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Gene Expression
in Prokaryotes

Master the operon model, understand how bacteria regulate transcription, and learn the difference between inducible and repressible systems.

MCAT Biological Foundations

Why Do Bacteria Regulate Genes?

Bacteria live in rapidly changing environments. Producing every protein at all times would waste energy and resources. Instead, prokaryotes turn genes on or off depending on environmental signals: nutrients present, toxins encountered, or growth conditions.

The Operon Concept

An operon is a cluster of functionally related genes controlled by a single promoter. This arrangement allows bacteria to coordinate expression of multiple genes in one transcription event, producing a polycistronic mRNA.

Promoter
The DNA sequence where RNA polymerase binds to initiate transcription
Operator
The DNA region where a repressor protein binds to block transcription
Structural Genes
The protein-coding genes transcribed together as a single mRNA unit

Anatomy of an Operon

Reg Gene
 Promoter Operator
Gene Z
Gene Y
Gene A
 Regulatory P O Structural Genes RNA Pol binds here Repressor binds here Transcription direction

The lac Operon: An Inducible System

The lac operon in E. coli controls genes for lactose metabolism. It is an inducible operon: normally OFF, it is turned ON when lactose is present and glucose is absent.

1
Without lactose: The repressor protein (encoded by lacI) binds the operator, blocking RNA polymerase. Transcription is OFF.
2
With lactose: Allolactose (an isomer of lactose) binds the repressor, causing a conformational change. The repressor releases the operator.
3
Transcription ON: RNA polymerase transcribes lacZ, lacY, and lacA into a polycistronic mRNA.

lac Operon: ON vs OFF

OFF State (no lactose) P O
lacZ lacY lacA
 Repressor ✕ No transcription ON State (lactose present, glucose absent) P O
lacZ lacY lacA
 Repressor Allo Allolactose binds repressor CAP mRNA transcribed Polycistronic mRNA

Positive Regulation: CAP-cAMP

The lac operon requires both negative regulation (repressor) and positive regulation (CAP) for maximal transcription. The catabolite activator protein (CAP) bound to cAMP enhances RNA polymerase binding.

High glucose
Low cAMP levels: CAP is inactive. Even with lactose, transcription is low.
Low glucose
High cAMP levels: CAP-cAMP binds the promoter. With lactose present, transcription is maximal.

The trp Operon: A Repressible System

The trp operon controls genes for tryptophan biosynthesis. Unlike the lac operon, the trp operon is normally ON and is turned OFF when tryptophan accumulates: a repressible operon.

1
Low tryptophan: The repressor is inactive (cannot bind the operator alone). Structural genes are transcribed, producing enzymes for tryptophan synthesis.
2
High tryptophan: Tryptophan acts as a corepressor: it binds the repressor, activating it. The active repressor binds the operator, blocking transcription.

Inducible vs Repressible Operons

Inducible (lac) Repressible (trp)
Default state OFF ON
Function Catabolic (breaks down substrate) Anabolic (builds product)
Small molecule role Inducer (allolactose) inactivates repressor Corepressor (tryptophan) activates repressor
Repressor alone Active (binds operator) Inactive (cannot bind)
Signal to turn ON Substrate present Product absent

Attenuation: Fine-Tuning the trp Operon

Beyond repression, the trp operon uses attenuation: a mechanism that prematurely terminates transcription based on tryptophan levels in the cell. This provides fine-grained control.

1
Leader sequence: A short leader peptide region at the 5' end of the mRNA contains tandem tryptophan codons.
2
High Trp: Ribosomes translate quickly through Trp codons. The mRNA forms a terminator hairpin, stopping transcription early.
3
Low Trp: Ribosomes stall at Trp codons. The mRNA forms an anti-terminator hairpin, allowing full transcription.

lac Operon: Four Conditions

Glucose Lactose CAP Repressor Transcription
Present Absent Inactive Bound to O OFF
Present Present Inactive Released Low
Absent Absent Active Bound to O OFF
Absent Present Active Released Maximal

Step-by-Step: Predict Operon Activity

1
Identify the operon type: Is it inducible (catabolic) or repressible (anabolic)?
2
Determine the default state: Inducible = OFF by default. Repressible = ON by default.
3
Check the small molecule: Is the inducer/corepressor present? How does it affect the repressor?
4
Check for positive regulators: For the lac operon, also check glucose levels (CAP-cAMP).
5
Combine: Transcription requires RNA polymerase access (repressor off operator) and, if applicable, activator binding.

Example 1: lac Operon Scenario

1
Glucose present: cAMP levels are low. CAP-cAMP complex does NOT form. CAP is inactive.
2
Lactose present: Allolactose binds the repressor, removing it from the operator. Repressor is released.
3
Result: RNA polymerase can bind, but without CAP assistance. Transcription is low (basal level).

Example 2: trp Operon Mutation

1
Normal trp repressor: Inactive alone. Tryptophan acts as corepressor, making it active.
2
Mutant repressor: Cannot bind tryptophan, so it stays permanently inactive. It can never bind the operator.
3
Result: The trp operon is constitutively ON: tryptophan biosynthesis enzymes are always made, even when tryptophan is abundant. This wastes energy.

Example 3: Operator Mutation

1
Normal operator: Repressor binds when no inducer is present, blocking transcription.
2
\(O^c\) mutant: Repressor cannot bind, regardless of lactose levels. The operator is always "open."
3
Result: lac genes are constitutively expressed. This mutation is cis-dominant: it affects only genes on the same DNA molecule.

Common Mistakes

✕ Confusing inducer with corepressor
An inducer inactivates a repressor (lac). A corepressor activates a repressor (trp). They have opposite effects.
✕ Forgetting CAP-cAMP
Removing the repressor alone gives only basal transcription of lac. Maximal transcription requires CAP-cAMP at the promoter.
✕ Mixing up cis and trans
Operator mutations are cis-dominant (only same DNA strand). Repressor and CAP mutations are trans-acting (protein diffuses freely).

Question 1 of 5

In the lac operon, what is the role of allolactose?

Question 2 of 5

Under which conditions is the lac operon transcribed at maximal levels?

Question 3 of 5

In the trp operon, what happens when tryptophan levels in the cell are high?

Question 4 of 5

A mutation makes the lac repressor unable to bind allolactose, but it can still bind the operator normally. What is the result?

Question 5 of 5

Why does attenuation work in prokaryotes but not in eukaryotes?