Monday, December 7, 2009

Genetics Practice Problems Solutions

Here are the answers and explanations for the genetics review problems from class today. There will be five problems on the test.

1. Colorblindness is a sex-linked, recessive trait. Remember that sex-linked traits are on the X chromosome, which means that men only have one copy of the gene. In this example, we are told that the man has colored vision, so his genotype must be XCY. The woman also has colored vision, so she could be XCXC or XCXc. Since one of her sons is colorblind, she must be XCXc, since sons inherit their X chromosome from their mothers.

2. This is a relatively simple dihybrid cross. If we use B for brown eyes and b for blue eyes; and H for brown hair and h for blonde hair, the genotype of the man is BbHH, and the woman is bbhh. Doing the cross, their children have a 50% chance of being BbHh and a 50% chance of being bbHh. Answering the question posed on the sheet, there is 0 chance their children will have blue eyes and blonde hair.

3. This is an example of a dihybrid cross where one of the genes displays incomplete dominance - red and white flowers give pink. We are crossing two F1 plants, so the phenotype of both parents is TtRr. For this type of dihybrid cross with complete dominance, we would normally expect the 9:3:3:1 ratio. However, with incomplete dominance there is a new phenotypic class, since the heterozygous individuals are distinct from the homozygous dominant individuals. The expected phenotypic ratios are then 3 tall, red-flowered; 6 tall, pink-flowered; 3 tall, white-flowered; 1 dwarf, red-flowered; 2 dwarf, pink-flowered; and 1 dwarf, white-flowered.

4. A dihybrid cross with a lethal allele. If an individual is homozygous recessive for the l allele, they will not survive, and are not counted in the phenotypic ratios for the answer. The parental genotypes are LlBb and Llbb. After throwing out the individuals with the lethal gene combination, the phenotypic ratio in the offspring is 1 normal-legged, brown; 1 normal-legged,white; 2 deformed-legged, brown; and 2 deformed-legged, white.

5. Gene linkage. You absolutely must know how to analyze these types of data, and tell the difference between parental and recombinant phenotypes. The data that are presented are from a testcross on the F1 generation. The genotypes for this cross are CcShsh crossed with ccshsh (remember, a test cross is always performed with a homozygous recessive individual). The phenotypes of the parents are colored, full seeds and colorless, shrunken seeds.

If we assume that these genes are going to follow the Mendelian laws of inheritance, we predict that the offspring would have equal numbers of the four possible phenotypic classes: colored, full; colored, shrunken; colorless, full; and colorless, shrunken. HOWEVER, that is NOT what the data show. Two of the phenotypic classes, colored, full seeds and colorless, shrunken seeds are MUCH more common than the other two. These two common phenotypes are called the PARENTAL phenotypes, since they resemble the parents of the cross. The other two phenotypes, which are much less common, are called RECOMBINANT phenotypes, since these gene combinations do not exist in the parental generation.

To calculate the map distance, we need to calculate the recombination frequency, which is simply the percentage of offspring that show recombinant phenotypes. For this problem, the answer is (515 + 489) / 8368 = 12%. This means that the genes are 12 map units apart.

6. This is an example of epistasis - one gene is influencing the expression of a second gene at a second location. In this case, dogs that are homozygous recessive for the e gene will be yellow, regardless of what alleles are at the location that determines pigment color (B for black and b for chocolate). The phenotypes of the parents are BbEe. Doing the cross results in a 9 black to 3 chocolate to 4 yellow labs.

7.

...........7..........3...................15..................5..........
-----/-----------/----------/---------------------------/-------------/---
.....b..........d...........a...........................c.............e

8. This is a simple incomplete dominance cross. The heterozygous individuals have green flowers. A cross of two green flowers gives results of 1 blue, 2 green and 1 yellow.

9. The genotype of the woman must be ii, since that is the only possibility for type O blood. Her baby, with type A blood, must have at least one i allele from the mother. Therefore, the babies genotype must be IAi. The IA allele must come from the father. The only man with an IA allele to contribute is man #2.

10. Pedigree A is an autosomal recessive trait. Pedigree B is a sex-linked trait because many more males exhibit the trait than females (7 vs 2). Pedigree C is a dominant autosomal trait. To differentiate recessive and dominant traits, there are a few things to look for. First is that recessive traits tend to skip generations. Look at generations I and III in pedigree A. For a dominant trait, at least one parent must exhibit the trait in order for it to be passed on to the offspring.

11. I treated this example like a regular dihybrid cross, but in this case the dominant allele will change based on the sex of the individual. The two parental genotypes are BbXX and BbXY. For female offspring, there will be 3 with hair for every 1 bald; and for males there will be 1 with hair for every 3 bald.

Wednesday, September 2, 2009

Summer Assignment: 9.2

Since this is the last post for the summer assignment, I would like to take the time to thank everyone for doing a great job. The comments were very thoughtful, and there seems to be some very interesting differences of opinion among you all; hopefully this will lead to some good discussions/debates in class.

There is no reading assignment this week. I want to know some of the topics you are interested in learning more about this year in class. It can be something that was covered over the summer, such as evolution, or anything else that you find interesting. We will do our best to cover as many of the topics as we can, but it may not happen till after the AP test.

Wednesday, August 26, 2009

Summer Assignment: 8.26

Tools Let Public Contribute to Massive Interactive Online Biodiversity Encyclopedia

Short update on the progress on the Encyclopedia of Life, an effort to catalog all of Earth's species. A very ambitious and worthwhile project. Another similar project is the Tree of Life, which focuses more on the phylogenetic (evolutionary) relationships between species.

Chris Jordan Photographic Arts

A blogger at Ready Made Magazine is trying to survive for a week without plastic. Very interesting concept, I have seen this done a few times before with other materials. But it reminded me of the artwork of Chris Jordan, who creates mosaics using certain numbers of items.



The example above is made of 10000 dog and cat collars, which represents the average number of unwanted dogs and cats euthanized in the US every day. The gallery at his website features close-up views of the work, and most of his others, so that the individual pieces can be seen.

Very powerful work, I highly recommend visiting the site and checking out the two Running the Numbers galleries. A great visual statement on our disposable culture in America.

Wednesday, August 19, 2009

Summer Assignment: 8.19

The Long and Short of It

Short essay about the evolution of size in animals. There are many factors at play here, and the process is not very well understood.

I found this to be very interesting
Take a salamander. Let’s say it’s a certain size, and it has a certain number of cells. Suppose you double the size of the cells. Do you get a salamander that is twice as big? No. You get a salamander that’s the same size as it was before. But it has half the number of cells. Somehow, the salamander’s body can measure how big it is and stops growing when it gets to the right size.

(These animals look like regular salamanders, and are perfectly healthy. However, they are a bit stupid, apparently because they have half the number of brain cells. They’re less good than regular salamanders at solving mazes.)

Poor salamanders, not only are they small, they can't find their way home.


Early Risers are Mutants


I always knew there was something weird about morning people. Well, I shouldn't point fingers, I usually do just fine on 5 hours of sleep a night. But still, being able to tell a morning person that they are a mutant is nice.

Wednesday, August 12, 2009

Summer Assignment: 8.12

Babies' Brains Churning With Activity

The idea of "mirror neurons" is very interesting...as you watch someone doing an action, your brain works as if you are doing the action yourself. Could be a very important part of learning motor control.

Tumor Suppressor Pulls Double Shift as Reprogramming Watchdog

Induced pluripotent stem cells (iPSC) could potentially be the key to the future of stem cell based therapies and research. They can provide patients with a population of stem cells that are an exact genetic match, without the moral/ethical issues surrounding other methods of obtaining stem cells.

Vertical Farms

I thought that this was an interesting method to address the food problem in the world. Not sure if they took into account the price of real estate in NYC....

Wednesday, August 5, 2009

Summer Assignment: 8.5

Microbes 'R' Us

Interesting ideas about the role of intestinal flora in human evolution. Why do specific groups have specific bacterial signatures? Do the diets fit the bacteria, or vice versa? Could this play a role in one of the posts from a few weeks ago about humans eventually evolving to be able to handle high-fat diets and not become obese: Since bacteria can evolve so much faster than humans, it is probably much more likely for a fat-metabolizing bacteria to arise than the human genome changing.

How Happy is the Internet?

Very interesting use of the internet in social research; the results from Twitter should be even more enlightening. Some interesting questions raised about popular music too: Is there a relationship between happy lyrics and popularity? As someone who listens to both "sad" (Radiohead, Elbow) and "happy" (Jack Johnson....umm, that's the only happy artist I can think of right now. Maybe I only like sad music...) artists, I think maybe the popularity of the artists may be a reflection of the overall mood of time. Happy mood = happy popular music.

But anyway, how can the internet not be happy when there is stuff like this on there. And this.

Tuesday, July 28, 2009

Summer Assignment: 7.29

Respect For the Fungus Overlords

Only one link today, it is a longer article and I am going out of town (again) tomorrow, and still need to pack...

Carl Zimmer is one of my favorite science authors/bloggers, there is a link to his blog The Loom on the left side of this blog. I recently read his book Parasite Rex, which was about how parasites are integral parts of ecosystems, and in many ways have directed the evolution of their hosts. One idea is that parasites are responsible for the evolution of sexual reproduction, which is actually quite costly and the reasons for it first appearing are unknown.

One thing that is made very clear throughout the book is that a parasitic life style may actually be the "norm" on Earth, rather than something odd or strange. Parasitic life forms may very well be found to outnumber "free-living" organisms.

This particular article highlights some current research on a fungal parasite (Ophiocordyceps unilaterius)of a specific species of ant (Camponotus leonardi). This parasite takes over the body of the ant and causes it to seek a high leaf. From there, the fungus grows out of the ant body and releases spores the forest floor below, which are then able to infect more ants.



The researchers wanted to know if the parasite was actually controlling the ants, or if the ants just got lost along the way, since ants normally do not occupy the specific leaf height where infected ants go to die and release the fungal spores.

And for those of you who may think this research qualifies as frivolous or wasteful,
Like their hosts, parasites face many threats to their survival these days. Just as overfishing may wipe out my dear namesake tapeworm, I worry about the rampant deforestation of tropical forests, which may wipe out not just trees, but the insects that depend on them, and the fungi that depend on them in turn. We should not wish extinction on Ophiocordyceps, as gruesome as it may be. It has much to teach us. We might even borrow some of its tricks–Ophiocordyceps antibiotics show promising signs of fighting against malaria and cancer. And it would be a true shame for this particular bit of science fiction to disappear from the world of science fact.

Also, parasites are just way creepy-cool. If you don't take my word for it, check out the book.

Thursday, July 23, 2009

Quick Comment

Just a quick note that I will be out of town, with no internet access, from Friday morning till Sunday night/Monday morning. If you make a comment between those times, it may take a few days to show up. I will read them all when I get back.

Tuesday, July 21, 2009

Summer Assignment Post for 7.22

Lots of great comments last week...seems like everyone likes to curse when they hurt themselves, and are somewhat skeptical of using rapamycin to increase life span.

Remember to vote in the polls if you have not, and to check back for other student comments all week; the comment section can be a great place for discussion/arguments.

Seemingly "Duh!" Scientific Studies Often Hold Value

I actually looked up one of the studies mentioned in this article: the one about the evolution of tickle-induced laughing. Granted, that may have been just because I had an image in my mind of a bunch of grad students in a lab tickling baby chimps and gorillas, and that made me happy.

And I also found their model of the evolution of this laughter to be interesting...



If you haven't heard this before, you definitely will this year in AP: Everything in Biology can be explained through evolution.

In regards to the original article, do you think there are "frivolous" scientific studies? Or is any and all knowledge worthwhile, simply for the sake of knowledge?


Coping With Excess

I thought this was an interesting idea...will humans eventually evolve to be able to handle Big Macs and not get obese? Not sure... the columnist makes a lot of good points, but I think the most important one may be one of the last ones:
Many factors — what you eat today, what you ate as a baby, levels of exercise, your gut microbes and so on — contribute to obesity.

Something very important to remember, all traits, especially human traits, are very complex and hard to ascribe a cause to.

And the pentailed tree shrew looks like a pretty cool guy...even if there is only the one picture of him.

Tuesday, July 14, 2009

Summer Assignment Post for 7.15

This is the first "official" post for the summer assignment. Take a few minutes to read the linked articles below and make a comment or two on them. You don't need to read all three or comment on all three to get credit...just read whichever ones interest you. Be sure to check back often during the week after you have posted your comment, as you may want to respond to other student's comments, or they may specifically address your comments.

Also, if you have not voted in the two polls on the left side, please do so. The polls are anonymous, so you will not be singled out for your responses.

Darwin's Mystery of Appearance of Flowering Plants Explained

Two ecologists present a possible explanation for the rapid (in evolutionary terms) expansion of angiosperms in the Cretaceous period (100 - 65 million years ago). This problem upset Charles Darwin greatly, and he had no explanation for it when he proposed his framework for evolution by natural selection. I have an essay around here somewhere that goes into more detail about angiosperm evolution, but I am not sure where it is right now....

Anyone have any comments/thought about the mechanism proposed in this article?


A Pill for Longer Life?

Rapamycin, a drug commonly used in humans to prevent transplanted organs from being rejected, has been found to extend the lives of mice by up to 14% — even when given to the mice late in life. [...]until now, the only robust way to extend life in mammals has been to heavily restrict diet.


In terms of the average US life span of 78 years, this would add about 10 years. Would you take a drug that may increase your life span if it meant that you may be more susceptible to infections?


Holy $@%#! Swearing Eases the Pain

I thought this was kind of interesting...but I don't need you to make a list like the researchers had their subjects do.

Tuesday, June 23, 2009

First summer assignment

Please vote in the polls to the right...be honest; they are anonymous, and are only for information gathering purposes. If you select other for the first poll, feel free to elaborate in the comments section.

Monday, June 15, 2009

Summer Assignment

Welcome to the AP Biology summer assignment for 2009. The assignment will officially begin on July 15, after which you will be responsible for a weekly comment on the post topic of the week. Until then, you can use this post to practice making comments, and determine if your screen name works. Comments are moderated, which means that I read them over before they will appear on the site, so it may take a while for your comment to show up.

Have a good summer, and see you here in July.

Friday, February 27, 2009

Links for 2.27.09

Transpiration Lab

Drink Up, Energy Hogs


Are people still drinking that much bottled water? Really??

Deconstructing the Ribosome


Interesting article on the evolution of a highly complex structure - the ribosome.

Sunday, February 15, 2009

Chapter 35 and 36 review packet answers

Answers for chapter 35 and 36 review packets

Chapter 35

MATCHING

1...H .6...A
2...F .7...C
3...B .8...D
4...E .9...J
5...I .10...G

MULTIPLE CHOICE
1...A .9...E
2...E .10...D
3...B .11...E
4...C .12...B
5...B .13...C
6...A .14...C
7...E .15...E
8...C .16...D


CHAPTER 36

1...B .11...A
2...E .12...C
3...D .13...E
4...A .14...B
5...C .15...C
6...B .16...D
7...D .17...D
8...D .18...B
9...A .19...D
10...C .20...C

Tuesday, February 10, 2009

Links: 2.10.09

Projected records: Baseball 2009

Wonder how it would feel in Tampa if the Rays have the second highest win total in franchise history, and yet miss the playoffs. Ouch. As far as the Orioles winning 76 games, which would be an 8 game improvement over last year, I think that sounds about right.

Flu: It's the humidity. Absolutely


Winter is flu season in the world's temperate regions, but scientists still aren't sure why. Now, it turns out that the answer may have been staring them in the face all along. A reanalysis of data from past studies suggests that low absolute humidity--not low relative humidity, the factor many scientists have studied--helps the virus survive and the flu spread.

"Immortal" Jellyfish Swarm World's Oceans

A potentially "immortal" jellyfish species that can age backward—the Benjamin Button of the deep—is silently invading the world's oceans, swarm by swarm, a recent study says.

Time to put Darwin in his Place

Charles Darwin would be 200 years old this week. And after all these years, people are still arguing about the theory of evolution that he fathered.
[..]
But there's another reason for the ongoing debate that may surprise you: The terms "Darwinian evolution" and "Darwinism" — used frequently by scientists and the media — are misleading.

Friday, February 6, 2009

New post format: Links for 2.6.09

I realized the other day that I have not posted anything here for a long time: Just about a month. I am going to start a new type of post - the links dump. Just a bunch of links to things around the Interwebs that I find interesting/important/amusing. They won't all be science-related - I do enjoy reading about things besides science.

Energy Drinks: The coffee of a new generation?

Several studies have demonstrated that strong doses of caffeine can increase hypertension, cause heart palpitations, provoke irritability and anxiety as well as cause headaches and insomnia. Health Canada does not recommend consuming more than two cans per day.

What causes schizophrenia?

Researchers in Sweden have revealed a surprising change in brain biochemistry that occurs during the training of working memory, a buffer that stores information for the few second required to solve problems or even to understand what we are reading. The discovery may have implications for understanding disorders in which working memory is deficient — such as schizophrenia and attention deficit hyperactivity disorder (ADHD).

Scientists find world's largest snake

The scientists estimate the snake lived 58 to 60 million years ago and was around 13 metres long. The giant, found in northeastern Colombia, dwarfs modern pythons and anacondas which usually don't exceed 6-6.5 metres and are thought to be the largest living snakes.

Amid rising childhood obesity, preschoolers found to be inactive

They found that the preschoolers were inactive for much of their preschool day, with 89 percent of physical activity characterized as sedentary. Even when they played outside, a time when children are expected to move around, 56 percent of their activities were sedentary


A much earlier start for animals


Where did all the animals come from? The fossil record is virtually animal-free up until the Cambrian Explosion 540 million years ago, and then--boom--thousands of critters of all shapes and sizes show up. The mystery has plagued scientists for more than a century and a half, beginning with Charles Darwin. Now, with a brilliant bit of detective work, researchers have located our missing ancestors.

Thursday, January 15, 2009

Darwinism Test and PowerPoint

I was a bit disappointed by the level of surprise in class today about the test on Friday. I hand out the monthly syllabus for a reason: For you to know what is happening in class. I expect you to use the schedule, and not rely on me to tell you when things are happening. There should be no surprises when it comes to tests, quizzes, labs, or any other class activity.

I want you to use the syllabus for a few reasons. One, it makes it easier for me to plan. It should also make it easier for you to study, since you have a few week's notice of tests and quizzes. If you are absent from class, you can look at the schedule and see what we are going over that day. One of the most important reasons I do this is that this is what happens in a college course. You will get a syllabus at the beginning of the semester that lists all the tests. You will be expected to know when they are. The professor/instructor may not remind you that they are coming.

Please use the syllabus. There is one posted in the classroom, and I can get you another copy if you lost yours. There are two more quizzes on the syllabus for this month. Make sure you know when they are. I may not remind you in class about them.

Anyway, here is the complete PowerPoint for Chapter 22. I will be moderating comments till 10.30 tonight.