3 Styles of Photosynthesis

     A. Capturing Light

     B. Use light to drive the synthesis of:

          1. ATP- Break terminal phosphate off. Result: Heat

          2. NADPH- chemical that has been REDUCED (REDOX)

Chemical Power

     C. Use ATP and NADPH (fuels) to drive the synthesis of Glucose from CO2 ( the calm sycle)

(C. is Light Independent and A &B are light dependent reactions) 

* Memorize - 6CO2 + 12 H2O ---light---- C6H206 + 6H2O + 6O2 

- Calvin cycle happens between inner and outer membrane.

Light- energy in the form of photons.

-Photons-tiny packets of energy

-Light energy is determined by wavelength-Distance between the crests or troughs.

-Nothing can travel faster than light.

Competitive Inhibition-occurs when an inhibiting molecule (poison) moves into the active site and blocks the substrate from entering

Adenosine triphosphate(ATP) is the main energy currency of the cell
-Each ATP molecue is composed of 3 parts
1. Adenine Triphosphate
2. Adenine disphate
3. Adenine mono-phosphate

Many reactions involve the passage of electrons from one atom/molecule to another
-Oxidation-is the loss of electrons and looses energy
-Reduction- is the gain of electrons and gains energy

Oxidation reduction reactions always take place together

PHOTOSYNTHESIS

Photosynthesis- process that captures and converts light energy into chemical energy in the form of glucose (carbohydrate)

It occurs in the:
-plasma membranes and some bacteria
-cells of algea
-leaves of plants

6CO2+12H2O--------light------>C6H1206+6H2O+6O2

Cuticle-clear waxy non-cellular layer-waterproofs
Epidermis-secretes cuticle
Palisade Mesophyll-Where most photosyntesis takes place
Spongy Mesophyll-Some Photosynthesis--gaps allow diffusion of CO2 in and O2
Vascular Bundle-Converts water up and sugar water down

CHLOROPLASTS
-double membrane system
-Granium=stack
-Grana=stacks
-Thylakoid= disk on stack-where light absorption happens
-Space between stacks=groma 
 
  

E. Factors that slow down Enzyme Activity

1. pH-there is an optimum pH for every enzyme; peak of the bell curve.  Moving away from that pH will slow down the activity gradually until it reaches 0.
2. Temperature- also has an optimum number for each enzyme. As temp. decreases activity decreases gradually; as temp. increases a point will be reached where the enzyme denatures and all activity will stop.

 F. Regulation of Enzyme Activity

1. Allosteric Enzymes- have 2 binding sites; 1, the active site, for the substrate & 2, the allosteric site, for regulatory chemical. 2 actions:
• Activation
• Enzyme will be inactive as long as its allosteric site is uninhabited
• When an activator molecule bonds to the allosteric site this changes the shape of the active site, making it "fit" the substrate. Result: Catalysis
• Repression
• an enzyme will remain active as long as its allosteric site is uninhabited
• Repressor molecule bonds to the allosteric site changing the active site and making it "not fit" the substrate. Result: Stops Catalysis

G. Enzyme Inhibition- 2 Ways

1. Allosteric Repression- Non-competitive inhibition- repressor molecule is not competing for the active site.
2. Competitive Inhibition-  another molecule similar in structure to the substrate bonds to the active site, not allowing the real substrate to come in and bond.

Energetics

How energy is transformed and utilized by the cell.

Energy: ability to do work

      Two states: Kinetic and Potential

I. Laws of Thermodynamics

 A. First Law- energy cannot be created or destroyed- it can only be converted from one form to another.

         Note: Most life relies on light energy being converted into a usable form.

Light >>> Glucose >>> ATP >>> Heat

 B. Second Law- Entropy Happens

         Death = Entropy

II. Enzymes- protein catalysts that lower the activation energy required for cellular chemical reactions.

        Enzymes neither add, nor subtract atoms from chemical reactions.

        Enzyme concentration does not change with the chemical reaction.

How can the rate of enzyme catalysis speed up?

   1. More enzyme

   2. More substrate

   3 Add energy

            a. heat

            b. kinetic- stir it

I. Exocytosis- vesicle, with cell product or waste, moves to the cell membrane and is "pushed out" of the cell.
J. Proton Pump- Pumps protons onto one side of a membrane creating a proton diffusional gradient.
K. ATP Synthase- This is how we generate ATP from glucose, pump the glucose through creating ATP. Uses light power or glucose power to generate ATP from the flow of protons back across a membrane.

VI. Other Membrane Proteins
A. Recognition Proteins (MHC marteors) - Allow the body's immune system to recognize cells as domestic.
B. Receptor Proteins- other free proteins bond to them and this illicit a series of chemical reactions inside the cell. Changing it. Protein hormones bond to these.

VII. Movement Inside the Cell-  A complex of proteins called:
A. Dyne actin Complex- bonds to a vesicle (with stored materials) and using ATP as fuel, it "walks" the vesicle along micro tubules in the cell to its destination.

C. Protein Channels- embedded proteins that are specific to certain atoms or molecules. Na+, Cl-, Ca2+. Many are "gated"

D. Endocytosis- Active movement of chemicals into the cell by:
      1. Phagocytosis- (Amoeba) When the cell envelops the solid materials, encloses it in a vacuole and digests it.
     2. Pinocytosis- Same as #1, but material engulfed is liquid.

E. Facillitated Diffusion- Passive movement of longer chemicals by bonding to a receptor protein on membrane surface and than the membrane folds around it.

F. Exocytosis- Active transport of chemicals out of the cell: usually membrane bound by the Golgi Apparatus.

G. Na+/K+ Pump (sodium/potassium pump)- Active transport of Na+ out of the cell and K+ into the cell.

Monday 9/17/2012

B. Osmosis

Stops:
   1. Isotonic
   2. Cell Bursts
   3. Pressure cancels Osmosis

Water Potential- The potential for H2O to move away from a source. Measured by the equation.
Ψ= Ψ_p + Ψπ
  Ψ=H2O Potential ( measured in Bars)
  Ψ_p=Pressure potential, is always zero or above (always +)
  Ψπ =  Osmotic Potential

Ψπ = -iCRT  (always 0 or negative)
    i= ionization constant (=1because we're working with sucrose) (never negative)
   C = Molar concentration of the solution (never negative)
   R = Pressure Constant (0.0831) (never negative)
   T = Temperature K  (Kelvin) (273+Celsius) can never be negative (never negative)

 Example:
 at time 0 in the cell.
Ψ= 0+ [-(1)(.6)(.08313)(293)
   = 0 + (-14.6)
  = -14.6
Ψ=[-(1)(.2)(.0831)(293)
  = -4.9
-4.9 wants to go into -14.6 until one of the stopping factors occurs.

 

Sept. 14, 2012

5. Movement into and out of cells. Remember, the cell membrane is a phospholipid bilayer.
     -What are the ways that substances can move into a cell?

     A. Diffusion - the idea that a substance moves from a high to a low concentration, or in other words, it moves down a concentration gradient. (So if you jump out of a tree, you will fall and hit the ground. Same thing like a cell.)
     - Examples:
          - O2, most cells needs oxygen.
          - CO2, requires no energy expenditure. (ATP) The greater the concentration difference the greater the force of diffusion.
     B. Osmosis - the diffusion of H2O. There are a couple of tricks to the diffusion of water. Water is polar, you can't just diffuse the membrane, so it diffuses through special H2O channels (proteins) called aquapurins. Do all cells have these? Yes. Water is absolute necessity for all cells.
     -H2O always moves from a low solute concentration (Hypotonic) to a high solute concentration (Hypertonic). Movement will stop when the two solutions are equal in concentration (Isotonic).
          - Scenario: Say you have a beaker of sugar solution. The sugar is a 1.0 molar sucrose. (To say the something is 1 mole, it's a mole per liter, so this is really sweet!) There is a cell in that solution. (the solution of sucrose is 0 mole) Can the sucrose move through the cell membrane? No, it's way to big to get through that membrane. What direction will the water move, into or out of? Water will move out of the cell. So then osmosis is backwards from a diffusion? False, we're talking about the diffusion of water. Water is at 100% concentration in that cell. Water is moving from a high water concentration to a low water concentration. When will the water movement stop? That's a trick question. It will never stop. The movement of water will only stop when the cell is completely dehydrated.

Edocytosis

A. Mitochondria- powerhouses of the cell

     1. Right Size- look like Bacilli: rod-shaped bacteria

     2. have their own DNA (circular-"plasmids")- Reproduce on their own

     3. Have a double membrane system. Cell being engulfed by a bigger cell causes an inner membrane from the "engulfed cell" and the outer membrane from the host cell. Inner membrane folds(drapes-curtains) like cristae in bacteria

    4. Ribosomes are similar to bacterial- make their own proteins

B. Chloroplasts- Photosynthesizesers in plants and algae(s).

     1. Right size- same as cyanobacteria: shape is similar

     2. have their own DNA

     3. Have a double membrane system- inner is similar to membrane system in cyanobacteria

     4. Ribosomes are similar to bacterial- make their own proteins

Cell Biology

I. The Cell Theory
     A. All organisms are composed of one, or more cells
     B. Cells are the smalles living things
     C. All cells come from previously existing cells (most contriversial)

II.Cell Size- cells are small. As volume increases, surface are does not keep up.

III. Types of Cells
     A. Prokaryotic- "Before the kernel"- Cells that have no nucleus nor do they have any membrane-bound organelles.
            - Archebacteria and Eubacteria. Evolved first. (3.5 billion years ago)
     B. Eukaryotic- "Now the Kernel"- cells with a nucleus and organelles. ex: animals, plants, fungi, protozoans, and algaes. (1.5 billion years ago)

IV. The Endosymbiotic Theory- complex cells (eukarotic) evolved from the endocytosis of other cells and subsequent cooperation between them.
          endocytosis- one cell taking in material or other cells
            certain cells "took in" other cells that had abilities to help the host cell and a symbiotic relationship developed. 2 organelles that "fit" this theory;

9/10/12

4. Nucleic Acids: 3
     a. DNA--Deoxyribonucleic Acid--genetic information
         Structure: Composed of subunits called nucleotides: PO4--Deoxyribose--Nitrogenous Base
                        1 phospate, 1 sugar, 1 base                     (P)        (S)              4 Bases: Adenine, Guanine,
                                                                                                                              Cytosine, & Thymine
                                                                                                    A & D are Purines (double rings)
                                                                                                   C & T Pyrinidines (single ring)

                                                                             OH in RNA
                                                                             H in DNA               (in the R-group coming off the sugar)
                           P                      P
                             \                  /
                            S--A... T--S
                           /                 /
                         P                 P
                         \                 /
                         S--G... A--S
                         /
                       P              So on so forth.
                        \
                       S--C

Chargaff's Rules: A Bonds to T always. G to C.
DNA is complimentary (one side compliments the other {A-T G-C})
Double Helix allows DNA to make exact replicates. Also allows for copying genetic information by RNA.
Allows for DNA repair.
DNA is anti-parallel. One side faces in the opposite direction to the other.


     b. RNA--Ribonucleic Acid. Same structure as DNA with the following exceptions:
                    i. Uracil replaces Thymine
                    ii. Ribose, not deoxyribose
                    iii. Single Strand, not double
      Function: Copies genes & translates that information into a protein.

A-T-G-C-A-T-G-G-G-A-T-G-C-C-A         DNA (gene)
U-A-C-G-U-A-C-C-C-U-A-C-G-G-U       mRNA (m=messenger)

Underlined part leaves nucleus of the cell & goes out into the cytoplasm where it anchors onto a ribosome. (amino acid)           (same shape as first)
     |             |          |             |           |
A-U-G C-A-U G-G-G  A-U-G C-C-A         tRNA
U-A-C-G-U-A-C-C-C-U-A-C-G-G-U         64 words in DNA


     c. ATP--Adenosine Tri-phospate--Our cell's energy currency

        Structure: PO4 bonds are High Energy Bonds.

                                                            Glucose
                                                           /
                                               <------
ATP<----------------------------------> ADP (di) + P
       \
        -------------> Heat

PROTEINS AND NUCLEIC ACIDS

Protein Structure continued:

Proteins have 4 levels of structure
....1) Primary - refers to the amino acid sequence or the chain of amino acids. No proteins function at this level.
...2) Secondary - when R-groups begin interacting forming Hydrogen Bonds.  Typical secondary structure would be the ALPHA HELIX - which is shaped like a spring (hair) and the BETA SHEET - like an interlocking mat (silk).  Some proteins function at this level.
...3) Tertiary - When R-group interactioons begin to form complex complex globular structures.  Most proteins (like enzymes) function at this level.
...4) Quaternary - This is when more than one polypeptide forms a single protein - it is multiglobular.  Hemoglobin has 4 Heme groups that can each carry an O2 molecule.  A few very complex proteins function at this level.

DENATURATION - Happens when heat and/or change in pH interferes with the R-group interactions and the protein reverts back toward its primary structure.  This will alter or destroy the protein's function.

4. NUCLEIC ACIDS - Chemicals that are found mostly in the nucleus of cells that have phosphate groups (PO4's) and Nitrogenous Bases.  3 Types:
....a. DNA - Deoxyribonucleic Acid - Contains the Genetic information.

Proteins

3. Proteins: we are proteins "Building blocks of life" (Polypeptide, not all polypeptides are proteins)
      a. Functions:
           i. Structure- Bone, Cartilage, Muscle, Hair, Nails, etc.
          ii. Carriers- Insulin (Glucose), Hemoglobin (O2)
          iii. Defense- Antibodies, etc.
          iv. Movement- Muscle Fribers (actin & myosin)
          v. Regulators- Hormones, Neurotransmitters,

          vi. Cell Membrane Proteins- I'on Channels, Aquaproins (H2O), Pumps.
        ***  vii. Catalysts- Enzymes : lower the activation energy of reactions
     b. Structure: composed of long chains( > or =100) of Amino Acids.
            Amino Acid Stucture: Our cells put the amino acids together by using Dehydration Synthesis
                                Uses a *Peptide Bond

*All Organisms are built from the same 20 Amino Acids.*
In humans, 10 of the 20, are Essential( - must be obtained in diet), the other 10 are Non- Essential (can be made by the cells). In Plants all are Non-Essential. (some exceptions)

Four Levels of Protein Structure:
 1. Primary Structure: the chain of Amino Acids. NO proteins funtion at this level.

 2. Secondary Structure: the hydrogen bonding between R-Groups. Some proteins will function at this level. Ex. Alpha Helix : Hair                                         Ex. Beta Sheet: Silk

                                                                                 

       

9/5/12 - Lipids

2. Lipids - Lightweight, High energy/Mass
    a. Triglycorides - Basic Fats. Storage Long-Term of Energy. Fats in our diet.

         Structure:              H  H  H
                                      |    |    |
                                 H-C-C-C-H       Glycerol
                                      |    |    |
                                   OH  OH  OH

                                       (Diagram of fatty acids)              }3 Fatty Acids that Break down from Dehydration Synthesis.

BAD----Saturated Fat: Full of Hydrogens
Good----Monounsaturated Fat: One double bond, can add more Hydrogens
GREAT----Polysaturated Fat:  Two double bonds, can add more Hydrogens

   Trans Fat  - Natural Fat that is Hydrogenated. Look for Partially Hydrogenated(on food labels)!!!!
                      
             H
              |
         H-C-H
              |
         H-C-H
              |
         H-C-H
              |
         H-C-H
              |
             H


     b. Steroids -- fat-derived hormones (People tend to think of Testosterone, Estrogen) also Cortisol (Cortizone) etc.
     c. Cholesterol -- long-term fuel storage
     d. Phospholipids -


             (Diagram)

Polar Hyrdrophilic- h20 loving
Non Hydrophobic- h20 hating

9/4/12

1. Carbohydrates
    a. Monosaccharides
    b. Oligosaccharides- short chains of monosaccharides
           -Sucrose: Glucose and Fructose molecules join and break off OH from glucose and H from fructose which = water (the bond forms and water breaks off)
           -This reaction is called dehydration synthesis (condensation): When and OH and and H group are removed from 2 monomers and this forms a polymer  
           -Hydrolysis: The chemical destruction of water in order to break chemical bons between the subunit of a polymer to form monomers. OH goes to 1 monomer, H gos to the other- when sucrose separates into glucose and fructose the H2O bond breads. (Also known as digestion, the reason you shouldn't eat when dehydrated)
           -Lactose: Milk Sugar=Glucose and Galactose
    c. Polysaccarides: long branching chains of glucose
              i. Glycogen: "Mid-term muscle fuel"-stored in the muscle and liver, first source to replace blood sugar.  Easily made from:
             ii. Starch: way that plants store glucose
             iii.Chitin (Kytin): structural carbohydrate- forms the exoskeletons of arthropods(insects, etc.)
             iv.Cellulose: forms the cell walls of plants(wood). Humans cannot break these bonds and get nutrition from cellulose.

2. Lipids: Composed of C, H, and ), but with far fewer oxygens that carbs.  This makes them lightweight and able to "carry" more energy/mass.  Purpose: long-term energy
-Lipids have much less oxygen, known as hydrocarbons because they are mostly hydrogen and carbon
-Oxygen is heavier than Hydrogen, making lipids much lighter than carbs.