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Q2 – Week 7 – 1/3 – 1/7

                                                                                                                               Jump to:  Tuesday,   Wednesday,  Thursday,  Friday                                                                                                                                   ___________________________________________________________

1/3 – Monday –  A Day

Main focus –   
                                                                                                                                                                                      a)  To introduce methylation of cytosine in its contribution to mismatch point mutations
b)  To describe methylation can result in gene regulation
c)  To introduce positive gene regulation in the Lac Operon.


1: Reviewed handed back the Gene to Protein Form 2 / and translation draw activity.

2: Reviewed negative Control of Trp Operon and Lac Operon

3. Introduced methylation as a form of gene – regulation and evolution of uracil exclusivity        on RNA as a possible error control mechanism.

                   a) Methylation – genetic imprinting

               b) Histone modification

               c) ncRNA – Non coding Rna that includes miRNA (micro RNA) – gene silencing

4: Review the pGlo lab results as a transformatiion (horizontal gene transfer) AND a Gene          regulation Lab

5: Positive Control of Lac Operon in E. coli – (in addition to the negative control in has with its                repressor protein made up stream in its regulatory gene).  


Trp Operon Notes: 

 The Trp Operon is segment on the bacterial DNA includes a single promoter for a group of genes.  These genes represent the 5 enzymes in a single metabolic pathway that will produce tryptophan.  This is an anabolic operon as it builds or synthesizes the amino acid tryptophan from other resources. It is an repressible operon that is on the “on” position until a repressor protein produced from an upstream regulatory gene that will turn the operon “off” when there is enough tryptophan present in the cell.

The switch of the operon is the operator position in the promoter region that the regulatory protein (repressor) can bind to and will prevent RNA polymerase from binding to promoter and turn the operon “off”.   

It is a negative control operon.


                                                                                                                                                                  Metabolic pathway in the synthesis of tryptophan:                                                                             –                                                                                                                                                                                                                 

Trp Operon Animation:


Lac Operon Notes: 

 The Lac Operon is segment on the bacterial DNA includes a single promoter for a group of genes.  These genes represent the 3 enzymes in a single metabolic pathway that will digest Lactose.  This is a catabolic operon as it breaks down a larger molecules (disaccharide)  into a smaller molecule it can metabolize for energy (glucose).  It is an inducible operon that is the “off” position until a repressor protein produced from an upstream regulatory gene is induced by allolactose to allosterically change its shape so that it can no longer bind  to the operator and thus will turn the operon “on” when there is lactose present in the cell.

It is a negative control and positive control operon.

                         Permease             —–>            B – Galactosidase – 

              aids in the absorption of Lactose in the cell                                    Hydrolyzes the 1,4 glycosidic bond in Lactose

                                   Currently is is unclear what the role of Transacetylase is.


Lac Operon:


Cytosine Methylation: 

DNA methylation occurs when DNA methyltransferase transfers a methyl group from S-adenosyl-methionine to cytosine in CpG dinucleotides. The methylation of 5’ methyl cytosine (5mC) nucleotides is an important epigenetic change that regulates gene activity and impacts several cellular processes including differentiation, transcriptional control and chromatin remodeling.


The first type of mark, called DNA methylation, directly affects the DNA in a genome. In this process, proteins attach chemical tags called methyl groups to the bases of the DNA molecule in specific places. The methyl groups turn genes on or off by affecting interactions between the DNA and other proteins. In this way, cells can remember which genes are on or off.The second kind of mark, called histone modification, affects DNA indirectly. DNA in cells is wrapped around histone proteins, which form spool-like structures that enable DNA’s very long molecules to be wound up neatly into chromosomes inside the cell nucleus. Proteins can attach a variety of chemical tags to histones. Other proteins in cells can detect these tags and determine whether that region of DNA should be used or ignored in that cell.


                                                              Cytosine                                               Uracil
So Cytosine will undergo spontaneous deamination into Uracil in the DNA chain that get removed by endo nucleases or other repair mechanisms.  This may be why uracil is exclusive to RNA.  We can remove any Uracils and prevent point mutations. If Thymine is made as in the case of the deamination of methylated cytosine a point mutation is more likely if an A is replaced instead of the novel thymine. There is a selective pressure to lower the amount of mutations from deamination.


1/3 – Monday’s Homework: –

1.  Please view the two videos below and complete the form posted below on epigenetics.

The first video is from Khan Academy regarding ncRNA – Non coding RNA:

The second is the X inactivation and Epigenetics posted below:

1: X inactivation and Epigenetics:

2: Epigenetics Form – 

End of Monday..



1/4 – Tuesday –  B Day – 

Main focus –                                                                                                                                                          
a)  To Review Epigenetics: gene imprinting by methylation, histone modifications
                                                                                                                                                                                                             b)  To identify the positive control of the Lac Operon of the E.coli.
                                                                                                                                                                                      1.  Epigenetics homework review:                                                                                                                                                                                                                                                                                                                                       2.  Positive control of the Lac Operon  –  glucose is the preferred medium for Energy so there is a mechanism in place the controls the how much the lac operon in “on’ based on the availability of glucose.                                                                                                                                                                                                                                                                                                                                                       3.  AP Multiple Choice Practice  –  Classwork:
                                                                                                                                                                                           Practice AP Genetics A .pdf
         View Download 


Gene Regulation:

Positive gene regulation lecture:

AP Genetics Practice A Form: Today’s Classwork




1/4 – Tuesday’s Homework: –

1. Please complete the AP Questions (1 – 14) from today’s classwork and enter your answers into the form posted above. You can have 3 submissions.   



1/5 – Wednesday –  A Day 

Main focus –                                                                                                                                                          
a) To investigate the bacterial Phage DNA through Gel Electrophoresis.

1. Crime Scene lab –

       a) pour gels

       b) Load gels with DNA from crime scene.

       c) Run Gels


2.  Start the Lab questions:

 Biorad – DNA Fingerprinting- Student .pdf                                                                                                   View Download                                                                                                                                                              


1/5 – Wednesday’s Homework: –


1.  Start DNA Fingerprinting Lab by answering the following questions on the following pages:
Biorad – DNA Fingerprinting- Student .pdf

View Download

Page 2: questions 1 – 5
Page 3: questions 1 – 3
Page 4: questions 4, and 5
2.  Please complete the Gene regulation HW Quiz

1: Gene Regulation Hw Quiz Form

End  of Wednesday…



1/6 – Thursday –  B Day 

Main focus –                                                                                                                                                          
a)  To able to read an electrogelphoris gel to identify base pair length and
       similarity in DN                                                                                                                                                
b)  To Plot a exponential graph and determine base pair lengths from a standard.                                                                                                                                                                                                             
1.  Download the images I took of your Gels.
                                                                                                                                                                                              2.  Measure the Band Distances.
3.  Plot an exponential graph
4.  Complete the lab packet.                                                                                                                                                  

How I read your completed gels:


Crime Scene Lab Data:
Lanes:              1.                   2.                   3.                   4.                    5.                   6.                  7.   
                     Standard      Crime Scene        Lukas             Abigal            Kaitlynn           Zeke               Zoey                                             
                       Table 1: Abigal and Lucy:                                 Table 2: Zeke, Gavin, Quinn, Alessandro:           

Table 3: Lukas, Drew: 

Table 4: Jordan, etc.

Table 5: Zoey, Lily P, etc.

                                        I went blank here..

                                Kaitlynn…Its time to get some representation!


1/6 -Thursday’s Homework: –

1. Please complete the following selected questions or pages of your Crime Scene lab Packet.

   pages 2,3,4, 12,
   page 18 but please only complete the following questions from page 18:
 You need a gel that has excellent clarity to answer some of these questions. Use any gel from   either class if you own gel that I posted here does not have good clarity.
            questions 1,3,4,5,6,7, 8 (use one of the gels posted instead)
                                                                                                                                                                                                                                  2. Please complete the following from the PCR Presentation posted below
 – WE begin our PCR Lab tomorrow.

PCT Taster Lab 2 (*We did an activity on Hardy Wienberg on bitter taste papers earlier this year.

2: The PCR and Taster 2 Lab Form – 21-22




1/7 – Friday – A Snow Day!

Main focus –                                                                                                                                                          
a)  To Enjoy the day off!
b)  To make snow (cross-over ) angels with your friends and send me the pic!



1/7 -Weekend’s Homework: –

1. Make a snow (crossover) angel and send me the pic (optional).

2.  Please complete the practice multiple choice questions below and enter your responses into the form below.  There will be only one response for the weekend and it is not on auto-grade. Please make your one submission count!

Genetics AP Multiple Choice Review Questions 3.pdf
View Download

2: Genetics AP MC Review Questions Form:


 End of week 7!