Difficulty: Intermediate | Prerequisites: Part 1 of these notes (Prokaryotic Gene Regulation and Bacterial Operons), plus basic understanding of enzymes, metabolic pathways, and end-product feedback inhibition.
The lac operon and the trp operon are the two classic examples of prokaryotic gene regulation, and they work in opposite directions. The lac operon is inducible: it switches on when lactose appears so the cell can break down a new sugar. The trp operon is repressible: it runs by default to build tryptophan but shuts off once there is plenty. Together, these two systems illustrate almost every principle of bacterial gene control you will be tested on, including negative regulation, positive regulation (via cAMP and CRP), and the interplay between enzymatic feedback inhibition and genetic regulation.
The lac operon is normally off; lactose (via allolactose) inactivates the repressor so the cell can make enzymes to digest lactose, and low glucose boosts transcription further through the cAMP-CRP system. The trp operon is normally on; when tryptophan accumulates, it acts as a corepressor, activating the repressor to shut down the genes. The trp pathway also uses enzyme feedback inhibition, so bacteria have two independent ways to stop making tryptophan.
lacZ
The gene in the lac operon that codes for beta-galactosidase, the enzyme that cleaves lactose into glucose and galactose. Think of it as: the main workhorse enzyme that actually breaks lactose apart.
lacY
The gene that codes for permease, a membrane transport protein that brings lactose into the bacterial cell. In simple terms, this means it is the door that lets lactose in.
lacA
The gene that codes for transacetylase, an enzyme whose role in lactose metabolism is less central but is co-transcribed with the other two. Think of it as: the third member of the lac operon gene cluster, always along for the ride.
lacI (regulatory gene)
The gene that codes for the lac repressor protein. It sits upstream of the operon and is transcribed from its own separate promoter. In simple terms, this means it is the gene that produces the "off switch" protein.
Allolactose
An isomer of lactose that acts as the natural inducer of the lac operon. It binds to the lac repressor and inactivates it. Think of it as: the signal molecule that tells the repressor "lactose is here, stand down."
cAMP (cyclic AMP)
A signalling molecule produced when glucose levels in the cell are low. In the context of the lac operon, cAMP binds to the CRP protein. In simple terms, this means it is the cell's way of saying "we are low on glucose."
CRP (cAMP receptor protein) / CAP (catabolite activator protein)
A transcription activator protein. When bound to cAMP, CRP binds near the lac promoter and helps RNA polymerase bind more effectively, boosting transcription. Think of it as: the accelerator pedal, only active when glucose is scarce.
Tryptophan (trp)
An amino acid that bacteria synthesise from a precursor molecule via a multi-enzyme pathway encoded by the trp operon. Tryptophan also acts as the corepressor for the trp operon. In simple terms, this means tryptophan is both the product of the pathway and the signal that shuts it down.
trpE, trpD, trpC, trpB, trpA
The five structural genes of the trp operon, encoding enzymes (as polypeptide subunits) that convert a precursor molecule into tryptophan step by step. Think of it as: five genes, five enzyme components, one assembly line.
trpR (regulatory gene)
The gene that codes for the trp repressor protein. The repressor is produced in an inactive form and is activated only when tryptophan binds to it. In simple terms, this means the repressor needs tryptophan to do its job.
The lac operon contains:
A regulatory gene (lacI), transcribed from its own separate promoter, which constantly produces the lac repressor protein.
A promoter where RNA polymerase binds.
An operator (between the promoter and the first structural gene) where the repressor binds.
Three structural genes: lacZ (beta-galactosidase), lacY (permease), and lacA (transacetylase).
All three structural genes are transcribed as a single polycistronic mRNA with three start codons (AUGs), one per gene.
The lacI gene produces the lac repressor protein, which is active by default.
The active repressor binds tightly to the operator.
RNA polymerase cannot move past the operator to transcribe the structural genes.
No mRNA is made. No lactose-digesting enzymes are produced.
This makes sense: why waste energy making enzymes for a sugar that is not there?
Some lactose is converted to allolactose (an isomer of lactose) inside the cell.
Allolactose acts as the inducer: it binds to the lac repressor protein and changes its shape.
The shape change causes the repressor to release from the operator.
With the operator clear, RNA polymerase can bind the promoter and transcribe all three structural genes.
The cell now produces the enzymes needed to import and break down lactose.
The lac operon is an inducible operon. The default state is OFF. The inducer (allolactose, derived from lactose) removes the block. When the inducer disappears (lactose is used up), the repressor re-binds and the genes turn off again.
Removing the repressor is only half the story. The lac operon also has a positive control mechanism that depends on glucose levels.
When glucose is low, the cell produces cAMP (cyclic AMP).
cAMP binds to the CRP protein (also called CAP), activating it.
The activated cAMP-CRP complex binds to a site near the lac promoter (the CRP-binding site).
This binding helps RNA polymerase bind the promoter more tightly, speeding up transcription.
Even if lactose is present and the repressor is off, transcription of the lac operon is relatively slow without the cAMP-CRP boost.
This ensures that when both glucose and lactose are available, the cell preferentially uses glucose (it is the more efficient energy source) and does not waste resources on lactose enzymes.
Maximum lac operon expression requires two conditions at once: lactose present (repressor off) AND glucose absent (cAMP-CRP active).
If lactose is absent, the repressor remains bound to the operator regardless of cAMP-CRP. The activator cannot override a bound repressor, so no transcription occurs. Both the negative control (repressor off) and the positive control (cAMP-CRP on) must be favourable for full expression.
The trp operon contains:
A regulatory gene (trpR), transcribed from its own promoter, which produces the trp repressor protein in an inactive form.
A promoter and operator.
Five structural genes (trpE, trpD, trpC, trpB, trpA) encoding the enzyme subunits that convert a precursor molecule into the amino acid tryptophan.
The trpR gene produces the repressor, but it is inactive by default.
The inactive repressor cannot bind the operator.
RNA polymerase binds the promoter and transcribes all five structural genes.
The enzymes are produced, and the cell synthesises tryptophan from precursor molecules.
This is the normal state: the cell needs tryptophan for protein synthesis.
Tryptophan itself acts as the corepressor.
Tryptophan binds to the inactive repressor, changing its shape and activating it.
The now-active repressor binds the operator and blocks RNA polymerase.
No mRNA is made. No more tryptophan-synthesising enzymes are produced.
This conserves energy: the cell already has enough tryptophan.
The trp operon is a repressible operon. The default state is ON. The corepressor (tryptophan itself) activates the repressor, which then shuts down transcription. When tryptophan levels drop, the corepressor dissociates, the repressor goes inactive, and the genes turn back on.
The trp operon is an important example because it demonstrates two independent levels of control over the same pathway.
Tryptophan, the end product, directly inhibits the first enzyme in its own biosynthetic pathway.
This is classic end-product feedback inhibition: the finished product binds to the enzyme's allosteric site and reduces its activity.
This acts immediately: excess tryptophan slows the pathway within seconds, even while the enzymes are still present.
Excess tryptophan activates the trp repressor (as the corepressor), which shuts down transcription of the trp operon genes.
This stops the cell from making new enzymes entirely.
This takes longer to have an effect because existing enzymes remain in the cell until they degrade naturally.
The enzymatic control is a rapid, fine-tuning response. The genetic control is a slower but more thorough shutdown. Together, they give the bacterium a layered strategy: quickly throttle the pathway when tryptophan spikes, then stop wasting resources on making the enzymes at all if tryptophan remains abundant. The trp operon is a good example of end-product feedback inhibition for both enzyme activity and gene activity.
Students often think lactose directly binds the repressor. Strictly, it is allolactose (an isomer of lactose) that acts as the inducer. Your exam may accept "lactose" in a general sense, but be precise if asked.
A frequent mistake is thinking the trp operon uses an activator protein. It does not. It uses removal of a repressor (the repressor goes inactive when tryptophan is absent). This is negative regulation, not positive.
Students sometimes confuse which molecule is the corepressor in the trp system. Tryptophan is the corepressor (it activates the repressor). The precursor molecule is not involved in regulation.
Many students forget that the cAMP-CRP system in the lac operon is a separate layer of control from the repressor. Removing the repressor alone gives low-level transcription; full expression requires cAMP-CRP as well.
⚠️ Be able to state whether the lac operon is inducible or repressible, and whether the trp operon is inducible or repressible. Know why each classification applies.
⚠️ The lac operon question "How are lac operon genes regulated?" has a specific answer: lactose sugar de-activates the repressor (answer B from the lecture clicker question). Lactose does not activate the repressor.
⚠️ Know all the conditions for maximum lac operon expression: lactose present AND glucose absent.
⚠️ Be ready to explain the two ways a bacterial cell can stop making tryptophan (enzyme feedback inhibition and gene regulation via the repressor).
⚠️ Mutation questions are heavily flagged in this lecture. Understand what happens to the whole operon when a single component (promoter, operator, one gene's start codon) is mutated.
True or False: The lac operon is a repressible operon. (False, it is inducible)
Fill in the blank: The inducer of the lac operon is ______. (Allolactose)
True or False: The trp repressor is active by default, even without tryptophan. (False, the trp repressor is inactive by default)
Fill in the blank: For maximum lac operon expression, lactose must be ______ and glucose must be ______. (Present; absent)
True or False: Enzyme feedback inhibition and gene regulation are two independent ways bacteria control the trp pathway. (True)
Q: Lac operon genes are: (A) usually turned off, turned ON in the presence of lactose sugar, or (B) usually turned on, turned OFF in the absence of lactose sugar?
A: A. The lac operon genes are usually off. They are turned on when lactose is present and the allolactose inducer inactivates the repressor.
Q: How are lac operon genes regulated? (A) Lactose sugar activates a repressor, or (B) Lactose sugar de-activates a repressor?
A: B. Lactose (via allolactose) de-activates the repressor. When the repressor is inactivated, it releases from the operator and transcription can proceed.
Q: The trp operon genes code for enzymes that make tryptophan. What are two different ways (one enzymatic and one genetic) a bacterial cell can turn off tryptophan production?
A: Enzymatic: tryptophan directly inhibits the first enzyme in the biosynthetic pathway through end-product feedback inhibition. Genetic: tryptophan acts as a corepressor, binding to the trp repressor and activating it. The active repressor binds the operator and blocks transcription of the trp operon genes, stopping production of new enzymes.
Q: Why is the trp operon a good example of end-product feedback inhibition for both enzyme and gene activity?
A: Because tryptophan, the end product, controls both levels. It inhibits the first enzyme in its pathway (enzyme-level feedback) and it also acts as the corepressor that shuts down transcription of the genes encoding those enzymes (gene-level feedback). One molecule regulates both the activity of existing enzymes and the production of new ones.
Q: Bacteria must make necessary amino acids from precursor molecules. Is this operon type A (inducible) or B (repressible)?
A: B, repressible. Amino acid synthesis pathways are anabolic, and their genes are normally on. They are shut off only when enough of the amino acid accumulates.
Q: Bacteria must make ATP by metabolising a sugar that has newly appeared in their cell. Is this operon type A (inducible) or B (repressible)?
A: A, inducible. The genes for metabolising the sugar are normally off and are induced only when the sugar appears.
The lac operon's cAMP-CRP system connects to signal transduction and second messengers (cAMP), which you may encounter again in eukaryotic signalling pathways.
The concept of repressible operons and end-product feedback ties directly to amino acid metabolism and biosynthetic pathways covered elsewhere in the course.
Eukaryotic gene regulation (Ch. 15.2) builds on these foundations but adds chromatin structure, enhancers, silencers, and post-transcriptional controls. Understanding the simpler prokaryotic system here makes the eukaryotic version far easier to follow.
Lac operon, trp operon, lactose operon, tryptophan operon, lacZ, lacY, lacA, lacI, beta-galactosidase, permease, transacetylase, lac repressor, allolactose, inducer, inducible operon, repressible operon, corepressor, trpR, trpE, trpD, trpC, trpB, trpA, operator, promoter, structural genes, regulatory gene, cAMP, cyclic AMP, CRP, CAP, catabolite activator protein, cAMP receptor protein, positive control, negative control, gene activation, gene repression, end-product feedback inhibition, enzyme feedback inhibition, anabolic pathway, catabolic pathway, polycistronic mRNA, bacterial gene regulation, prokaryotic gene expression, BIO 314, Chapter 15, intro biology, University of Texas