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Q2 – Week 1 – 19-20

week 1

Week of 11/5- 11/9

11/4 – Monday – period 7,8 
TEST 2 – It will count for the 1st quarter!!!
11/4 – Monday – Homework:
1.  Complete the take-home portion of the test.
End of Monday..

11/5 – Tuesday – period 7 – Academic Study Hall
1. Complete Test 2 – Take home due
                                period 8 – 

1. Review origin of life presentation through Amino acids
2.  Periodic table formation, Elements, Periodic trends, atomic radii
Large Organic Molecules Lewis Structures.pdf
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11/5 – Tuesday Homework:
1.  BioChemistry – 
Please watch both lectures on Covalent Bonds (1st one only the 1st 10 minutes).
and then watch the second one with the Covalent ditto 1 -Electron Dot Diagrams worksheet we worked with today in class. (backside).
I mention R – groups from Amino Acids. these are parts of the amino acids that can be polar or non- polar.  

So these molecules are amino acids! They are what the DNA codes for and when you connect these amino acids you get a protein!

The R groups are the part of the amino acid that is in green and these can be polar and non- polar!

Covalent ditto 1 -Electron Dot Diagrams worksheet.pdf
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Covalent ditto 1 -Electron Dot Diagrams key p.pdf
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2.  Complete the entire worksheet (write the Lewis dot structure) and label each molecule as either polar or non- polar.
3. Review with the key above.
Lecture on covalent bonds:


Lecture for Covalent ditto 1 -Electron Dot Diagrams worksheet:
End of Tuesday..

11/6 – Wednesday  – Period 7.8 
1. Test 2 – Review
2. Continue Biochemistry with Lewis Dot Diagrams
Large Organic Molecules Lewis Structures.pdf
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3.  Polar vs. Non- polar molecules- 
        a)   Polar molecular atractions – (H – bonds)  – HYDROPHILIC
        b)   Nonpolar attractions – (LDF’s) – HYDROPHOBIC
4.  Amino Acid Structure – using electron dot diagrams
5. Complete Polar vs, Nonpolar Molecules Form.

Polar vs. Nonpolar Molecules 1920

End of Wednesday…

11/7 – Thursday – period 7 – academic study hall

                                period 8
1) Amino acid worksheet – Classwork!
Origin of life 3a – amino acids.pdf
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Essential, Nonessential,  Conditionally Essential
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)

“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!
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 week??   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.
Using the H-Bonding – Organic Molecule worksheet : Classwork
H-Bonds – attractive forces.pdf
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1:  Polar molecular atractions – (H – bonds)  – HYDROPHILIC
2: Nonpolar attractions – (LDF’s) – HYDROPHOBIC
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.

Intermolecular Attractions AP

Origin of life

11/7 – Thursday – Homework
Origin of life 3a – amino acids.pdf
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1. Please make one more submission to last nights form if you need it.
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 from 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!
The bonding between amino acids is is called dehydration synthesis or condensation and it creates a peptide bond and water!
Complete the form below based on all of this above:

Amino Acid Organic Analysis 1920

End of Thursday..

11/8 – Friday – period 7,8 
1. Review Homework Forms- 
2.  Complete demos – 

Today’s polarity demo:

3.  attractive forces – 

Intermolecular Attractions AP

Origin of life

4:  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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11/8 – Friday – weekend homework – 
There are 3 assignments for this weekend!
Please do them in the correct order!
1) Make another submission to last nights form!
2) Amino Acid worksheet and Form:
3) Protein packet with videos
Amino Acid worksheet
1. Please complete the Amino Acids worksheet 1718-New.pdf worksheet and follow along with me using the video below.
Amino Acids worksheet 1718-New.pdf
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2.  Read the entire section from the reading link below, and using the information from the video that helped you with the Amino Acids worksheet 1718-New.pdf  complete the form below.


Weekend’s Form:

Protein Concept Form 1920

Protein Packet assignment:
1:  Watch the disulphide video.
This represents the a covalent bond between R groups that have a S (sulfur).  This is the final type of way that proteins (R groups) can attach to themselves and fold into their “active” shape.
2:  Watch the protein folding video.
*Notice the primary structure, secondary, tertiary, and quaternary structure that proteins can have by attracting themselves by R groups attracting or bonding(cysteine – disulphide bonds) with other R groups.
* 3 ways that amino acids can attract each other:
                A) polar attractions (H – bonds)
                B) Nonpolar attractions (LDF’s)
                C) Ionic attractions (some R groups have charges and thus a negative charge R group from one amino  
                                                       acid will attract positive charged R groups from another amino acids.)
    *1 way they bond between  R groups
                A) Disulfide bridges         
3: Complete the protein packet and review with the key – do your best here and I will review.  I do have video below that reviews parts of the packet.
Origin of life 3 – Protein form and function.pdf
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Origin of Life 3 – protein key p.pdf
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Video 1:  

Video 2:
Optional video on Mr. Grodski reviewing a little bit of the packet.
Optional video of Extra help session explaining H-Bonding:
End of week 1…