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.

Worked example

A child has the genotype IA i at the ABO blood group locus on chromosome 9. The locus is the position of the ABO gene. The two alleles are IA (dominant for A antigen) and i (recessive, produces no antigen). The gene is the stretch of DNA at that locus that codes for the glycosyltransferase enzyme that builds blood-group antigens. The genome is the entire 3 billion base pairs across all 46 chromosomes. The phenotype is blood type A, because IA is dominant to i.

Common traps

Saying "she has the gene for cystic fibrosis". Everyone has the CFTR gene. Carriers and affected individuals have specific disease-causing alleles of the CFTR gene.

Confusing locus and allele. A locus is a position; an allele is one of the variants found at that position.

Mixing up "homologous chromosomes" and "sister chromatids". Homologous chromosomes are a pair (one from each parent), with the same genes but possibly different alleles. Sister chromatids are two identical copies of one chromosome, joined at the centromere after DNA replication.

Treating the genome as just genes. Genes are about 2% of the human genome; the other 98% is non-coding regulatory and structural DNA.

Saying "genotype = phenotype". Genotype is the genetic make-up; phenotype is the observable trait. Many genotypes can give the same phenotype (PP and Pp both produce purple flowers), and one genotype can produce different phenotypes in different environments.

In one sentence

A gene is a length of DNA at a specific locus that codes for a functional product, an allele is one of the variants of a gene in a population (each diploid individual carries two alleles per autosomal gene), and a genome is the complete set of DNA in a cell, including all genes and the non-coding DNA between them.