Biology Name: _______________________________
Introduction:
Over the past thirty years we have witnessed a phenomenal growth in our ability to both collect and assess genetic information. Biologists have determined the entire genetic sequence for many individual species. Likewise, biologists are becoming increasingly adept at using this information to evaluate the genome of specific individuals. Technology exists that can be used to determine your specific genotype for a number of different traits.
The light cycler, or real time polymerase chain reaction (PCR), is one piece of equipment that is used for such diagnostic purposes. Using PCR, fluorescent molecular tags, and the knowledge of single nucleotide polymorphisms (SNPs) within an allele, the light cycler can determine the homozygosity or heterozygosity of an individual for a specific allele. The device relies upon the “melting” of DNA, or the temperature at which the two strands of DNA will denature and separate from one another. During the light cycler/PCR process, fluorescent markers attach to the DNA double helix at a SNP. The light cycler device records this fluorescent glow. The temperature of the DNA sample is then continually raised until the two strands denature. At this point the fluorescent markers let go of the DNA and stop “glowing”, also measured by the light cycler. Different base pairs within DNA will “melt” at different temperatures, depending upon the hydrogen bonds between them. Remember, also, that alleles are different due to differences within the sequence of bases of which they are comprised.
Check: Based on the above information:
Predict what a graph of fluorescence data will look like for
A heterozygous individual. A homozygous individual.
Temperature (C) Temperature (C)
Given the title of the activity, you may be wondering why all the fuss over the light cycler? Well, you know that Hardy-Weinberg can be used to calculate the frequency of alleles within a population and to predict the expected percentage of heterozygous and homozygous individuals. In the 70 or so years since Hardy-Weinberg has been widely applied to living populations, data on allele frequency has been obtained through the analysis of phenotypes through the context of a pedigree… much like what we have done in class. However, with technology such as the light cycler, biologists can now screen the DNA itself for SNPs and determine the genotype of an individual. This data, compiled for a population, can then be analyzed using the Hardy-Weinberg model. You will do this in the following activity.

Biology
Review/ Pre-Lab: Before you begin the activity, answer the following questions.
1.
Define the following terms: a.
Allele b.
Genotype c.
Single nucleotide polymorphism (SNP) d.
Hardy-Weinberg equilibrium e.
Founder effect f.
Genetic drift
2.
Describe a reason why genetic equilibrium may shift from one generation to the next.
Please be specific.
3.
Describe three factors that have an effect upon genetic equilibrium.

Biology
Look at http://www.karymullis.com/pcr.shtml
. This will describe the basic process of PCR, or polymerase chain reaction.
4.
In a few sentences, describe what PCR can do with a very small sample of DNA.
5.
Given your answer for question 4, why do you think PCR has drastically influenced the field of forensic investigation (it has)?
Look at the light-cycler handout which describes how a light cycler works.
6.
For the light cycler/ real time PCR: a.
What is the advantage of using the light cycler (what can it do quickly and cheaply)? b.
Why must other technologies be used alongside of the light cycler in genome research (think of the limitations of the light cycler)?

Biology
Scenario: ...and now the fun part.

In July of 1969, human beings first set foot upon the moon. In the years since, human exploration of the solar system continues, primarily through robotic probes that send data back to scientists on Earth. In fact, some scientists agree that continued robotic exploration may confirm the presence of living organisms elsewhere in the solar system. This could even occur within our lifetimes. Though robotic exploration is effective, there are those who feel that human exploration should continue, with the planet Mars being the next target. Since 1969, engineers have proposed a number of strategies for reaching the Red Planet. Generally, these include some version of a 3 year time period spent in a vehicle the size of a mobile home, with a limited amount of time spent poking around the surface of Mars. Yes, imagine the ultimate road trip…except that leaving the car is never an option. Thanks goodness for iPods!

Of the strategies for manned exploration of Mars, one of the more radical approaches has been referred to as the “one-way-trip”. This is exactly what it sounds like; a person or select group of people would volunteer to travel to Mars. Upon reaching Mars, they would stay there permanently, spending the rest of their life exploring the planet and reporting back to Earth. This person or group would be resupplied from time to time, but they would stay on Mars.
Biologically, a group of explorers embarking on a “one-way” mission could constitute a founder population. This is, of course, if males and females of reproductive age were among the explorers. If the “one-way” explorers were to have children, the eventual descendants of the explorers would be similar in genotype to the founding explorers themselves. Your goal is to analyze such a founding population and speculate as to how the genotypic makeup of the descendants will compare to that of the initial founders.
Essential Questions:

Can you use the light cycler data to determine the genotype of each of the founding
Martian colonists (hypothetical colonists, of course)?

Can you calculate the frequency of alleles within the founding population?

Can you calculate the percentage of heterozygotes and homozygotes within this population?

Can you use modeling software to predict the allele frequencies of future “Martian” generations?
Task:
It is the year 2023 and the United Nations is organizing a “one-way” mission of volunteers to study the planet Mars. Fifteen couples from around the world have signed up for the mission. They will travel to Mars, begin study of the planet in depth, and set up a permanent habitat on the planet. Your genetics study group has been contracted by the UN to assist in developing a crew profile. You are responsible for generating data on relevant genetic traits of the crewmembers. Likewise, the UN has asked you to write a summary outlining the genetic makeup of future generations of children born on Mars. Remember that the original colonists will be considered a founder population. Good luck!

Biology
Mars Project: Data Task One. Genotypes.
Target Trait: Eye color, blue vs. non-blue
Target Gene: HERC2, SNP rs12913832
Task Summary: The Mars Project crew will travel to Mars as two separate groups.
Review the light cycler data for each contingent and determine their genotype for the target trait. Record results in the table below.
Crew Contingent One
Crew Member Hetero or Homozygous
One
Two
Molecular Genotype
(gg, GA, or AA)
Phenotype, Blue or
Not-Blue
Three
Four
Five
Six
Seven
Eight
Nine
Ten
Eleven
Twelve
Thirteen
Fourteen
Fifteen
Sixteen
Crew Contingent Two
Seventeen
Eighteen
Nineteen
Twenty
Twenty One
Twenty Two
Twenty Three
Twenty Four
Twenty Five
Twenty Six
Twenty Seven
Twenty Eight
Twenty Nine
Thirty
Mars Project: Data Task Two. Data Totals.

Biology
Task Summary: Use the table below to count and calculate data totals and percentages where indicated.
Data Totals.
Total Mars population, both contingents
Total Number of alleles,
Both blue and non-blue
Total number of Blue
Alleles
Total number of Non-blue alleles
Frequency of each allele within the Crew
Population
Mars Project: Data Task Three. Hardy-Weinberg Analysis.
Task Summary. Given the frequency of each allele within the population of the Mars
Crew, calculate the expected percentage of homozygous dominant, heterozygous, and homozygous recessive individuals. Remember that the Non-blue allele is dominant over blue allele.
In the space below, calculate p 2 , 2pq, and q 2 . Show work please.
Next, use your data from part one to calculate the actual percentage of each genotype within the thirty-person Mars crew. Please show work.
Finally, compare the predicted Hardy-Weinberg values to the actual values. Answer the following in a few sentences.

Are they the same or are they different?

Biology

What might explain any similarity or difference between the predicted and actual values? Hint, think about how the crew was chosen. Crew members were analyzed for eye color but eye color was not a criteria for inclusion in the final mission crew.
Mars Project: Data Task Four. Population genetic analysis.
Task summary: In this step, you will use ‘Allele A1’ software to analyze possible allele frequencies for the descendants of the Mars Crew. Assume that the couples of the crew will have children. These children will in turn will grow and have their own children. As generations pass, what will happen to the allele frequencies within the
Martian population?
Proceed to http://faculty.washington.edu/herronjc/SoftwareFolder/AlleleA1.html
Download and open Allele A1 as directed.
Allele A1 screen shot.
Allele A1 simulates two alleles.
Designate the
Non-Blue allele as A1 and the blue allele as A2
Click this arrow to expand Data window.
Set the nonblue frequency here… and here.
Set your starting population here, this is population” it is possible the a child

Biology
Once you have set your parameters within Allele A1, you will simply click “Run” in thew bottom left to run a simulation. This will demonstrate what occurs to the frequency of the two alleles over a span of 50 generations.
Simulation One: Run the simulator once and answer the following:
 Describe what has happened to the frequency of the two alleles.
 Did the population eventually reach an equilibrium for the blue/non-blue eye trait?
 Why may you have obtained the results you did for this simulation?
Remember the factors that effect Hardy-Weinberg equilibrium.
Simulation Two: Run the simulation again.

Biology
 Describe what has happened to the frequency of the two alleles.
 Did you get the same or very similar results as the first simulation?
Why or why not?
Simulation Three: Run the simulation a number of times until you get a result that is drastically different than either of the first two simulations.
 Describe what has happened to the frequency of the two alleles.
 What may have happened with successive generations of the Mars colonists to make these results differ from those of your first two simulations?
Please be as specific as you can.
 What role does genetic drift play in each of the Mars Population simulations and why is its effect so pronounced?

Biology
Simulation Four: Remember that the Mars Project Crew is a relatively small population of 30 people. Change the parameters of Allele A1 so that it reflects a typical population. Use the same allele frequency, but set the population to at least
1,000,000 people. Run the simulation again.
 What occurs in this simulation that does not occur in any of the Mars
Crew Member simulations?
 In terms of Hardy-Weinberg, how does this final simulation differ from those involving the Mars Crew members?
Final Summary: Summarize your findings to the United Nations below. Be sure to detail the genetic make-up of the initial Mars Crew in terms of the target trait.
Also, describe how, according to models of population genetics such as Hardy-
Weinberg, the Mars population will change over successive generations.
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________

Biology
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
______________________________________________________________________________________
__________________
Finally…bonus question. The title of this activity refers to an older and relatively obscure song that was, for a brief time, a number one hit. For a few bonus points research and tell me the following:
 What is the song and who is the artist?
 When was it on top of the music charts?
 What other very significant event occurred when this song was a number one hit.

Biology
Yes, you must have all three for credit.
