Overview of DNA Fingerprinting Lab: to be done on Monday, Wednesday, and Friday of next week

Day 1: (Monday, April 22).  Label 4 microfuge tubes.  Add 5 microliters of one of the DNA samples (crime scene, suspect 1, suspect 2, suspect 3).  Add 5 microliters of restriction enzyme (EcoR1) into each of the tubes.  Restriction Enzyme must be kept on ice!  Put your tubes in your styrofoam "floatie" and put in the water bath for an hour!  After an hour, remove your labeled tubes and put them in the designated rack, which will be refrigerated until Wednesday.

Day 2 (Wed, April 24):  Take your samples from Monday and warm them up in your hands.  Add 2 microliters of dye to each of the 4 samples and spin in the centrifuge.  Carefully load 10 microliters of each of the 4 samples into a gel.  Make sure that you make a key so that you know which sample is where.  After both groups have loaded their samples into the gel, one group needs to load the "ladder" in one of the leftover lanes in the middle.  The gels will be hooked up to the power source and turned on.  You can watch bubbles form and then watch the blue dye migrate across the gel.  You should label the baggy that your gel was in with your groups' names and then put it near your gel.  This will ensure that I will put your gel in your labeled baggy after the gels are done running (because they will be done after you leave).

Day 3 (Fri, April 26).  You will get the baggy with your gel.  Go into the microscope room with your gel and put it in the "illuminator".  Turn the lights off, turn the illuminator on, and view your gel!  Have a few different people take photos of the gel.  When you leave the room, determine which photo works best and share it with your group numbers.  You can also send it to me!

Write up details to follow.

Boston Children's Hospital Virtual Stem Cell Laboratory

This activity can be done in pairs.  Go to the Boston Children's Hospital Virtual Stem Cell site and do the following.  Answer on a separate sheet of paper and turn in during class on Friday 4/12 or Tuesday 4/16.

1. Go to the Boston Children's Hospital Virtual Stem Cell Laboratory (linked on my website)
2. Read the Introduction and about Embryonic Stem Cells
3. Start the simulation by choosing a coaxing agent (one of the 5 colors).  If that coaxing agent works in the ES cells, you will see movement along a pathway.  If not, try a different coaxing agent until you get some movement.
4. Write down the coaxing agent that you chose and what new cell type you went to.  Read about that cell type.
5. Continue with the coaxing agents until you reach the end of a pathway.  Write down the ending stem cell and what it can be used to treat.
6. Start over with a whole new pathway (or just back up one step to get to another), writing down the coaxing agents and products as you did above.
7. Repeat this process for 5 different complete pathways.
8. Summarize what you learned about embryonic development and how these early cells can be used to treat different disorders.
9. If time:  Discuss the ethical pros and cons of using embryonic stem cells for treating patients and write down 2 pros and 2 cons.

Enzyme Lab Details

We will be discussing the lab write-up this coming week (Wed, 4/10), but for those of you who want to get ahead, here is what you will be required to include in the Enzyme Lab (first draft due Tuesday, 4/16).  Final Draft due Wednesday 4/24 through turnitin.com

1. Focused Question (1 pt)
2. Background Information.  Should be relevant to your lab.  For example if you are changing pH, you should include background about pH and pH buffers.  Start with general information and get specific by the end.  2 paragraphs approximately.  (4 pts)
3. Variables (manipulated, responding, controlled--describe how you control at least 5 variables)  (3 pts)
4. Procedure/Methodology.  Most people include a materials list and many people include a diagram or photo of their set up.  Procedure can be written step by step or in paragraph form.  It needs to be specific and clear enough that another person could follow it.  You should include how you measured things, specific amounts, etc. (4 pts)
5. Data Table (neat, organized, labeled, includes uncertainty).   Observations need to be included as well.  Some students put in the same table, others put as notes under the data table, and some have a whole table just for observations)  (4 pts)
6. Data-Processing:  Calculate averages and uncertainties.  Where appropriate calculate rate.  Show work for 1 sample calc of each type.  (2 pts)
7. Graph:  good title, labels, units, uncertainty bars, line of best fit, annotation  (4 pts)
8. Conclusion:  Refer back to question, use data to back yourself up, discuss patterns, how uncertainty impacts results, refer to scientific context (what does science say should happen and why?)  (5 pts)
9. Evaluation:  Discuss strengths of your investigation.  Outline weaknesses (at least 3 good ones).  Many people present weaknesses/limitations in a chart.  Suggest realistic improvements to the procedure for each weakness/limitation.  Do NOT just say something like, we need more time.  You need to explain specifically what you would do differently to get better results.  (5 pts)
10. Communication:  Up to 3 points for clarity, spelling/grammar, and overall presentation.

Total Points:  35

April 2019

• Mon 4/1:  4 Levels of Protein Structure.  Basic Enzyme Notes.  Work on Enzyme Worksheet.  Due at the beginning of class on Wed 4/3.  Read 2.5.
• Wed 4/3:  Check off Enzyme Worksheet.  Introduce Enzyme Lab.  Groups will work with 3 protocols, determine which protocol they want to do, and determine which manipulated variable they will change.  Make sure you tell me which you will be doing before you go.
• Fri 4/5:  Data-taking day for the Enzyme Lab.   Carefully take enough data, clean up when you are done, and start processing data.  When everyone is done, we will discuss how to process the data and write a conclusion.
• Wed 4/10:  Discuss the Enzyme Lab.  Enzyme inhibitors.  Read 8.1.  First draft of Enzyme Lab due Tues 4/16 for Peer Review.
• Fri 4/12:  Finish up enzymes.  Introduce stem cells and do stem cell computer activity.  
• Tues 4/16:  First draft of Enzyme Lab due for color-marking (peer review).  Polymerase chain reaction.  Discuss gel electrophoresis.
• Thurs 4/18:  Micropipetting practice for the DNA Fingerprinting Lab.
• Mon 4/22:  Start DNA Fingerprinting.  While you are waiting, learn about Genetic Modification.
• Wed 4/24:  Part II of the DNA Fingerprinting Lab.  

Now Until Spring Break!

• Tues 3/5:  Structure of DNA and RNA.  Discovery of the double helix.  Work on 2.6 and 7.1 questions, to be checked off on Thursday.  Read 2.6 and 7.1 if not already.  
• Thurs 3/7:  Check off questions and go over.  Process of DNA replication.  Do simulation in groups and get it checked off.  Start Transcription.  Read 2.7.
• Mon 3/11:  Science Testing for Juniors.
• Wed 3/13:  Transcription to Translation.  The genetic code.  Read 7.2. and 7.3.
• Fri 3/15:  Review the whole process of translation.  Short video on Epigenetics.
• Tues 3/19:  Review of DNA Replication, Transcription, and Translation.
• Thur 3/21:  Replication, Transcription, and Translation Test.  Start Reading 2.5 on Enzymes and work on Enzyme Worksheet, which is due after break on Wed 4/3.

2.6 and 7.1 Work for After the Test on 3/1/19

When you finish the test on Friday (and/or for homework), please do the following questions in your notebook about material in Sections 2.6 and 7.1.  I will check them off on Thurs 3/7, but get them started now!

1. (Starting in 2.6) What are the 3 parts of a nucleotide?
2. Describe 3 differences between DNA and RNA.
3. Do the DBQ on Chargaff's rules on p. 107.
4. Draw and label a simplified diagram of DNA.
5. Outline the structure of DNA
6. (Moving to 7.1)  What were Hershey and Chase trying to determine in their experiment?
7. Outline the Hershey-Chase experiment, including the results.
8. Who was Rosalind Franklin and how did her work influence the discovery of DNA structure?
9. What  is the semi-conservative model of DNA replication?
10. What is a nucleosome and what is its role in DNA packing?
11. Do the DBQ on p. 349 (this one is tricky, but I will give some background on it in class)

Genetics Test Update

Due to the Snow Day on Wed 2/27, the Genetics Test has been moved to Fri 3/1.  Prepare yourself by learning about 2 single gene genetic disorders, review how to set up a dihybrid Punnett Grid and complete it, review how to do a chi-squared test, calculating expected values, plugging into the equation, and interpreting the results.  Much of this information is in 10.2 and can also be found in the Genetics Notes on-line.  We will start Sections 2.6 and 2.7 right away after the test because we will have to cover the next unit before Spring Break!