the structure of genes including exons, introns and promoters and the role of regulator genes, including the role of the trp operon as an example of a regulatory process in prokaryotes

What this dot point is asking

VCAA wants you to label the parts of a gene (promoter, exons, introns), explain what a regulator gene does, and use the trp operon as a worked prokaryotic example of how gene expression is controlled.

The answer

A gene is a length of DNA that codes for a functional product, usually a polypeptide. Eukaryotic and prokaryotic genes share some features but differ in detail.

Parts of a eukaryotic gene

Promoter

A non-coding region upstream of the start of transcription. It contains binding sites for transcription factors and RNA polymerase, often including a TATA box. The promoter is not transcribed; it positions the polymerase.

Exons

The coding regions, retained in the mature mRNA and translated. The order of exons (and their alternative combinations through splicing) determines the protein sequence.

Introns

Non-coding regions inside the gene, transcribed into pre-mRNA but removed by the spliceosome during RNA processing.

Terminator

A sequence at the 3' end that signals RNA polymerase to release the transcript.

Regulatory elements

Enhancers and silencers (further from the gene) can be bound by transcription factors that increase or decrease the rate of transcription.

Regulator genes

A regulator gene codes for a protein (often a transcription factor) that controls the expression of one or more target genes. Regulator gene products may be:

• Repressors that bind DNA and block transcription.
• Activators that recruit RNA polymerase or stabilise the initiation complex.

Regulator genes are usually expressed continually so the regulatory protein is available whenever the cell needs to switch the target gene on or off.

The trp operon (worked prokaryotic example)

An operon is a cluster of genes under a single promoter, transcribed as one mRNA. They are common in prokaryotes such as Escherichia coli.

The trp operon controls the synthesis of the amino acid tryptophan and contains five structural genes (trpE, trpD, trpC, trpB, trpA) that together code for the enzymes of the tryptophan biosynthesis pathway. Upstream of these genes are:

• A promoter for RNA polymerase.
• An operator sequence where the repressor binds.

A separate regulator gene (trpR) lies elsewhere on the chromosome and constantly produces an inactive trp repressor.

When tryptophan is low. The repressor stays inactive and does not bind the operator. RNA polymerase transcribes the operon, the five enzymes are made, and tryptophan is synthesised.

When tryptophan is high. Tryptophan acts as a corepressor and binds the trp repressor. The repressor changes shape and now binds the operator. RNA polymerase is blocked, transcription stops, and the cell stops making more tryptophan.

This is a repressible operon: it is normally on but switched off when the end product accumulates. It is a classic example of negative feedback in gene regulation.

Why this matters

Regulating gene expression lets cells:

• Save energy by only producing enzymes when their substrate or product demands.
• Respond to the environment (nutrient changes, stress, hormones).
• Specialise (in eukaryotes, different cells express different sets of genes despite having identical DNA).

Examples in context

Example 1. Eukaryotic gene structure at Walter and Eliza Hall Institute. WEHI's structural biologists work on the haemoglobin gene cluster, a textbook eukaryotic example. The beta-globin gene has three exons separated by two introns, a promoter region containing TATA and CAAT boxes 30 and 80 base pairs upstream of the transcription start site, and tissue-specific enhancer elements thousands of base pairs further upstream. WEHI uses this knowledge to design gene therapies for sickle-cell anaemia; one strategy is to add a beta-globin transgene with its full promoter and enhancer regions so the cell expresses functional haemoglobin only in red-cell precursors. VCE students learn that gene structure (exons, introns, promoter) matters as much as gene sequence.

Example 2. E. coli trp operon in food microbiology at CSIRO. CSIRO's Werribee laboratory studies E. coli contamination in raw milk. Tryptophan, an essential amino acid, becomes limiting when bacteria grow in milk that has been temperature-abused. The trp operon then activates: low tryptophan leaves the trp repressor inactive, RNA polymerase transcribes the operon, and the bacterium synthesises its own tryptophan from precursors. When milk is refrigerated and bacteria stop growing, accumulated tryptophan binds the repressor, which then binds the operator and blocks transcription - the operon is "off". The trp operon is therefore a repressible operon: present by default and switched off when its product is plentiful.

Try this

Q1. State three structural components of a eukaryotic gene and their function. [3 marks]

• Cue. Promoter (binding site for RNA polymerase and transcription factors); exons (coding sequences retained in mature mRNA); introns (non-coding sequences spliced out).

Q2. A geneticist deletes the operator sequence from the trp operon. Predict the effect on transcription when tryptophan is plentiful, and explain. [3 marks]

• Cue. Without operator, repressor has no binding site; transcription continues regardless of tryptophan level; operon is constitutively on.

Q3. Refer to the trp operon in E. coli. (a) Distinguish a repressible from an inducible operon. (b) State what happens at the operon when tryptophan is low vs high. (c) Explain why operons are common in prokaryotes but rare in eukaryotes. [2+2+2 marks]

• Cue. (a) Repressible: on by default, off when product binds repressor. Inducible: off by default, on when substrate inactivates repressor. (b) Low tryptophan: repressor inactive, operon transcribed. High tryptophan: repressor binds operator, operon off. (c) Prokaryotes have polycistronic mRNA, no nucleus, so co-regulation of metabolic pathway genes is efficient; eukaryotes regulate genes individually through transcription factors and chromatin.