the distinction between genes, alleles and a genome, and the use of pedigrees, Punnett squares and other tools to predict inheritance

What this dot point is asking

VCAA wants the precise distinction between three related but different terms: gene, allele and genome. These are the language of inheritance, used in every Unit 2 question that follows.

The answer

Gene

A gene is a length of DNA at a specific location (a locus) on a chromosome that codes for a functional product. Most genes code for a polypeptide (a protein or part of one) by being transcribed to mRNA and translated. Other genes code for functional RNAs (tRNA, rRNA, microRNAs).

A gene is the basic unit of inheritance: it is what is passed from parent to offspring and what is expressed as a trait.

The human nuclear genome contains around 20,000 protein-coding genes, plus many more that produce non-coding RNAs.

A gene has a fixed locus on a chromosome. The locus for the human ABO blood group gene, for example, is on chromosome 9; the locus for the gene that causes Huntington's disease is on chromosome 4.

Allele

An allele is a variant of a gene. Most genes exist in two or more allelic forms in a population because of historical mutations.

Examples:

• The pea flower colour gene has at least two alleles: P (purple, dominant) and p (white, recessive).
• The human ABO gene has three common alleles: IA, IB and i.
• The gene for the CFTR protein has one common functional allele and many disease-causing alleles (the most common is delta-F508), responsible for cystic fibrosis.

In a diploid organism (like humans), each individual has two alleles for each autosomal gene, one on each homologous chromosome, inherited one from each parent. The pair can be:

• Homozygous: the two alleles are identical (PP or pp).
• Heterozygous: the two alleles differ (Pp).

Alleles differ from each other by mutations in the DNA sequence: a single base change, an insertion, a deletion, or a larger rearrangement.

Genome

A genome is the complete set of DNA in a cell, including:

• All genes (coding sequences).
• All non-coding DNA between genes (regulatory regions, introns, repetitive elements, much of which once called "junk DNA").
• In eukaryotes, the nuclear genome plus the small genomes in mitochondria (mtDNA) and chloroplasts (cpDNA).

The human nuclear genome is about 3 billion base pairs organised into 23 pairs of chromosomes (22 autosome pairs + the sex chromosomes XX or XY). The mitochondrial genome is a single 16,569-base-pair circle inherited from the mother.

A genome is usually referred to per species (the human genome, the wheat genome, the E. coli genome). Within a species, individuals share the same genome organisation but differ in their specific alleles at many loci.

Genotype and phenotype

Two more essential terms that build on the above.

Genotype is the genetic make-up of an individual at one or more specific loci: the combination of alleles. Examples: PP, Pp, pp; IA IB; or for two genes, AaBb.

Phenotype is the observable trait produced by the genotype, often influenced by the environment. Examples: purple flower colour; AB blood type; tall plant.

The relationship genotype to phenotype is set by the rules of inheritance (dominant/recessive, codominance, incomplete dominance, sex-linkage, polygenic). It is also shaped by the environment and epigenetic factors. Identical twins have the same genotype but can have different phenotypes if they grow up in different environments.

Other essential terms

• Locus (plural loci): the specific position of a gene on a chromosome.
• Chromosome: a single DNA molecule wrapped around histones. Humans have 23 pairs.
• Homologous chromosomes: a matching pair, one from each parent, with the same genes at the same loci (but possibly different alleles).
• Dominant allele: masks the effect of a recessive allele in a heterozygote.
• Recessive allele: only expressed in a homozygote.
• Wild type: the most common allele in a natural population.
• Polymorphism: the existence of multiple alleles of a gene in a population at appreciable frequency.

Why the distinction matters

Sloppy use of "gene" when you mean "allele" is the single most common mistake in VCE genetics responses.

Wrong: "She inherited the gene for blue eyes."

Right: "She inherited a recessive allele of the eye-colour gene that, in homozygous form, produces blue eyes."

Markers reward precision: the gene is the locus; the allele is the variant.

Examples in context

Example 1. Wollemi pine population genetics at Royal Botanic Gardens. The Wollemi pine (Wollemia nobilis), discovered in 1994 and now propagated at the Royal Botanic Gardens (Melbourne and Sydney), has fewer than 100 wild adults. DNA fingerprinting found that every wild individual is essentially genetically identical, sharing the same alleles at every locus tested. In other words, the species' genome is present but allelic diversity is near zero. This makes the population highly vulnerable: a single pathogen targeting the shared phenotype could wipe out every plant. The example clarifies the gene-allele-genome distinction. Every Wollemi pine has the same genes (the species genome) but lacks the allelic variation that normally protects populations.

Example 2. Punnett squares for autism risk counselling at Royal Children's Hospital. Genetic counsellors at Royal Children's Hospital Melbourne use Punnett squares and pedigrees to predict the inheritance of conditions such as fragile-X syndrome, where the FMR1 gene on the X chromosome can carry a CGG-repeat expansion. The gene is the locus; the alleles are the normal length and the expanded length. By drawing the cross between a carrier mother (Ff) and an unaffected father (FY), the counsellor calculates a 50 percent risk for sons and a 50 percent chance of carrier daughters. The pedigree shows transmission across three generations and validates the Punnett-square prediction.

Try this

Q1. Define the terms gene, allele and genome, and give a one-line example for each. [3 marks]

• Cue. Gene: DNA sequence coding a product. Allele: alternative version (e.g. A vs a). Genome: total DNA content of a cell.

Q2. A monohybrid cross between two heterozygotes (Aa x Aa) produces 240 offspring. Predict how many are homozygous dominant, heterozygous and homozygous recessive. [3 marks]

• Cue. 1:2:1 ratio: 60 AA, 120 Aa, 60 aa.

Q3. Refer to the Wollemi pine. (a) Explain the difference between having the same genome and having the same alleles. (b) Suggest why low allelic diversity threatens the species. (c) Outline how Royal Botanic Gardens uses cuttings rather than seed for propagation and what this means for genetic diversity. [2+2+2 marks]

• Cue. (a) Same genes but identical allelic versions; no variation between individuals. (b) One pathogen could affect all. (c) Cuttings are clonal so diversity stays low; seed from cross-pollination could increase variation.