The first exam will be Thursday, March 14. If you will be absent that day, e-mail me by the end of the day on Thursday, March 7, so that we can schedule your makeup exam.
You may not use your notes during the exam. You will not need a calculator.
The exam will consist of about 15 questions. Each of your answers should consist of one or two sentences. You will get points off for writing long, rambling answers that say the same thing over and over.
Here are some practice questions. Try answering them, then highlight the invisible text inside the red box (drag your cursor across it) to see my answer.
1. Based on their similar size, short tails, and cute noses, you think that guinea pigs and rabbits are more closely related to each other than they are to rats and mice. How would you test this hypothesis? What result would be consistent with your hypothesis?
Answer: I would collect DNA sequence data from one or more genes in the four species. If my hypothesis were correct, I would expect the difference in the DNA sequences between guinea pigs and rabbits to be smaller than the difference between them and rats or mice. [If a question asks for one answer, and you can think of more than one possible answer, just put down the one that you think is most likely to be correct. You won't get extra credit for having both correct answers if only one was asked for, and if one of your answers is right and one is wrong, you'll get graded based on the wrong answer. For example, if you wrote: "I would collect DNA sequence data from one or more genes in the four species. If my hypothesis were correct, I would expect the difference in the DNA sequences between guinea pigs and rabbits to be smaller than the difference between them and rats or mice. I would also look for rabbit-guinea pig hybrids in the Precambrian fossil record; if my hypothesis were correct, I would find them", you would get zero points, because the second half of your answer is very wrong.]
2. DNA polymerase is an important protein involved in replicating DNA during reproduction. One DNA polymerase protein in the bacterium Escherichia coli is 351 amino acids long; here is its sequence, using the single-letter amino acid abbreviations:
>gi|89107104|ref|AP_000884.1| DNA polymerase IV [Escherichia coli W3110] MRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLT LLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASA GVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVM LLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPD LLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDPQMERQLVLG L
If you put amino acids together randomly, the probability that a random molecule would have this sequence is 1/20351. This is such a ridiculously small number that if the whole universe were made of amino acids, randomly associating into new molecules every second for the last 13 billion years, this sequence would never have occurred. Creationists use this kind of calculation to argue that life could not have originated by random, natural processes. What's wrong with their argument?
Answer: There are many different sequences that would function as a DNA polymerase, so the numerator in their expression should be much greater than 1. This makes the probability much higher than the creationists calculate.
3. You've decided to write your term paper about ammonites. What are the three most important things you would do to find scientific literature about ammonites?
Answer: 1. Do a topic search for ammonites in the Web of Science.
2. Pick some of the articles from the topic search and look at their reference lists for good older papers.
3. Pick some of the best papers from steps 1 and 2 and use the Web of Science to find more recent papers that cite them.
[Note that if a question asks for more than one answer, be sure to give the correct number of answers. Numbering the answers, as I've done here, may help you keep track of this.]
4. You are trying to estimate the phylogeny of several species of pine trees in the genus Pinus. You sequence the RBCL gene in a white pine, lodgepole pine, yellow pine, bristlecone pine, and pitch pine. You also sequence the RBCL gene in a blue spruce, Picea pungens. You analyze your data on RBCL in pines using the neighbor-joining technique and it gives you the tree on the left, while the maximum likelihood technique gives you the tree on the right. What do you conclude about the relationship of white pine, yellow pine, and pitch pine? What should you do next?
Answer: Because the two techniques give different results, you conclude that you don't know whether yellow pine is more closely related to white pine or pitch pine. Your next step would be to collect more data, such as DNA sequences of more genes.
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This page was last revised February 25, 2013. Its URL is http://udel.edu/~mcdonald/495studyguide1.html