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Q2 – Week 4 – 12/6 – 12/10

                                                                                                                             Jump to:  Tuesday,   Wednesday,  Thursday,  Friday                                                                                                                                   ___________________________________________________________

12/06 – Monday –  A Day

Main focus –   
                                                                                                                                           
a)  To complete the voice over project using the storyboard slides                                                    
b)  To Begin the Lab 4 Sordaria Firmicola Lab

1: Sordaria Fimicola Lab begins – Lab book note-taking

 
            a) Set up out fungi cultures –
 
We are culturing 2 types of fungi (decomposer), Tan –  mutant and Brown – wild type. We put them in four alternating quadrants in the petri dish so that the mutant and wild type will sexually cross to make hybrids.  We then placed the petri dishes in the incubator (38 degrees Celsius) for about a week so that we can take samples of the hybrids and view the hybrids ascospores  (group of eight spores).    The color of the fungi is due to the color of the ascospores and we will determine the crossover percentages by viewing the pattern of the ascospores (tan or brown).  I will explain this completely again when we get to the next phase in this lab. 
                   
2: Voice Over DNA Replication

Please use your storyboard and all the vocabulary that you have used to add audio to the following video to describe the animation of Video.  Please upload it into one of the students google drive and link the video into your last slide (#10).  This will complete this activity.

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

Lab 4 – The Genetic cross between mutant and wild type fungi: 

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12/06 – Monday’s Homework: –

1. Please complete the form below on Chapter 16 of the textbook.

 
1: Chapter 16 Textbook Form :

End of Monday..

 

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12/7 – Tuesday –  B Day – 

Main focus –                                                                                                                                                          
a)  To complete DNA replication voice over activity    
b)  To discuss the Linked genes (non- sex linked) and develop the ideas of recombinants, 
      cross over, through the Test cross of our Fast Plants                                                                                                                                                                                                                                                                       
1:  Linked Genes – Non – Mendelian genetics and how cross over can lead to recombinant offspring,
                                                                                                                                                                                                                 We test for recombinant offspring or genetic linkage through a genetics Test Cross. 
                                                                                                                                                                                                                  We did a test cross in our Fast Plant Lab (Thanks Lily P and Zoey):                                                                     
Testcross:         (double recessive)  anl/anl, ygr/ygr      X       (Dihybrids)  ANL/anl, YGR, ygr 
                                                                                                                                                                                               Expected Punnet Square :   purple,  green       purple, yellow    non-purple, green    non-purple, yellow
                                                  ANL/ YGR,       ANL/ ygr,     anl/YGR,      anl, ygr   
                                                                                                                                                       anl/ygr    ANL/anl, YGR/ygr       ANL/anl, ygr/ygr.   anl/anl, YGR/ygr   anl/anl, ygr/ygr 
                                                                                                                                                                                                                            If non-linked:                1                   :                  1                :               1               :                 1                                                          
                If Linked:                     Parental                      Recombinant               Recombinant               Parental                      Our Data This year:         4                                            5                                     8                                    19 
                              
       The recombinant offspring have new combinations due to Cross Over!!!  This how new combinations of phenotypes (Recombinants) can occur if the genes are linked (on the same chromosome).   If the genes are linked the Recombinants will be in lower in number than the parental genotypes, which are chromosomes that are linked that are not involved in the crossover because ONLY the inside homologous chromosomes are involved.                                                                                                                               
Now if these 4 gametes combine with a double recessive gamete of a/a, b/b in a test cross then 4 possible genotypes are :
                                       A/a,B/           A/a, b/b            a/a, B/a            a/a, b/
                                            Parental        Recombinant     Recombinant        Parental                                                      
Look at the Black letters in front as they represent the Linked A and B alleles from the original parent..  Notice the Parental genotypes have the same combination as the chromosome on the outside of the chromosomes THAT CANNOT CROSS OVER.  Offspring with A,B or a,b do not result from crossover but offspring with A,b and a/B MUST occur from crossover as they do not originally exist in the original parent.  The blue letter alleles come from the test cross individual and since it is double recessive the only change that occurs is due to the crossover event in the original parent.
                                                                                                                                                                             
We can also identify whether an organism exhibiting a dominant trait is homozygous or heterozygous for a specific allele, a scientist can perform a test cross. The organism in question is crossed with an organism that is homozygous for the recessive trait, and the offspring of the test cross are examined. If the test cross results in any recessive offspring, then the parent organism is heterozygous for the allele in question. If the test cross results in only phenotypically dominant offspring, then the parent organism is homozygous dominant for the allele in question.                                                                            

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12/7 – Tuesday’s Homework: –

                                                                       

1. DNA Duplication Voice Over Activity Make sure you use all the vocab words in your story boards.   
 
                                   This is a group lab activity.  Make sure it is accurate! It is due Friday!
 
 
2. Please complete the form below on Morgan’s second ground breaking Drosophila experiment. 
 
                                   You will have 1 submissions to this form.

 

 2: Morgan’s Drosophila Experiment 15.9 

End of Tuesday….

 

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12/8 – Wednesday –  A Day 

Main focus –                                                                                                                                                          
a) To  review cross-over events in meiosis that can unlink genes.     
b)  To  introduce gene mapping in terms of percent recombination frequency.
c) To redefine a linked gene and thus Non- Mendelian Genetics                                                                                          
1.  Review the test cross using the notes posted yesterday to review and teach parental and recombinant genotypes or chromosomes.                                                                                                                            
2.  Introduce what percent recombinant frequency provides us in terms of the ability unlink the chromosomes. Calculate the percent recombinant frequency on our test cross data. What does it tell us? What is the maximum recombinant frequency and why  does this value demonstrate alleles that are unlinked even though they are on the same chromosome? 
  
    I spent a lot of time on the drawn diagram on the board of the test cross  to accomplish the following.
 
    a. Mieosis – tetrad
    b) DNA duplication in the S1 phase
    c) Homologous, sister chromatids
    d) Dihybrid cross
    e) Testcross!!!
    f) Expected ratios
    e) recombinants – due to crossover!!
    f) what are really linked genes?
    g) % recombinants and relative distance that genes of 2 alleles are on a chromosome

    f) Morgan Units = mapping the chromosomes!                                                                                                                                                                                                                                                                                                                                 

NOW one last thing. What are LINKED genes? 
 
2 different genes on the same chromosome THAT ARE CLOSE ENOUGH so that they will move together in Crossover events!  There is no independent assortment! No Mendelian genetics!
 
What are UNLINKED genes?
 
Unlinked genes are 2 genes on different chromosomes OR GENES on the SAME CHROMOSOME THAT ARE FAR APART SO THAT Cross Over will always separate the 2 gene to different chromosomes. There is independent assortment and Mendelian genetics is upheld!
 
If Crossover ALWAYS moves genes to another chromosome (100% crossover )and separates them from distant genes on the same chromosome then these genes act as if they are on different chromosomes! Gregory Mendel was lucky that he studied pea plant alleles that were Unlinked.  We now know that some of his experiments were with genes on the same chromosome but were far apart on the same chromosome so that he was able to develop the law of independent assortment!
 
One last point. If recombination frequency (percent of  individuals with alleles different from parents) is 50% then isn’t that the percentage of getting the maternal or paternal allele in meiosis if they independently assort on different chromosomes?  (Remember flip of a coin?) YES!!!! 
And therefore recombination frequency cannot exceed 50%!  
 
Recombinant frequency is the frequency of individuals that do not have the parental genotype AND Crossover frequency that unlinks genes are NOT the same!   If crossover is 100% then the recombinant frequency will max out to 50%.
 
Please read page 296 if I was not clear!!

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12/8 – Wednesday’s Homework: –

                                                                       

1. Please make another submission to the Last nights form.  Today’s lesson should have helped.

2. Complete the written form below using chapter 15.

 

 

 2: Linked Genes Form 2

Wednesday….

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12/9 – Thursday –  B Day 

Main focus –                                                                                                                                                          
a)  To discuss the concepts of recombination, cross-over, meiosis, mitosis in the life cycle 
       of the Sordaria Fimicola (fungi) that we cultured.
 
b)  To calculate the Chi – squared value of our fast plant lab in order to verify IF OUR two alleles tested (stem color and leaf color) ARE LINKED!!
                                                                                                                                                                                                          1.  Take notes on the Sordia Fimicola Lab:  Its a recombinant lab!!!!
Explained the Lab fully with a class lecture – posted above homework:            
 
We are culturing 2 types of fungi (decomposer), Tan –  mutant and Brown – wild type. We put them in four alternating quadrants in the petri dish so that the mutant and wild type will sexually cross to make hybrids.  We then placed the petri dishes in the incubator (38 degrees Celsius) for about a week so that we can take samples of the hybrids and view the hybrids ascospores  (group of eight spores).    The color of the fungi is due to the color of the ascospores and we will determine the crossover percentages by viewing the pattern of the ascospores (tan or brown).  I will explain this completely again when we get to the next phase in this lab. 
                                                                                                                                                                                                                                   This is the culture from one of my previous AP Bio student groups.  
Can you see where the boundary between the mutant (tan) and brown (wild type) is?
We will be looking for the hybrids between the true breeders and they should be found where?
 
                                                                                                                                                                                                                                   
We will carefully scrape where the two types of Fungi meet and are producing Hybrids and then using a light microscope will be counting the ascus (pod of eight ascopores) that are recombination and parental to determine the percent recombination frequency.
 
                                                                                                                                                                                                                                         Percent Recombinants =        number of recombinants on all pics  =     % Recombinants
                                                                       Total Acsci counted
 
Because each asci (pod) that we count as a crossover (alternating brown and tan ascospores) also has individuals that did not crossover WE will divide OUR Number above by 2 to correct for the fact that only 2 haploid ascospores our of the possible 4 (after Meiosis II ) actually are recombinants.
 
                                        % Recombinants/2 = Corrected % Recombinants
 
Now that we have the corrected % recombinants we want build a map on the chromosome on the Fungi that contains the color of the ascospores in relation to the Centromere.  The idea is very simple.  The closer that the gene for the tan or brown ascospore is to the centromere the harder it will be for Crossover to swap the gene from one chromosome to another.  The farther that this gene is from the centromere the more likely Crossover will be able to swap the color genes.
 

Look at the diagram above and notice that the allele for the brown or tan is far away from the centromere and thus the crossover will more than likely INCLUDE the color allele (black line).

 
If the the color allele was closer to the centromere (middle region) the crossover would be less likely to swap the tan and brown alleles AND if the gene was farther away (as in the diagram above), there will be a greater chance!  Understand that where crossover occurs (close to centromere or far from the centromere) is totally random BUT it will cause more recombinants if the genes are farther away!
 
The greater the recombinant frequency the greater the distance between the gene and the centromere on the actual chromosome!
 
So we can build a gene map with % recombinants as this value represents a “distance” from the centromere.  THUS YOUR % recombinant value is a “distance” on a gene map. If we had another allele to test for % recombination on the same chromosome then we could determine how far apart the other allele is from the color allele we just tested.  This is how we first mapped genes that are in relation to each other on the same chromosome.
 
Thus our recombinant data can also be related to a distance from the centromere!
 
                                           Corrected % Recombinants = Gene to Centromere distance
 
                                                               % recombination = map unit 
 
How many map units away is the gene for the color of the ascospore from the centromere?
 
This is figure 15.12 of your text.  This was a genetic map made from recombinant frequencies or percentages.

Notice the the Aristae Gene has a 0 on this gene map of a single chromosome of the drosophila.  This gene is the closest to the Centromere.

The Body Gene is 48.4 distance away from the Aristae Gene and thus would have a much higher chance of recombinants.

The other genes are even farther away and almost certainly are always included in a cross over event and are always moving to another chromosome.  We would say these genes are unlinked even being on the same chromosome.

2.  Calculate the Chi – squared for our lab data for Lab 1.  We already know that based on recombinant frequency that it appears that the two alleles studied are in fact linked:                                         

Expected Punnet Square :   purple,  green       purple, yellow    non-purple, green    non-purple, yellow
                                                  ANL/ YGR,       ANL/ ygr,     anl/YGR,      anl, ygr   
                                                                                                                                                      anl/ygr    ANL/anl, YGR/ygr       ANL/anl, ygr/ygr.   anl/anl, YGR/ygr   anl/anl, ygr/ygr 
                                                                                                                                                                                                                           If non-linked:                1                   :                  1                :               1               :                 1                                                          
                If Linked:                     Parental                      Recombinant               Recombinant               Parental                      Our Data This year:         4                                            5                                     8                                    19 
                                                                                                                                                                                                                                     % Recombinants    =       13 Recombinants      x      100    =    36%
                                                                                           36 total offspring                                                                                                     
           Because the % Recombination is less than 50% the genes for stem color and leaf color are linked!                                                                                                                                                                                                                       Does the Chi- Squared value for our data on the dihybrid cross support the chi- squared value?              
                                       Expected Ratios                                                                                Observed  Data
               Purple Stem/Green Leaf              :  9
               Purple Stem/Yellow Leaf             :  3
               Non-purple stem/ Green Leaf    :  3
               Non-purple stem/ Yellow Leaf   :  1  
            Purple Stem / Green leaf : 173                                            Purple Stem / yellow leaf: 52                                              Non-purple stem/ Green Leaf: 98                                      Non-purple stem/ Yellow Leaf: 23

Lab 4 – The Genetic cross between mutant and wild type fungi: 

Sordaria Fimicola Lab introduction:

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b12/9 – Thursday’s Homework: –

                                                                       

1. Please complete the form Below on your understanding of the Sordaria Fimicola lab.

 

 1: Sordaria Fimicola Form

End of Thursday…

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12/10 – Friday –   A Day 

Main focus –                                                                                                                                                          
a)  To practice AP Genetics questions.                                                                                                                                                                                                                                                                                                        AP Biology – Genetic Questions Practice.pdf                                                                                              View Download     
                                                                                                                                                                                               AP Biology – Genetic Questions Practice key.pdf                                                                                    View Download                                                                                                                                                                                                     

 _____________________

12/10 – Friday’s Homework: –

                                                                       

1. Review your AP Question Packet with the key posted above.

2. Start your write-up of Lab 1 with both the Chi-squared data of expected phenotypes of the F2 generation AND the Recombinant Test Cross. 

Was Mendelian genetics supported? Why or why not?

I expect that you include a well presented punnet square of the dihybrid cross (we did this together in class) to obtain expected outcomes along with all calculations utilizing the information below:

To Review Mendelian Genetics through a dihybrid Cross                                                              
1. We identified the 4 possible phenotypes that resulted from the F1 cross of the dihybrids by drawing a punnet square to determine the expected ratios of the phenotypes of the cross.

 

WE actually completed a dihybrid cross (F1). Your lab needs to show this information:
 
P1: (this was the parents of our original seeds)  :                         ANL/ANL  YGR/YGR              x                anl/anl  ygr/ygr
                                                                                                  Purple Stems   Green Leaves            Non-purple stems   yellow leaves
 
F1: (this was the genotype of the seeds we first planted) :               ANL/anl  YGR/ygr   x   ANL/anl  YGR/ygr                                                                                                                                 Purple Stems   Green Leaves     Purple Stems   Green Leaves
 
F2: (this was the generation of the seeds from the cross above (OUR second planting):  There will be 4 different phenotypes:                                             
Today we determined the expected phenotypical ratio of the offspring of the F1 generation by completing a punnet square of the dihybrid cross. 

 

This is what I modeled on the board today (actually this is what I did a couple of years ago):
                                                               
From the Punnet square:
Purple Stem/Green Leaf              :  9
Purple Stem/Yellow Leaf             :  3
Non-purple stem/ Green Leaf    :  3
    Non-purple stem/ Yellow Leaf   :  1    

Recombinant Data:

Expected Punnet Square :   purple,  green       purple, yellow    non-purple, green    non-purple, yellow
                                                  ANL/ YGR,       ANL/ ygr,     anl/YGR,      anl, ygr   
                                                                                                                                                      anl/ygr    ANL/anl, YGR/ygr       ANL/anl, ygr/ygr.   anl/anl, YGR/ygr   anl/anl, ygr/ygr 
                                                                                                                                                                                                                           If non-linked:                1                   :                  1                :               1               :                 1                                                          
                If Linked:                     Parental                      Recombinant               Recombinant               Parental                      Our Data This year:         4                                            5                                     8                                    19 

 

You will need to include the Null Hypothesis, and the alternative Hypothesis.  Your are investigating whether the observed frequencies from the F2: generation support the expected frequencies from Mendelian genetics.
 
You will need to include your calculations of the Chi- Squared math.
 
This Lab will have the same format as the last lab EXCEPT you are adding Calculations section in your Data Section.
 
You must provide a LEAP of what the outcome of your analysis means. 
The leap should include what we are learning about in genetics!
 
Hmmm.. Maybe page 296 of the text could help.
 
You will complete the writeup of your FAST PLANT LAB. Please have the following completed on the shared google doc that will be sent your way by the weekend:
 
         A) Title Page
        B) Background – Chapter 14 and 15!!!!!!
        C) Hypothesis – (alternative) and Null Hypothesis
        D) Data Table and Punnet square of the F1 Cross of the dihybrids
                I need you to make it clear what the phenotypes are and what the genotypes for each of the                        generations:  P1, F1, and F2.  It needs to clear what we did by providing this information!
 
        E) Calculations Page – Chi – squared value calculated with calculations with % recombinants!
         F) Results – What was the outcome of the Chi-squared Test?
         G) Conclusion – Analysis!!! – You can get this done another time.
         H) Sources
 
 Please have the FAST Plant Lab completed by Next Wednesday.
 
Please use the following video to help with the FAST plant lab:
 
Fast Plant lab Help:
 
The conclusion is not due yet but when you write it 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.
   
                     Was there any genetic Drift between the FI and F2 generations?  We may have calculated it!                                                                                                                                                                                                
* 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.  

Fast Plants: