What are some examples of genes being active in Slug cells?

[Q_Goest]

In a http://www.sciam.com/article.cfm?chanID=sa003&articleID=CF2AA0B2-E7F2-99DF-34CD01DE3E68F8ED&ref=rss", it says:

Kandel and Leonid Moroz of the University of Florida teamed up with other researchers to methodically identify genes expressed in Aplysia brains. They found that at any given time, more than 10,000 genes could be active within a sea slug brain cell.

What do they mean when they say 10,000 genes "could be active"? What are these genes doing in the brain cell which is interpreted as 'being active'?

 

[Monique]

The answer is in the first sentence of your quote: they looked at the genes that were expressed, thus making protein. An unexpressed gene is not active, an expressed protein might be active. The only way to make sure that it has a function in that brain cell, is to turn the gene off and see whether there is a phenotype when you do that.

 

[iansmith]

An active gene is usually a gene that is actively transcribed into mRNA. There's techniques to measure levels of mRNA for several if not all the predicted genes of one organism. Microarrays is a technique that is often use but there's also macroarray and other techniques that work as well.

 

[iansmith]

http://www.ncbi.nlm.nih.gov/entrez/..._uids=17190607&query_hl=2&itool=pubmed_docsum

so they look at the transcriptome i.e. transcribed genes

Just to complement the information that given.

The problem is that an gene can be actively transcribed but the transcript is not translated into proteins. Also, some genes might not be transcribed but an active protein might be present. Transcriptome analysis is often complemented with the analysis of proteins (i.e. proteome).

 

[Q_Goest]

Hi Monique. Sorry, but I know almost nothing about biology. I don't know what "expressed" means nor what turning on and off a gene is. Ok, wait, I looked it up and it seems to be what Iansmith is talking about. . . . when you say "making a protein" are you referring to mRNA? ie: is mRNA the protein you're referring to? If so, why the different terminology?

Also, not sure what you meant by "phenotype" as it doesn't make sense in context with what I'm looking into right now. Per http://en.wikipedia.org/wiki/Phenotype" :

The phenotype of an individual organism is either its total physical appearance and constitution or a specific manifestation of a trait, such as size, eye color, or behavior that varies between individuals.

Hi Iansmith.

An active gene is usually a gene that is actively transcribed into mRNA.

I think I understand what you're saying here. An "active gene" has been duplicated from a small section of DNA and is now an mRNA which is somewhere, doing something, inside the cell. I assume that's what "expressed" means, is that right?

So the article is saying there are 10,000 mRNA molecules floating around inside the cell, doing something, is that correct? If so, what in general terms, are they doing? Are they mostly the same or different mRNA?

Thanks for the help both of you - fascinating! :)

 

[iansmith]

Some basic biology

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html

DNA (gene) is transcribed to RNA (mRNA) which is translated to protein.

Expression usullay referes to both transcription and translation

The 10 000 numbers refers to unique and individual genes not the to number of mRNA molecules in a cells. There often more than one mRNA molecules produce from one gene. So a cell can have 10 to 100 of thousands of mRNA molecules at any given time. mRNA numbers can also be a bit more complicated depending on the organism.

Also, one mRNA molecules can code for more than one protein (i.e. more than one gene per mRNA). It's called a polycistronic mRNA. This is usually seen in bacteria, in some archea and in rarely in eukaryotes (group that includes the slug), exluding chloroplast and mitochondria.
For example 2 genes = 1 mRNA = 2 proteins
http://en.wikipedia.org/wiki/Polycistronic_mRNA

One gene also can produce more than one mRNA due to alternate splicing (see the transcription link above). This is often seen in eukaryotes and rarely seen or absent in bacteria and archea.
For example: 1 gene = 2 mRNA = 2 proteins

 

[Monique]

Hi Monique. Sorry, but I know almost nothing about biology. I don't know what "expressed" means nor what turning on and off a gene is. Ok, wait, I looked it up and it seems to be what Iansmith is talking about. . . . when you say "making a protein" are you referring to mRNA? ie: is mRNA the protein you're referring to? If so, why the different terminology?

Also, not sure what you meant by "phenotype" as it doesn't make sense in context with what I'm looking into right now. Per http://en.wikipedia.org/wiki/Phenotype" :

Iansmith already explained it largely. I'll just explain it a little bit further: every cell in your body carries the same genetic information, every cell has the same genome.

So how is it that every cell has its own program. That is because every cell has its own subset of genes that are transcribed into mRNA and then translated into proteins.

Proteins are the functional units in the cell that carry out a function [although there is also recent evidence that miRNAs (micro RNAs) have a regulatory function, but that is a whole other discussion].

Every gene has a promoter that can be activated or repressed, this is done by transcription factors (a subset of proteins that can bind to DNA).

By analyzing mRNA (messenger RNA) in a cell, you can see which genes have been activated. As said, this does not tell you anything about the protein levels or the actual function of the protein.

If the gene IS important, you should get a phenotype when you remove it. With a phenotype I meant that there will be a difference in the characteristics of the organism that you can measure. A genotype is the genetic makeup of an organism (how many copies of a gene it has), while a phenotype is the appearance of an organism resulting from the interaction of the genotype and the environment.

Thanks for the help both of you - fascinating! :)

You are only scratching the surface here, it is indeed very interesting, especially to find out what is conserved between the sea slug and us humans.. and also what is different.

 

[Q_Goest]

Some basic biology

http://users.rcn.com/jkimball.ma.ult...scription.html

DNA (gene) is transcribed to RNA (mRNA) which is translated to protein.

Thank you. As difficult as it is to read without a background, it's been some help.

I see I was mistaken about mRNA and how it is created. The link points out the mRNA is not a duplicate of some portion of the DNA as I'd thought, but that it is "transcribed":

Thus for each C encountered on the DNA strand, a G is inserted in the RNA; for each G, a C; and for each T, an A. However, each A on the DNA guides the insertion of the pyrimidine uracil (U, from uridine triphosphate, UTP). There is no T in RNA.

Got it. I went through the example with all the …TACCGG<etc> and figured this created an mRNA with …UTGGCC<cte> And this is called "transcription". Think I got this right now!

The 10 000 numbers refers to unique and individual genes not the to number of mRNA molecules in a cells.

Ok, still trying to wrap my last remaining (and functional) brain cells around this. The gist of what I'm getting from both of you (iansmith & monique) is that depending on the cell type (ex. of cell type: liver cell, muscle cell, brain cell) the cell will have a set of genes (not necessarily in series) along this enormous DNA chain that are making mRNA molecules. But this set of genes will be different for different cell types, even though all the cell types in a single organism have identical DNA. Is this what is called expression? That is, the set of genes in a given cell type are expressed (or activated) when they are of that set which create mRNA.

Also, the molecule performing this "transcription" is called "RNA polymerase", is that right?

So the 10,000 number referred to is the number of genes in this set, which are inside this brain cell, which are creating mRNA molecules. yes/no?

Still pondering here... Is there a way to catagorize what all these activated genes are doing? That is, like a colony of ants, some of these mRNA molecules must be creating proteins that are in the energy food chain, things that shuttle energy into or out of the cell. Others are repairing the cell. Still others are communicating with other cells. Is there a catagorized list of what all these 10,000 molecules are doing?

 

[iansmith]

Got it. I went through the example with all the …TACCGG<etc> and figured this created an mRNA with …UTGGCC<cte> And this is called "transcription". Think I got this right now!

you just learn the basic concept of transcription

The gist of what I'm getting from both of you (iansmith & monique) is that depending on the cell type (ex. of cell type: liver cell, muscle cell, brain cell) the cell will have a set of genes (not necessarily in series) along this enormous DNA chain that are making mRNA molecules. But this set of genes will be different for different cell types, even though all the cell types in a single organism have identical DNA. Is this what is called expression? That is, the set of genes in a given cell type are expressed (or activated) when they are of that set which create mRNA.

You got the concept but the wording is not best.

Gene = region of DNA that encodes a protein
Transcriptome = mRNA produce by a given type of cell at a given time
Proteome = protein present in a given type of cell at a given time
Expression = transcription+translation

Basicly, all cell in a multicellular organism has the same genetic material and the set of genes. The difference is in the transcription level of each genes and combination of expression. So it's the transcriptome and the proteome that are different from cell types.

For example, both liver and brain cell possesses gene A, B, C and X. The liver cells have a high transcription level of gene A and B whereas the brain cell have high level of C and X mRNA. So

Also, the molecule performing this "transcription" is called "RNA polymerase", is that right?

Right

So the 10,000 number referred to is the number of genes in this set, which are inside this brain cell, which are creating mRNA molecules. yes/no?

number of genes that are actively transcribed in the brain cells

Still pondering here... Is there a way to catagorize what all these activated genes are doing? That is, like a colony of ants, some of these mRNA molecules must be creating proteins that are in the energy food chain, things that shuttle energy into or out of the cell. Others are repairing the cell. Still others are communicating with other cells. Is there a catagorized list of what all these 10,000 molecules are doing?

It`s what research is trying to figure out. some of the function are know.

 

[bross7]

Still pondering here... Is there a way to catagorize what all these activated genes are doing? That is, like a colony of ants, some of these mRNA molecules must be creating proteins that are in the energy food chain, things that shuttle energy into or out of the cell. Others are repairing the cell. Still others are communicating with other cells. Is there a catagorized list of what all these 10,000 molecules are doing?

Once the function of the gene is known, absolutely.

There are databases for known genes and their function on the internet.

From the sequence, if you find a gene in another organism that has a similar function you can predict that it probably has a similar role in the organism of your choice, but it would have to be proven correct.

 

[Q_Goest]

Thanks again for the info. (Also for confirming/clarifying - that's a great tool to learn to use if you haven't already.)

iansmith said: You got the concept but the wording is not best.

I'll try again... So "expressed" genes are 'transcribed' from DNA to mRNA (transcriptome), and then 'translated' from mRNA to protein (proteome). And these 10,000 genes are active when they are going through this process. <do I sound like a biologist yet?> lol

bross7 said: ... if you find a gene in another organism that has a similar function you can predict that it probably has a similar role in the organism of your choice, but it would have to be proven correct.

Ok, this is strange. I believe I read that some genes can create more than one type of protein. So either the transcription to mRNA or the translation to protein must be able to propogate along more than one path. Is that what you're saying? Isn't the purpose of expressing a gene (in the most simple terms), "to create protein molecules"? And if that's true, then I'm still a bit lost as to what all these proteins are doing. They must interact with other portions of the cell in some way, so I wonder if there's a very simple way of catagorizing the function of these proteins, and hence the expressed gene.

One other thing strikes me as odd here. With all these proteins floating around, some of them being used to transcribe genes and others with various other functions, it seems strange that these things seem to 'know' what they are doing. Why don't all these different molecules end up turning into a pile of goo inside the cell instead of doing what they're supposed to do? Any good references that helps explain that would be appreciated.

 

[iansmith]

I'll try again... So "expressed" genes are 'transcribed' from DNA to mRNA (transcriptome), and then 'translated' from mRNA to protein (proteome). And these 10,000 genes are active when they are going through this process. <do I sound like a biologist yet?> lol

You got the concept and almost sound like a biologist . However, keep in mind that this is a very simplified concept and that reality is not as clear cut as that.

For example, the study you linked only looked at the transcription and not at expression. As I said before, transcription does not always equate to protein expressed. Also, expression does not necessarly equates to an active protein. So what the researcher meant by active genes were those that were actively transcribed.

Ok, this is strange. I believe I read that some genes can create more than one type of protein. So either the transcription to mRNA or the translation to protein must be able to propogate along more than one path. Is that what you're saying? Isn't the purpose of expressing a gene (in the most simple terms), "to create protein molecules"? And if that's true, then I'm still a bit lost as to what all these proteins are doing. They must interact with other portions of the cell in some way, so I wonder if there's a very simple way of catagorizing the function of these proteins, and hence the expressed gene.

You are right, one gene can produce more than 1 protein. You usually end up characterizing each protein despite the fact that they are coming from the same gene. I'll like to give you a good example but I just can't think of a good one right now. I study bacteria and not eukaryotes. Monique studies eukaryotes so I'm sure she could find an example.

As far as the transcription or translation path is concern, we are getting into the more complex part of expression. For transcription, RNA polymerase can bind to different sites and initiate transcription at different point. Therefore you end up with different mRNA. That one way to produce 2 "different" proteins.

The initial transcription does produce an immature form of mRNA and that immature mRNA must be process prior to translation. Processing of the mRNA into a mature form can produce different mature mRNA and thus produce more than 1 protein. As fas translation goes, it will only produce one protein per mRNA molecules but post-translation processing will produce different form of the protein. There several different post-translation processing and each modification will have an impact of the function of the protein. Again, this is the more complex part of protein expression and function. I am barely scratching the surface.

One other thing strikes me as odd here. With all these proteins floating around, some of them being used to transcribe genes and others with various other functions, it seems strange that these things seem to 'know' what they are doing.

Protein don't float around. Proteins often have specific location and proteins are directed to their location by other proteins. They "know" what to do because they are in the right place and they can interact with other protein or DNA. Those interaction are very specific and therefore limits the type of "jobs" a protein can do.

Why don't all these different molecules end up turning into a pile of goo inside the cell instead of doing what they're supposed to do? Any good references that helps explain that would be appreciated.

Protein will sometime form "pile", at least in bacteria, when protein processing fails or is not under optimal condition. Protein will also be degraded if they are not properly process. The system is far from being perfect and a lot of mistake happens but the cell has mechanism to deal with the mistakes.

 

[Monique]

You are right, one gene can produce more than 1 protein. You usually end up characterizing each protein despite the fact that they are coming from the same gene. I'll like to give you a good example but I just can't think of a good one right now. I study bacteria and not eukaryotes. Monique studies eukaryotes so I'm sure she could find an example.

Of the human protein that I'm studying right now, three different splice variants are known.

There are four different ways of getting alternative splicing: alternative selection of promoters, alternative selection of cleavage/polyadenylation sites, intron retaining mode, exon splicing mode.

The Dscam Drosophila (fruitfly) protein has over 38,000 alternative splicing forms from four variable exon clusters