March 6, 2012
Nick Ewing
Freckles, Farts, and Earwax
I. Introduction: How does genetics determine our traits? We all know that our
DNA contains genes that control our traits--or phenotype. Let's look at some
specific examples to see how genes can control traits.

We will use the commercial site 23andMe to help us understand more about
what genes are and how they control traits. Their website is at
https://www.23andme.com/.

23andMe is a company that analyzes individuals' DNA. This isn't an ad for
them! Their site is really a fun place to explore and use to understand
genetics. The cost for their service is dropping all of the time.

You can send in a sample and they will look for key differences in genes.
These single base changes are called SNPs (short for Single Nucleotide
Polymorphisms). These different versions of genes are the alleles that you
have learned about. Take a look at the link on their site if you'd like to see
how they test DNA (either click the "How it Works" button or go here
https://www.23andme.com/howitworks/)
One of the most important things to realize is that many of the bits of DNA sequence
they examine only point to an increased chance of getting a disease or having a trait-not that you necessarily will!
1. Would you like to know that you have a slightly increased chance of a deadly
disease?
2. Would you like to know that you have a greatly increased chance of getting
an untreatable disease? How might knowing this affect you?
This is something to think about before having your genotype analyzed! The time is
very rapidly approaching that we will all know our DNA sequences and know the
chances that we will come down with a wide variety of diseases during our lifetime.
Genetic counselors can help us all understand what all of these predictions mean for
our lives. Consider a career as a counselor if this field sounds exciting for you.
Let's get to the genes! Do you remember the basics from your classes? Take a look
at the "What are Genes" videos (at https://www.23andme.com/gen101/genes/) on
the 23andMe site and try to answer the following questions.
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Nick Ewing
3. How many genes do the 23andMe folks say that we have? (Their number
may be a bit low.)
They say there are fewer than 20,000 genes. They are referring to protein
coding regions here.
4. How long is all of the DNA in a single cell? 2 meters
5. What percentage of our DNA do we share with the rhesus monkey?
Chimpanzees?
Rhesus = 93% Chimpanzee = 98.5%
6. What percentage of our DNA sequences do we share with other humans?
We share at least 99.5% of our sequence with other humans.
7. All of our nucleated cells have the same DNA. What makes cells different
from each other? (Hint: are all genes on all of the time?)
The differences in cells results largely from the pattern in which genes
are turned on and off.
II. Earwax...hey, get your finger out of your ear! Have you noticed what your
earwax is like? There are two major types of earwax, moist and dry. The 23andMe
site describes some of the biology and genetics behind earwax.
Take a look at that here: https://www.23andme.com/health/Earwax-Type/
Here is some of the genetic info:
The genotype column shows the nucleotides at a single position in our DNA. This is
a site that has been identified to be important for this trait for which our sequences
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Nick Ewing
differ. Since these genes differ at this site these are different alleles. These single
base changes, that we often call point mutations, are also called Single Nucleotide
Polymorphism or SNPs. (Want to know more about SNPs? Take a look at the the
tutorials: "What are SNPs" https://www.23andme.com/gen101/snps/)
8. The Genotype that is shown represents the sequence at a single base in our
DNA. Two bases are shown for this site (C or T). Why are there two bases
listed as the genotype?
We have two copies of each gene on autosomes.
9. So, these SNPs represent two different alleles of this gene (for every gene
there probably are many alleles...but we tend to find those that have an effect
on traits). Think about Mendel's experiments (Gregor Mendel...not Greg
Mendel whose genotype is given here.) Which of these alleles is dominant?
Why do you conclude that?
The wet earwax allele is dominant. Having either one or two copies of this
allele leads to the wet earwax phenotype. Dry earwax is recessive since the
individual must have two copies of the allele for the phenotype to be
observed.
10. Can you think of how earwax might be made by your body? Write at least
one possible explanation here (hint: it is made inside cells first before it ends
up in your ear canal).
Perhaps made in cells and secreted?
11. If a material such as earwax is made in a cell it needs to somehow get across
the cell membrane. Do you know some of the ways in which cells move
materials across membranes? Describe how this could occur.
Would they possibly think exocytosis? Membrane transport proteins? Both
are possible mechanisms. Since it is hydrophobic, it is also reasonable to
think they it could diffuse directly through the membrane.
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Nick Ewing
12. It turns out that the SNP here is in the gene ABCC11. This gene encodes a
protein that pumps materials across membranes. In this case, it pumps some
of the material in earwax across membranes. The single base change of this
SNP is in the region of the gene that codes for the protein and causes an
amino acid change from glycine to arginine. Can changing just one amino
acid have a dramatic effect on a protein's function? Do you think changing
any one amino acid would necessarily have a big effect? Explain why you
conclude this.
Yes, single amino acid changes can have a big effect since a difference of even
one amino acid can affect a protein's structure. It can also affect its ability to
bind reactants or other molecules such as receptors that are essential for its
function. While some amino acid changes are dramatic, many amino acid
changes have no effect, especially if it results in the substitution of a similar
amino acid.
13. If the whole protein is 1380 amino acids, at least how long must the mRNA
be? (Show your calculations.)
Since there are three bases per codon the mRNA must be at least:
(3 bases/codon) x (1 codon/ amino acid) x (1380 amino acids) = 4140 bases
The SNP is at base 538 of the mRNA. At this site the sequence is either a G or an
A on the coding strand but the 23andMe site shows the SNP as a C or T because
23andMe reports the sequence of the complementary strand.
14. Look at the genetic code on the last page of this handout. Could a single G to
A change cause a change from Glycine (abbreviated Gly or G) to Arginine (Arg
or R)? Which base of the codon must this be?
If the first base of either of the glycine codons GGA or GGG is changed to an A
this will cause a change to arginine.
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Nick Ewing
III. Taste Blindness! It probably is not surprising that we differ in our ability to
taste. These differences are probably a big part of why we like different foods. Here
is an introduction to this trait: https://www.23andme.com/health/Bitter-TastePerception/
15. What does the gene code for?
It codes for a taste receptor.
16. If individuals have two of the bad alleles they have an 80% chance of not
tasting bitterness. Considering what the gene codes for can you propose an
explanation for why we have to have two bad copies of this gene to not be
able to taste?
If you still have one functional receptor you will still be able to taste bitter
compounds.
17. What is a possible evolutionary advantage of being able to taste bitter
compounds?
Many toxic compounds are bitter so this may have helped us avoid eating
toxic plants and animals.
If you'd like to learn more about the biology of bitter taste perception here is more
detail-- https://www.23andme.com/health/Bitter-Taste-Perception/howitworks/
IV. Freckles: Let's take a look at a bit of the biology behind freckling.
Go to: https://www.23andme.com/health/Freckling/
18. How many different genes do they examine for this trait?
Three.
19. With what other traits are these genes associated?
Hair color, eye color, and sun sensitivity.
20. The two traits we looked at above (earwax type and taste-blindness) are
largely determined by genetics. Many traits are affected by the environment
and not just determined by genetics. Do you think freckles may have a big
contribution from the environment also?
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Nick Ewing
V. Farts...oops, safety! Do you like ice cream...but does it not like you? Many
people are not able to digest lactose. Take a look at the page on lactose intolerance:
https://www.23andme.com/health/Lactose-Intolerance/.
This is an interesting example that adds some new twists.
21. What enzyme do we all produce as babies to digest lactose?
Lactase
22. People who can digest lactose as adults continue to produce this enzyme.
The ability to produce the enzyme is determined by genetics. Look at the
panel "Genes vs. Environment". How can the environment affect this
phenotype?
The bacteria in our gut can affect this trait since they may be able to digest
lactose.
23. In the previous examples SNPs were in the coding regions of genes. The
SNPs identified here aren't in the coding region, but are near by. How can
mutations near a gene affect whether or not the protein is made.
Changes in promoters--the genetic switches that controls genes--can cause
them to be turned on or off or expressed at different times or at different
levels.
Other interesting links at 23andMe:

For a fun look at some other really interesting the links between genes and
disease click on "Discoveries" on the 23andMe homepage or go to:
https://www.23andme.com/about/factoids/

List of all traits examined by them: https://www.23andme.com/health/all/

Lots more good stuff if you look around their site.
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Nick Ewing
The Genetic Code:
Image from: Godfrey-Smith, Peter and Sterelny, Kim, "Biological Information", The
Stanford Encyclopedia of Philosophy (Fall 2008 Edition), Edward N. Zalta (ed.), URL =
<http://plato.stanford.edu/archives/fall2008/entries/information-biological/>, accessed
Feb. 27, 2012
Feel free to copy, modify, or distribute this exercise.
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