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Q2 – Week 1 – 11/15 – 11/19

                                                                                                                                Jump to:  Tuesday,   Wednesday,  Thursday,  Friday                                                                                                                                   ___________________________________________________________

11/15 – Monday –  A Day 

Main focus –                                                                                                                                                          
a)  To review polar and Non-polar molecules.
a)  To identify H-Bonding (hydrophobic) and London Dispersion Forces (hydrophobic).
1.  Polar vs. Non- polar molecules- 
        a)   Polar molecular atractions – (H – bonds)  – HYDROPHILIC
        b)   Nonpolar attractions – (LDF’s) – HYDROPHOBIC 
        c)   proteins , carbohydrates, Lipid review
2. H – Bonding
3. London Dispersion Forces                                                                                                                                                                                      
Demo – 
    1.  – electrostatic streams of water
    2.  Like dissolves like – intermolecular attractions.
          a) Sweat and sharpie –
           b) acetone and Polystyrene
           c) starch and water. 

          d) Demonstrated the 2 bottles with 2 types of dyes.                                                                                                                                       

 4. Using the H-Bonding – Organic Molecule worksheet : Classwork

         H-Bonds – attractive forces.pdf
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attractive forces vs covalent bonds
R groups  – polar – H – bonding – Hydrophilic
                     polar – LDF’s –            Hydrophobic
                     Ionic  – ( ions attracting) – IONIC
                     Disulphide bridges   – cysteine (sulfur covalent bonds)                                                                                                            

Amino Acids worksheet 1718-New.pdf
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  Polarity animnation:


Class Notes:
Like dissolves Like” because the intermolecular attractions between molecules are similar.  
Hydrophilic (water loving) molecules prefer to ATTRACT molecules that are also like water.
 Water has strong INTER molecular attractions because it is polar.  The electron rich oxygen end is negative and the electron deficient end of hydrogen is positive.  Water will orientate itself correctly liquid or in the solid phase so that positives (H end) attract the negatives (oxygen).
These are not Bonds!! Bonds are intramolecular forces that are determined by valence electrons filling their outermost energy level. The only molecules that can GET into water must also have positive and negative ends to dissolve in water!

Notice the negative charges of water (RED = Oxygen) will attract the positive charges of water (white = hydrogen).  These are called H-Bonding and its the primary way polar molecules attract other polar molecules.

Water is polar and thus has positive and negative (poles).  Other molecules that are polar will also have positive and negative poles that water can attract to and mix into water.
                                 polar glucose ( C6H12O6) molecule                                          glucose dissolved in water
The diagram is illustrating the Hydrogen Bonding between the polar water and polar glucose molecules.  H – Bonding, is NOT a bond but an attractive force between polar molecules that have electron deficient hydrogens.
*Notice that the oxygen end of the water molecule is Attracted to the positive end of the Hydrogen that is BONDED to an atom that that has a large attraction for electrons.  The Hydrogen must be electron deficient in order for it to be positive. THAT means that is must be bonded to either F,O, or N to create this electron deficient hydrogen. 
These three element pull the shared electrons (electrons in the bond) AWAY from the hydrogen ENOUGH to make the Hydrogen positive enough so that it can ATTRACT to electron rich (negative end) of another polar molecule.
The reason elements F,O, or N create electron deficient Hydrogens is because they have the greatest electronegativity (attractions for electrons).  Here is a list of electronegativity values for some of the elements of the periodic table.
                                                                                                                                                                                                                                                                    Hmm.  Does this trend follow the atomic radii trend that we looked at last Wednesday??   YES!
Notice which elements have the greatest attraction for electrons (electronegativity). F , O, and N!
Also Notice that Hydrogen (2.20) and Carbon (2.55)  have electron configurations differences less than .40 and generally any difference in electronegativity less than .40 between 2 elements in a sharing bond (covalent) is considered “equal sharing’ and thus will not create electron rich or electron deficient areas of a molecule.  THIS MEANS THAT HYDROGENS THAT ARE BONDED TO CARBON ARE NOT ELECTRON DEFICIENT AND WILL NOT H-BOND!
Molecules that are not polar do not have Electron deficient Hydrogen and thus MUST attract each other by another method – LDF’s or non-polar attractions.                                                                                                        


H – Bonding (hydrophilic)- LDF – (hydrophobic) review: 



11/15 – Monday’s Homework: –

1) Review Test 2 and make three unique entries in the TEST 2 Forum and respond to three people in the forum.  Please use the key posted in Power School to review. Bring your questions tomorrow.

Origin of life 3a – amino acids.pdf
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                                                                                                                                                                                                          2) Please continue with the front of the worksheet that we ended with in class, Origin of life 3a – amino                     acids.pdf worksheet and 
            a) continue to add carbons (in the carbon backbone) or hydrogens
            b) label each amino acid as either polar (hydrophilic) or non-polar (hydrophobic)
                                                                                water loving                   water fearing
             c) on the back of this same worksheet there is a molecular diagram of a small protein            
                (polypeptide) that causes discomfort to people who have Celiac Disease.
The HLA genes known to increase susceptibility to celiac disease are called HLA-DQA1 and HLA-DQB1. These genes provide directions for making proteins used by the immune system. They belong to a family of genes called the human leukocyte antigen (HLA) complex, which helps the immune system distinguish between proteins that belong in the body from those made by foreign invaders such as viruses and bacteria. The proteins made by these 2 genes attach to each other to form bigger proteins called heterodimers, which attach to proteins outside cells and help the body decide if they are foreign.[2] The heterodimers respond differently depending on the versions (alleles) of the HLA-DQA1 and HLA-DQB1 genes a person has.
The bottom line is that people who are more susceptible to having celiac disease have genes (code in the DNA that codes for specific amino acids) that make proteins (polypeptides) that help the bodies immune system (white blood cells) determine if the protein structures coming off cells surface belong to us or are viruses or bacteria.  Our immune system works by recognizing proteins that are similar or dissimilar.  
Remember when we talked about blood types?  If you are type B blood you have a certain protein on top of your blood cell that makes it a B type.  If you give type B blood to a person who is type A, that person with type A will have its immune system attack that blood and cause coagulation or clotting (due to antibodies which are also proteins)in the blood stream to immobilize the foreign invader.  This leads to certain death to the individual.
Okay so celiac disease is due to proteins being made that make white blood cells incorrectly recognize GLUTEN as a foreign invader in the stomach.  Gluten is protein found in many grains like wheat that help give it structure and this is sticky.  Gluten because it sticks to the intestinal lining of the gut will cause OUR OWN WHITE BLOOD CELLS TO ATTACK OUR OWN CELLS IN OUR digestive system.  When our own body attacks our own cells it is called an autoimmune disease. 
Polypeptides are long chain proteins made of amino acids bonding together in a certain way.
Please watch the video below and then please do the following on the GLUTEN diagram:
                     1) Please label all carbons and add Hydrogen as you did on the first side
                     2) Identify the peptide bonds
                     3) identify the amino acids in this polypeptide.
                                You will need the first side of your worksheet to help.                                                                                 
                     4) Draw the correct water molecules that were produced in making this                                                                              polypeptide (amino acids boding to each other).
                     5) Complete form below!


 Dehydration Synthesis –  monomers become polymers (polypeptides)

 5: Polar and NON- polar Form:

End of MondaY….


11/16 – Tuesday –  B Day – 

Main focus –                                                                                                                                                          
a) To simulate and model dehydration synthesis by building a primary polypeptide structure from amino acids.
                                                                                                                                                                                                           1.  Protein activity start-   We will build a primary chain of a polypeptide of at least 30 amino acids per lab group. Make sure you add the H on one of Carbons to correct a printing Mistake.                                                                                                                                                                                                                                                                                                                                                             a) Cut out individual amino acid from your colored sheets (each team will have a different colar)                                                     b) Remove the water (dehydration synthesis) and make peptide bonds between the amino acid chains.                                           c) Tape the H and -OH together to make water molecules.


11/16 – Tuesday’s Homework: –

                                                                                                                                                                                                                                  No homework tonight!


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11/17 – Wednesday –  A Day – 

Main focus –                                                                                                                                                       
a)  To review some basic properties of proteins and their structures. 
     Please complete the following questions from chapter 5 of the text. If you want a textbook please grab one. They are located to the left of the refrigerator underneath the microscopes.  You may work together and you will have 3 graded submissions to this form. Please return the textbooks when you are done.

 The Protein Classwork Form:

End of Wednesday..


11/17 – Wednesday’s Homework: –

                                                                                                                                                                                                                                  1. If you did not complete today’s classwork’s form please finish for homework.



11/18 – Thursday – B Day

Main focus –   
a)  To identify the different types of R groups and their attractive forces through the protein building activity.
1  Protein Lab Activity –  linking the amino acids in peptide bonds
    A) complete primary protein structure with R groups
    B) Label the amino acid using abbreviation from worksheet.
    C) Highlight the hydrophobic R groups.
Amino acid activity double sided p.pdf
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11/18 – Thursday’s Homework: –


1:  Use the form below and the text book to answer the questions 1 – 10: Text page 86, concept 5.5 : 

2:  Then watch the complete video below and then complete question 11 and 12 :

YOU WILL ONLY HAVE ONE RESPONSE FOR THIS FORM and it will not be on auto-reply.

 DNA – The Secret of photo 51 –  

Text page 86, concept 5.5 : 

End of Thursday..


11/18 – Friday –  A Day – 

Main focus –                                                                                                                                                       
a)  To write a protein amino acid primary sequence of your model
b)  To Fold your protein model based the type and availability of your R groups in your               model.
c)  To observe a secondary protein structure.                                                                                           
    1)  Review the Origin presentation slides (16 – 22) to view how proteins are made – preview the genetics                                                                                                                                                                                                                                                                    2) Protein Lab Activity –  linking the amino acids in peptide bonds
    A) complete primary protein structure with R groups
    B) Label the amino acid primary chain using abbreviation from worksheet.
    C) Highlight the hydrophobic R groups and hydrophobic R groups
    D) Fold your protein into a tertiary structure based on the following rules:
             a) Link the hydrophobic R groups first deep inside your protein
             b) LInk your Ionic R – groups next
             c) Link your cysteines into the disulphide bridges
             d) LInk your Hydrophilics on the outside of the protein.      

     E) Write the amino acid primary sequence.                                                                                                                                                   F) Write the triplet codon for the protein.                                                                                                              

Origin of life Presentation: 

Protein Folding video – how proteins take their 3-D shape.

 Last Years Folded protein time lapse –  

Folded protein on molecular level –  


11/12 – Friday’s Homework: –

1. Please make one more submission to Thursday nights  form – DNA and its discovery

2.  Please complete the Form below with your textbook.  I expect complete answers that are fully  

 End of week 1!