Basics of Genetics

In trying to solve the puzzling results he found in his experiment, Mendel developed a hypothesis that explains what genes do on chromosomes when they are transmitted, even though he had no idea what genes or chromosomes were. We can divide Mendel’s hypothesis into four related ideas. First, Mendel argued that the different versions of what he called “heritable factors” must be responsible for producing the different traits. A “heritable factor” was responsible for the purple flower, and a different one was responsible for white flowers. What Mendel called heritable factors are what we now call genes. The different versions of the genes are what we call alleles. For example, the gene responsible for flower color in peas has two alleles, one for purple flowers and the other for white flowers.

Mendel’s second idea was to conclude that each individual had not one but two different particles for each character. In other words, each individual has two alleles for each gene. Mendel made this conclusion knowing nothing about chromosomes, but microbiologists confirmed this by showing that each offspring has two copies of every gene.

Mendel’s third suggestion was that one allele of the two that an individual possesses might actually be dominant over the other one. In other words, one allele is expressed even if the other allele is present. We say that one allele would be dominant, and the one that is not expressed we call recessive.

Let’s go back to Mendel’s experiment to clarify this. He started with true breeding lines of purple and white flowers. He argued that these true breeding lines, that produce only one or the other flower color, must always have two of the same kind of allele. The purple flower plant has two purple alleles and the white plant has two white alleles.

The offspring of this cross must receive one allele from each parent, and thus have one purple allele from one parent and one allele from the other parent. Because all of the offspring in the F1 generation had purple flowers, Mendel argued that the purple form must be dominant over the recessive white form.

Mendel’s forth idea was that when a parent produces gametes in preparation for sexual reproduction; each gamete only gets one of the two alleles that that parent possesses for a particular gene. If we are talking about flower color, if a parent possesses two of the same kind of allele, when it produces gametes, all of the gametes would have only that kind of allele. For example, purple plants from Mendel’s parental generation would only make gametes that have purple flower alleles. The same would be true of the parental white plants.

Here’s the kicker. When we have individuals that have two different kinds of alleles, for example individuals in the F1 generation, can produce two kinds of alleles. They have both a purple allele and a white allele, so they can produce gametes that have either purple or white alleles. In fact, they do so in a 50:50 ratio. It is equally likely that their gametes would have one or the other allele.

The original parental plants Mendel started had two alleles for the same color. We call individuals that posses two of the same kind of allele “homozygous”. The parental plants were homozygous. By contrast, when an individual possesses two different kinds of alleles for the same gene, we say that it is heterozygous. Individuals in the F1 generation were heterozygous.

We give some labels to the alleles. We’re going to give the purple flower allele the capital letter P, and the white flower allele the lowercase p. Giving the uppercase and the lowercase versions of the same letter is one common way that geneticists designate different alleles for a gene.

Because the original in Mendel’s cross were homozygous, they could produce only one kind of gamete. We’ve already said why their offspring should have all purple flowers. If the purple allele is dominant to the white allele, the F1 offspring all have one big P and one little p. Because they all have a big P, which is dominant, they’ll all be purple, regardless of the fact that they have the little p too.


Now I want to introduce two new terms: phenotype and genotype. An organism’s phenotype refers to what it looks like. It refers to the traits that organism expresses. For example, we would say of a purple plant that it has the purple phenotype. The genotype of an organism represents its genetic makeup. The genetic makeup of an organism clearly would have something to do with the traits that the organism expresses. It is important to keep in mind, though, that a given phenotype might be produced by different genotypes.

Let’s go back to our pea plants. Because the purple allele is dominant over the white allele, there are two possible genotypes that could give rise to the purple flower phenotype. Individuals having two big P alleles clearly would have the purple phenotype. So would individuals having one P and one p allele. Both the PP and the Pp genotypes yield the purple flower phenotype. That’s because the purple allele is dominant over the white allele.

On the other hand, the only way we could get the white flower phenotype is if we have a genotype that has both p alleles. This helps us explain the surprising findings from Mendel’s first cross. The white flower phenotype had disappeared completely in the F1 generation, but not the white allele, which was hidden in the heterozygous genotypes of those individuals.

Let’s look at what Mendel found when he crossed these heterozygous F1 individuals together. He found that the offspring in the F2 generation produced both purple and white phenotypes in the ratio 3:1. To understand that 3:1 ratio, let’s consider again the kinds of gametes and the proportions of gametes that those F1 individuals could produce. Because these individuals were all heterozygous, they could produce two kinds of gametes, either a purple allele or a white one. Indeed, each individual would produce equal numbers of both types of gametes.

This makes an intuitive sense. This is very like flipping coins. We’ve got two possibilities; we could come up with a heads or a tails. The key question to ask is what proportion of individuals in the F2 generation would have the possible genotypes that could be formed by joining the gametes that the F1 individuals produced.

An easy way to think about this is to use a convention that we call a Punnett square. Along the top of the square we have one column that has big P on top of it and one column that has little p. Along the side, we have one big P and one little p.

The point of making this grid is that it helps us think about how these different gametes can combine to form genotypes in the offspring. If you fill out the grid by connecting the two alleles possible for each cell, you’ll see that you’ll get three different genotypes. We have PP, Pp and pp individuals. What you also see is that both PP and Pp have the dominant allele, which is the represented in the phenotype. Looking at this you’ll expect to see three purple individuals for every one individual.

With this we can explain why Mendel found a 3:1 ratio in his experiment in the F2 generation. Mendel’s brilliant insight was to put all of this together without knowing anything about genes or the physical basis of chromosomes.

We now refer to this key idea of the existence of two different alleles in each individual as “Mendel’s Law of Segregation”. This law is significant for a number of reasons. First, it completely refuted the blending hypothesis and demonstrated that heritable factors must be particulate. Second, what Mendel did was to provide a framework for looking at more complicated patterns of how traits are transmitted between parents and offspring, which allow us a more complete understanding of the genetic basis of inheritance.