Regulation of Gene Expression: Operons, Epigenetics, and Transcription Factors

Professor Dave here.

Let's examine how a cell regulates gene expression.

We have talked a lot about chromosomes and the genes they contain, as well as the genetics that dictate what kinds of phenotypes are expressed in an organism, like with Mendel's pea plants.

But how does gene expression work on the molecular level, and how is it regulated?

We have already discussed transcription and translation in the biochemistry series, so if you missed those tutorials, it is absolutely mandatory that you view at least this one before moving forward.

It is through transcription and translation that we see how the genetic information of an organism serves as a code for the manufacturing of everything within that organism.

If you've already viewed the biochemistry tutorials, then we can briefly summarize and expand by including some details we previously skipped over.

In transcription, the DNA within a gene codes for an mRNA, which then undergoes post-transcriptional modification.

Each end gets a special cap tacked on, like the 5' cap, which is a modified guanine, and the poly-A tail, which is 50 to 250 adenines.

Then a protein complex called a spliceosome will cut out sections called introns, and other sections called exons, come together to form a smaller mRNA, which then moves from the nucleus to the cytoplasm.

This is where translation occurs. In translation, the mRNA, a ribosome, and many tRNAs work together to produce a polypeptide.

Some of these polypeptides will then be complete.

But others will instead undergo folding, likely in the endoplasmic reticulum, and sometimes modification in the Golgi apparatus,

where groups like sugars, lipids, or phosphates are attached.

Then the proteins are delivered to where they need to go.

This sum process, otherwise known as the central dogma of molecular biology,

illustrates how gene expression generates all of the proteins in your body.

Once again, please watch my biochemistry tutorials on DNA replication and transcription and translation, as these are some of the most important concepts in biology.

Once those processes are understood, we can begin to analyze all of the complex interactions that regulate gene expression.

We know from learning about mitosis that every cell in your body, except your gametes, contains all of your genetic information, and therefore all of your genes.

But different cells in your body serve different purposes: some are muscle cells, some are nerve cells, some are liver cells.

So different cells need to express different genes.

How does a cell know which genes to express and which to leave dormant so that it can serve its particular purpose?

This is done through regulatory mechanisms.

These evolved very early in the timeline of life on Earth because single-celled organisms had an advantage if they only expressed the genes that code for proteins that are needed by the cell in a given moment.

If a particular resource that the organism needs is plentiful nearby, it should stop self-producing that substance to save energy.

If it is sparse in the environment, it needs to kickstart production to survive.

This kind of metabolic control is self-regulated because the products of certain enzymatic pathways act as inhibitors for those pathways.

So if there is a lot of a certain metabolite accumulating in a cell, it slows down the pathway by which it is generated.

This is called feedback inhibition.

But how exactly does this work on the molecular level?

Well, bacterial cells utilize operons.

So even though eukaryotes don't have these, they will be important for us to understand.

Operons work like this.

Let's look at a particular metabolic pathway present in the bacterial species E. coli.

The amino acid tryptophan is synthesized in three steps, with each step catalyzed by a different enzyme.

And it takes a total of five genes to produce these enzymes.

These genes are found very close to one another on the bacterial chromosome, and a single promoter serves them all,

producing one huge mRNA that produces all five enzymes during translation when ribosomes anneal at any of the various start codons on the chain.

This means that these five genes are coordinately controlled.

Any influence on the transcription of these genes will impact the production of all of these enzymes.

There is a segment of DNA, in this case, in between the promoter and the first gene, which operates as an on-off switch.

This is called an operator, and it controls whether RNA polymerase has access to transcribe or not.

The promoter, the operator, and all these genes are all together called an operon.

Normally, the operon is on.

But something called a repressor can bind to the operator, which then blocks access to the promoter, so RNA polymerase can't do its job.

If the genes can't be transcribed, the enzymes can't be produced, and the cell can't build tryptophan.

This repressor is specific to this particular operator, so it doesn't do anything to other genes.

And it is a protein, which is a product of a different gene somewhere else in the DNA.

This tryptophan-specific repressor is produced regularly, but in an inactive state that has little affinity for the operator.

When tryptophan binds to the active site of the repressor, it changes shape to become an active form that has much more affinity for the operator, so it will bind and stay on for quite some time,

thus turning the operon off, inhibiting gene expression,

and limiting further tryptophan production.

The more tryptophan there is in the cell, the more repressors that will be activated to inhibit gene expression.

The less tryptophan there is, the less inhibition there will be.

While we just saw an example where a gene is typically on unless repressed,

there are also genes that are typically off or silenced unless activated.

In E. coli again, there are genes that when expressed, produce an enzyme that will metabolize lactose, a disaccharide, into individual monosaccharide units, glucose and galactose.

There is typically a repressor bound to the operator that corresponds to these genes.

But an isomer of lactose called allolactose will bind to the repressor and deactivate it,

thus allowing for transcription of the gene, enzyme production, and higher levels of lactose metabolism.

These two examples both demonstrate negative gene regulation.

One repressed gene expression, and the other deactivated a repressor.

So the signaling molecules do not interact directly with DNA.

There can also be positive gene regulation, where a signaling molecule like cAMP will bind to a protein called an activator, which will then bind to DNA and directly stimulate gene expression

by increasing the affinity that RNA polymerase has for the promoter.

So negative and positive gene regulation are both methods by which signaling molecules interact with operators, repressors, and promoters to regulate the frequency with which certain genes are expressed.

But it gets much trickier than this.

Regulation gets more complicated than this, however.

Many cells need to do more than respond to levels of glucose or lactose.

When a fetus grows, cells are dividing and becoming specialized, and each cell acquires a distinct role on the basis of selective gene expression.

Nerve cells and liver cells and skin cells are very different from one another,

even though they all possess the same genetic material.

And the secret behind this is strict regulation of gene expression.

In any given cell, some genes are expressed and some aren't.

An easy way to turn genes on and off has to do with the way the DNA is wrapped around histones to form nucleosomes.

When bound to histones, genes can't be expressed.

In order to express a gene, the gene must become accessible.

This can happen if an enzyme modifies a histone through acetylation, methylation, or phosphorylation, thus decreasing its affinity for DNA.

When a gene is no longer coordinated to the histone, it is available for transcription.

In order for transcription to proceed, proteins called transcription factors are necessary.

Some of these bind to a section of a promoter, usually in a region called a TATA box, as thymine-adenine pairs are easier to pry apart, given that they make one fewer hydrogen bonds than a CG pair.

Binding to DNA occurs due to a binding domain that has affinity for a specific sequence of nucleotides in the promoter.

The transcription factor also has an activation domain, which will bind to other regulatory proteins that enhance transcription.

In addition, there are other control elements farther away from the gene called enhancers that interact with proteins called activators.

When activators bind to the enhancer, another protein can bend DNA to bring the activators closer to the promoter where the transcription factor can be found.

Other proteins mediate interactions that produce the complete transcription initiation complex, which allows RNA polymerase to do its job.

So we can see that transcription is quite a bit more complex than we previously discussed in biochemistry.

There are many proteins involved when any gene is being transcribed.

And so regulation of the levels of these proteins can regulate the expression of other genes.

Some genes can only be transcribed when specific activator proteins are present.

And this may only occur at a specific time, like hormones carrying a message to promote the expression of genes

whose products trigger development during puberty.

Combined with the acetylation and deacetylation of histones to either activate or silence genes,

proteins that bind to mRNA to prevent translation,

and other phenomena, the cell has several strategies at its disposal to regulate gene expression.

A combination of these regulatory strategies therefore allows a relatively small number of inputs to regulate thousands of genes independently.

Although these interactions are much more complex than we have depicted here,

they tend to follow these principles.

And with a basic understanding of both gene expression and cell division, we are now ready to look at more complex systems.

Let's move on to some of these now.

Thanks for watching, guys.

Subscribe to my channel for more tutorials.

Support me on Patreon so I can keep making content.

And as always, feel free to email me, [email protected].