GENETICS VOCABULARY

 

GENE – A location on a chromosome that codes for a general trait (protein).  Example:  Plant Height Gene

 

ALLELES – Different forms of the same gene.  Examples:  A and a.

 

PHENOTYPE – The physical appearance of an organism due to its genetics.  Examples: Tall and Dwarf.  PHENOTYPIC RATIO: 3:1 Tall:Dwarf

 

GENOTYPE – The genetic combination of alleles in an individual.  GENOTYPIC RATIO: 1:2:1  AA: Aa: aa.  3 Basic Genotypes:

1. HOMOZYGOUS DOMINANT – both alleles are dominant – AA

2. HOMOZYGOUS RECESSIVE – both alleles are recessive – aa

3. HETEROZYGOUS – the alleles are different from one another - Aa

Thursday 11/21/13 Gregor Mendel and Monohybrid Crosses

Gregor Mendel- (1850's) Often called "Father of Genetics" Austrian monk, Worked with pea plants. (Plant pass down genes in the same way that animals, so this worked out.) Identified seven traits within pea plants to work with.

• Flower color, position, plant height, pod color, pod shape, pea color and seed shape

I. The Monohybrid Cross- cross between parents that have different characteristics for 1 trait.

_______________________________________________________________________________
Parental (P)              True-breeding Tall(M)    x    True-breeding dwarf(F)  (Truebred is like purebred)

1st Filial (F1)                                             All Tall

2nd Filial (F2)                                        Tall : Dwarf
(Inbreeding of F1's)                                    3 : 1 ratio
_________________________________________________________________________________

Key:                               P       Male plant (TT)      x       Female plant (tt)    

T = Tall plant                             Sperm ~~(T)                         Egg (t)
t = Dwarf plant
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
                                     F1      Male offspring (Tt)    x    Female offspring (Tt)
- - - - - - - - - - - - - - - - - - - - - - -- - - - - - - - - - - - - - - - - - - - - - -- - - - - - - - - - - - - - - - -
                                     F2                  Punnet Square

Genetics

I. Probability

Product Rule- The probability of 2 or more independent events occurring together is the product of those events.

Take the odds of each event and multiply them together, this will give you your probability

Sum Rule- When there are more than one combination of ways to get an event, the probability is the sum of those combinations.

Meiosis - 2 divisions that result in 4 haploid cells (sperm/egg cells).

I.   The 9 phases of Meiosis.
        
      A. Interphase - DNA is duplicated
         
      B. Prophase I - Chromosomes appear; the nuclear envelope breaks down.
          The chromosomes form tetrads;  two homologous chromosomes
          connected.
                       - In the tetrad, Crossing-Over takes place.  Random bits of
                         information are exchanged between the two homologous         
                         chromosomes. This accounts for the genetic-variability in
                         Gametes.

      C. Metaphase I - Tetrads line up at equator.

      D. Anaphase I - Homologues split apart from 1 another and move toward 
         the poles.

      E. Telophase I - Cytokinesis.  Cell divides into 2 intermediate cells.  This is
           a know as Reduction Division.
                          -Reduction Division has its name because the chromatids 
                           remain together. This means that the amount of genetic
                           information in each of the new cells is significantly reduced.

                    
      F. Prophase II - DNA doesn't replicate again, and no tetrads form
          therefore no cross-over occurs.



      G. Metaphase II - Chromatid Pairs line up at the equators.

      H. Anaphase II - Chromatids split apart and move toward the poles.

       I. Telophase II - Cytokinesis divides the 2 cells into 4 unique haploid 
         cells.

5. Cancer- There are 2 types  of Genes that, if mutated, can potentially lead to cancer:
     A. Proto-Oncogene- encode for proteins that, when ready, stimulate cell division. If mutated, they are Oncogenes- automatically signal cell division.
     B. Tumor Suppressor Gene- encode proteins that inhibit cell division. Cell will continue onto the Cell Cycle w/o inhibition if these genes are mutated

P53- is a tumor suppressor gene that 1) either repairs the DNA to allow the Cell Cycle to continue, or 2) triggers PCD if DNA is irrepairable.

Meiosis- Cell Division that results in the formation of 4 genetically unique haploid cells (sperm and egg).

1. 2 Divisions and 9 Phases 
    A. Interphase- Includes the G1, S, and G2 Phases and their checkpoints. Same as Mitosis.
DNA Replication: S-phase









Homologues- have the same genes, but not necessarily the same alleles.
Chromatids- 2 exact copies of DNA.

IV. Controlling the Cell Cycle- 3 "checkpoints"
    A. G1 Checkpoint- at end. Is it ready to replicate the DNA?
    B. G2 Checkpoint- at end. Had the DNA replicated correctly?
    DNA polynerases (enzymes) assess and repair "damage" to DNA.
    C. M Checkpoint- Had the DNA separated correctly? If yes, Cytokinesis finishes the process; if no, the cell/s will undergo a programed cell death.
V. Cancer and the Cell Cycle- an uncontrolled growth of cells is a cancerous tumor. 2 types:
    A. Benign- Encapsulated- contained within a membrane. Most can be surgically removed.
    B. Malignant- Non-encapsulated- invasive- can spread into ANY part of the body- Metastis- when the malignancy spreads to another tissue or organ.
    C. Mutations in 2 types of genes are dangerous in term of Cancer.
        1. Proto-oncogene- Code for proteins that simulate cell division. Activated, or not, at the G1 Checkpoint. If mutated they might become Oncogenes- Automatically be activated no matter what. (Bad)
        2. Tumor-suppressor Genes- Inhibit cell division
          P53- Monitors the integrity of DNA. If the protein is damaged, the protein stops cell division and stimulated repair. Will simulate PCD (programed cell death) if the damage is beyond repair. (Good if it isn't mutated)

11/6 Cell Division cont.

(Chapters 9-10)

II. Mitosis- Cyclic (never stops). The Cell Cycle:
    A. G1 Phase- ("1st growth") Cell elongates and becomes "normal" size.
    B. S Phase- ("Synthesis" of DNA) DNA is replicated in this phase.
    C. G2 Phase- ("2nd growth") Organelles are "doubled."
    (Collectively these three phases are called Interphase)
    D. M Phase- ("Mitosis") When the cell undergoes division.
    E. C Phase- ("Cytokinesis") When the cell/s re-form membranes and other cytoskeletal structures. This starts in the M Phase. Cell divides completely here.

III. M-Phase
    A. Interphase (G1, S, G2)- DNA replicates here but this process is invisible, because the DNA is in the form of Chromatin- DNA is "uncondensed" and not wrapped around histames. The DNA is going from 46 pieces to 92 pieces of DNA.
    B. Prophase- DNA condenses around its histomes and forms Chromosomes (visible). In chromosomes, two identical pieces of DNA called Chromatids, are joined by a small bead called a Centromere. The Nuclear membrane breaks down and the Chromatid pieces spread randomly through the cell. 2 Centrioles break from the Centrosome and move to the poles of the cell.
    C. Metaphase- Chromatid pairs line up at the equator of the cell, and spindle fibers (made from microfiliments) develop from the centrioles and attach to them.
    D. Anaphase- Chromatin pairs separate and are pulled apart by the spindle and begin moving towards the poles.
    E. Telophase- Chromosomes reach the poles and Cytokinesis begins (the actual division of the cell)

Cell Division

1. 3 Types:
    A.Binary Fission- happens in prokaryotes. Simple, cell divides and Circular DNA is copied.
    B. Mitosis- happens in eukaryotes. Cyclic. Happens in Somatic Cells (Non-gamete producers). Used for growth and repair of tissue. Result: 2 identical Diploid (23 Pairs=46 Total, in Humans) daughter cells that are genetically identical to the parent cell.
    C. Meiosis- eukaryotic. Not Cyclic. Happens in gamete producing cells. Used for reproduction. Result: 4 unique Haploid (1 of each of 23 Chromosomes) daughter cells that have 1/2 the information of the parent cell.

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

VI. Properties of Cell Membranes
    E) Other processes that move substances through the cell membrane.
            1. Facilitated diffusion- Carrier protein will bond to a molecule that would normally not be able to pass through the membrane. The act of bonding facilitates its transport across the membrane. Goes with the force of diffusion, because of this, it is passive.

 
         2. Coupled Transport- One molecule moves with its concentration gradient through a protein called a transport channel and this "force" will move another molecule into the cell against its concentration gradient.
Example: Insulin and Glucose.
        
  




        3. Endocytosis- When the cell engulfs materials and moves them into a cell in a vacuole or vesicle.
               a) Phagocytosis- Surrounding and engulfing particulate material and digesting it.
               b) Pinocytosis- Same as Phagocytosis but the material is a liquid.
               c) Receptor Mediated Endocytosis- Particles bond to specific receptor sites in a pit on the cells surface and this initiates the formation if a vesicle that moves into the cell.
     
         4. Exocytosis- Materials moving out of the cell enclosed in a vacuole or vesicle.

Diffusion, Osmosis & Cell Membrane

V. Diffusion & Osmosis
Example 2
-Solution 0.4 M sugar
-Cell 1.0 M sugar
Water goes into the cell by osmosis

When will water movement stop (net) ?
1. when concentrations solutes are equal (Isotonic);
2. when cell would bursts;
3. when the cell fills enough to create a positive pressure that cancels out the force of Osmosis. (Pressure cancels Osmosis) - This is called Turgor Pressure

VI. The properties of the cell membrane ( The fluid mosaic model ) 

Composed of phospholipids, cholesterol (structural) and proteins (functional)

Functional Proteins:

 A. Channels :

1. Aquaporins (dedicated of movement of water)
2. Ion channels (devoted to Na+, Cl-, Ca2+, K+, etc.)

B. Carriers - Could be either active or passive. One molecule could be carried against the force of diffusion (ATP must be burned) or with the force of diffusion

C. Markers - Identify the cell as your own and also identify it as the type of cell

D. Pumps :

1. Proton Pump - pumps H ions to 1 side of the membrane , creating a proton gradient that is used by ATP (synthase to make ATP)
2. Sodium-Potassium Pump - uses ATP to pump Na+ out of the cell (neurons) and K+ ions back into the cell. Uses the energy from ATP to cause the protein to change its tertiary structure

11. Central Vacuole: large storage vesicle in a plant cell (lipid storage)
       Note: There are other types of vacuoles, like contactile is some protists
12. Chloroplasts: where photosynthesis happens
       -Double membrane

C. Outside the Cytoplasm
1. Cell Wall: (not in animals) rigid structure made of glucose (cellulose in plants, chitin in fungi)
       -This gives the cell rigidity
2. Cell Membrane: phospholipid bilayer (also some cholesterol and many functional proteins)
       -Fluid Mosaic Model: the ability of the membrane to be selectively permeable
       -Selectively Permeable:
                    a. What can move freely though? = Non-polar, neutrally charged (not an ion), and small
                                  Examples: O2, CO2, NH3
                    b. What can't? = Polar, Ionic, or Big

V.  Diffusion and Osmosis: Passive Processes- No ATP is "burned" here
       A. Diffusion: the passive movement of a substance from a high concentration to a low concentration.
                -Force is determined by the difference between the high and low concentrations
                Example: (find a friend with the picture)
                         #1                                  #2
                     Higher O2                    Lower O2
                       Couch                         Marathon
                             *O2 would have a higher force to #2, O2 would have a lower force to #1
       B. Osmosis:  the passive movement of water (H2O) from a low solute concentration across a 
      membrane to a high solute concentration  
                - Movement stops when the 2 concentrations are equal 
                Example: (find a friend with the picture)
               0.4 M Cell <--------> 0.4 M Sugar
                *"Isotonic": Net movement of a solution is zero
               0.4 M Cell ------>1.0 M Sugar
                *Hypotonic and Hypertonic 
               1.0 M Cell <------0 .4="" m="" nbsp="" span="">
                *Water goes into cell





        

friday notes

we watched the you tubes video. a tour of the cells bozeman.

B. cytoplasm,
       1.ribosomes, where the proteins are made in a cell. not where the information is found, the RNA that run through it and it make the proteins
       2.vesicle, it is the storage unit in the cell, it can have water,  fat, or other thing in it. also anything needed to be transported out of the cell. 
       3. rough ER. endoplasmic reticulum. it has ribosomes on it, where most ribosomes are found, also where most proteins are made in also make vesicles. make membranes in cells.
       4. Golgi, is an extension of the ER, it is a shipping part of the cell, it tells where to move the thing around the cell or out of the cell.
       5. Cytoskeleton, they are the structure of the cell. three different function, structure, movement, and to provide a rail system inside the cell. it is composed of two different type of structure, micro tuberculin, micro filaments.
       6. smooth ER, make carbohydrates and lipids, it is your detox unit of your cells. if you drink, or a alcoholic you will have more of this.
      7. mitochondria, it generates energy in the form of ATP. it has a double membranes that pumps the protons, and kind of dams it up, and uses the protons to get the power like a hydroelectric plant. they have there own DNA
      8. vacuole, found mostly in plant cells. only in plant cells are they really big, and stores water and help keep shape.
      9. Cytosol, kind of the same thing as cytoplasm. it is the fluid in a cell.
      10. Lysosome, it is a digestion place, it open thing from incoming things, it also breaks down cellular wast. it also destroys the cell.

Cells- September 17 & 18, 2013

Cells-Units of organisms
I. The Cell Theory
   A. All organisms are made of cells
   B.Cells are the smallest living unit
   C.Cells only arise from existing cells
II. Why are Cells Small?
    As volume increases in a cell, surface area also increases, but, it does not keep up with volume
     If volume increases 100x, then surface area increases 10x
    Cells need to move outside nutrients in through the cell membrane
    The smaller a cell is, the more efficient it is moving materials into (nutrients) and out (waste) of the cell
III. 2 Basic types of Cells
    A. Prokaryotic- "before the kernal," kernal meaning nucleus. Have no nucleus, nor do they have organelles - internal,   membrane-bond structure. Do have internal membranes. Two kingdoms: Bacteria & Archea. Earliest of these on the planet 3.5 billion years ago.
    B. Eukaryotic- "the nucleus now" Have a nucleus, and organelles. Four kingdoms: Animalia (organ systems are unique to this kingdom, along with the ability to move on your own from place to place, and they are multi-cellular), Plantae, Fungi, Protista.
IV. Structure of a Eukaryotic Cell
    A. Nucleus- "Control Center" Surrounded by a selectively permeable membrane (made of phospholipids, which repel polar substances, and substances with a charge)

1. Nucleolus- Makes nucleotides (Phosphate-Sugar-Base)
2. DNA- 46 strands in every human cell, called Chromosomes (when it is condensed, "visible", and wrapped around proteins called histones) or Chromoatin (uncondensed, "invisible")

*test Monday*

Nucleic Acids
    A. DNA
4 Bases:
A-Adenine
T-Thymine
G-Guamine
C-Cytosine

Pairing Rules:
A always pairs with T
G always pairs with C
 

Backbone is made of:
P= Phosphate (PO4)
S=Sugar (Deoxyribose)

Nucleotide= 1 P, 1 S, and 1 Base

Each pair is bonded with a hydrogen bond
( ex. Adenine is bonded to Thymine)

It's a weak bond because when genes are read they need to be "unzipped" or pulled apart


    B. RNA- Ribonucleic Acid-transcribes genes in DNA and then translate them into a protein. 
3 differences from DNA:
1. Single Stranded
2. Ribose Sugar
3. Another base called Uracil (U) replaces Thymine (T)




Uracil has a much shorter life than Thymine
You can make more RNA, but you can't make more DNA

    C. ATP-Adenosine Triphosphate-"Energy Currency."
Really good energy compound

P-P-P
          \
            S-A


ATP--> ADP + P
releases heat

1 Glucose yields 36 ATP on average


 

Thursday, September 12 Notes

III. Protein
      A. Stucture
            4 Quaternary-(few)-Multiglobular
                              Hemoglobin-carries Oxygen through our bodies

Denature- breaking the bonds that hold a protein in its 3-D structure. This destroys the proteins function. Heat and pH will do this.

*A protein's function is based completely on its 3-D structure* 
       
       B. Functions
            1. Structure- Hair, Muscle, Bone, Cartilage
            2. Pigment- Melanin
            3. Carriers- Insulin, Hemoglobin
            4. Defense- Antibodies
            5. Contraction- Muscle
      ***6. Enzymes- Catalyze every chemical reaction in an organism. They are exclusive (meaning that every different chemical reaction has a different enzyme).

Catalyze-speeds up chemical reactions by decreasing the level of energy required for the reaction to take place (activation energy)

IV. Nucleic Acids- Made in the Nucleus.
     A. DNA- Deoxyribonucleic Acid- Genetic information.
Gene= Recipe for a protein.
                                 

C. Phospholipids: form the cell membrane for ALL cells, water cannot pass through the membrane but can pass through channels in the cell.

     III.  Proteins: building blocks of life. Long chains of Amino Acids. There are 20 different amino acids in organisms.  All living things are made of the same amino acids, just in different order.
         A. 4 levels of Protein structure:
             1. Chain of Amino Acids-Primary structure (1^0) long chains  of amino acids are non-functional.
             2. Hydrogen Bonding will now cause the chain to begin to "fold up" on itself - 1 and or 2 distinct structural configurations occur:
                 a. Alpha Helix ex: hair                       b. Beta Sheet ex: silk
                                                   

        

Some proteins function at this level- All are structural proteins. Secondary Structure (2^0)

                  3. Interactions between R-groups form the Tertiary Structure (3^0) Globular  This shape determines the function of the protein, change it and the function changes.Most proteins function at this level. Some proteins are multi-globular. - 2 or more polypeptides.

Lipids Continued

4. Trans-fat- partially hydrogenated fat, man made fat, breaks down the carbon bonds and sends hydrogen into the fat to bond with the carbon atoms aka hydrogenated fat

           stacks very easily increases risk of heart disease

           

other lipids

    a. steroid hormones- testosterone, estrogen, cortisol

    b. chlorophyll - green pigment in plants

    c. phospholipids- what our cell membranes are mostly composed of
                polar head- hydrophilic-h2o loving

                non-polar tails-hydrophobic-h2o hating

Final Paper - Due Oct. 7

1. Original w/ rubric attached ( Add title page if necessary)

2. Do the experiment

3. Write up

         A. results- 3 things

                   Table

                    Graph 

                   Paragraph - Point out important data

              explain table and graph

         B. Conclusion/ Results- was the hypothesis supported if yes how so? explain speculate what went right, Why?

              if no, why? what went wrong? why?

LIPIDS - CONTINUED

Lipids have much more Carbon than Oxygen and because of that, they are: 
* Lightweight - Oxygen weighs 16 amu's whereas Carbon weighs 12 and Hydrogen only 1.
* Higher Energy Level - 1 gram of lipid has almost twice the number of calories as 1 gram of Carbohydrate

This is a significant adaptation because organisms use Lipids as long-term energy and they are the last energy compound to come out of storage.  So their light weight and high energy yield allows us to survive better and longer.

STRUCTURE OF A TRIGLYCERIDE (most common form of fat)

So, notice that the head (Glycerol) has a chain of 3 Carbons and more closely resembles a sugar while the 3 tails (fatty acids) have very little Oxygen and this is why they're lightweight.  This is a SATURATED FAT because there are no double bonds in the carbon chains of the fatty acids.  MONOUNSATURATED FATS - have one double bond in the chain (missing 2 hydrogens) and POLYUNSATURATED FATS - have 2 or more double bonds and have even less Hydrogens.  The more hydrogens the "straighter" the molecule and so they "stack" in your arteries more easily causing cardiovascular disease.

Ap Biology Notes

9/5



Reversing Hydrolysis
When water is being taken out of a Polymer:  It's called Dehydration Synthesis or Condensation
Condensation
 Reaction- When an OH and an H are stripped off of 2 Monomers to form a Dimer (Polymer). After this process you get H20 as a byproduct.

2. Lactose = Glucose - Galactose
       Water is then used to break up the bond between the two sugars, which then gives you another Glucose as the product of the reaction.                                         
                                                        Glucose- Galactose -------> Glucose
                                                                    ^
                                                                  H20
C. Polysaccharides - Long chains of Glucose
                   1. Starch - the way that plants store glucose before the winter. (almost all plants use starch to store glucose except for Annuals)  ( Starch can be easily converted to glycogen my our body)
                   2.  Glycogen - The way that animals store glucose.  It is stored in our muscles and  Liver. "Muscle Fuel"  Midterm Energy
                   3. Cellulose - Forms the cell walls of plants- this is what gives then their rigidity---WOOD

II  Lipids - Generally serve as long-term fuel storage compounds.  They are composed of Carbon, Hydrogen, and Oxygen (but very few Oxygen atoms)
Jonas Johnson

September 4th

Chapter Four Macromolecules of Life

I. Carbohydrates -Sugars  *Carbo -consists of Carbon *hydrate -water *CH2O.
   Ratio of 1 carbon to 2 Hydrogen to 1 Oxygen.
   Quick Energy + Mid-term energy compounds (not longest energy burst)
A. Monosaccharides  -single sugars. Glucose, Dextrose, Galactose, Fructose, Ribose, etc...
           Glucose -Blood sugar
              *Product of Photosynthesis Transported into cells/storage by Insulin         C6H12O6

Basic function is Quick Energy and they are easily converted into ATP, or are stored in ions as branching chains
B. Disaccharides -Pair of sugars
         and Olgosaccharides -2-4 monosaccharides in a chain.

1. Sucrose -Glucose bonded to Fructose. Table sugar. @room temp glucose & fructose are gels, but sucrose is a sold @ room temp.

Hydrolysis is shown by an arrow pointing up.
 Hydrolysis- *hydro-H20  *lysis-chemical Destruction
-Destroying a H2O in order to break a bond between 2 monomers. Main reaction in Digestion The water breaks the bonds in Sucrose

September 3rd

VI. H2O
  D. Stores Heat - allows organisms to maintain heat more efficiently.
  E. High heat of Vaporization - allows for evaporative cooling. (sweat)
  F. H2O is most dense at 4 degrees Celcius (frozen water is less dense than liquid water)
      -Spring Ice-off is very important for the ecosystem in a lake, it causes turnover which brings nutrients up from the bottom and jump-starts food chains. This also happens in the fall.
  G. pH - proportion of H+ ions to OH- ions in a solution.
       H2O ionizes: H2O=H+ + OH-
       Pure H2O   H+ = OH-    pH 7 is Neutral
       Pure H2O + HCl     H+ > OH-    pH < 7 to 0 - Acidic
       Pure H2O + NaOH     H+ < OH-    pH > 7 to 14 - Basic or Alkaline
       Caustic - because the pH is not 7 (neutral), either (+) or (-) ions will be pulled from a substance (a nail, as an example) and it will dissolve. Going in either direction from 7 (a neutral pH) is equally caustic.
       Buffers - any chemicals that bond to either H+ or OH- that neutralize pH.

Biochemistry 8/30/13

Properties of Water

• Adhesive (Sticks to itself)
• This is why water beads up
• Due to water's polarity

• Cohesive (Sticks to Other Polar Things)
• Think of Water soaking into a towel
• Once again, due to water's polarity

• The Best Solvent
• The polarity of each water molecule makes it the universal solvent
• Water dissolves polar things very well

In a solution, the dissolving substance is called a solvent and the dissolved substance is called a solute

Solute + Solvent = Solution
Kool Aid (solute) + H2O (solvent)  = Liquid Kool Aid

 

When a solvent is dissolving a solute it is hoping to achieve saturation.

Saturation - When "all" hydrogen bonds are formed between solvent and solute

Super Saturation - When ALL hydrogen bonds are formed between solvent and solute AFTER heat,     agitation and pressure are added. (heat, pressure and agitation increase saturation and speed it up)

Things don't really like to be super saturated, this is why when you open up a can of soda, it will go flat after some time.

• Heat Storage
• Retains heat well
• Keeps humans warm
• Keeps us from cooling down too fast

• High Head of Evaporation
• Allows for evaporative cooling

Most warm blooded organisms use a technique to cool themselves down called evaprotive cooling (Sweat)

Sweat doesn't cool you down by itself. Evaporation does. Your body takes a significant amount of heat to evaporate the sweat and so it cools down.

• Ice
• Water expands when it freezes (Less dense when solid)
• Water is most dense at 4 degrees C (39.2 degrees F)

5. bonds-
   b. covalent 
       1. non-polar- O2: H-H O=O,  N2: N=N, NH3: H    H, CH4: H    H
                                                                                    N                  C
                                                                                    H               H    H
 * cant find good pictures of the diagrams, ask somebody you sit by if they can show you the diagrams.
Life's building blocks-
Hydrogen chain (H)- one single bond
Oxygen (O)- O= 1 double bond,  -O- 2 single bonds          -
Nitrogen (N)- N -= 1 triple bond, -N= 1 double, 1 single, -N- 3 single      -
Carbon (C)- -C-=1 triple 1 single, =C= 2 double -C= 1 double 2 singles -C - 4 singles
                                                                                                                  -
      2. Polar Covalent Bonds- electrons are shared unequally
    H2O     (-)
             ee--ee
            (    O  )      Na+    Cl-
            ee--ee           C. Hydrogen- weak bond that forms between 2 polar molecules
           (          )
             H    H
                (+) 
6. Properties of H2O- H2O is polar and because of the it (is):
        A. Cohesive- sticks to itself ( helps overcome gravity)
        B. Adhesive- sticks to other polar substances.