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Q2 – Week 3 – 11/22 – 11/23

                                                                                                                              Jump to:  Tuesday,   Wednesday,  Thursday,  Friday                                                                                                                                   ___________________________________________________________

11/29 – Monday –  B Day

Main focus –   
*Ordered  Sordaria Firmcola from Wards to arrive this Friday                                                                                                                                                      
a)  To identify all the components of 3 dimensional DNA from our 2 dimensional cutouts.
       
b)  To measure the biomass from Lab 2.
1: Lab 2    Gather Biomass data – 
                                 
 a) We will cut our plants from the second generation and count how many plants we have per group and place in the oven to dry. This data will be added to out lab 2.
                                                                                                                                                                              
 2.  DNA RACES – make a 3 segment DNA with the code:
                                                                                                                5′ TGT 3′
                                                                                                                3′ ACA 5″                                                 
                                                                                                                                                                         
 3: Part 1 – DNA Activity   We may start part 2
Everyone needs to have a completed 6 nucleotide fragment that codes for 2 of your first 2 amino acids in your protein you folded last week.
   
        a) Reviewed important structural aspects of DNA
        b) Students makes 2 dimensional cutouts of 6 nucleotides.
        c) Labeled Nucleotides, Direction, and code on the cutout that student keeps as notes.
 
You should now have slides 1 – 4 completed of the presentation – The guidelines are posted below.

                                                                              

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

  

 Building a nucleotide fragment –  Mr. Grodski and the DNA cutouts!

Origin of life Presentation: 

___________________

11/29 – Monday’s Homework: –

1.  Please use Chapter 15 to complete the following Form on Linked Genes.
2. If you have not already done so please complete the DNA molecules that codes correctly for the first 2 amino acids in your folded protein from your protein activity. We completed this in class Last Tuesday:
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′.  Use the codon chart below to identify your code.
 
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
 1: Linked Genes – Non-Mendelian Form:

End of Monday….

 

_______________________________________________________________________________________________________________________

11/30 – Tuesday –  A Day – 

Main focus –                                                                                                                                                          
a)  To identify all the components of 3 dimensional DNA from our 2 dimensional cutouts.       
b)  To assemble. the double helix structure of DNA.                                                                                             
c)  To identify sex linked characteristics and why it is not Mendelian genetics.
 
1: Thomas Hunt Drosophila Experiment (#1) – Sex- linked!
 
What was important about this experiment was that is was the 1st time that an allele was associated on a particular chromosome (the X chromosome).  It was the 1st evidence of the chromosomal line of inheritance and although it used parts of Mendelian genetics (dominant and recessive alleles) it also demonstrated that the Law of Independent assortment was not always the case. THERE ARE SCENARIOS where alleles travel on the same chromosome!  This is not rare as we have 30,0000 genes in our human DNA and only 23 different chromosomes!
Most genes are linked.  Mendel was lucky to pick alleles on pea plants that were not linked so that he could establish the Punnet Squares and the laws of probability that result from unlinked alleles. 
 

 image from Khan Academy

2: We will continue with the DNA Google Slide Activity:

You should now have slides 1 – 4 completed of the presentation – The guidelines are posted below.

                                                                              

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 – we are picking up from this point today
 
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

   

This will be graded as Lab grade.

                                                                                                                                                                     

  _____________________

11/30 – Tuesday’s Homework: –

                                                                       

1:  Watch the lecture on the Pedigree Diagrams and take notes using the Pedigree Diagram Notes 1718.pdf worksheet that I gave you in class or posted below.  If you cannot  print then just do so with a piece of paper.
 
Pedigree Diagram Notes 1718.pdf
View Download
                                                                                                                                                                                                         2:  Complete the Pedigree autosomal and linked.pdf worksheet and review with the key.
      
Pedigree autosomal and linked.pdf
View Download
 
Pedigree autosomal and linked key p .pdf
View Download
 
3: Complete the Pedigree Diagram Form below:
You will have 3 submissions to this form.

 

 1. AP Biology Pedigree Diagram Lecture

 
3: Pedigree Diagram Form 21 – 22

End of Tuesday….

 

_____________________________________________________________________________________________________________________

12/1 – Wednesday –  B Day 

Main focus –                                                                                                                                                          
a)  To identify all the components of 3 dimensional DNA from our 2 dimensional cutouts.       
b)  To assemble. the double helix structure of DNA.                                                                                            
       
1: 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

Some images that might help:

sugar phaosphate backbone:

                             

A 4 segment DNA molecule:                                                                                                                             

Today’s Class Lesson:

1.  Types of pedigree’s –  
                                                A) autosomal recessive –  sickle cell anemia, Tay Sachs, types of hemophilia
 
                                                B) autosomal dominant – Huntington’s disease
 
                                                C) X – linked recessive – color blindness, Duchenne muscular dystrophy
 
                                                D) X- Linked dominant –  Rett syndrome
 
                                                E) Y – linked  –  Y – chromosome infertility
From Wikipedia:
Tay–Sachs disease is caused by a genetic mutation in the HEXA gene on chromosome 15, which codes for a subunit of the hexosaminidase enzyme known as hexosaminidase A.  It is inherited from a person’s parents in an autosomal recessive manner. The mutation disrupts the activity of the enzyme, which results in the buildup of the molecule GM2 ganglioside within cells, leading to toxicity.[1] Diagnosis may be supported by measuring the blood hexosaminidase A level or genetic testing. Tay–Sachs disease is a type of GM2 gangliosidosis and sphingolipidosis.
 
From Grodskipedia:   
Chromosomes (coiled up DNA) segregating in anaphase into gametes in meiosis is the mechanism that these pedigree diagrams are based on.  There is a 50 – 50 chance that you get the allele from the chromosome recessive or dominant that causes the disorder.
 
The disorder results from the cells of an organism not being able to to its normal functions BECAUSE its proteins are NOT being coded for properly due to a mutation in the nitrogenous bases of the DNA.  These proteins will have the WRONG amino sequence due to the WRONG DNA code that results from mutation.  These proteins have different 3 dimensional shapes due to different R – groups on the Wrong amino acids that result from the mutated code.  These proteins with a different shape or form will no longer have the same function which results in all of the disorder patterns or pedigree diagrams above.
 
Where do these mutation originate from?

 Look at the chromosomes!

WHY IS THIS DIAGRAM INACCURATE?

When are the chromosomes duplicated?

When do these mutations that lead to
disorders occur?

  Do individuals that have the disorders
discussed develop a  mutation? Why or
why not?

     

 
 DNA Replication: Note taking!!!
 
2. Whiteboard activity – Draw the replication fork in DNA Replication
    aIdentify and label the template strands with 5′ and 3 ‘ ends. 
    b) Draw in with a different color primers and the daughter strand.
    c) Identify the Leading and Lagging strand.
    d) Identify the Okazaki fragments and direction of nucleotide addition by DNA polymerase III
 
Here is a picture of my whiteboard:
 

 

 

  _____________________

12/1 – Wednesday’s Homework: –

                                                                       

1. You can make one more submission on last nights form if you need to.

 
2: Please view the three college lectures to answer the questions from the form below. 
    THE FORM WILL DIRECT YOU TO EACH VIDEO!       

 

 
2: 5′ to 3′ Directionality Form 21 – 22

 

College Lecture #1:

College Lecture #2:

College Lecture #3:

_______________________________________________________________________________________________________________________

12/2 – Thursday –  A Day 

Main focus –                                                                                                                                                          
a)  To study DNA replication, Origin of Replication, Replication Bubble, Replication Fork, DNA Polymerase I, DNA Polymerase III, Primase, Ligase,  Helicase,  Topoisomerase, SSB, RNA, eukaryote vs. prokaryote differences.
    
                                                                                           
Where do these mutation originate from?

 Look at the chromosomes!

WHY IS THIS DIAGRAM INACCURATE?

When are the chromosomes duplicated?

When do these mutations that lead to
disorders occur?

  Do individuals that have the disorders
discussed develop a  mutation? Why or
why not?

     

 
 DNA Replication: Note taking continues.
 
1. Whiteboard activity – Draw the replication fork in DNA Replication
    aIdentify and label the template strands with 5′ and 3 ‘ ends. 
    b) Draw in with a different color primers and the daughter strand.
    c) Identify the Leading and Lagging strand.
    d) Identify the Okazaki fragments and direction of nucleotide addition by DNA polymerase III
 
Here is a picture of my whiteboard:
 

 

                                                                                  
2: 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

DNA Replication animation:

  _____________________

12/2 – Thursday’s Homework: –

                                                                       

1. You can make one more submission on last nights form if you need to.

 

2. Please read the article below from Newsday  a few years ago.

 
3: Please view my lecture on DNA replication to the lecture below:
 
4:  Please read the article on Telomeres.
 
5:  Answer the questions on the DNA Duplication form.
*Be prepared to have only 1 submission!

 

Newsday article: –  You could also read it online with this LINK:


3:  Grodski Lecture on DNA Replication:

 4:  Article on Telomeres:

 

Telomeres –  A very interesting article on the current research in Telomeres.
 

 
5: DNA Duplication Form – 21-22
<

 End Of Thursday!

______________________________________________________________________________________________________________________

12/3 – Friday –  B Day 

Main focus –                                                                                                                                                          
a)  To study DNA replication and link to how mutations arise.
b) To construct a class DNA molecule. 
 
Classwork questions:
#1 Correct Choice was Choice D that was discussed in class.
    #2 Correct Choice was Choice D that was discussed in class.
                                                                                                                                                                                                                                    1. Construct a class DNA molecule for our final slide of the DNA presentation activity. 
2.  VOICE OVER PROJECT” – DNA replication                                                                                                                                                     
 Your group will make a story board of all the steps of DNA Replication.

Please place a screenshot of the video into a new page of the Google Doc and add as many screenshots of the animation as necessary to completely and thoroughly describe the video using captions that you will synthesize from your text book.

Link to video file for “VOICE OVER PROJECT” – DNA replication”

You will need to use your text pages 313 – 318 to help learn or review all the important steps of DNA replication. Whenever you use an important vocab word please bold it and add its definition below the caption.  Presentation counts and well as content.  

So you will need to make screenshots of the video that you will open on your computer.  These screen shots will be placed into the Google Doc THAT I SHARED WITH YOUR GROUP. Each screenshot will have words below it that you will makes with your group (using the textbook) to describe the step in the replication of DNA.  Make as many as slides as possible to describe the entire process.                                                                                

Work together by adding comments and chatting by clicking comments above. Do not let the LVP (least valuable player) off the hook. Get them involved.  Everyone is responsible for understanding the content. This graded project will be based on presentation, content, and accuracy. Humor is appreciated but accuracy is still important.

You will need a minimum of 10 slides to accomplish the goal of describing DNA replication.                                                                                          

_____________________

12/3 – Friday’s Homework: –

                                                                       

1. Complete the storyboard of your DNA Replication Activity as group. I have linked a Google doc to each member of each group to begin the storyboard.  Only one project is needed per group. Make sure your title page has all the names of the students in each group and that everyone is contributing. 

2:  Please make sure your Brine Shrimp Lab is complete as I will be reading them this weekend.

                                                                                                                                                                                                                                   End of week 3!