VIII. Anaerobic Respiration-without Oxygen (O2)
        A. Organisms that use Inorganic TEA's
             1. Methanogens (Archaea)- use CO2 as their TEA and it is reduced it is converted to CH4 (Methane)
             2, Sulfur Bacteria- use Sulfate (SO4) as their TEA and it is reduced to H2S (Hydrogen Sulfide). Hot Springs
        B. Fermentation- allows a cell to regenerate NAD+ so that the process of glycolysis can continue as long as glucose is present. This is done by Oxidizing NADH and reducing an organic TEA. 2 types:
             1. Lactic Acid Fermentation- Lactate is the reducing agent for NADH
                 Pyruvate ->Lactic Acid
                  NADH->NAD+
             2.  Alcohol Fermentation- yeasts convert Pyruvate into Acetaldehyde and then Oxidize Acetaldehyde into ethanol.
                  

Krebs Cycle continued

Part D starts at the bottom of cycle and goes till the next C-4

October 30th 2014

Krebs Cycle Continued

     D. The 4-C molecule and strip the rest of the high energy election off, making   more NADH and FADH2.

 4-C ----->4-C (starter material) + 2NADH + 2FADH2 

NEG:  4 ATP, 10 NADH, 2 FADH2 




VII     The Electron Transport Chain - Consists of 3 major protein complexes (I, II, III) these are all proton pumps and are embedded in the Inner Mitochondrial Membrane.
      
     A. NADH donates the electrons to complex I and then they're passed to II and III, pumping protons the whole way through

     B. FADH2 - Donates its electron to complex II and then III, pumping protons. This makes the process more efficient because the electron from FADH2 have not lost any energy yet when they reach Complex II.

     C. The exhausted electrons, once they've passed through the Electron Transport chain have O2 as their terminal electron acceptor (TEA)
                                                                

Equation: 2e- + 2H+ + 1/2O2 ----->H2O

So, O2 is crucial to provide a sink for electrons. Without it, the whole system backs up to Pyruvate.  (Back to Pyruvate Oxidation) 

    

    D. A proton gradient has now been created in the Inter Membrane Space, and the power of the diffusion of protons is used for Chemiosmosis to make the final 32 ATP.

NEG: 36 ATP, 0 NADH, 0 FADH2

 

October 29, 2013

IV. Glycolysis
          A. Phosphorylation
               Net Energy Gain (NEG): -2 ATP
          B. Breakdown of Glucose into two 3-C's
               NEG: -2 ATP
          C. Conversion to Pyruvate
               NEG: +2 ATP
                         -2 NADH

V. Pyruvate Oxidation
- Pyruvate diffuses into the Mitocondria. Pyruvate is converted to Acetyl CoA and a CO2. In this process two electrons are given off to form NADH.

                               Enzyme in
          o   o   o     ---------------->   o   o   +    o
          o   o   o       Intermembrane     o   o         o
      2 Pyruvates           Space                2          2
                                                 Acetyl CoA   CO2
                           ---------------->
              NAD+ + H+ + 2e- = 2 NADH
                         NEG:  2 ATP
                                    2 NADH

VI. The Kreb's Cycle
- Takes place in the Mitochondrial Matrix. 9 enzyme catalyzed reactions that strip the rest of the high energy electrons off and onto NADH and FADH2.Also more ATP is made.
4 Stages:

          A. Acetyl CoA bonds to a 4-C Molecule making a 6-C molecule.
Look in book for Diagram
                       
                               o  o  2 Acetyl CoA
                               o  o
                                 +
o  o  o  o ----------------------------------->  o  o  o  o  o  o
o  o  o  o                                                          o  o  o  o  o  o
                            NEG: 2 ATP
                                      2 NADH

          B. The 6-C molecule has a Carbon break off forming CO2 and 2e- are harvested to make more NADH.
 Look in book for Diagram
 NEG: 2 ATP
           6 NADH

           C. 2 5-C molecules are converted to 2 4-C molecules by losing another carbon each. More electrons are stripped off to form NADH and this is an exergonic reaction that forms more ATP.
Look in book for Diagram
NEG: 4 ATP
          8 NADH

An Overview of Cellular Respiration

Cellular Respiration- Is the harvesting of energy to form ATP from the breakdown of Glucose

I. Summary Equation



II. 2. Stages
         A. Glycolysis- splitting Glucose into 2 molecules (Happens in the cytoplasm)
         B. Oxidation- stripping electrons off (Happens in the mitochondria)

Overview of Aerobic Respiration

Between Glycolysis and the Krebs Cycle a Process called Pyruvate Oxydation occurs producing Acetyl-CoA and NADH and CO2

III. Glycolysis

     !. Takes place in the cytoplasm

     2. Occurs in the presence or absence of oxygen

     3. Involves ten enzyme-catalyzed reactions (Don't need to know all of them just know there are 10)

     4. Broken down into 2 molecules of pyruvate

     5. Steps

         A. Glucose is converted to a 6-C diphosphate. This uses 2 ATP's

         B. The 6-C molecule is broken down into 2, 3-C molecules

         C. The 2, 3-C sugars are converted to Pyruvate, gaining 4 ATP and 2 NADH

NAD+ + H+ + 2e- ----------> NADH

IV Pyruvate Oxidation

2 Pyruvate is converted into 2 Acetyl Co-A. 1 Carbon is stripped off (2 CO2) and 1 NADH per pyruvate is formed. This happens in the Mitochondria

You can use Acetyl Co-A to make either fat, or more ATP or some Proteins

Mitochondrial Structure

Tuesday, October 22-Notes-C4 photosynthesis

IX. C4 Photosynthesis-Solves the photo-respiration problem. 2 types of plants that run a C4 photosynthesis:
     A. C4 Plants- sugarcane, corn

         1. CO2 enters a Mesophyll cell where it is fixed onto a PEP molecule by PEP carboxylase forming a 4-C molecule (malate).
             PEP (3-C)  + CO2 (1-C) ==> malate (4-C) (this is where the C4 cycle gets its name-there are 4 carbons)
         2. The Malaate diffuses into a Bundle-Sheath cell where it gives off a CO2 to the Calvin Cycle (same as C3 photosynthesis) The 3-C molecule "left over" is pyruvate. So, all of the sugars are made in Bundle-Sheath Cells.
         3. The pyruvate diffuses back into the Mesophyll cell, is converted back to PEP (uses an ATP) and the cycle starts over.
     B.CAM Plants-Cacti, Pineapple
 

      
         1. CO2 is fixed during the night when stomata are open into the C4 pathway.
         2. C4 molecule gives up its CO2 during the day to the Calvin Cycle.

VII. Photosynthesis
        B. Light-Independent Reactions
AKA The Clavin Cycle AKA C^3 Photosynthesis
ATP provides energy to drive endergonic reactions and RADPH provides REDOX Power.
Happens in the Stroma.
                1. 1RuBP  combines with one CO2 to form 2 Phosphoglycerates. This is catalyzed by the enzyme RUBISCO.

RuBP + CO2---- 2 Phosphoglycerates

Note: C^3 Photosythesis refer to the # of carbons in the comound formed when CO2 enters the cell

               2. 2 phosphoglycerates undergo a series of reaction to form 2 Glyceraldegydes.
ATP and NADPH are now used to make glyceraldehyde a "High Energy" compound
(it now has the electrons from PSI) Excess Glyceraldegyde "leaves" the calvin cycle and it takes 2 to form 1Glucose.
Every turn of the calvin cycle adds 1 extra carbon. So, 3 turns will give you 2 glyceraldehydes and 6 turns will give you 2 glyceraldehydes, which will yield 2 glucose.
 
               3. The Glyceraldehyde that remains in the cycle is catalyzed by a series of reactions (some requiring ATP) to regenerate RuBP, the starting material.

VIII. Photoresperation- Happens under hot, dry conditions when a plant closes its stromata in order to conserve H20. Result: O2 cant escape and CO2 cant get in. So, RUBISCO will "fix" O2, not CO2, into the Calvin Cycle. This will stop the production of Glucose and potentially kill the plant.
So, how do plants (like-desert plants) survive?:

IX. C4 Photosynthesis
     

Oct 16 Light Dependent Reactions

This process is called noncyclic photophosphorylation.

Difference between Photosystem 2 and Photosystem 1. Ps2 has a water splitting enzyme while Ps1 does not. Also the wavelengths of the reaction center are slightly different.


E. These electrons are now passed down a 2nd electron transport chain of cytochromes and are finally transferred onto NADPH (serves as an intermediate electron acceptor). These electrons will now be transferred, in the light-independent reactions onto Glucose.

Reaction
*NADP+ + H+ + 2e- ------> NADPH * must have this equation memorized.

VI. Pigments- chemicals that absorb part or all of the visible spectrum. Plants use 4 pigments;
     A. Chlorophyll A- deep green (most common)
     B. Chlorophyll B- yellow-green (2nd most common)
     C. Xanthophyll- red
     D. Carotene- yellow-orange

Note: these pigments are organized into large protein complexes imbedded in the thylakoid membranes of the chloroplasts called photo-systems.
VII. Photosynthesis
     A. Light Dependent Reaction
          1. Photo/s are absorbed by a chlorophyll molecule in Photo-system. II (PS II) This causes the energy to be transferred (kinetic) to the rest of the chloroplast until it reaches the reaction center chloroplast. Here, h2o is split by an enzyme that "harvests" electrons.
Equation: (2)h2o-------->4e- + 4h+ + o2 (oxygen gas) or h2o ----> 2e- + 2h+ + 1/2 o2
          2. The kinetic energy is then transferred to one of htese electrons and this boosts its energy level.
          3. This electron is then transferred down a chain of proteins in the membrane called cytochromes (electron transport chain). One of the cytochromes is a proton pump- this uses energy from the electrons to pump protons from the stroma into the thylakoid space creating a proton gradient. These then pass back through ATP Synthase which creates ATP from ADP+P. Now the electrons have lost most of the energy they gained from PS II. CHEMIOSMOSIS.

Note:  these are known as the LIGHT DEPENDANT reactions of photosynthesis.
C. Converting the energy from ATP and NADPH into glucose from CO2 and H2O.
(These reactions are known as the LIGHT INDEPENDANT reactions of photosynthesis)


The summary equation of photosynthesis is:
 6 CO2 + 12 H2O + Light Energy --------> C6H12O6 (glucose) + 6 H2O + 6 O2
V. LIGHT - light is composed of subatomic particles called PHOTONS.  Photons always move at the same speed (light-speed) and travel in waves.  The distance from peak to peak of the waves are known as a WAVELENGTH.  The shorter the wavelength, the the higher the energy.

B. Electromagnetic Spectrum  - The entire spectrum of photon radiation.

Photosynthesis uses the visible light portion of the spectrum to work. 

C. Pigments - are chemicals that absorb a portion of the visible spectrum.  There are 4 pigments that are used by plants to absorb light:
   1. Chlorophyll A - reflects green
   2. Chlorophyll B - reflects yellow/green
   3. Xanthophyll - reflects red
   4. Carotene - reflects orange/yellow

Xanthophyll and Carotene together are known as the carotenoids.
 Together these 4 pigments work to absorb the majority of the high energy, short wavelength portion (violet, blue) of the spectrum.

Fall colors occur because the Chlorophylls denature 1st when the plant leaf cells stop photosynthesizing and the carotenoids  break down later so the leaf will turn yellow ----> red.

October 11, 2013 Process of Photosynthesis

The process of photosynthesis is molecular, so it's important to be able to visualize the things that are happening.

Photosynthesis
I. Overview- Photosynthesis is the process that captures light energy and transforms into the chemical energy of carbohydrates (glucose)

• It occurs in

-Plasma membranes of some bacteria
-Cells of algae (60 % of photosynthesis is done by these)
-Leaves of plants

II. Leaf structure

Cuticle- Clear, waxy coating on top of the leaf
Palisade Mesophyll- Photosyntheis happens here, more than the spongy mesophyll. (90%)
Vascular Bundle- (This is found inside the Bundle Sheath cell in the picture)
Spongy Mesophyll- Mops up the rest of the light that wasn't absorbed by the Palisades.
Stoma- A "doorway" that goes in and out of the cell. The oxygen that is made by photosynthesis is given off, and CO2 is taken in. Water can also escape through this.

III. Chloroplast Structure

Outer Membrane-
Thylakoid-
Granum-
Stoma- The space between the Thylakoids and the outer membrane
Thylakoid Space

IV. 3 Stages of Photosynthesis
A. Capturing energy from sunlight
B.Using energy to make ATP and NADPH to power the synthesis of carbohydrates from CO2

Enzyme inhibition

D. Inhibition 1. Non-Competitive Inhibitios-When a repressor molecule bonds to the allestoric site and inhibits the activity of the enzyme. The active site is not competed for. 2. Competitive Inhibition- A second moolecule that has a similar characteristics to the substrate. gum in the lock. this inhibits the enzyme's activity by blocking the substrate from fitting into the active site (Poisons and toxins) V. ATP Adenosine Tri_Phosphate What ATP is used for in the cell Muscle contractions pumpthings across membrane biosynthesis cytoplamic transport chemical activation Flagella or Cilia Motor Protiens Cell Crawling Heat can be generated directly from ATP VI. REDOX- Reactions (Reduction/Oxidation)-transfer of electrons from one chemical to another. A. Reduced Chemical-receives the electrons. (electrons are negative so when it gains electrons its charge goes down, reduces) B. Oxidized Chemical- Gives off its electrons. The reason the word oxodized is used is because Oxogen (O2 is the best and most commonen electron accepter.) [fire is a common example of a redox reaction. When you but a lid over the fire it goes out because the electrons no longer have a place to go.)

5. Enzymes (catalysts)
Enzyme level does not change. What would increase the rate?
1. More substrate
2. More enzymes
3. Increase temperature
4.Agltate
5. Optimize pH
B. Temperature-

C. pH-
D. Allosteric Enyzmes- have a 2nd bonding site for a chemical that will alter the active site of the enzyme. 2 types:
1.Repression- happens when the molecule that bonds to the allosteric site makes the active site less likely to bond the substrate. Feedback Inhibition- excess product acts as the represses molecule.
2. Activation- happens when the molecule that bonds to the allosteric site makes the active site more likely to bond the substrate. Vitamins

Energy

Important Announcements:
**New section started today
**Next exam will be on chapters 6 and 7
**It will be testing energy, photosynthesis, cellular respiration, etc.

ENERGY - the ability to do work.

 - Energy Flow:  It exists in two states: Kinetic and Potential. Classic example: boulder on the hill. While the rock sits on top, it has potential. When it is pushed or rolls down, it now has kinetic energy.
 - Thermodynamics: 2 laws
      A. Energy cannot be created nor destroyed, it can only be converted from one form to another. Whenever energy is converted from one to another, energy is always lost (usually in the form of heat).
      B. Entropy happens/Disorder (Entropy) in closed systems is continuously increasing. Entropy is a measure of the disorder of system. Classic example: eating, cleaning your room every week.
 - Chemical Reactions:
      A. Begin with reactants (substrates) which are converted to products.
      B. 2 Types: Exergonic reactions (leaving/exit) - products contain less energy than the reactants.This reaction would feel extremely hot.
                        Endergonic reactions - products contain more energy than the reactants. ATP allows for this. This reaction would feel extremely cold. This is because the reaction is absorbing heat from the environment. Example: cold packs for althetes.
Graph -

Energy of Activation (the humps on the graph): extra energy required to destabilize chemical bonds and so initiate a chemical reaction.
Catalysts: lower the activation energy of a reaction, and thus increase its rate. **However, they cannot make an endergonic an exergonic. Dotted line on the graph.

 - Enzymes: proteins that lower the activation energy required for a reaction to take place. Hydrogen Peroxide, H2O2 = H2O + O2 This equation is NOT balanced. Balance to 2H2O2 = 2H20 + O2. This happens very, very slowly. First enzyme ever discovered: Catalase. Active site - where the substrate(s) (reactant) will "fit". Remember as "the key". Because of this reaction, hydrogen peroxide is not the best antiseptic. The bubbling is actually indicating that the reaction has quit (release of oxygen gas).

      A. Enzyme Activity: Graph b is the correct graph. Compare this reaction to an easter egg hunt. 1 egg every three seconds, but there's only so many easter eggs and the amount of kids are the same. Fewer eggs to be picked up and eventually get to 1 egg per minute. So in the reaction, the amount of catalase stays the same, but the amount of reactants decreases so the graph flattens out. 

TEST ON THURSDAY       
          4. Coupled Transport - One material (molecule) diffuses in passively and it, or the power of its diffusion will move another material against its concentration gradient.

 Insulin/Glucose

    B. Phagocytosis- engulfing particulate matter into the cell by engulfing it and then containing it into a vesicle.

    C. Pinocytosis- same as phagocytosis but the material is liquid.

    D. Receptor Mediated Endocytosis - molecule bonds to a receptor protein on the cell's surface and this activates a system that "pulls" the material in and contains it in a vesicle.

    E. Exocytosis - the direct opposite of phagocytosis

VII. Protein Identification Markers - found on the external surface of a cell and ID's it as Foreign or Domestic and also as the type of tissue it is.


VIII. Endosymbiotic Theory- Eukaryotic Cells evolved from the phagocytosis and symbiotic cooperation of prokaryotic cells.  Watch "Bozeman Biology-Endosymbiosis."  Mitochondria and chloroplasts in particular show evidence that this has happened
    A. Size and Shape are the same as aerobic bacilli Bacteria and Cyanobacteria (photosynthetic)
  
    B. Mitochondria and Chloroplasts have a Double Membrane system:
         1. Outer- came from the host cell.  Same characteristics
         2. Inner - folds and stacks just like Bacterial membranes.  Used for the same purpose - make ATP

    C. DNA
         1. Have their own
         2. DNA is circular