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Q2 – Week 2 – 19-20

week 2

Week of 11/11 – 11/15

11/11 – Monday – Veterans Day – OFF

11/12 –  Tuesday – period 7 – Academic Study Hall
                                – period 8 – 
1: Collect Protein packet – last week
2. Protein folding activity continues!
11/12 – Tuesday’s night Homework:
1:  Use the form below and the text book to answer the questions 1 – 10:
2:  Then watch the complete video below and then complete question 11 and 12 :
Secret of Photo 51:
Text page 86, concept 5.5 : 

DNA and its Discovery 19/20

End of Tuesday!

11/13 – Wednesday – period 7,8 Lab!
1) Form Review HW:
2) Protein Folding activity
11/13 – Wednesday Homework:  
1.  Please complete the Form below with your textbook.  I expect complete answers that are fully developed.
2.  You will have a RAT Quiz in Thursday based on the Tuesday’s and Wednesday’s HW.

DNA 2 – early experiments 19/20

Origin of Life Presentation for Class discussion:

Origin of life

Cold Spring Harbor- X-ray crystallography of DNA:

End of Wednesday!

11/14 – Thursday – period 7  – Academic Study Hall
1. Finish folding your proteins
                                    period 8 –
1. DNA activity begin
DNA is another example of a polymer because it is made up of repeating nucleic acids.
Remember that proteins are also polymers because they are made up repeating amino acids.
Each individual nucleic acid bonds to other nucleic acids by removing water to make a phosphodiester bond that links the phosphate group to the sugar. An H is removed from the phosphate and and OH is removed from the sugar and thus a water is removed. This is another example of dehydration synthesis!
Now we have 2 nucleic acid, RNA and DNA.  They only differ by they type of sugar in the nucleic acid AND they use the nitrogenous base uricil instead of thymine.
Given the differences between ribose found in RNA and deoxyribose in DNA what nucleic acid was being synthesized above?
Here is the Codon Chart that represents the nucleic acid code for all amino acid.
11/14 – Thursday Homework – 
1.  Please watch my video below that will complete the slide that we were working on today.  Please work with with me to finish the slide that we were working in class with. I will give you instructions on how to complete your homework from the sheets that I gave out today in the video as well.
Please take a look at my screenshot that I did after you guys left today. All I did was number the carbon in the deoxyribose (sugar). We always count starting from the Carbon next to the Oxygen.
Also notice that I bonded the third nucleotide by creating a phosphodiester bond that links 3 Carbon (on the sugar) to the phosphate of another nucleotide. I used white boxes to take out the 2 hydrogens and 1 oxygen (that becomes water in another example of dehydration synthesis).
Please add this to your presentation before you begin viewing the video.


2.  Please correctly cutout, tape a double stranded DNA molecule that correctly codes for the first 2 amino acids in your protein that you folded last week. It must be anti-parallel!  You will need a total of 12 nucleotides that will make a 6 nucleotide code from 5′ to 3′.
A) Make sure that you create phosphodiester bonds by cutting out 2 H’s and 1 O atom (removing  
      water) to link nucleotides AT THE 3rd Carbon.  
B) Make sure you mark with dots the correct H-Bonding that occurs between nucleotides.
C) Make sure you put a A,T,C,or G inside the nitrogenous base of each nucleotide.
D) Make sure you label each of the four ends with 5′ or 3′ ending!
E) Make sure that your DNA correctly codes for your amino acid sequence from the 5′ to the 3′          direction.
F) Put your name on your DNA!
IF you need more nucleotides!
nucleotide 1920.pdf
View Download
It will be collected and graded.
I have posted each lab’s groups primary amino acid sequence ( the first 2 amino acids from the 
N terminus from your protein that was constructed.
Purple Group: Asn – Leu
Yellow Group:  Cys-Leu
Green Group: Cys – Cys
Peach Group: Phe – Ser
Blue Group: Tyr – Ser
End of Thursday..

DNA Activity Instructions:

1: Title Page, with your name: slide page 1

2: 1st Notes page:
General Label Nucleotide: nucleotide, sugar, phosphate and nitrogenous base on slide page 2
3. 2nd Notes pagePyrimidines, Purines, Name of the nucleotides based on nitrogenous bases on slide page 3
4: 2nd Notes page with small DNA fragment(6 nucleotides total with 3 on each complimentary strand):
Illustrate and label:  phosphodiester bonds, identified all nucleotides (Adenine, Thymine, Guanine, Cytosine),
On slide 4                          5′ or 3′ direction of DNA fragment, correct H-Bonds with dots between the nucleotide  
                                             pairs,  Make sure your nucleotide pairs are correct and your orientation of your  
                                             complimentary strands.
Write the DNA’s fragment code for both strands:   example:   5′ ATA 3′
                                                                                                                               3′ TAT 5′
Part 2 : 3D DNA model building.
5:  Take a photo of the 4 nucleotides of the model kit of your color and
Label: nucleotide name, Purines, Pyrimidines and place carbons, Nitrogens and oxygens on top of the models
On slide 5   
6.  Take a photo of the Sugar Phosphate backbone and 
Identify and label:  the phosphate, and deoxyribose (sugar).  
On slide 6   
Number the carbons on the sugar.
7.  Build the SAME 6 nucleotide DNA segment that you created in step 4 above.
8.  Take a Photo of the DNA segment and label the image with arrows and labels with the same list from step 3.
On slide 7   
9. Connect your segment with others in your group or class to create a very large DNA segment.  
      a) Take a photo and label the direction on a new slide On slide 8 
      b) and Write the DNA Code for both strands on the slide
10.  Make sure you have Titled every page.

11/15 – Friday – period 7/8 – *Ordered  Sordaria Firmcola from Wards to arrive Next wed.



1:  DNA activity – with Google Presentation file I shared with everyone.
2. Connections with Evolution, mitosis, meiosis with DNA
      and auto immune disorder of celiac, AIDS (HIV virus), fever, denaturing
3. Instability of wrong base pairing = mutations
4. DNA Races!

11/15 – Friday – Homework (2 parts)

1.  Please the double stranded DNA of the following code:
                                                                5′ CTGCAT 3′
                                                                3′ GACGTA 5″
Please make these perfect and I will award everyone who completes this DNA completely will earn a 100 in place of a lower quiz grade. Because we are taking this home I expect more than if we did this as a race in class.
Please follow the following  requirements:
A) Make sure that you create phosphodiester bonds by cutting out 2 H’s and 1 O atom (removing  
      water) to link nucleotides AT THE 3rd Carbon.  
B) Make sure you mark with dots the correct H-Bonding that occurs between nucleotides.
C) Make sure you put a A,T,C,or G inside the nitrogenous base of each nucleotide.
D) Make sure you label each of the four ends with 5′ or 3′ ending!
E) Make sure that your DNA correctly codes for your amino acid sequence from the 5′ to the 3′          direction.
F) Put your name on your DNA!
2: Brine Shrimp Lab write-up complete!
This is a simpler Lab than the lab 2 write-up in that we have only one independent variable, the swimmers who represents hatching viability.
There is a shared google sheet that has the data.
You need to make a data table with error bars!! 
We also adjusted the % hatching viability to the number of swimmers, if you remember.
Brine Shrimp Lab requirements – 
If I get to your lab with comments you have a guide.
  If not read the conclusion rubric below.
Conclusion:  This section will be heavily scrutinized. YOU NEED 3 PARTS.
    1. FROM YOUR DATA, determine whether the hypothesis was supported or not supported!  Your hypothesis is never wrong!!! You need to explain in detail why you believe your hypothesis was not supported.  This is not a one word or one sentence response.  It requires you to think!!!  Think of the data that is obvious but also think hard about what the data may be implying.  Error bars should be part of the discussion, and a description that you are using +/- 2 SEM.  Error bars are helpful in our discussion but they are not the end of the story. Even if the error bars overlap there may still be some “possible” trend.  You need something to sink your teeth into.  There is always something that you can imply from the data.  Think of a prosecuting attorney.  You are building your case or arguments for or against your Hypothesis.
    2. MAKE A LEAP from your DATA.  What does the data imply or suggest about the Biology of the Brine Shrimp?  Do not get lost in the sauce. What was the major purpose of the lab?  What was you question that you tested with your hypothesis?  That question is what you are trying to answer based on the data!  Make a leap from numbers (data) and try to logically describe what this means in term of the living organism. You cannot be wrong here unless you use poor logic.  This area is conjecture and IT MAY NOT BE TRUE and that is why OTHER experiments are needed to test these ideas.  Experiments in the future will measure your ideas.  I am asking you to fully develop your ideas regarding how the data reflects the Brine Shrimps biology.  This takes thought!
    3. Write and error analysis.  Discuss the limitations of this experiment.  Every experiment has limitations as these limitations will affect our outcome by some margin.  Most experiments test one dependent variable against the independent variable by controlling other dependent variables.  What was the control and did we control the other variables that COULD affect the Hatching viability besides Saline percentages?  Fully develop your ideas on how these limitations may have affected you results. DO not just list the possible error but describe how these errors or limitation could have skewed our data.  DO NOT INCLUDE HUMAN ERROR.
General Comments:
If you get vague you will lose points. You must fully develop your points and support them with logic! Remember that many experiments are built from the conclusions of other labs.  This means your points in your discussion will not be facts but just very good possible explanations.  Another experiment would be needed to test the validity of these statements. However,  if you support your statements with solid logic from evidence collected in the lab then you are addressing all the possible implications from YOUR WORK or experiment.  In this point of your conclusion you will be MAKING A LEAP from your work based on data analysis to a POSSIBLE implication BIOLOGICALLY for the Brine Shrimp.  If you do this by tying the Background discussion with your discussion here it will result in very will impressive lab write – up! 



Please make sure your conclusion covers three basics:
            A:  DATA analysis:  complete detailed analysis of the the hard data collected.
                      This has nothing to do with error analysis!!! You should be taking into consideration the                      error bars that you have created in your graph.  The error bars tell us something about                          the reliability of the data.  Also we are NOT proving a hypothesis correct or wrong. The   
                     data “suggests” or there is a possibility..
            B:   A LEAP:  You need to explain what the data means in terms of the biology of the organism. The data    
                        suggests that the Brine Shrimp ……. This really the reason for the investigation.  Fully develop your  
                        thoughts based on your evidence.  Be logical and make your case as if you were a lawyer trying to  
                        convince a jury of your argument.
             C:  Error Analysis:  What are the possible limitations in your lab.  Every experiment has limitations. What    
                       were the limitations in this experiment. What could be done to narrow our approach to better the 
                        questions you laid out in this lab.
* DO NOT MAKE comments that are not logical and are not supported by the evidence.  This is an area of conjecture and speculation so it cannot be wrong unless you do not fully develop your thoughts and support your statements with sound logic.