Tuesday, April 14, 2015

Teaching Resources

Earth Systems Science Modules Index

Understanding Science: How It Works

PDF:Dispelling the Myths of Science

Applications in Instructional Planning and Presentation in Science

Student Blog Post.

Review the Deseret News article from March 30, 2015 entitled: The morality of parents playing God with their baby's DNA

Questions to guide student learning:

·         (1) Would you, as a parent want to know if your child is going to be born with a genetic disease?

·         (2) Do you think knowing your baby’s DNA could cause discrimination to choose a different phenotype (looking child)—i.e. choosing blue eyes and blonde hair over brown eyes and brown hair.

·         (3) Over time, if PGD allows us to choose what our children look like, how will the population demographics change? 

·         (4) If population demographics change, would different races cease to exist?  Is this discrimination?

·         (5) Do you think PGD is ethical?  As a politician/public policy maker, do you approve or disapprove of PGD testing?  What constraints should the government enact to control PGD?

Monday, March 2, 2015

Muscle Contraction




Chloroplasts: Site where it occurs in Eukaryotes.

Thylakoid Membrane: Where the light reaction occurs

Granum: Stack of Thykaloids

Stroma: liquid in chloroplasts between Thykaloids where the Calvin Cycle occurs.

  1. Light Reactions: In Thylakoid membrane.  Water & light produce NADPH, ATP & 02 (waste).
  2. Calvin Cycle (a.k.a. Dark Reactions): In the Stroma.  Energy transfers where CO2 enters and Glucose comes out.
Essentially, PSII, Cyt B6f and PSI take electrons from light and put it through an electron transport chain.  (Protons are pumped into the inside of the Thylakoid called the Lumen).  ATP Synthase finishes the proton pumping process to make ATP.  Then ATP leaves and goes in the Stroma to the Calvin Cycle.  Waste Product: O2

Calvin Cycle: 5C molecule RUBP combines with CO2 through the leaf stromata, breaks into 2 3C molecules.  ATP adds energy in G3P to make useable sugars (sucrose, glucose, fructose and etc).

Problem: Photorespiration: occurs when we do not have enough CO2.  O2 jumps in and uses RuBisCo and makes junk (bad in all C3 plants).

Hot environments, CAM plants (pineapple)--only open stomata at night to avoid water loss.  Store CO2 in malic acid & enters the Calvin Cycle as they need it.  Stomatas can be closed during the day.  C4 (i.e corn) plants make 4C Oxalate which then moves to the bundle sheath cells, introduce CO2 to enter the Calvin Cycle.  Don't have to wait for CO2 to fuse in.

Cellular Respiration


Respiration: Breaks down food to make ATP or energy in the Mitochondria.  Requires oxygen.

Bacteria use their outer membrane.

Aerobic Respiration: Respiration  in the presence of Oxygen

Anaerobic Respiration: (Turbo button) Respiration without Oxygen and leaves lactic acid (pain).

Heterotrophs (Animals, Fungi): convert organic compounds (food) in the presence of Oxygen to create ATP (energy) & Carbon Dioxide (CO2).

Autotrophs (Plants, Algae): Converts Carbon Dioxide to Oxygen

  1. GLYCOLYSIS: (In cytoplasm) Glucose (6c) converted to Pyruvate (two 3C & 2ATP &NADH)
    1. Pyruvate diffuses into the Mitochondria where it is converted to acetyl CoA (2 C molecule to enter Krebs Cycle & gives off CO2).
  2. KREBS CYCLE: AcetyleCoA gives of 2 ATO & CO2.  Adds energy to NADH and FADH2. 
  3. ELECTRON TRANSPORT CHAIN: NADH and FADH2 transfer eletrons to this series of proteins to pump protons to the inner membrane space.  By products are combined here to produce water.  Produces 32 to 34 ATP in this last step.  ATP Synthase (in this ETC) : as every proton goes through, it converts ADP to ATP.
Anaerobic Problem: In Glycolysis, protons are given to NAD+  to make NADH  and uses up all the NAD+ so glycolysis breaks down and stops.


Lactic Acid Fermentation: Glycolysis goes to form Pyruvate and then Lactate (which makes more NAD+ to recycle NADH).   This what builds up the toxin lactic acid.  O2 will remove it eventually.

Alcoholic Fermentation works the same, and makes Ethyl alcohol instead of Lactate.



Enzymes: chemicals that speed up a reaction but are not consumed.  (It is a chemical catalyst that reduces the activation energy needed to start the reaction.)

Catalase: A protein enzyme that breaks down hydrogen peroxide in Eukaryokes.

Active Site: The part of the enzyme where substrates go into to let the reaction go.  (The hole in the key hole of the door).

Substrate: (The key to open the door of reaction).

Activation: Cofactors (inorganic i.e. Heme group {iron} in blood) & Coenzymes (organic, thymine/Vitamin B1--or other vitamins).

Inhibition: Competitive and Allosteric

Activation: adding something to an enzyme to make it work, or turned on by DNA regulation


Friday, February 27, 2015

Osmosis and Diffusion


Diffusion: movement of a chemical from high concentration to low concentration against a gradient. (energized by kinetic energy of particles bouncing around to get equilibrium)
  • solvent: higher concentration of a chemical in a mixture (called a "solution") (more of)
  • solute: lower concentrated chemical in a mixture (It has been "dissolved" into the solvent. (less of)

Osmosis: solvent is water because it is polar (and only works in water).  Concentrations of chemical will move to get equilibrium (how cells work in attracting water).
  • In osmosis, the solute chemical is too large to leave the membrane (container) and blocks the solvent from escaping
  • Water can go in and out so it is "semi-permeable".
  • Net effect: more water goes in.  Solute goes from hypotonic to hypertonic-why it goes against the gradient.

Hypertonic solutions: higher in concentration of the solute than the  solution

Hypotonic solutions: lower in concentration of a solvent

Chemical goes from hypertonic solution to the hypotonic solution

Tour of the Cell


Prokaryote-no nucleus, Bacteria and Archaebacteria
·         No Nucleus-free floating DNA
·         Cell Membrane
·         Cytosol
·         Ribosomes
Eukaryote-animals, plants, fungus, protists (much larger)
·         Organelles including:
·         Cytoskeleton: structure inside the cell (works like a bridge)-microtubules (compressional support) and microfilaments (tensional support)
·         Nucleus (contains DNA and controls cells, makes proteins and enzymes) & Nucleolus (within nucleus, holds the chromosomes that make ribosomes only & where ribosomes are synthesized)
·         Ribosome (mrNA goes through then tRNA comes and builds proteins on it)
·         Mitochondria-generate energy (ATP); endosymbiotic theory (have own DNA & binary fission)
·         Cell Membrane
·         Cytosol-fluid with solutes
·         Lysosome-digestive enzymes that will break down vesicles or if it pops can kill the cell itself “apoptosis” (suicide)
·         Centrioles: positioning in cell, including positions nucleus & roles in cell division (forms division)
·         Cytoplasm
·         Secretory Vesicle (membrane bound container that moves material i.e. vacuole)
·         Rough Endoplasmic reticulum)-membrane continuous with the nucleus. Rough have mRNA to make proteins & produces membranes.
·         Smooth Endoplasmic reticulum:  produces lipids, cholesterol & detoxification
·         Flagellum
·         Vacuole-large are in plants only; stores water & maintains turgor pressure (cell pressure)
·         Golgi Body:  where proteins are modified (shipping/sorting part of cell)
How things go in and out of cells:
·         Diffusion
·         Osmosis

Nucleic Acids DNA and RNA


DNA-directions that make our genes and tell how to make proteins
RNA-shuttles/worker to make Proteins in ribosome
Nucleotides: building blocks of DNA and RNA.  3 parts
1.       Phosphate group
2.       Pentose sugar (5 carbon)
3.       Nitrogenous base (contains nitrogen)
·         Adenine, Guanine (Purines)
·         Cytosine, Thymine (Pyrimidines)
·         In RNA, it is Uracil not Thymine.
·         Done via. dehydration reaction to form covalent bonds.
·         Hydrogen bonds form between Adenine and Thymine; and Cytosine and Guanine.
DNA is a more stable structure as it is two copies going reverse paired from one another.  RNA is simply one copy opened up through DNA replication.
·         DNA backbone is basically a sugar-phosphate-sugar-phosphate alternating base.
Video game  or simulation of this science:  Build section of RNA (and build it and see how it does).



  • Triglyccerides: 3 fatty acid tails (stores energy in body)
  • Lipases: enzymes that break down triglycerides into energy
  • Phospholipids: cell membrane-two fatty acid tails with a head and a negatively charged phosphate group.  (Tails are uncharged).  These form spheres or “Micelles”.  All cells are phospholipid bi-layers.
  • Cholesterol: maintains fluidity of cell membranes.  It holds fatty-acid tails of phospholipids.  It maintains integrity of cell membranes by inter-locking and over-lapping the phospholipid tails.
  • Hydrocarbons: give energy on the carbon tail of the triglyceride (stuff that burns)
  • Glycerold head and fatty-acid tail
  • Saturated: Hydrogen on the outside-straight line hydrocarbon tail.  Solid at room temperature (worst fat for us).
  • Unsatruated-double bonds between carbons eliminate hydrogen and creates kinks.  Liquid at room temperature.

Why water is required for life to exist.



Water is polar: Oxygen holds its Hydrogen bonds strongly (covalent bond) so much that it polarizes it towards the oxygen (oxygen is highly “electronegative”).
As a molecule whole, Hydrogens are + and O2 are – so a second bond forms between the molecules allowing ice to float—a new lattice.  It also creates a high heat capacity (holds heat) allowing for thermoregulation and a conduit for metabolism to occur.  It dissolves materials as well.  Water is a good solvent because it is polar (having a + and – side on the molecule).  It breaks solutes (NaCl) into its parts.




Covalent Bonds:

Hydrogen Bonds:

Ionic Bonds:




Simulations from the University of Colorado: