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Q2 – Week 5 – 19-20

week 5

Week of 12/2 – 12/6  

 
12/2 – Monday – Period 7/8 – Lab  
 
3.  Review common mistakes from Last 2 Forms using Classwork worksheet below.
     *Connections – Sex Linked vs Linked genes
        Linked Genes = < 50% Recombination due to CROSS OVER!!!
        An unlinked gene could also be 2 different genes on the same chromosome that are so far away that
        the % Recombination is 50% – The same if on a different chromosome!
       Mendelian Genetics is not upheld when genes are linked!!!!
Classwork sheet given out:
Pedigree Form: Morgan Drosophilia – Most Common mistakes 1819.pdf
View Download
 
1.  Sordaria Firmicola Lab 
2. Sordaria data collection/ picture taking.
12/2 – Monday Homework:  2 parts
1: Complete the form below using your text!
 
***You should work on a Word Doc or another program like it and then paste your answers when you are finished to prevent the page from timing out or any other connection issues.
 

Gene to Protein Form 1 – 1920

2.  START the Fimicola lab write-up:  
 

Sordoria Firmicola Data collection and (Slide-UP
)
      You will work on making a Google Presentation for the Sordaria Firmicola Lab
       This will be started in class and you will make an abbreviated lab write-up that will completed on Google Slides.
        Every Lab group will be linked to a blank google slide file that only the group has access to.  
 
YOU WILL USE THE DATA FROM PICTURES from CLASSES wet mounts that were taken FROM VARIOUS SLIDES OF THE MATING FROM THE TAN (mutant)  AND DARK (wild type) Fungi to determine the % recombinants and the relative distance to the centromere.
 
I am staying late today to find these hybrids!
 
Please Read everything below to get a sense of what this experiment is all about!
    
The Presentation must have:
 
        1: Title Slide- I need all the names of your group to give a grade.
        2: Background SLIDES
        3: Objective SLIDE ( no hypothesis here as we are determining gene linkage in terms of   
                                                distance to centromere.)
                                
        4: PROCEDURE SLIDE – explain what we are looking for .
        5: DATA:  Include the pictures that you used or the pictures taken from other groups to get 50                              or so asci. They will be posted below.
 
                           The must be hybrids (brown and tan colored ascospores ) that you can identify.
                                An identified hybrid is a group of eight that you can see from the pic that has 2  
                           different colored ascospores (individual little spores in the pod).
 
                          As you identify a hybrid, determine if it is 
 
                                                a) a recombinant – has alternating light and dark ascospores OR
                                                    “Cross Over” at the color ascospore locus
 
 
                                                b) non-recombinants – Has 4 light or 4 dark ascospores in a row.
                                                    “Crossover did not occur at the ascospore locus”
 
                        MARK IT ON YOUR DATA SLIDE! EVERY PICTURE YOU USE 
                                                        MUST BE MARKED like below:
            
Date table example:
 Recombinants Non-recombinants Total Asci (pods)
 Picture #
Picture #

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.

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 move them to another chromosome. 
They 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!!
            
        6: RESULTS
        7: CONCLUSION:  Please use the concepts that I discussed above!
        8: SOURCES
                           
*This lab will be graded as a group

Evan’s Data:

 

Evan IMG00046.jpg
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Evan IMG00049.jpg
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Evan IMG00051.jpg
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EvanIMG00052.jpg
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EvanIMG00053.jpg
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Link to all images

 

Theresa’s and Emma’s Data:
 

 Theresa IMG00122.jpg
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THeresa IMG00113.jpg
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THeresa IMG00119.jpg
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Theresa IMG00122.jpg
View Download

 

Theresa IMG00127.jpg
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Link to all images

 

Kristina’s and Jacks Data: 
Maximus, Kade, and Dan
Morgan, Morgan, Christie
End of Monday..

Tuesday – 12/3 –  period 7 – Academic Study Hall 
 
1.  Work on the Group Slide – Up of the Sordaria Fimicola Lab.
      Instructions above. Everyone was mailed a link to their gmail account to Begin the lab       
      yesterday. You will graded as group.
 
2) Start Tonight’s Homework
 
                                 period 8
1.  Give back Last weeks Linked Gene 2 form and Review.
2. Classwork Form on the Gene Edited Babies
 
Classwork: 
Gene edited babies?  A Chinese researcher has declared that he has edited the first human babies using the CRISPR/Cas 9 system.
1st Article:
2nd  Article:
A simple guide to CRISPR, one of the biggest science stories of the decadehttps://www.vox.com/2018/7/23/17594864/crispr-cas9-gene-editing

Gene Edited Babies 1920

Interesting videos to play on the bus.
Tuesday – 12/3 –  period Homework: 
 
1.  Please make another submission on the CRISPER Classwork Form.
 
              “Bacteria IS IN YOGURT!!!”
2:  Please complete the form below with the text book:
 

Gene to Protein Form 2 1920

 

End of Tuesday!

Sordaria Fimicola Lab – when we get data!

Genetic Crosses of Sordaria fimicola .

End of Tuesday!

12/4  – Wednesday – Period 7/8- Lab 
 
1. Crisper  reviewed.
 
2.  Work on the Sordaria Fimicola Slide-Up
 
3.   mRNA activity begin – build DNA template strand.
 
You may need the digital file to see if your strand is correct!  You are acting like a CRISPER/Cas- 9 enzyme cutting and adding DNA. 
 

mRNA activity student copy .pdf

 
Please Follow the Instructions below to complete the mRNA activity:
 
Please find your work in the back lab table under the light.
 
1. Complete the Template strand of the DNA by writing the correct complimentary code below the coding strand.
 
2.  Connect a single stranded blank strand that is almost as long your DNA strand. This will be eventually be your mRNA but for now it will be your pre-mRNA (or primary transcript)
This blank strand sheet that needs to be cut out and assembled are on the first desk next to the scissors and tape box.
 
3.  Mark on your DNA strand with a highlighter the promoter region and the termination sequence. If you forget what these small bits of code are for each then grab the text in Chapter 17 and look it up.  
 
The promoter region is telling where to start represents the INITIATION step.
 
*When you look for this code it is helpful to look and the coding strand (The printed code above the Template strand that you filled in).  The coding strand will reveal what the mRNA Strand will look like EXCEPT THAT thymine will be Uracil!
 
4.  Lay your blank RNA strand along the Template Strand (that you filled out) and start making the RNA primary transcript from 15 or so UTR’s  downstream from your promoter region.  It must be in front of the start CODON: AUG which will look like ATG on the Coding strand!   So start coding the mRNA strand remembering to use Uracil instead of  THymine.  
 
Writing the code on the single strand mRNA is the ELONGATION step.
 
5. Keep coding until you complete the terminating sequence. At this point your primary transcript (pre-mRNA) will be detached from the Template Strand of the DNA. This is where RNA polymerase detaches from the template strand of the DNA.  
 
Stopping the code and detaching the pre-RNA is the TERMINATION step.
 
6.  Now you have to make your pre-RNA into the processed mRNA that can leave the nucleus of a eukaryote cell and move into another area of the cell that will Translate the mRNA Codons into proteins.  
 
Alteration of the mRNA Ends
 
7. You must modify the ends of this pre-mRNA. You may have look up in the text (page 334) or look below to remember how the ends of the RNA are modified.  You may have to add some blank strands to the ends to make the caps.
This modification facilitates the export of the mRNA out of the nucleus, protects it from it being broken down by enzymes, and helps ribosomes to attach it for Translation.
 
RNA Splicing
 
8. On your pre-mRNA that has its end capped appropriately in step 7, use a highlighter to identify the EXONS.  The Exons are the triplet codons that are expressed.  In your packet you have the code for the entire gene including the start codon and stop codon.  So highlight  ONLY the Triplet CODON in the RNA strand that is in your packet or below.
 

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The code will go in order but it will have many UTR’s (Untranslated REgions) that are not part of the code and these are INTRONS!!!!

After you have highlighted all of the EXONS Physically cut away all of the INTRON in between the start and stop codon and retape (splice) the RNA back together so that there is a continuous code of EXONS from start to stop.  At this point you are acting as snRNA (snurps) in a splicesome!

Your pre-mRNA IS NOW a mRNA and can leave the nucleus to begin Translation.

9.  Roll up your DNA and completed mRNA and place on top of your packet with group names and return this back to the lab area you picked up your work today.

 
 
A fun presentation:
 
12/4  – Wednesday Homework :
 
1. Please use your book from chapter 17 to complete the multiple choice questions in the form below:
 

Gene to Protein Hw Quiz -1920

 

End of Wednesday.

12/5  – Thursday – Period 7 – Academic Study Hall – Not really..
 
1.  Drosophila lab set-up- Sexting Your Flies.
 

 

 

 

                                     
2. mRNA activity continues:
 
mRNA activity:
        Complete  the “processed mRNA” by splicing out the Introns and make a continuous  triplet code for the nucleotides that are coding for the following polypeptide:
 

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 *Remember to include start and stop codons, any additional UTR’s that are necessary, other additional items that you may have to add. Color code your DNA strand and your completed mRNA molecule. 

For instance the Exons on both molecules should be highlighted with the same color. Please take a picture of:

A) DNA molecules (both strands)

B) pre-RNA strand

C) completed mRNA molecule

 
12/5 THURSDAY Homework:   This is important!!!
 
1. Complete the Sordaria Fimicola SLIDE – UP
2: complete the form below: 

Translation Form 1718

 

End of Wednesday

12/6  – Friday – Period 7/8

 
1: mRNA activity – complete
 
    Hand in 
 
    a) Double Stranded DNA (with Highlighted Promoter region and Termination sequence)
      and with the template strand correctly filled out.
 
    b) mRNA (not the primary transcript) with processes ends!  
 
2.  Played the following animation of Transcription and reviewed Gene to Protein 1 Form through   
      the animation. 
3. Handed back Graded Gene to Protein Form 1
 
4.  Lab 1 discussion and requirements
 
F2 PhenotypesMax/Edgar/KadeTheresa/EMorgan’sDan/Evangroup 5 wreck Mr. GTotal
purple stem, green leaf411210 627
purple stem, yellow leaf2210 510
non-purple stem, green leaf4151135 1066
non-purple stem, yellow leaf2800 414
FAST PLANT Tutorial:

Wisconsin Fast Plants

 
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            Green 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 of OUR second planting:  There will be 4 different phenotypes:
                                                                                     
                                                                                      Purple Stems, Green Leaves
                                                                                      Purple Stems, Yellow Leaves
                                                                                      Green Stems, Green leaves
                                                                                      Green Stems,Yellow leaves
 
You will need to complete the Punnet Square for the DiHybrid cross in the F1 and include in your lab report. (Data section)
This will produce the seeds that produced the F2 generation.
This punnet square will produce all the genotypes and frequency of the phenotypes which was just like the Summer assignment 2. I have posted the punnet square that must be in your Lab
Summer assignment 2 question 2a Key.pdf
View Download
 
You will need to include the data table of the observed phenotypes from your class.
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.
 
12/8  – Friday – Homework – 
 
1. Complete the Sordoria Fimicola Lab!
2. You will begin 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) Chi – squared value calculated with calculations
         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.
 
* 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.  
 
End of week 5!