Double sided RNA

[invert_nexus]

Got a quick question for our DNA boys. (Or girls.)

What's the difference between double sided RNA and DNA?
I know that DNA is deoxy and so RNA must have oxygen involved somehow? But I always thought that RNA was simply 1/2 of a strand of DNA.

Does it use different base pairs?

 

[zyncod]

Ok - this would be so easy to look up online. Or figure out by the nature of the name. RNA is ribonucleic acid - DNA is deoxyribonucleic acid. Hence, DNA has an oxygen (actually, a hydroxyl) missing from the ribose sugar moety. Hence, the "deoxy"ribo... But that's the only diffeence between dsRNA and dsDNA except for the pesky uridine/thymidine difference in nitrogenous bases.

 

[invert_nexus]

Or figure out by the nature of the name. RNA is ribonucleic acid

You mean something like this: "I know that DNA is deoxy and so RNA must have oxygen involved somehow?"

Anyway. Thanks.

And there is U/T difference. Ok. I thought I remembered something along those lines.

And yes. A search probably would have answered this... eventually. But I was feeling lazy and thought I might find more useful information on the subject from the kindly folks in our forums.

Edit:
Bah. It was a lot easier to find than I thought. I didn't feel like poring over pages for a relevant link but this is one question that answered too easily with a web search.
Bah!

Anyway. The answer is answered. And my thanks to you, sir.

 

[spuriousmonkey]

and it would be double stranded and not double sided.

 

[invert_nexus]

Oops. Now that was a typo. Must have been thinking dice or maybe double sided tape or something.

 

[Hercules Rockefeller]

Double stranded RNA (dsRNA) is a rare occurrence in nature – pre-spliced RNA is single stranded, mRNA is single stranded, rRNA is single stranded, tRNA is single stranded. Of course, dsRNA viruses are a prime example, but viruses aren’t living organisms. (Yes, I went there! I realize that the definition of what is “living” is a semantic issue, so I won’t be discussing it here – it’s been done to death.)

The only instances of dsRNA in living cells that I am aware of are the relatively new (and very exciting) area of microRNAs (miRNAs). First discovered in the nematode <I>C. elegans</i>, this ~22 nt long class of noncoding RNAs are now thought to be expressed in all metazoan eukaryotes. Hundreds of different miRNAs from a variety of organisms have now been identified. Although their biological functions are still somewhat of a mystery, one function has been identified: posttranscriptional regulation of mRNA by binding to complementary sites in the 3’UTR. Other than viruses, this is the only “natural” instance of dsRNA that I can think of.

Of course, there is a laboratory example of dsRNA that I am sure you are all thinking of – RNA interference (RNAi). Cells have a natural defense against infection by dsRNA viruses whereby a protein complex cleaves the infecting dsRNA into small pieces. These pieces of short interfering RNA (siRNA)/protein complexes can then cleave any other complementary dsRNA molecules that enter the cell, thus providing “immunity” long after the original infecting dsRNA has been degraded. This cellular mechanism has been exploited by cell biologists – introduction of siRNA into cells or embryos that is complementary to an endogenous mRNA of interest will lead to the degradation of that mRNA and a “knockdown” phenotype. <P>

 

[invert_nexus]

Thank you, Hercules. MicroRNA and RNA interference are exactly what I was looking into and I kept coming across references to double stranded RNA which stood in the face of what I thought I knew about DNA and RNA.

I feel somewhat stupid asking such a simple question here, but since I already have, how about making this thread a general DNA question and answer thread. Feel free to comment on anything about DNA, RNA, plasmid, protein, whatever you might think people would find interesting.

I do have another question.
When DNA is transcribed to RNA and the introns are cut out of it, how does the enzyme know which segments are extrons and which are introns? Is there a marker at the end and beginning of each extron or intron?

And. I've seen references (specifically wikipedia) that say that this splicing takes place in the nucleus. But, I'm relatively sure that I read in Scientific American that the splicing takes place outside the nucleus.

 

[Maddad]

This is what I love about the science forums. You think you know the basics about a subject like DNA and RNA, and then discover that RNA can be double stranded! Amazing!

 

[Hercules Rockefeller]

MicroRNA and RNA interference are exactly what I was looking into and I kept coming across references to double stranded RNA which stood in the face of what I thought I knew about DNA and RNA.

These are hot topics at the moment so it shouldn’t be hard to find lots of info.

I've seen references (specifically wikipedia) that say that this splicing takes place in the nucleus. But, I'm relatively sure that I read in Scientific American that the splicing takes place outside the nucleus.

Inside the nucleus.

Mitochondria and chloroplasts have their own genomes, but being of bacterial origin, most of their genes have no introns. However, I believe that <I>some</I> mitochondrial/chloroplast genes have acquired introns. I assume that these are spliced out in the organelles, so perhaps this would be an example of extra-nuclear RNA splicing(?).

When DNA is transcribed to RNA and the introns are cut out of it, how does the enzyme know which segments are extrons and which are introns? Is there a marker at the end and beginning of each extron or intron?

Short answer: yes. <small>(Read on for more detail.....)</small>

Pre-mRNA splicing remains a mysterious process (and my knowledge is limited). We know a little bit about how it works.....

Introns range in size from very small (only a few nucleotides) to well over 100,000 nucleotides. I have worked with a gene that has a 1Mb intron! When looking at the DNA sequence of a gene, picking out the precise borders of an intron is very difficult (even with the aid of computers). The possibility of alternative splicing greatly compounds the problem of predicting protein sequences solely from a sequence. The position of exon-intron boundaries and alternative splicing still needs to be determined experimentally. Yet somehow each cell in our body recognizes and rapidly excises the appropriate intron sequences with very high fidelity.

The answer to your question is yes: there are specific sequences that mark to beginning and end of each intron. The protein/RNA complexes that excise the introns (called “spliceosomes”) recognize these sequences. According to <I>Molecular Biology of the Cell (4th Ed)</I> by Alberts et al., intron sequence removal involves three positions on the RNA: the 5’ splice site, the 3’ splice site, and the branch point in the intron sequence (about 2/3 through the intron) that forms the base of the excised "lariat". In pre-mRNA splicing, each of these three sites has a consensus nucleotide sequence that is similar from intron to intron, providing the cell with cues on where splicing is to take place. However, there is enough variation in each sequence to make it very difficult for scientists to pick out all of the many splicing signals in a genome sequence.

Have a look through these:
RNA splicing schematics

...or at this...

<img src="http://www.mit.edu/people/holste/MIT.Teaching/splicing.overview.gif"><P>

 

[invert_nexus]

Alright.
Thanks for all your help, Hercules. I'm glad you're around.
I have another question related to DNA. Specifically about Adenosine and ATP.
I've seen a couple of discrepant images of these molecules and I'm wondering if there's a difference between ATP and AMP (which is part of DNA and RNA) or if the pictures are just whonky.

Here. This is a pic of AMP:

Note the position of the double bonded Oxygen atom.

Now. Here's a picture of ATP from the same book:

The double bonded oxygen atom is in the same position.

But. This is from Wikipedia (probably the source of the problem...):

In this one the double bonded oxygen is on the side. Does this matter to the structure of the molecule? I would think that it would, am I wrong? Is it just this last diagram that is in error? Or does it not even matter?

I must admit that I'm somewhat surprised that ATP is actually the nucleotide Adenosine with extra phosphate groups tacked on. Is there anything significant in this that you might care to share or is it just a coincidence?

 

[spuriousmonkey]

They are exactly the same things. It doesn't matter for the real structure where you put the double bonded oxygen, up, down or on the side.

It is just an annotation.

 

[invert_nexus]

Hmm. I would have thought that it was somehow significant seeing as how it does limit and define what structures can form with it, and how they would look.

For instance, much is made of assymetric carbon atoms. The D and the L isomers of amino acids. Why shouldn't it also matter here? The double bond is significant, isn't it? Doesn't it lock the molecule in a certain way? Provide a certain stability?

 

[Idle Mind]

The D and L isomers are mirror images on paper, but all the bonds are reversed, and thus the chemistry is different.

What spurious means by "it's just annotation", is that since the bonds between the Phosphorus and Oxygen atoms in the chain are single bonds, they can rotate along that axis. So, writing the double bond facing downward is the same (since it may have just rotated).

 

[invert_nexus]

But that's just it. I can understand if it was up and down but to the side? Does the single bond allow that much leeway for it to move around that much?

And. If so, why do the single bonds allow such leeway here but not in the D and the L isomers based around carbon? They're single bonds too and so should be able to flip willy nilly. Or something. Is it something to do with the properties of carbon?

Edit:

I suppose one major difference is that we're dealing with only oxygen atoms around the phosphorus with only one being distinguished from the others by a double bond while there are different molecules in the amino acide based around carbon. But, they're still single bonds.

 

[Idle Mind]

Okay, now we're into resonance. You could correctly write the double bond on any of the three oxygen atoms because they technically "share" the electrons. The negatively charged oxygen atom has an extra 'lone pair' of electrons that can move between the P and O, and create a double bond, which will kick the pair of electrons in the other double bond out onto an Oxygen atom. This happens all the time, and electrons are constantly redistributing the negative charge.

 

[invert_nexus]

Alright. That makes sense. So. The difference here and between the D and L isomers is the fact that we're dealing with all oxygens then, right? This enables them to swap electrons in a way that the carboxyl, amino, hydrogen, and R side chain of the amino acid can't?

Is this true of all similar bonds? Or does it require a negatively charged atom? It probably does, right? Because there need to be an excess of electrons.


Oh. And while I'm at it. Why is it that it's only the L isomer found in most lifeforms? (I seem to remember it saying some deep sea creatures use D.) I'm forgetting right now (it's late) but the L form is used in proteins whereas the D from is used in... nucleotides? Or... something else. I'm blanking. Right? But why does it differentiate like this? Any particular reason or is it just one of those weird arbitrary things about cellular functioning?

Edit:
Sugars. Nearly all sugars are D isomers while amino acids are L.
Why?

 

[zyncod]

There's no reason why the L isomer is predominant - life just started off that way (the same reason why all cells have DNA as their genetic material). Proteins are very specific as far as the molecules they recognize, which is why there is specificity for certain isomers.

And resonance doesn't require negatively charged atoms. In fact, molecules that are fluorescent (like the black light paint stuff) have a number of double bonds between carbons (usually) that are shared. Resonance is just the way of spreading out the electrons - making molecules more stable. And by the way, the square configuration of the phosphate group has nothing to do with the chemical reality. Those oxygens are arranged in a pyramid with the phosphorus in the middle - to spread out the positively charged nuclei from each other. This is another general thing - nature tries to keep positive and negative charges away from like charges.

 

[QuarkHead]

I have another question related to DNA. Specifically about Adenosine and ATP.
I've seen a couple of discrepant images of these molecules and I'm wondering if there's a difference between ATP and AMP (which is part of DNA and RNA) or if the pictures are just whonky.

I must admit that I'm somewhat surprised that ATP is actually the nucleotide Adenosine with extra phosphate groups tacked on. Is there anything significant in this that you might care to share or is it just a coincidence?

In view of your recent grump at me, I dare say this won't be welcome. But others might be interested.
Let's start with the bases. In the case under discussion this is Adenine. It is a highly nitrogen-rich carbon double ring structure. Adenine is one of five bases. The other four are guanine, cytosine, thymine and uracil. To any of these a 5-carbon sugar can be added; if the sugar is ribose, the resulting compound is referred to as a Ribonucleoside. If the sugar is deoxy-ribose, it become a deoxyribonucleoside.
Now any of these can be phosphorylated (its called esterification if you want to posh) up to three times. In the case of the ribonucleoside adenosine, you get adenosine mono- di- and tri-phosphate. The importance of this in metabolic terms is that phosphate groups carry a lot of energy, i.e. if you can remove a phosphate enzymatically you are in the money.

So your question was is there anything significant in the extra phosphates on ATP? Yes, highly. ATP is the fuel for life. And that is not an exaggeration, it literally is.
And if you're thinking about nucleic acids, the tri-phosphorylated nucleotides are of course able to participate in nucleic acid synthesis by virtue of their energy content.

 

[invert_nexus]

In view of your recent grump at me, I dare say this won't be welcome. But others might be interested.

On the contrary. I don't know what kind of a person you take me for, but my recent 'grump' at you was because of a certain attitude and stinginess with knowledge. You haven't displayed either in here and I thank you for your help.

I thank all of you for your help.

Keep your eyes tuned to this thread, this will be my general question and answer thread on the subject of genetics and cellular biology.

So your question was is there anything significant in the extra phosphates on ATP?

Actually, my question was more related to the adenine than the phosphate. All the nucleotides have a phosphate group attached to the sugar. But it's adenine that is the one used for the power source. Why not a TTP or a UTP or GTP?
Chance again? Just the vagaries of fate?

And if you're thinking about nucleic acids, the tri-phosphorylated nucleotides are of course able to participate in nucleic acid synthesis by virtue of their energy content.

Ah. Ok. I haven't made it that far yet, but this makes sense. In a normal ATP reaction, the severed phosphate group is attached to the reactant with the positive delta G to power the reaction. But, in the case of DNA formation the molecule itself provides power to itself directly, yes?

Or does the energy go with the severed phosphate...?
I suppose that if this is the case, then the phophates severed from the previous molecules could be used to power the next in the chain...
If this is the case, it would lead me to think that a genetic chain would always begin with Adenine, but I doubt that this is the case.

This brings me back to the concept of UTP and GTP and etc... In DNA and RNA formation is ATP required to power their addition to the chain or do they power themselves?


Another question. Concerning that extra hydroxyl group in RNA as compared to DNA. AMP also has this extra hydroxyl, so my question is when is the oxygen atom removed from it to change the ribose to deoxyribose? Does DNA formation occur this way? From AMP (plus the other bases) to DNA? Or must it occur seperately so as to incorporate deoxyribose instead of ribose?

And resonance doesn't require negatively charged atoms.

But what about different elements? Such as the case of the asymetrical carbon? Do all the atoms have to be of the same type for this resonance to occur?



Ok. That's it for now. Expect more later. Your answers will probably also inspire more questions as is the way of things.

By the way, anyone else with similar questions feel free to ask.

 

[QuarkHead]

On the contrary. I don't know what kind of a person you take me for, but my recent 'grump' at you was because of a certain attitude and stinginess with knowledge. You haven't displayed either in here and I thank you for your help.

Good. All friends again

Actually, my question was more related to the adenine than the phosphate. All the nucleotides have a phosphate group attached to the sugar. But it's adenine that is the one used for the power source. Why not a TTP or a UTP or GTP?
Chance again? Just the vagaries of fate?

OK. Let's go back to the bases. Adenine and guanine are classified as purines, thymine, uracil and cytosine as pyrimidines. Let's just say they have a different chemical structure (please don't ask - you'd be asleep in 5 minutes). The point is that that purine tri-phosphonucleotides are more useful as a general energy store/source. Yes, GTP is used in this way, but not as much as ATP

But what it basically means is that the nucleotides derived from the purines are more active in general metabolic processes. By general I mean the whole bannana - anything that involves energy exchange or conservation (yes! TD1 appies in biochemistry too!)

In a normal ATP reaction, the severed phosphate group is attached to the reactant with the positive delta G to power the reaction. But, in the case of DNA formation the molecule itself provides power to itself directly, yes?

Yes more or less. The energy locked in the tri-phosphorylated nucleotides is used in the synthesis of RNA and DNA, but ATP is also used as an adjunct energy source for the enzyme reactions required for synthesis.

Or does the energy go with the severed phosphate...?

Bingo. Energy is almost all in the terminal phosphate linkage. Adenosine is the sucker.

In DNA and RNA formation is ATP required to power their addition to the chain or do they power themselves?

Have I answered this already? How's this. Yes and no. In removing the terminal phosphates to make RNA or DNA, you release energy, which is always handy when you're making something big out of something small. But ATP is required in addition to do ..oh..all the other things that synthetic machinery requires (sorry - if you want me to expand on that, ask)

Concerning that extra hydroxyl group in RNA as compared to DNA. AMP also has this extra hydroxyl, so my question is when is the oxygen atom removed from it to change the ribose to deoxyribose?

I see your problem. I blame my (long dead) colleagues. We have, strictly speaking 5'-monophospahte ribonucleotides (AMP is one) and 5'-monosphate deoxyribonucleotides (dAMP). What that mouthful is meant to convey is that the difference between, AMP and dAMP is in the sort of sugar that is attached to the base. Before anybody even thought abou making RNA or DNA.