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Q1 – Week 11 – 11/8 – 11/12

                                                                                                                                Jump to:  Tuesday,   Wednesday,  Thursday,  Friday                                                                                                                                   ___________________________________________________________

11/8 – Monday –  A Day 

Main focus –                                                                                                                                                          
a)  Review of Stanley Miller, RNA world Hypothesis and Origin of life
a)  Test 2 begins

1.    Stanley Miller Review:

Origin of life 1 – Stanley Miller RAT.pdf.                                                                                                        View Download

2.    RNA Hypothesis Review:

Origin of life 2 – RNA World Hypothesis RAT.pdf                                                                                          View Download

3.  Origin of Life form review:

Origin of life Presentation: 


11/1 – Monday’s Homework: –

1)  Study for test 2.


Here is the Key to The Hardy Weinberg form form Sunday night.



11/9 – Tuesday –  B Day – 

Main focus –                                                                                                                                                          
a) To Continue with Test 2 – Part 2
                                                                                                                                                                                                             Test 2 continues!!!!                                                     


11/9 – Tuesday’s Homework: –

                                                                                                                                                                                                                                    We left off in class before test 2 going back in time discussing the origin of life, the age of the planet, and Stanley Miller’s Experiment that tested to see if life can begin from the basic compounds that the early earth had.  Although he was not successful in creating life in his laboratory he was able to see that organic (life based) compounds could be made. So no life was created but molecules or compounds that support life were made!

Can you guess where we are headed?

 Yes we are headed in the direction of the details that support life exactly how hereditary actual works in the atomic level. We are going to study how alleles are delivered to offspring by looking at the biochemistry and the genetics that supports evolution and the chromosomal line of inheritance. 
The first day should connect to the last day!
In order to understand the microscopic details of hereditary we need to study chemistry or biochemistry.
What we will be doing is studying the basics of chemistry in order to work towards understanding 
           1) how amino acids make proteins
            2) How different amino acids create different proteins that will function differently
            3) What is DNA, RNA and their roles in coding for alleles (amino acids —> proteins)
            4) How Chromosomes (DNA) actually replicates in the S1 phase of the growth cycle of a cell.
 This introductory lectures are made to gain a basic understanding of the patterns that occur in nature in terms of atoms that are in proteins, amino acids, and DNA (etc).    
1.  Please watch the lecture below and add notes to your blank periodic table. It will be important for you to also look          at a real periodic table of elements while you do this.
2.  Then watch the lecture below it with Elvira.
3.   Complete the Form below and yes you will have 3 submissions to the form.                                                                                
       Blank periodic table with Reference Periodic Table 1213.pdf
       View Download


1: Periodic Table and Trends screencast lecture:

2: Classroom Periodic Table lecture with Elvira (the outermost electron):

 3: Acid base intro Lesson Form

End of Tuesday..


11/10 – Wednesday –  A Day – 

Main focus –                                                                                                                                                       
a)  To identify Metals, Non-metals and their differences in Electronegativity.
b)  To identify the stable elctron configurations, covalent bonds, ionic bonds, and write 
       lewis structures for molecular compounds (organic compounds)..                                                
1. Complete Origin of Life slides up to amino acids.
2. Elvira the Outer most Electron/homework review.
3.  Lewis dot Diagrams of organic molecules
Valence electrons/covalent bonds/stability – organic molecule
Amino acid structure – R groups, different Amino acid differ by R groups
Peptide bond basics – water leaves (dehydration synthesis) and the N and C bond maintaining proper stability.                                             We drew an amino acid and made lewis structure by using valence electrons to determine the number of bonds per molecule.                 
Polar molecule vs. Non- polar molecule. (we did not get to this in class)
Classwork – 
Large Organic Molecules Lewis Structures.pdf
View Download
Covalent ditto 1 -Electron Dot Diagrams worksheet.pdf
View Download


Amino Acids worksheet 1718-New.pdf
View Download



Origin of life Presentation: 


11/10 – Wednesday’s Homework: –

1. Please watch the lecture (below the form) and with the Covalent ditto 1 -Electron Dot Diagrams worksheet I gave out today.
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
View Download
Covalent ditto 1 -Electron Dot Diagrams key p.pdf
View Download


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.
4. Complete Polar vs, Nonpolar Molecules Form.

1: Lewis Structures of Covalent molecules lecture without Elvira (the outermost electron 🙁

 2: Polar and NON- polar Form:

End of Wednesday..


11/11 – Thursday – Veterans Day – OFF – enjoy!



11/12 – Friday –  B Day – 

Main focus –                                                                                                                                                       
a)  To review the monomers of proteins and carbohydrates
b)  To review the concepts of Lewis Dot diagrams and identify polar and non-polar                        molecules                                                                                                                                                                
1.  Amino Acid Structure – using electron dot diagrams
2.  Polar vs. Non- polar molecules- 
        a)   Polar molecular atractions – (H – bonds)  – HYDROPHILIC
        b)   Nonpolar attractions – (LDF’s) – HYDROPHOBIC
3. Resubmit form from last night,                                                                                                                                                                           
4. 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.
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.                                                                                                        

 Today’s Demo – acetone has non-polar characteristics that can dissolve other non-polar                                     molecules. (non-polar likes non-polar)


11/12 – Friday’s Homework: –

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
View Download


2:  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.
3:  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 ION R group from one                                                                amino acid will attract positive charged ION R groups from another amino acids.)
                                                 (+) ION —– (-) ION is a IONIC ATTRACTION!
4: Complete the protein packet and review with the key – do your best here and I will review.  I do have video (Optional video below ) that reviews parts of the packet. WATCH THIS VIDEO FIRST! SO I guess it is not optional!                                             
Origin of life 3 – Protein form and function.pdf
View Download
Use this to name you amino acids in the above packet:
Amino acid activity double sided p.pdf
View Download

1: Disulphide video – cysteine amino acid making covalent bonds

2: Disulphide video –cysteine amino acid making covalent bonds

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

4: Origin of Life 3 review – I review a little of the packet for you.