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).

Worked example

A culture of E. coli is grown in a medium with no added tryptophan. After several hours, abundant tryptophan is suddenly added.

Predicted change. Within minutes, tryptophan binds the trp repressor; the active repressor binds the operator; RNA polymerase is blocked; trp mRNA levels fall; production of the biosynthesis enzymes (trpE through trpA) slows; tryptophan synthesis declines.

If a mutation deletes the operator. The repressor has nothing to bind, so the operon is transcribed continuously regardless of tryptophan levels. Tryptophan will be over-produced.

Common traps

Calling the trp operon "inducible." It is repressible (normally on, turned off by a corepressor). The lac operon is inducible (normally off, turned on by an inducer); do not confuse the two.

Saying the regulator gene is inside the operon. It is a separate gene at a different location. The operon contains the promoter, operator and structural genes.

Forgetting introns are in the pre-mRNA. Introns are transcribed; they are removed during processing. Prokaryotes generally do not have introns and do not splice mRNA.

Mixing promoter and operator. The promoter is where RNA polymerase binds; the operator is where the repressor binds.

In one sentence

A gene is a stretch of DNA with a promoter, exons, introns and a terminator, and its expression can be controlled by regulator genes that produce proteins such as the trp repressor, which in the presence of tryptophan binds the operator of the trp operon and blocks transcription of the biosynthesis enzymes.