h2g2 The Hitchhiker's Guide to the Galaxy: Earth Edition

I think I should know this but can't quite put it together so perhaps time to have it explained again.

What exactly is meant by a gene being switched on or off? And what is the mechanism through which this works?

There are numerous ways of doing it. For example, a gene can be 'switched on' by splicing a constitutively active promoter next to it, in place of the gene's normal promoter region. A gene can be 'switched off' by methylation or, post-transcription, by inhibitory RNA molecules.

Is that the sort of thing you had in mind..?

hmmm.

"a gene can be 'switched on' by splicing a constitutively active promoter next to it, in place of the gene's normal promoter region"

So does that mean it doesn't need the RNA polymerase thing stuff?

What's methylation? Getting drunk under a bridge?

Sorry...

"a gene can be 'switched on' by splicing a constitutively active promoter next to it, in place of the gene's normal promoter region"

> So does that mean it doesn't need the RNA polymerase thing stuff?

Not quite. Any gene will need RNA polymerase to transcribe the DNA to messenger RNA as the first step. All genes have a promoter region, to which the polymerase initially binds. Most (all?) genes also need other 'transcription factors' to bind to the promoter at the same time. It is often the presence or absence of these factors that determine whether a gene is 'on' or 'off' (a gene that is only expressed in the skin, for example, will require transcription factors that are only present in the skin. In the other cells of the body, the factors are not present, so the gene is not expressed).

For example, let's say gene X is expressed in the skin, but not in the liver. This is probably because it requires transcription factors that are not present in the liver. If, however, you take the promoter from a liver-specific gene and attach it to gene X, then gene X will be 'switched on' in the liver. Am I making sense?

> What's methylation? Getting drunk under a bridge?

Sadly not

Methylation is the process of adding methyl (CH3-) groups to CpG DNA sequences within genes (it stands for cytosine-phosphate-guanine). This prevents the RNA polymerase from transcribing the gene. It can (I think) be done artificially these days, but is also a part of the normal control of gene expression in cells.

Absence of promotion can also mean a gene - or more correctly, expression of a gene - is switched off.

There are various 'operons' which require a series of events to occur for genes to be activated for expression usually. There can be suppressor activity as well as promoter activity too...

here's the lac operon which is probably the most well understood and widely known way of controlling gene expression (at least in my field) as it is used to control the expression of cloned genes in e. coli cells.
http://en.wikipedia.org/wiki/Lac_operon

Most genes will not be actively expressed at any one time and their expression has to be tightly controlled so that cells function as they need to.

"Am I making sense?"

Yes!

When talking about transciption factors, these are other molecules that bind to the gene? And when enough molecules have bound to the right places then transcription can take place as the correct chemicals and so forth can be release?

I know eukaryote (complex cells such as wot we have, is that the right name?) have rather complex activation/transcription processes that I don't hope to properly understand without a decent bit of grounding!

"When talking about transciption factors, these are other molecules that bind to the gene? And when enough molecules have bound to the right places then transcription can take place as the correct chemicals and so forth can be release?"

More or less! Not so much that 'the correct chemicals and so forth' are released, just that the right collection of transcription factors puts the polymerase in the correct position to begin copying the DNA gene into messenger RNA.

correct position?
I think we might be oscillating between functional and mechanical descriptions here. Fine with the functional, but mechanically are talking about a docking zone where the various factors lock in and guide the polymerase to its correct position to start? So the factors are guides or markers to indicate where to start transcription?

that's weird, just posted that and it says it is one hour old <?>

"mechanically are talking about a docking zone where the various factors lock in and guide the polymerase to its correct position to start? So the factors are guides or markers to indicate where to start transcription?"

The promoter of the gene is the guide where to start transcription. It has binding sites for the polymerase and for the various transcription factors. Only when everything necessary has bound to the promoter will transcription start.

[This is very simplified, as there are other regions, often some distance from the gene, that also appear to affect transcription. At the time I stopped studying genetics they still didn't know how this worked! They may do now... ]

[Also - yes, I've noticed the 1-hour thing. Obviously all the down-time this morning has done something to the clock...]

"This is very simplified"

I gathered that, but very simplified is what I need right now

"The promoter of the gene is the guide where to start transcription"
So what are the transcription factors doing then? I realise probably lots of things but some examples as I don;t understand their role at the moment?

[Also - yes, I've noticed the 1-hour thing. Obviously all the down-time this morning has done something to the clock...]
good, not just me then! Seems to be back to normal now though.

The role of the transcription factors is:

1. Mechanical: create a docking site to allow the polymerase to bind to the promoter. No transcription factors -> no polymerase binding -> no gene transcription.

2. Specificity: the transcription factors present in a particular cell determine which genes are 'on' or 'off' at a given time.

There may be others, but those are the most obvious ones.

ah, I get ya.

Thanks for the explanations, I have a rough idea in my head now of what people mean by these things now rather than just a basic on/off concept.

Another important thing to realise is just how much* DNA is within the nucleus, and also how, when its err 'resting' I.E., not active, its very tightly coiled up, bound round pieces of protein which help the chromosomes maintin this tightly coiloed arrangement....

some of the job of the transcription factors is to alter the gross conformation of the chromosome at the area wehre the enzymes need to join, in order to provde space for this pretty big enzymes like DNA polymerase to actually be able to get in and contact the right area to begin transcription.

At least part of the roll of the very distant areas that seem to be involved in a genes transcption are often other genes involved in making spaecific transcription factors, or inhibitory factors for that gene, these need not even be on the same chromosome...some transcription factors can be very specific for a given gene, others will act apon several genes, and some pretty-much on any gene; though most genes require multiple TFS to make transcripton begin.

I used to know a great deal about certain factors involved in the activation/promotion of a specific gene (TNF alpha), but to be honest I've forgotten most of it now No, it was* interesting... I think but really quite complicated
You can get all kinds of funny things:

membrane receptor protein, outside bit of it binds say TNF-alpha.

this binding induces conformation change in the intracellular bits of the recptor, sometimes these bits insdide the cell can physically break off to form proteins that directly travel to the nucleus as transcription factors, or inhibitors, etc...

often instead, the broken off inside bits of the recptor become activated enzymes, which in turn 'alter' soem other protein in the cell (phosphyralate it, methylate it or some such); turnign that* secon protein into an active molecule that can either be a transctiption factor itself, or then itself, activate a further dosntream protein which becomes a transcription factor; often multiple receptors for fdiffernt molecules (like hormones etc), may share part of the downstream pathways as they provide alterntive routes to activate simular or identicle genes in the target cell
It relaly was a long while ago I did anything on this though

"some transcription factors can be very specific for a given gene, others will act apon several genes, and some pretty-much on any gene; though most genes require multiple TFS to make transcripton begin."

That's interesting cos that seems to plug into the idea of Gene regulatroy networks I have planned to read here:
http://scienceblogs.com/pharyngula/2009/08/gene_regulatory_networks_and_c.php#more



today I have learnt...

Yes there is just so much complexity in biology, and especially within the cell itself....
multiple extracellular receptors recieving very differnt extracellular signaly and then triggering the identicle response inside the cell; differnt responses inside the cell. these respnses themsevelses will have differnt or the same next reaction in differnt cells, differnt cells at difernt times in their development; often depending on what else jsut* happened to the cell
and all that multiple biochemical signalling pathways that might be triggered by differnt receptors, often these interact with each other at differnt points in differnt ways; not all, but pretty much all these pathways ultimately* end up in genes being transcribed, or genes stopping being transcribed, and that is either through transcription factors, inhibitors etc
and I used* to know a lot about this... I don't think I can remember anything cept the general anymore actually maybe I should go read by masters thesis

Wow, I learned a lot about biology. I blame 2legs.