-Cyclic Photophosphorylation
b)  To identify the individual  reactions and metabolic pathways in the Calvin Cycle


1. Review the notes posted yesterday based on both cyclic and non-cyclic, which came first, how are they different. Is there any evolutionary similarities in cellular respiration?
2.  Use the detailed notes of the Calvin Cycle to introduce carbon fixation.
Photosynthesis diagram  – Cyclic vs Noncyclic Photo phosphorylation , Diagram photosynthesis diagrams.pdf
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2/4 -Weekend’s Homework: –

1.  Please view the Photosynthesis Light Reaction Video below.

2.  Please complete the form below.

Photosynthesis Light reaction Homework video:

2: Photosynthesis Form 2 :