What is a Gene?

What is a gene?

(Key terms will be in
First, a general observation: offspring tend to look like parents. No surprises there. We say that
traits are general descriptions of how an organism appears or behaves and that these traits are inherited from parents. The study of inheritance is called genetics.
What is a gene? I will use two definitions here, both of which are incomplete.
  • A gene is the unit of inheritance. It is the thing that is passed from parent to offspring that results in the inherited trait.
Since we now know that the information in living things is encoded in DNA and that most traits are mediated by proteins (which are encoded by DNA) I can add a second definition.
  • A gene is a stretch of DNA that encodes a protein and the regulatory sequences that tell the cell when and where the gene is turned “on” and the protein is made.
There are a couple of points here. First, since a gene is a physical sequence of DNA, a gene must therefore have a physical location in the long double strand of DNA we call a chromosome. Second, recall that all genes are not “on” in all cells at all times. The thing that makes one cell in your body a liver cell and another a muscle cell is that different proteins are made in different amounts. All those structural variations you studied in the beginning of the year to know how each cell is different come down to which genes are “on” and “off.”

The physical location on a chromosome that contains a particular gene is called a
locus (plural, “loci”). So, let’s pick blue eyes versus brown eyes as an example. It should be said that the details of the genetics of eye color are much more complicated than you may have been previously told. You can find a really good description of how it works here. However, there is a major gene involved in eye color, called “OCA2.” I’ll tell you what the protein it encodes is later. It is encoded by a stretch of DNA on chromosome 15. Like all humans, you have two copies of chromosome 15, one from Mom and one from Dad. A “map” of the chromosome is below. It is approximately 100,000,000 base pairs long and the OCA2 gene is located between base pair 28,000,020 and base pair 28,344,457 on chromosome 15. On every person’s chromosome 15, the gene for OCA2 is in that spot (give or take 10,000 base pairs). This is its locus.
Chromosome15In the diagram, the constriction in the chromosome is where the centromere is. Standard nomenclature refers to the “bands” visible when metaphase chromosomes are stained with a particular dye. The site labeled 15q21.3 is about where the gene resides. “15” refers to the chromosome number, “q” means the longer of the two arms separated by the centromere and 21.3 refers to the band and sub-band. Note that there is not an exact relationship between how thick a band is and how many base pairs are there.

However, even though every one of us has a copy of OCA2 at the same spot on each of the two copies of chromosome 15, the exact sequence of the DNA may be different (due to inherited changes to the sequence in the DNA called
The different forms of the gene are called “
alleles.” There is an allele associated with brown eyes and one with blue.

What does OCA2 do? Well, it encodes a membrane protein that transports an amino acid called tyrosine, which is converted by a specific enzyme into a dark brown pigment called “melanin.” Melanin is the source of the brown color in our skin or hair, and increased melanin in cells in our skin leads to us getting a “tan.” There is no “blue” pigment in my eyes…just the lack of brown pigment in the front of my iris. If you were to cut into my eye, you would find I have melanin in the back of the iris (though, please don’t).
The problem with my eyes that leads to them being blue is
where the transport protein is expressed…or, where it isn’t. The mutation associated with blue eyes is in the regulatory sequences around the sequence that encodes the protein. The transport protein is not expressed (turned on) in the front part of the iris, no melanin gets put there and my eyes are blue.

So, let’s over simplify eye color and say that there is only “brown” and “blue.” Brown results from the transport protein being made in the front of the iris as well as in the back, so melanin is in both places.
Blue eyes result when the transport protein is not expressed in the front of the eye and less melanin is put there. (again, over simplified).

Blue eyes are recessive and brown eyes are dominant.
Consider this: suppose you have people that come in two varieties: ones that pour water on the floor and ones that don’t. If you have two people who don’t pour water in a room, the floor is dry. If you have two people who do pour water on the floor, the floor is wet. If you have one of each…the floor is still wet. The effect of the person pouring water on the floor is
dominant to the effect of not pouring water.

Let’s suppose you got one copy of the “blue” allele from your mom and one copy for the “brown” allele from dad. Since the two
loci contain different alleles, you are said to be heterozygous (having different alleles at the each of the two loci).
The copy you got from mom does not result in the transporter being made in the front of the eye…but the one from dad does, so you have the transporter there and the eyes are brown. The blue allele is busily not doing anything…but no one notices because the brown allele makes the protein. That’s why “blue” is recessive.
In order to have blue eyes, you have to have both copies of the gene be the form that does not function in the eye (just like to have a dry floor, you have to have both people in the room not pouring water on the floor). If you have two copies of the “blue” allele, no transporter, therefore no melanin in the front of the eye, therefore blue.
You are “
homozygous” for the recessive allele. If we abbreviate the allele that results in expression of the transporter as “b” and the allele that results in proper expression in the front of the iris as “B,” you can have three possible arrangements of the alleles at your two loci.
B,B (
homozygous for the dominant brown eyes);
B,b (
heterozygous, one of each allele);
b,b (
homozygous for the recessive allele)

We call this your “
genotype.” Genotype tells you what two alleles at a particular locus you have.
BB and Bb both result in brown eyes. Brown eyes is the “
phenotype,” the person has. Phenotype describes the actual trait.
Only the homozygous recessive (bb) results in blue eyes.