Gene control

1. Overview

Cells do not make every protein all of the time; they switch genes on and off so that proteins are produced only when they are needed, saving energy and resources. The point most often controlled is transcription - whether a gene is copied into mRNA. This topic compares structural and regulatory genes, and repressible and inducible enzymes. It then explains two real control systems: the lac operon of the bacterium Escherichia coli (a prokaryote), and gene control in eukaryotes by transcription factors, including how the plant hormone gibberellin switches genes on by triggering the breakdown of DELLA repressor proteins.

Key Definitions

• Structural gene: a gene that codes for a polypeptide with a structural, enzymatic or transport role in the cell, rather than one that regulates other genes.
• Regulatory gene: a gene that codes for a protein, such as a repressor or transcription factor, that controls the expression of other genes.
• Repressible enzyme: an enzyme that is normally produced but whose synthesis is switched off when its end product accumulates.
• Inducible enzyme: an enzyme that is normally not produced but whose synthesis is switched on when its substrate (the inducer) is present.
• Operon: a length of DNA made up of structural genes and the control sites (promoter and operator) that switch their transcription on or off together.
• Operator: a region of DNA next to the promoter where a repressor protein can bind to block transcription.
• Promoter: a region of DNA to which RNA polymerase binds to begin transcription of the structural genes.
• Transcription factor: a protein that binds to specific DNA sequences in a eukaryote and increases or decreases the rate of transcription of a gene.
• DELLA protein: a eukaryotic repressor protein that inhibits transcription factors and is broken down in response to gibberellin, switching target genes on.

Content

Structural genes and regulatory genes

A structural gene codes for a polypeptide that does a "working" job in the cell - for example an enzyme that catalyses a reaction, a membrane transport protein, or a structural protein such as collagen. A regulatory gene does not code for a working protein in that sense; instead it codes for a protein, such as a repressor or a transcription factor, that controls whether other genes are switched on or off.

In short:

• Structural genes carry out the cell's tasks.
• Regulatory genes decide when those tasks happen.

Repressible and inducible enzymes

Both terms describe how the production of an enzyme is controlled, but they work in opposite directions:

Feature	Repressible enzyme	Inducible enzyme
Normally being made?	Yes	No
What changes its synthesis	A build-up of its end product	The presence of its substrate (the inducer)
Effect of that trigger	Switched off	Switched on
Typical pathway	Biosynthetic (building-up)	Catabolic (breaking-down)
Why it makes sense	Stops making more of something the cell already has enough of	Avoids making an enzyme that would have nothing to act on

The lac operon: an inducible system in E. coli

E. coli can use the sugar lactose as an energy source, but it only makes the proteins for handling lactose when lactose is actually available. The genes are organised as an operon - a cluster of genes controlled together.

The lac operon contains three structural genes (lacZ, lacY and lacA). Their products are proteins, not all of which are enzymes:

• beta-galactosidase - an enzyme that hydrolyses lactose into glucose and galactose;
• lactose permease - a membrane transport protein that carries lactose into the cell (it is a transporter, not an enzyme);
• transacetylase - an enzyme with a minor role in the pathway.

Next to the structural genes are two control sites: the promoter, where RNA polymerase binds to start transcription, and the operator, which overlaps the promoter region. A separate regulatory gene (lacI) codes for the lac repressor protein.

The two states of the operon are easiest to compare side by side:

Stage	Lactose absent	Lactose present
Repressor protein	Active; binds the operator	Changed shape by the inducer; detaches from the operator
Operator	Blocked by repressor	Free
RNA polymerase	Cannot move past to the structural genes	Binds the promoter and transcribes the structural genes
Transcription	Switched OFF	Switched ON
Result	lactose-handling proteins not made	beta-galactosidase, permease and transacetylase made

Working through the two states in words:

• When lactose is absent: the regulatory gene makes the repressor protein, which binds tightly to the operator. Because the operator overlaps the promoter, the bound repressor physically blocks RNA polymerase from moving along to transcribe the structural genes. Transcription is switched off, so the proteins are not made - the enzymes are inducible and lactose is the inducer.
• When lactose is present: some lactose is converted to a related molecule (called allolactose) that acts as the inducer. The inducer binds to the repressor protein and changes its shape (a conformational change). The altered repressor can no longer fit the operator, so it detaches from the DNA. With the operator free, RNA polymerase can bind to the promoter and transcribe the three structural genes, so beta-galactosidase, lactose permease and transacetylase are produced and the cell can use lactose.

(Note: at A-Level you are not expected to know about the role of cAMP in this system - the explanation above, based on lactose acting as the inducer that inactivates the repressor, is sufficient.)

Worked example

Exam-style question: In E. coli, the structural genes of the lac operon are not transcribed when lactose is absent, but are transcribed when lactose is present. Explain how the presence of lactose switches these genes on. [4]

Model answer:

• When lactose is absent, the repressor protein (made by the regulatory gene) binds to the operator.
• Because the operator overlaps the promoter, the bound repressor prevents RNA polymerase from transcribing the structural genes.
• When lactose is present, lactose (or a derivative) acts as the inducer and binds to the repressor, changing its shape so it can no longer bind the operator.
• The repressor detaches, so RNA polymerase can bind the promoter and transcribe the structural genes, and the proteins are made.

Transcription factors in eukaryotes

Eukaryotic genes are also controlled mainly at transcription, but they do not use operons in the same way. Instead, control depends largely on transcription factors - proteins that bind to specific DNA sequences (often near the promoter of a gene). A transcription factor can either increase the rate of transcription of its target gene (by helping RNA polymerase attach and begin transcribing) or decrease it. The same cell can switch different genes on or off by using different combinations of transcription factors, which is how cells with identical DNA become specialised.

Gibberellin, DELLA proteins and gene activation

A clear example of transcription-factor control is the action of the plant hormone gibberellin. Some genes a plant needs - for instance genes for enzymes that break down stored food during germination - are kept switched off by repressor proteins called DELLA proteins. A DELLA protein is itself the product of a regulatory gene: just like the lac repressor in E. coli, it is a control protein that does no "working" job but instead governs other genes. A DELLA protein works by binding to and inhibiting transcription factors (such as PIF-type factors) that would otherwise switch those genes on - so the same repressor logic seen in the prokaryote applies here, simply acting at the level of the transcription factors.

When gibberellin is produced (for example when a seed begins to germinate), it triggers the breakdown (degradation) of the DELLA proteins. With the DELLA repressors removed, the transcription factors are released and become active, so they bind to the DNA and switch on transcription of the target genes. In this way gibberellin activates genes indirectly - it does not switch the genes on itself; it removes the repressor that was holding them off.

A worked illustration is barley seed germination. Gibberellin made by the embryo travels to the aleurone layer, where the breakdown of DELLA proteins frees transcription factors that switch on the gene for the enzyme amylase. The amylase then hydrolyses stored starch in the endosperm into maltose, providing sugars for the growing seedling.

Worked example

Exam-style question: During germination, a barley seed produces gibberellin. Explain how gibberellin switches on the gene that codes for the enzyme amylase. [4]

Model answer:

• Before gibberellin is made, DELLA proteins act as repressors by binding to and inhibiting the transcription factors needed to switch on the amylase gene.
• Gibberellin causes the breakdown (degradation) of the DELLA proteins.
• With the DELLA repressors removed, the transcription factors are released and become active, so they bind to the DNA.
• The active transcription factors switch on transcription of the amylase gene, so amylase is produced (gibberellin therefore acts indirectly, by removing the repressor rather than switching the gene on itself).

Key Equations

This is a qualitative topic - there are no equations to learn. Marks come from describing control mechanisms accurately and in the correct sequence.

Common Mistakes to Avoid

• Defining a gene loosely as "a piece of DNA". Define it precisely as a sequence of nucleotides (DNA) that codes for the amino acid sequence of a polypeptide; for a regulatory gene, make clear its product controls other genes.
• Mixing up structural and regulatory genes. Structural genes code for working proteins (enzymes, transporters, structural proteins); regulatory genes code for control proteins such as repressors and transcription factors.
• Confusing repressible with inducible enzymes. A repressible enzyme is normally made and switched off by its end product; an inducible enzyme is normally absent and switched on by its substrate (the inducer).
• Saying the repressor binds the promoter. The repressor binds the operator; because the operator overlaps the promoter region, this is what blocks RNA polymerase - keep the two sites distinct in your wording.
• Forgetting that lactose changes the repressor's shape. It is the change in the repressor's shape caused by the inducer binding that stops it fitting the operator - do not just say "lactose removes the repressor".
• Bringing cAMP into the answer. At this level the lac operon explanation does not need cAMP; explaining control through the repressor and inducer is enough.
• Saying gibberellin switches the genes on directly. Gibberellin causes the breakdown of DELLA repressor proteins; this releases transcription factors that then switch the genes on - state the indirect chain in order.
• Treating transcription factors as only "turning genes on". They can increase or decrease the rate of transcription, so describe the direction of the effect.

Exam Tips

• In lac operon answers, name the parts in the right order: regulatory gene to repressor to operator (overlapping the promoter) to RNA polymerase to structural genes - the logical sequence is what earns the marks.
• Always state clearly whether transcription is switched on or off in each scenario, and link it to whether RNA polymerase can reach the structural genes.
• When you compare repressible and inducible enzymes, write a single comparative sentence (e.g. "a repressible enzyme is switched off by its product, whereas an inducible enzyme is switched on by its substrate").
• For gibberellin questions, build the answer as a cause-and-effect chain: gibberellin then DELLA breakdown then transcription factors freed then genes transcribed then enzyme made - each link can earn a mark.
• Use precise verbs - binds, blocks, detaches, changes shape, breaks down - rather than vague phrases like "stops" or "lets it work".
• If a question asks you to explain rather than describe, give the mechanism (what binds to what and what effect that has), not just the outcome.
• In a lac operon "explain" question, describe both states, not just the "on" half. A 4-mark answer credits the off-state baseline (lactose absent: repressor binds the operator and blocks RNA polymerase) as well as the on-state (lactose present: inducer changes the repressor's shape so it detaches) - answering only how lactose switches the genes on typically caps you at 2 marks.