Lesson Explainer: Alleles

In this explainer, we will learn how to define and explain the key terms in genetics and explain how alleles provide genetic variation in humans.

Have a look at your family members or some of your friends. We, as the species Homo sapiens, all look quite similar, do we not? We generally have two legs, a head, and ten fingers, but we still look very different. We can easily distinguish two people, because they have different hair colors, different nose sizes, and other features or characteristics that are different from one to the other. The different variants of characteristics are called traits in biology.

Key Term: Characteristic

A characteristic is an observable feature, like, for example, hair color.

Key Term: Trait

A trait is a variation of a characteristic. Traits of the characteristic “hair color” are, for example, red hair or brown hair.

What is behind all of this similarity within a species and the variation between individuals of the same species?

How a body is formed and how it works are defined in genetic instructions. These genetic instructions are found in specific sections in DNA sequences called genes. Once a gene is expressed, it will produce a specific unit, for example, a protein, that controls a particular characteristic. For example, the gene for hair color is converted to a hair color protein that will make your hair appear in the corresponding color!

Key Term: Gene

A gene is a section of DNA that contains the information needed to produce a functional unit, for example, a protein.

In almost all cells in our body, the entirety of the genetic information can be found. The whole of the human genetic material, which is called the human genome, is over 3 billion base pairs long. It was found that if stretched out, all the DNA of one human body cell would span about 2 metres in length. So, how does so much DNA fit into a tiny body cell?

Key Term: Genome

The genome is all the genetic material of an organism.

The secret lies in the packaging of the DNA. Coiled tightly around specific proteins and arranged in an orderly fashion, DNA is packaged into structures that are called chromosomes. This process is illustrated in Figure 1.

Key Term: Chromosome

Chromosomes consist of long molecules of DNA that are coiled around proteins.

**Figure 1**: A diagram showing how the DNA double helix is packaged into a chromosome.

The human genome is packed into 23 pairs of chromosomes. When a baby is conceived, 23 of their chromosomes are inherited from the father, and 23 are inherited from the mother. A human body cell therefore contains a total of 46 chromosomes. You can find an illustration of the human chromosomes in Figure 2.

**Figure 2**: A diagrammatic representation of the 23 pairs of human chromosomes.

Specific genes are found on dedicated chromosomes. We explained previously, in a simplified manner, that there could be a gene causing the coloring of hair. If a gene that specifically determines hair color existed, it would be stored on a specific chromosome, for example, chromosome 1. This means that the gene would be found on chromosome 1 in all humans.

Different versions of the same gene are called alleles. The two terms gene and allele can be thought of in parallel to the two terms characteristic and trait. We recall that a characteristic is a common feature among the members of a species, and our previous example was hair color. The characteristic “hair color” is encoded in a “hair color” gene. Traits, since they are versions of a characteristic, like red or brown hair, are based on the coding of alleles an individual inherits from their parents.

Key Term: Allele

An allele is an alternative version of a gene.

Example 1: Defining the Term Alleles

What are alleles?

Same forms of different genes
Similar forms of the same gene
Different forms of different genes
Different forms of the same protein
Different forms of the same gene

Answer

A gene is defined as a sequence of DNA that contains the information needed to produce a functional unit that can produce a certain characteristic. Different genes code for different characteristics such as the hair color of a person or the shape and size or their nose!

Some appearance features are encoded by one (and only one!) gene. Let’s assume the color of the hair is encoded by only one gene. How can it be that someone has blonde hair and someone else has red hair if there is only one gene coding for hair color?

There have to exist variants of the gene to produce these different outcomes. One form of the gene codes for a functional unit, causing the hair to appear in a specific color, for example, blonde, and another variant of the same gene codes for a slightly different functional unit, which causes the hair to be red. These variations of a gene are called alleles.

Therefore, the correct answer is E: different forms of the same gene.

The introduction of alleles seems to explain how it can be that we all look similar but at the same time very different. We all have genes, defining that we have hair and a nose, but the appearance of the hair and that of the nose are defined by alleles. Alleles are responsible for the diversity of individuals in the species, leading to each individual being genetically unique.

Let’s look at a specific example in humans that demonstrates the vast diversity that alleles can cause: the human leukocyte antigen (HLA) system.

How To: Calculating Genetic Diversity in the Example of the HLA System

Almost every cell in the human body contains some distinctive features that are specific and unique to a person. One of the unique features, carried by all nucleated cells, is the composition of certain cell membrane surface proteins that belong to the HLA system.

The HLA system plays an important role in the immune system. If a body cell is infected by a pathogen, the cell membrane surface proteins of the HLA system will present parts of the pathogen on the cell’s surface. This allows specialized immune system cells to recognize infected cells and fight the pathogen.

There are three main genes needed for the coding of functional HLA system proteins on human body cells, which are called HLA-A, HLA-B, and HLA-C. The three genes are all located on chromosome 6. There are thousands of known alleles for each of these HLA genes.

So, for the sake of curiosity, how many different combinations of HLA proteins are there?

To simplify the task, we will assume that for the gene HLA-A, there exist 82 alleles in humans, for HLA-B 188 alleles, and for HLA-C 63 alleles. We name the first allele variation of the HLA-A allele A1, the second one A2, and so on. The last variant would be called A82. We do the same for the other two HLA genes.

One possible combination of alleles to build a functional HLA system protein would be A1B1C1. Note that all three genes are needed to form a functional HLA system protein. Therefore, A1B1 would not be a valid combination because the part of the protein encoded by the HLA-C allele is missing.

How can we calculate all possible combinations of the variations of the three genes?

Let’s start with a simplified example. Assume that gene 1, gene 2, and gene 3 each have two possible alleles. Let’s call each allele A or B. For a functional protein, an allele from each gene must be present.
For example, a person may have the combination gene1A, gene2B, and gene3B. A different person may have the combination gene1B, gene2A, and gene3A.
But how many different possible combinations are there? Because there are two possible options at each of the 3 gene positions, we simply multiply . So, there are 8 possible combinations!
Let’s revisit our HLA example.
We found out in our simplified example that the general formula to calculate the total number of combinations is

With the given numbers of known alleles, we can calculate .

Let’s just think about this number for a moment. It is close to a million. This is how many possible combinations there are to produce slightly different variants of the HLA system proteins! And this is simply the combination of variants of three genes!

We know that the human genome encompasses around 20‎ ‎000 genes. It is not known how many alleles of all of these genes exist. But having seen that the alleles of three genes already give us the possibility of almost a million slightly different individuals, it is now understandable why it is safe to say that every living human being is genetically unique.

Let’s now return our focus to the key terms in genetics. You might have wondered previously why it is so important to clarify the difference between characteristics and trait and genes and alleles.

Before we can discuss why those differences are important, we first need to look back to the composition of our genome.

You have learned that humans have 23 pairs of chromosomes (46 chromosomes), half from the mother and half from the father, and that specific genes are found on dedicated chromosomes. This means that almost every gene exists twice in the human genome, once on each of the chromosomes from the chromosome pair. In our previous, hypothetical hair color example, we said that the gene coding for hair color is found on chromosome 1. Because we have two chromosomes 1, one from the father and one from the mother, the gene coding for hair color exists twice in our genome.

You have also learned that since traits are versions of a characteristic, like red or brown hair, they are based on the coding of alleles, versions of a gene. As every individual’s gene for a characteristic exists twice in their genome, they have two alleles of that gene; both alleles can be the same (both alleles are coding for brown hair) or they can have two different alleles (one coding for brown hair and one coding for red hair).

To clarify this concept further, let’s have a look at an example.

Example 2: The Location of Genes and Alleles on Chromosomes

The diagram provided shows the basic outline of a chromosome.

What is represented by labels A and B?
1. Different alleles
2. Different genes
3. The same gene
4. The genotype
5. Chromosomes
What is represented by labels A and C?
1. Different alleles
2. Different genes
3. The same allele
4. The genotype
5. Different loci

Answer

The entirety of the genetic material in a human is coiled tightly around specific proteins and arranged in an orderly fashion to form chromosomes.

A gene, the coding unit for a characteristic of an organism, is always found on a dedicated spot, called a locus, on a specific chromosome. For example, the gene coding for the blood group in a human is always found in the same place on a human’s chromosome 9.

In the diagram, we can see a typical chromosome pair. One chromosome comes from the mother and the other comes from the father. Because there are two chromosomes, every human has two genes coding for the same characteristic.

You might know that humans have different blood groups. This is because there exist variations of the gene coding for the blood group. As a matter of fact, there are three variations of this gene. One variation codes for blood group A, one for blood group B and, one for blood group O. These variations of a gene are called alleles.

As every human has two genes coding for the same characteristic, there might be two different alleles present in a human’s genome. A person could, for example, carry the alleles for blood groups A and B or for blood groups A and O.

With that knowledge, let’s have a look at the labels in the given diagram.

Part 1

Labels A and B point out two different locations on one specific chromosome. Because we know that a gene is always found on a dedicated spot on a specific chromosome, these labels must indicate two different genes. The correct answer is B: different genes.

Part 2

Labels A and C point out the same location on the two chromosomes. As the two chromosomes belong to the same chromosome pair, they most probably point out the same gene but different alleles. Looking back at our blood group example, if this diagram was showing us chromosome pair 9 in humans, the indicated genes could be coding for the blood group.

The correct answer is A: different alleles.

Example 2 just gave us a glimpse of the importance of the differentiation between the terms gene and allele. Let’s dive a little deeper into the example of the blood groups.

We know that the human’s blood group is encoded by one, and only one, gene, which is found on chromosome pair 9. If the alleles on both of the homologous chromosomes code for the same blood group, for example, blood group A, the person carrying these alleles is said to have a homozygous genotype, or simply “be homozygous,” for blood group A. They will therefore have the phenotype of blood group A.

Key Term: Homozygous

An individual is homozygous for a characteristic if they have a pair of identical alleles for a gene.

Key Term: Genotype

The genotype is the genetic makeup (alleles) of an organism.

Key Term: Phenotype

The phenotype is the observable trait of an organism and is determined by its genotype.

But what happens if on one of the chromosomes the allele codes for blood group A and on the other chromosome the allele codes for blood group O?

When the alleles are different, the person is known as heterozygous. When a person has a heterozygous genotype for a specific trait, its phenotype depends on which allele is more dominant than the other.

Key Term: Heterozygous

An individual is heterozygous for a characteristic if they have two different alleles for a gene.

Key Term: Dominant Allele

A dominant allele is an allele that is always expressed in the phenotype if present in the genotype.

A dominant allele “dominates” over the recessive allele. In our example, the allele coding for blood group A is the dominant allele. The person will have blood group A, even though they have an allele for blood group O in their genotype.

The allele coding for blood group O is called recessive. A person can only have the phenotype blood group O if in its genotype both alleles code for blood group O.

Key Term: Recessive Allele

A recessive allele is an allele that is only expressed in the phenotype if two copies are present or a dominant allele is not present.

In order to make our life easier, as we do not always want to spell out “dominant allele” and “recessive allele,” biologists have created a nomenclature. Dominant alleles are written as an uppercase letter and recessive alleles are written as a lowercase letter.

For example, instead of saying “the dominant allele for brown hair,” we can simply write “B” and use “b” for the recessive allele that, for example, could code for blonde hair.

Example 3: Identifying Homozygous Genotypes, Heterozygous Genotypes, Dominant Traits, and Recessive Traits

A pea plant has the following two alleles (PP) for purple flowers. Which of the following terms can be used to describe this pea plant?

Homozygous recessive
Heterozygous dominant
Homozygous dominant
Heterozygous recessive

Answer

In diploid organisms, organisms that have pairs of chromosomes, almost every gene is present twice. This is because a gene can be found on a dedicated locus on a specific chromosome.

However, there are variants of a gene, called alleles. Let’s say there is a gene coding for the flower color in a pea plant. There could exist two alleles for that gene: an allele coding for purple coloring and an allele coding for white coloring.

The combination of alleles is called the genotype. If the two copies of the gene are of the same allele type, for example, coding for purple coloring, the genotype is called homozygous. If, however, two different alleles are present, the allele coding for purple coloring on one chromosome and the allele coding for white coloring on the other, the genotype is called heterozygous.

When the genotype is heterozygous, often only one of the alleles is expressed. As this allele “dominates” over the other allele, it is called “dominant” and annotated with an uppercase letter. The other allele is called recessive and annotated with a lowercase letter. A recessive allele is only expressed if the organism is homozygous for the recessive allele.

In our example, the allele for purple coloring dominates over the allele coding for white coloring; we annotate the allele coding for purple coloring with a P and the allele coding for white coloring with a p.

The genotype of the pea plant in our question is given by PP, two capital letters. The dominant allele coding for purple flowers is present twice, meaning that the genotype is homozygous.

Therefore, the correct answer is C: homozygous dominant.

Sometimes, both alleles in a heterozygous genotype are fully expressed. None of the two alleles dominates over the other; therefore, none of the alleles is dominant or recessive in respect to the other allele. These alleles are called codominant. The phenotype of an individual with codominant alleles for a trait is a combination of the phenotypes of the two alleles.

One classic example for codominance is found in blood groups. Because we can find codominance and because we have to consider three alleles and not only two, the annotation for the blood type alleles is a little different than the classic uppercase–lowercase annotation. We note them as I^A, I^B, and I^O.

The interaction of these alleles results in four options for the blood group: A, B, AB, and O. Table 1 shows how the combination of alleles gives rise to the different blood groups.

Alleles Present	I^A I^A or I^A I^O	I^B I^B or I^B I^O	I^A I^B	I^O I^O
Blood Group	A	B	AB	O

We already discussed that the allelic combination I^A I^O results in blood group A, and that therefore I^A is a dominant allele in respect to the allele I^O. The same is true for allele I^B. As the phenotype “blood group O” is only achieved when both alleles are I^O, I^O must be a recessive allele with regard to I^A and I^B.

This is where it gets interesting. There are two dominant alleles, namely, I^A and I^B. What happens if an individual has both of those dominant alleles present in their genotype? They are codominant to each other. Both alleles are expressed and therefore an individual with the genotype I^A I^B has blood group AB.

Let’s summarize what we have learned about the key terms in genetics and how alleles provide genetic variation in humans.

Key Points

The human DNA is packaged into distinct chromosomes.
Sections of the DNA, called genes, code for the characteristics of an organism.
Alleles are variations of a gene.
Every individual is genetically unique.
A genotype refers to an individual’s combination of genes and alleles, and the interaction of these genes is expressed in the phenotype.
If the alleles of a present gene are heterozygous, the “dominant” allele will be expressed.
Phenotypes of “recessive” alleles only appear if the genotype is homozygous for the recessive allele.
Some alleles, such as those that control blood groups in humans, can be “codominant.”