Evolutionary Genetics Honors
Homework Assignments
September 27, 2010 – November 26, 2010
(The homework is for the night assigned and due the next day unless otherwise noted)
Day/Date / Week 6 / Period 49/27/2010 / Day 1 / Read Chapter 3 in The Making of the Fittest. Answers to the following questions should be updated on your google document, if they are not already, by Tuesday at 4:00 p.m.
This first set was originally assigned on Monday, 9/20/2010.
1. What is the Antarctic icefish, and what makes its blood different from other fish?
2. How does a regular fish regular oxygen transfer? How does the regulation of oxygen in the icefish differ?
3. Why did the icefish make adjustments to the way that it regulated oxygen regulation in the first place?
4. What are the two key principles of evolution, which are so beautifully illustrated in the icefish?
This second set of questions was originally assigned on Tuesday, 9/21/2010.
5. Give your thoughts on these three excerpts from Darwin’s On the Origin of Species . . .FIRST … this preservation of favorable variations and the rejection of injurious variations I call Natural Selection …SECOND… and families of organic beings, with which this world is peopled, have all descended, each within its own class or group, from common parents, and have all been modified in the course of descent …AND THIRD . . . all the organic beings which have ever lived on this earth have descended from one primordial form, into which life was first breathed. (from three excerpts on page 30 of Carroll’s book).
6. What are the three main ingredients of evolution? Discuss the interplay of these three main ingredients (if you need a hint, look to page 42) in your answer).
7. Answer Carroll’s question as he posed it on page 31, So why have his great ideas endured such as struggle?
8. Why is the “sufficient time” required for evolution to do its work far less than one might think. Give an example of such an event from Carroll’s book.
9. How did mathematics ultimately prove to undergird genetics?
10. What is a mutation? Are all mutations bad? Give an example of two different types of mutations. Give an example of two different types of neutral mutations.
I also emailed you the take-home portion of your test that will be due on Monday, October 4, 2010.
9/28/2010 / Day 2 / UGA Greenhouse Tour –This will be LOTS of fun! We will leave from the SA parking lot at break. Get there quickly!
Please also answer the survey monkey questionnaire again this evening or sometime before class on Thursday!
http://www.surveymonkey.com/s/KF28CLY
9/29/2010 / Day 3 / Drop Day
9/30/2010 / Day 4 / Read Chapter 2: Intro to Bioinformatics, Genome Browsers & Genetic Analysis and define the bold terms. Also, we will be going over pages 13-19 in the experimental protocols section of your notebook. You will want to make sure that you are familiar with the bioinformatics that we worked through together in class in preparation for our upcoming experiment.
10/1/2010 / Day 5 / Take home portion of your Unit One Test is due at the beginning of class on Monday.
Day/Date / Cycle / Period 4
10/4/2010 / Day 2 / Answer the following questions from Chapter 3 of Carroll’s book:
11. What was the creature thermus aquaticus, and what have the implications been on science as a result of finding such a cool creature in the hot springs of Yellowstone?
12. What does Carroll term as “immortal genes?”
13. Why is the fact that the genetic code is the same in all species have profound evolutionary significance?
14. What are coding regions in DNA? Non-coding regions? Why are coding regions conserved in higher proportions than non-coding regions?
15. What is meant by a synonymous mutation vs. an injurious mutation? What would be the likely result of an organism who suffered an injurious mutation to an immortal gene during development?
10/5/2010 / Day 3
10/6/2010 / Day 4 / Get Unit One Test Signed and Corrected and Make sure your analysis from the actin experiment is up to date and ready to be handed in for grading. Also, remember to keep up with all that we are doing on the computer as we gear up for our 2nd experiment analyzing polymorphism within the actin gene.
10/7/2010 / Day 5 / Actin analysis in notebook is due by tomorrow. Make sure gel is well labeled and analysis of experiment is thoroughly documented.
10/8/2010 / Day 1 / Enjoy the long weekend. We will extract DNA from our the maize we are growing on Tuesday, so refresh your memory with protocol so you are ready to get back on the bench first thing!
Day/Date / Cycle / Period 4
10/11/2010 / Faculty Work Day / Student Holiday . . . Enjoy! J
10/12/2010 / Day 4 / No Homework because of the PSAT tomorrow!
10/13/2010 / Day 5 / Short Period today
We will finish DNA Extraction tomorrow. So, look through your protocols from last time and make some notes in your lab notebooks so you are prepared at the bench for tomorrow.
10/14/2010 / Day 1 / DNA Extraction and possible Dilution (Nanodrop??)
Read Chapter 4 in The Making of the Fittest.
Answer the following questions on your respective google document:
16. The colobus monkey is a ruminant where digestion is concerned. What does this mean exactly? Do you know of other mammals that are also ruminants? How does this help them expand their nutritional intake?
17. According to Carroll, what are the three elements of the evolutionary process?
18. What is gene duplication, and how is this an important tool for the potential development of new traits in species?
19. What are SINES and LINES and why do they work as perfect genealogical tracers?
20. With respect to color vision, why does Carroll make the point that it may not be a trait that denotes superior complexity (ie – nonprimate mammals are impoverished compared to other more primitive groups of vertebrates)?
21. What is the most likely story of how the 3rd opsin gene resulting in trichomatic vision evolved in primates?
22. Walk through another example of evolution outlined in this chapter (such as blue-shifted rhodopsin in deep-sea fish, UV-light seeing capabilities of birds and/or ruminating monkeys).
This question set will be due on Monday, October 18, 2010.
10/15/2010 / Day 2 / Finish designing primers using bioinformatics learned in class. Organize growing google document. You should have your needed sequence, a picture of your targeted region, your primer sequences and you will ultimately learn how to draw a picture of your targeted region electronically on your google document.
Day/Date / Cycle / Period 4
10/18/2010 / Day 4 / Finish Polymorphism theory, finalize and unify primers among four groups and get primers ordered. Make sure everyone has google doc started with the following FOUR items:
1. Gene Model Picture (captured from DNA Subway)
2. Selected Sequence (for Primer 3 Plus; it was hot pink/light pink representing exons/introns)
3. Primer 3 Plus Output to include F1/R1 primers, product sizes, etc….
4. Electronic Drawing of targeted region of actin gene (we will show you how to do this in your google document)
10/19/2010 / Day 5 / Pour Gels, Resuspend DNA and prepare for loading (add loading Dye), Reload Tip Boxes
10/20/2010 / Day 1 / Load Isolated DNA and Run on Gel
10/21/2010 / Day 2 / Drop Day – Homecoming Schedule
10/22/2010 / Day 3 / Drop Day – Homecoming Schedule
Day/Date / Cycle / Period 4
10/25/2010 / Day 5 / Analyze Gels and Prepare for setting up PCR tomorrow. Make sure to print your pictures and do analysis in your notebook for homework.
10/26/2010 / Day 1 / Set up PCR reactions. Your group should have all the strains covered! We will also need to pour gels today.
10/27/2010 / Day 2 / Run gels in class today! Read Chapter 5 in Sean Carroll’s book for Friday’s class.
10/28/2010 / Day 3 / Drop Day
10/29/2010 / Day 4 / Class Discussion on Carroll’s book.
Day/Date / Cycle / Period 4
11/1/2010 / Day 1 / Prepare DNA Dilutions for 2nd Run of Actin Polymorphism PCR
11/2/2010 / Day 2 / Set up 2nd Run of Actin Polymorphism PCRs
11/3/2010 / Day 3 / Drop Day
11/4/2010 / Day 4 / Run Gels
11/5/2010 / Day 5 / Analyze Gels and Make Plan of Attack for Getting Results
Day/Date / Cycle / Period 4
11/8/2010 / Day 2 / Hopefully, the 3rd time will be the charm for the Actin Polymorphism PCR! A notebook check will be required after the 3rd run of this experiment. I will check to make sure all of the following requirements are in your notebook:
1. Clear outline of what you have accomplished
2. Protocols for each experiment (which should include extraction and isolation of original DNA, running of genomic DNA, and then set up of THREE PCR reactions.
3. You should include the DNA you tested in each protocol, the different dilutions you tried, clearly labeled gel pictures, analysis from each experimental run, and where your group currently is in working through the process.
Remember, our end goal is to get some PCR products that are good enough for us to be able to send off for sequencing! We hope to accomplish this goal by the middle of the week. So, let’s hope for some good lab work this week! Unfortunately, science is not always predictable!!!!
NOTEBOOKS WILL BE DUE ON FRIDAY!!!
11/9/2010 / Day 3 / Drop Day
11/10/2010 / Day 4 / Finish setting up PCR and run some gels during long period! Notebooks due on TUESDAY. Read Chapter 6 in Carroll’s Book.
11/11/2010 / Day 5 / Run Gels and start organizing notebooks! Make sure you are caught up with your reading in Carroll’s Book through Chapter 5 and Chapter 6.
11/12/2010 / Day 1 / Analyze gels & prepare samples for sequencing. NOTEBOOKS will be DUE on TUESDAY!
Questions from Chapter 5 & 6 from Carroll’s book should also be uploaded to your google document by Tuesday evening by 11 pm!
CHAPTER 5:
23. What is a coelacanth, and why does it hold such a special place in natural history? (page 119)
24. What are fossil genes, and how are the same, yet different from living fossils?
25. Describe the cardinal rule of fossil genes, “use it or lose it?” Why does this rule so beautifully explain the evolution seen in fossil genes (hint – your answer should include what happens when natural selection is relaxed on a given gene)? (Last three questions all start around 119 – 123)
26. Cite a couple of examples where gene fossilization has occurred based on examples given in this chapter. (Opsin genes, olfactory smell in humans)
CHAPTER 6:
27. What is convergent evolution? Give at least two examples of animals that represent this phenomenon.
28. Why does it just make sense, practically, for evolution to repeat itself?
29. What role does gene duplication seem to play in an organism’s ability to evolve?
Date / Cycle / Period 4
11/15/2010 / Day 3 / Drop Day
11/16/2010 / Day 4 / Class Discussion, The Making of the Fittest. How has your view of evolution changed over the course of the year so far? Are you making connections about what we are working on at the bench and what we are reading in Carroll’s book.
11/17/2010 / Day 5 / Plant Arabidopsis today. Go over Actin Polymorphism Information sheet. Read “How your DNA Samples will be Sequenced?” for Homework
11/18/2010 / Day 1 / DNA Sequencing and Review of the DNA Subway
11/19/2010 / Day 2 / US SERVICE DAY
Date / Cycle / Period 4
11/22/2010 / Day 4 / Review for Test
11/23/2010 / Day 5 / EvoGen 2nd Test on Polymorphism, our 2nd Experiment, Bioinformatics, the DNA Subway and Primer Design and Experimental Design!
11/24/2010 / Day 1 / Enjoy the
Thanksgiving
Break!! J
11/25/2010 / Day 2
11/26/2010 / Day 3
Date / Cycle / Period 4
11/29/2010 / Day 5
11/30/2010 / Day 1
12/1/2010 / Day 2
12/2/2010 / Day 3 / Drop Day
12/3/2010 / Day 4
Date / Cycle / Period 4
12/6/2010 / Day 1
12/7/2010 / Day 2
12/8/2010 / Day 3 / Drop Day
12/9/2010 / US Review Day
12/10/2010 / US Review Day
Date / Cycle / Period 4
12/13/2010 / US EXAMS
12/14/2010 / US EXAMS
12/15/2010 / US EXAMS
12/16/2010 / US EXAMS
12/17/2010 / US EXAMS / ENJOY THE HOLIDAY BREAK!