Key for the practice problems

Here are the answers to the practice problem set I gave out in class this week:

Extrachromosomal inheritance

It's time to read Chapter 9, and do problems 1, 2, 3, 7, 9, 10, 11, 13.

The final tally

Here are the final tallies of the data for the whole lab in our trihybrid mapping experiment!

F1 totals for the reciprocal cross

In the female wmf x male +++ cross:
1155 wildtype females, 423 wmf males.

In the female +++ x male wmf cross:
958 wildtype females, 984 wildtype males.

F2 totals for the test cross of female wmf/+++ x male wmf/y:

Now: calculate and analyze and figure out what it all means.

Fun for Spring Break!

Read chapter 5 in your textbook.

I know, that doesn't sound like a lot of fun, but we are about to start talking about some of the more difficult concepts of the term, linkage and mapping. This stuff will not be on the second exam, but don't procrastinate about trying to grasp it all — I lose more students every year when we start doing the quantitative genetics that is needed to understand linkage. It's also material you'll need to understand in order to do the upcoming experiments in the lab.

Also, take a stab at the following problems: chapter 5, problems 8, 9, 10, 11, 12, and 13. Once we've covered the methodology of the triple point cross, after spring break, you'll be better prepared to do 14, 15, 16, 17, 20, and 24. Don't panic if that last batch look impossible right now, we'll be going over that sort of problem in great detail later.

Sex!

You should be reading Chapter 7. We've jumped ahead a bit — sex is a simpler case than linkage that skews ratios, and can be thought of as a kind of linkage, too — but we'll be coming back to linkage later.

Do problems 5, 8, 9, 22, 14, 15, 18, 20, 23, 25, 26.

An answer key for the practice exam

The answers are here.

Tuesday, 19 Feb Lab

We will be meeting in the computer lab on the 3rd floor of Briggs Library. Don't panic if you forget -- I'll put a big notice on the whiteboard in the usual genetics lab.

Problems for chapter 4

Do 1, 2, 4, 5, 6, 10, 11, 14, 18, 23 - 29, 31, 33.

Note that some of these problems do involve some more advanced concepts, like epistasis, and I'm not certain we'll get to those topics before the exam. Don't panic if some look hopelessly difficult at this point!

Problems for chapter 3

Do 1, 2, 6, 7, 8, 9, 15, 16, 17, 21, 23, 26, 27.

Mitosis and meiosis

For next week:

Read chapter 2 in Klug, Cummings, and Spencer.

Answer problems 2, 4, 5, 9, 11, 16, 17, and 20.

Any genetics students going to be staying in Morris this summer?

We're going to be doing a search for a temporary faculty member to teach Genetics next spring term. If you're going to be living in town this summer, and are interested in serving on the search committee, send me a note!

I'm not being replaced, if that's what you're wondering. Dave Hoppe is retiring, and we'll need someone to briefly fill his shoes for a little while, while we carry out a bigger search for a permanent replacement.

The penultimate grade update!

All of the grades on WebCT are now updated, including your last lab report. All that remains is the final exam.

The most important thing for everyone to look at is the column titled "CurGrade". This is what you are getting in the class right now: it is the minimum grade you are guaranteed to receive. If you do not take the optional final, you will get that grade. If you do take the optional final and bomb out horribly, that is still the grade you will get — the final cannot hurt your grade.

The next important column is titled "MaxGrade". If you take the final, this column optimistically assumes that you get 100%, and that that perfect score replaces your lowest exam grade. This is the very best grade you can possibly get in the class at this point.

I'm getting a lot of requests asking me to figure out exactly how well you have to score in the final exam to raise your grade a notch. There's too many of you for me to calculate that for everyone! It also sets yourself inappropriate goals — don't study to get a 79 on the test, always aim for 100. But here's what you can do to estimate whether you should take the final for yourself:

1. Look at your scores for exams I, II, and III.
2. Look at your lowest exam score.
3. If you think you can get a score on the final that is 10-15 points higher than that lowest exam score, you can expect to be able to raise your grade — for instance, from a B- to a B. You should take the final.
4. If all three of your exam scores are consistently in the same range, you should expect to have to study much harder for the final than you did for the other exams. You can take the final — it can't hurt you — but if it means compromising on studying for your other classes, think about it … it's not likely to improve your grade.

If you want to take the final just for fun, of course, feel free to do that, too.

Exam III

The grades are posted on WebCT, the answer key is outside the door to the genetics lab, and you can pick up your exam from the box outside my office door. I'll be available Monday afternoon if you have questions.

Exam III is done — ouch!

Exam III is graded and the scores have been uploaded to WebCT. The mean was 68.6, range was 20-97. Quite a few people were hit hard by this exam, and in particular, question 4 on page 2 was one of those problems where you either got it and did well, or missed the key insight and spent an hour pounding your head against the desk trying to figure it out.

Here's the problem:

4 (20 pts). You have mapped a set of markers on chromosome 2 of the fruit fly such that the wild type chromosome can be diagrammed like so: A—o—B—C—D—E The (o) marks the location of the centromere, and assume that all of these genes are close together (< 5mu) except A, which is about 20 mu from B. You also have a mutant stock of flies which carries recessive alleles in all 5 genes and in which chromosome 2 looks like this:

a—o—d—c—b—e

You cross the wild type and your mutant stock to create a heterozygous line. You then do a test cross of a heterozygous fly with one of the mutant stock flies. List all of the phenotypes you expect to see in descending order of frequency, as near as you can estimate.

And here's the answer.

The key here is to recognized that the inversion will prevent any crossover events within the inversion from appearing. The only places where detectable inversions will occur are

A—x—BCD—x—E

This greatly simplifies the problem because you can just treat BCD and bcd as one inseparable block. If you were sitting there trying to enumerate all possible combinations of 5 different pairs of alleles, you were completely missing the point. (Hint: exam questions won't have that kind of tedious, plodding, repetitious work in them. If you find yourself trying to chip away at a problem with brute force, you're missing something important in the question.)

Most common phenotypes: noncrossover
ABCDE
abcde

Next most common: single crossover between A and B
Abcde
aBCDE

Next: single crossover between D and E
ABCDe
abcdE

Least common: double crossover
AbcdE
aBCDe

Week 15: 30 April-3 May

No lab this week!

Monday in class we'll spend a little time going over a few Hardy-Weinberg problems, and then we'll just open the floor to questions and review.

Tuesday I will be in my office from 9-4; got questions? Come on by.

Wednesday we'll have Exam III, covering Chapters 8, 9, 12, 23, and 25 (25.1-25.4). Subjects covered: chromosome mutations, extrachromosomal inheritance, chromosome structure, developmental genetics, and population genetics. Whew!

The optional final exam for this course will be on Friday, 11 May, at 11:00. I will have all the material for this course (the last lab report and Exam III) graded by Friday, 4 May, and the grades on WebCT so that you can decide whether you need to take the final. Basically, if you already have an A or if your exam scores have been extremely consistent, you probably shouldn't bother with the final; it's main intent is to help students who just had one bad exam day, and would like to replace a poor exam score with a more representative value.

Week 14: 23-26 April

No class or lab! Catch up on your reading, especially of chapter 25.

Problems: Chapter 25, 1, 3, 4, 5, 7, 17.

Week 13: 16-19 April

A little fugu to wind up the discussion of chromosome organization, then chapter 23, Developmental Genetics.

Problems: Chapter 23, 6, 8, 13, 17, 18.

Week 12: 9-12 April

We wrap up Extrachromosomal Inheritance and move on to chapter 12, DNA Organization in Chromosomes.

Problems: Chapter 12, 3, 5, 7, 12.

Week 11: 2-5 April

This week, we'll finish up the discussion of chromosomal abnormalities and move on to chapter 9, Extrachromosomal Inheritance.

Problems: Chapter 9, 1, 3, 8, 11, 13.

Final results of the triple point cross

Here are the final tallies of our triple point cross experiment:

Using these numbers, I calculate a distance from white to miniature of 29.3 map units, and from miniature to forked of 23.6 map units. Be sure to show how those values are calculated in your final lab report!

Exam II is done

The grades are all available on WebCT Vista right now, I think. If you only knew how awkward and cumbersome that horrible little program is from the instructor's perspective...anyway, I'm pretty sure that you'll be able to see the scores if you look. If not, let me know and I'll wrestle and cuss with the program some more.

One very important note: there are two columns there labeled CurGrade and MaxGrade. "CurGrade" is your current letter grade in the class, taking into account exams and labwork. This is the grade you'll probably end up with, assuming that your exam average doesn't change from what it currently is, and is what you should use to get an idea of your current standing. If you bomb out on the remaining exams and skip lab, of course, this grade can plummet. "MaxGrade" is not your real grade; it is an extrapolation that assumes that you get perfect scores on all the remaining work in the course. It is therefore the most optimistic prediction possible — it give you an idea of what you can aim for with the remaining time in the semester.

Week 10: 26-29 March

I won't be teaching you anything new this week — it's all review.

Monday: come to class with questions. I'll open the floor to review any material we've covered so far.

Wednesday: Exam II. This exam will cover chapter 4 (Extensions of Mendelian Genetics), 5 (Chromosome Mapping in Eukaryotes), 7 (Sex Determination and Sex Chromosomes), and sections 1-5 of chapter 8 (Chromosome Mutations).

The lab this week will meet in room 2530, the computer lab near the division office. We're going to talk about the writeup for the triple point cross and learn how to use some genetics databases.

Week 9: 19-22 March

Everyone should be going insane in the lab this week, scoring many hundreds of flies. That will be completed this week, and next week we'll be working on analysis of the data.

In class, we're finishing up chapter 5, and will begin chapter 8, on chromosomal mutations.

Problems: Chapter 8, 1-5, 9, 10, 13-15, 17, 23, 31 (these problems are identical in the 7th and 8th editions)

Week 8: 5-8 March

This week, we start on chapter 6 5, linkage and mapping. This will also be a light lab week—we're just going to make sure your cultures are cleared and that the larvae are thriving. Don't think you're getting off too easy, though, because the week after spring break will demand lots of scope time and fly-counting beyond the regular lab time.

Problems: Chapter 6 5, problems 1-5, 13, 14, 16, 22, 23

Useful tip: The Biology Club is offering tutoring in the BioClub Room (Sci 1040) on Monday and Tuesday nights from 7-9 pm.

Week 7: 26 February-1 March

Here are the results of the recent fly cross for all of the lab sections. There are a few errors in the results, largely due to experimenter error: a few groups did not clear the bottles of the parentals before the F1s eclosed. We'll make very sure that that mistake isn't repeated with the next cross.

Results for the ♀ wmf x ♂ +++ cross:

Note that the progeny in blue are the F1 flies that we are using for our next cross.

Results for the ♀ +++ x ♂ wmf cross:

Be sure to get these numbers into your notebooks. You might also try doing some chi square tests. What numbers would you expect if these genes were not X-linked, and are your results significantly different from that? What numbers would you expect if, as I've told you, they are X-linked? Are the differences in the numbers of males and females significant?

Week 6: 19-23 February

Lab: Some of the flies are being recalcitrant, and people are struggling to get the complete set of crosses done. If you have all of your crosses set up, move your flies now to the incubator at the back of the room. If you have a stock bottle that's been working well to produce virgin flies, remove any post-its you have on it and leave it out for others to use.

Exam: The mean was 70, range 30-97. We'll go over the answers in class today, and finish up chapter 4, I hope.

Readings: We're going to skip ahead a little bit in the book. Read chapter 7 for Wednesday — we're going to look at sex and genetics.

Problems from Ch. 7: 1, 2, 3, 5, 6, 9, 11, 16, 17.

Week 5: 12-16 February

This is an exam week. Monday will be spent working through some assigned problems and opening up the class to questions and review.

The exam on Wednesday will cover all of chapters 1-3 and the basic blood groups (multiple alleles, codominance, incomplete dominance) in chapter 4.

I won't be assigning new problems this week—just study, study, study!

(By the way, if you are reviewing the answer key for exam 1 from previous years, problem #3 will be a killer. It requires an understanding of epistasis, something we won't be getting to until next week—don't panic if you find yourself completely bewildered by that particular question!)

Week 4: 5-8 February

You should be reading chapter 4, where we'll start to learn about all the complexities that cause simple Mendelian genetics to fail.

Problems: Chapter 4, 1, 3, 4, 8, 14, 24, 25, 26, 28, 34.

Apologies for yesterday's absence

Sorry, gang -- I had a minor family medical issue to take care of, and the appointment went on and on far longer than it should have, so when it looked like there was no way I'd escape in time, I had to call in and cancel class. I'll try not to have that happen again.

There will be lab this afternoon. All is well and back on schedule now.

Week 3: 29 Jan-1 Feb

This week, we will be covering the basics of Mendelian genetics. Read chapters 3 and 4.

Some of you will find this very simple, but don't get too cocky. I guarantee you that if you don't understand Mendel's basic rules almost by pure reflex, you will be floundering when we get into all the exceptions.

Problems!

Chapter 3: 1, 2, 4, 6, 7, 8, 9, 10, 15, 33, 38, 39, 41.