Students of biology are usually very eager to learn about genes, the molecular units that carry biological information from one generation to the next. At the undergraduate level they grasp that genes are made up of long stretches of DNA present in chromosomes. They have no trouble agreeing that the subtle differences in the DNA sequence across individuals brings about the variations of a trait, say human eye colour. They are happy to realise that most of these variations arise due to viable mutations, possibly from the same original variety or allele. Mention that the population harbors several alleles of gene A — and several concepts assimilated until then seem to evaporate in a bunch. 

Now suddenly, in spite of visual illustrations, it becomes difficult for students to understand that 

a) a given diploid individual can possess only one combination of these alleles,

b) all cells of the body, including most parts of the reproductive organs have exactly the same combination of alleles,

c) alleles of a given gene are located on only one pair of chromosomes among the many chromosomes in each cell, and

d) each set of alleles occupies the same chromosomal locus in all individuals, hence there are only two seats for them to fill in a given diploid cell/​individual.

The confusions arising from lack of clarity on these details get carried forward into many lessons in genetics, molecular biology as well as evolution. Teachers can identify these early by simply turning the above statements into true or false questions or framing them in the context of inheritance of a trait in a population. 

Sample questions:

1. True/​False: In a diploid individual, one allele each of gene A can be found on chromosomes 6 and 7. 

Answer: False. The locus for gene A can be present on only one of those chromosomes, not on both.

2. Siblings Vidya, Ankita and Sneha all have one allele for gene B in common, but the second allele is shared only by Vidya and Sneha. How many different alleles for this gene do their parents together possess? 

Answer: at least 3 in total.

Answers of the students can be discussed in groups, facilitating them to reach sound conclusions. 

Here I will first explain the correct meanings of (a) alleles at a locus and (b) alleles in a population and then illustrate this using a simple tangible example.

First of all, it is important to remember that the DNA sequence of a gene need not be identical across individuals. Subtle differences in DNA sequences give rise to gene variants, referred to as alleles of the gene. Since the alleles of the same gene in individual 1 may be different from the alleles present in individuals 2 or 3, and so on, the population as a whole may contain any number of alleles of that gene. Some alleles may occur more frequently than others.

In diploid organisms, each individual harbors only two alleles of each gene, one from each parent. These alleles may or may not be identical to each other. So when we say a gene has ten alleles, it means that ten variants of that gene are represented in the population, in different proportions, with two of them being present in each diploid individual of the population. 

To simplify this further with a mundane example, imagine a room with fifty children in it. Now imagine that we have many candies of the same shape but different colours to serve them – say, a total of one hundred candies of ten different colours. The number of candies of each colour may be different – there may be six yellow candies and seventeen red candies. If each child picks up two candies arbitrarily, then the variety of candy colours in the whole ​“population” in the room still remains ten, with any two candies of either the same colour or two different colours available with each person. 

Since a diploid individual inherits one copy of each chromosome from each parent, the number of loci for a given gene in the zygote is limited to two – one on each chromosome of this particular pair of chromosomes. So, alleles once assigned to the gene locus are faithfully replicated to all cells of the body – only a mutation (one that survives and shows up: which is another topic by itself!) can alter an allele in a cell. Even then the number of alleles of the gene in the cell remain the same as before, barring exceptional cases (e.g., if an abnormal cell division results in a missing or an extra chromosome, thereby resulting in a missing or an extra locus, respectively).

Teachers can use the above explanation to dispel confusions regarding (1) alleles in the population v/​s individuals (2) ploidy and number of alleles. I hope this makes subsequent discussions more fruitful for everyone!