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Why does RNA have 5 bases and DNA has only 4?


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#1 RyanJ

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Posted 17 November 2005 - 08:16 PM

Why does [acr=Ribonucleiic acid]RNA[/acr] have 5 bases and [acr=Deoxyibonucleiic acid]DNA[/acr] has only 4?

I really don't understand why! [acr=Ribonucleiic acid]RNA[/acr] is used in the replication of proteins (Because it can fit through the nuclear pores and the [acr=Deoxyibonucleiic acid]DNA[/acr] cannot) so why would it need to ahve a 5th base when only 4 are needed to complete [acr=Deoxyibonucleiic acid]DNA[/acr]?

There must be a reason why it has 5 when [acr=Deoxyibonucleiic acid]DNA[/acr] has only 4 and [acr=Ribonucleiic acid]RNA[/acr] is supposed to be a simpler form of [acr=Deoxyibonucleiic acid]DNA[/acr] so why would it need 5 bases?

This question has me stumped and my biology teacher could not provide much information it either so I was wondering if you guys could help answer this!

Cheers,

Ryan Jones
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#2 Ophiolite

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Posted 17 November 2005 - 09:15 PM

I think you are getting confused. RNA has only four bases. One of the bases is different from the corresponding one in DNA. Specifically:

DNA Bases:
Adenine
Guanine
Cytosine
Thymine

RNA Bases:
Adenine
Guanine
Cytosine
Uracil

So both RNA and DNA employ four bases each, its just that in RNA Uracil takes the role of Thymine in DNA.

If your biology teacher did not know this you need to change schools! I suspect you may have asked the question in an ambiguous way: perhaps they thought you were asking why is there that difference of a single base between RNA and DNA.
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#3 RyanJ

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Posted 17 November 2005 - 09:30 PM

I think you are getting confused. RNA has only four bases. One of the bases is different from the corresponding one in DNA. Specifically:

DNA Bases:
Adenine
Guanine
Cytosine
Thymine

RNA Bases:
Adenine
Guanine
Cytosine
Uracil

So both RNA and DNA employ four bases each, its just that in RNA Uracil takes the role of Thymine in DNA.

If your biology teacher did not know this you need to change schools! I suspect you may have asked the question in an ambiguous way: perhaps they thought you were asking why is there that difference of a single base between RNA and DNA.


It does? I must have miss-understoood the informaiton given in my textbook then.
Probably was that because of the way it was listed - in the groups not of the type RNA and DNA) but of another method I am not even shure of.

Thats probably why my teacher did not understand, it was because I asked him a question that was not correct (Maybe he thought I meant why is Uraciil present instead of Thymine :-)

Thanks for the help but I wonder if you could help me with an altered version of my quesiton on that case, why is Uracil present and not Thymine?

Cheers,

Ryan Jones
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#4 Ophiolite

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Posted 17 November 2005 - 09:42 PM

Ah! That one is more difficult. I think it is simply a matter of chance, but I do not know that. I'll google a little and if I find anything relevant I'll post it.
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#5 Ophiolite

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Posted 17 November 2005 - 09:53 PM

That wasn't so hard.
Here is another example of the cell going to a great deal of trouble to put a methyl group on the C-5 of uracil. It is a major energy-requiring process that needs a very special enzyme and vitamin cofactors in order to occur (thymidylate synthetase). The reason is not, however, all that obvious unless you step back and look at the chemical reactivity of the bases. The amino group on cytosine is somewhat vulnerable; under even physiological conditions, cytosine residues will undergo a small but finite deamination reaction. The result, of course, is to convert C to U. This means that a measurable population of RNA molecules have defects; but since several RNA molecules can be made from one template and the probability that a large fraction will have that defect is very small, the net effect is negligible. But if that happened in DNA, it would result in a permanent, heritable change in the genome, since there is but one copy of it. Indeed, the cell takes this seriously enough to have evolved a repair system that hunts out any uracil in the DNA and replaces it with the base dictated by the complementary strand. Pretty neat!

Taken from http://uhura.rpc.mso...w/sec4/4-20.htm
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#6 Dak

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Posted 18 November 2005 - 04:55 AM

Not directly in answre to your question, but:

Actually, RNA does use more than 4 bases, due to the fact that more than one codon can code for the same amino acid.

For example, alanine is coded for by CGA, CGC, CGG and CGT; in otherwords, CGx.

this would nessesatate 4 different types of tRNA: CGA, CGC, CGG and CGU; the last base is referred to as the 'wobble' position, because it can be changed to another base without changing the amino acid that it codes for.

The non-standard base inosine (I) can pair with C,A or U; meaning that you only need two different types of tRNA for alanine: CGI and CGC.

There are other non-standard bases that will bond with both pyramidines (ie U and A) or both purines (ie C or G), allowing greater flexibility in the genetic code, and cutting down on the amount of tRNA molecules needed.

In addition, the bases dihydrouridylate, thymine, and pseudouridylate are present in two of the four arms of the tRNA molecule, and i believe they play a role in joining the tRNA molecule to the ribosome during protien synthesys (tho im not too sure on that bit)
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#7 sunspot

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Posted 18 November 2005 - 06:20 PM

DNA and RNA also differ by the pentose sugars. RNA's pentose sugar is more oxidized (extra -OH group) and the DNA's pentose sugar is more reduced (-H instead). The same is also true of thymine and uracil. The extra -CH3 group on thymine of DNA is more reduced than the -H group on uracil of RNA. Two big differences between DNA and RNA that appear to reflect thse differences in reduction potential, are that the DNA always forms the double helix, while the RNA has more options. Secondly, the DNA is much larger than the RNA. Amazing what a little extra reduction or oxidation potential can do.

#8 RyanJ

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Posted 19 November 2005 - 02:07 PM

Thanks all!

sunspot, your description fits perfectly with the information given - a great explination! And your right, small difference in a small molecule make a huge difference!

Cheers,

Ryan Jones
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#9 sunspot

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Posted 20 November 2005 - 10:27 PM

If we look at DNA and RNA, the hydrogen bonding along the DNA occurs between the two DNA helixes. While the RNA can form double helix, loops, hairpins, and single helixes, etc. This implies that the hydrogen bonding potential defined by the DNA is higher than that defined by the RNA. In other words, if RNA had the same potential to form hydrogen bonds, it would lose its variety and try to become a double helix since this is the most efficient way for minimizing the hydrogen bonding potential within all the hydrogen bonding hydrogen on the bases.

If we add the more reduced state of the DNA to its greater observed hydrogen bonding potential, there should be a correlation between the two. The question becomes how can the extra reduction within the DNA cause the DNA to increase hydrogen bonding potential so it needs to more efficiently hydrogen bond than the RNA?

The extra electron density defined by the extra reduction of the DNA implies more electron density sharing within the hydrogen bonding. While the lower reduction value of the RNA implies less electron density sharing within the hydrogen bonding. This suggest that the primary potential within a hydrogen bond is the electrophilic potential of the hydrogen; the more available electron density that the H has to share helps the hydrogen lowers its electrophilic potential better. In RNA, the nucleophilic potential of the O and N are higher, yet the hydrogen bonding potential is lower because the electrophilic potential of the H is the primary potential.

This anomaly makes sense if one considers HCl in water. The Cl- is a very weak base while the H+ is a very strong acid. As such, HCl has more electrophilic potential in its H, in proportion to the amount of nucleophilic potential within its Cl-, even though the charge dipole might suggest their being equal. This is primarily due to the much higher electronegativity of the Cl-, allowing it to hold extra electron density and become a stable anion that does not need much positive charge to be stable, i.e., very low nucleophilic potential. The higher electronegativities of O and N, relative to their covalantly bonded H (hydrogen bonding hydrogen), should do a similar thing, but to a lessor degree, giving the H more electrophilic potential, and the O or N less proportional nucleophilic potential.

This irregular distribution of potential with a hydrogen bond explains why the extra electron releasing groups within DNA can increase the potential to form hydrogen bonds, i.e., better lowers the electrophilic potential of the H via the increased electron density within the O and N. In RNA, the opposite occurs, with the O and N having less electron density to share, this lowers the potential with the hydrogen bonding hydrogen. The result for RNA is looser H-bond variety.

#10 Nashyboyo

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Posted 21 March 2006 - 01:57 PM

...This implies that the hydrogen bonding potential defined by the DNA is higher than that defined by the RNA. In other words, if RNA had the same potential to form hydrogen bonds, it would lose its variety and try to become a double helix since this is the most efficient way for minimizing the hydrogen bonding potential within all the hydrogen bonding hydrogen on the bases.


It may imply that but that's not the case.

The question becomes how can the extra reduction within the DNA cause the DNA to increase hydrogen bonding potential?


Answer: A reduced form of DNA results in the negative charge on the sugar phosphate backbone being neutralised by hydrogen. By eliminating the negative charge the backbones can move closer, increasing the association (H bonding) between the bases.

This anomaly makes sense if one considers HCl in water. The Cl- is a very weak base while the H+ is a very strong acid. As such, HCl has more electrophilic potential in its H, in proportion to the amount of nucleophilic potential within its Cl-, even though the charge dipole might suggest their being equal. This is primarily due to the much higher electronegativity of the Cl-, allowing it to hold extra electron density and become a stable anion that does not need much positive charge to be stable, i.e., very low nucleophilic potential.


That is absolutely correct, but irrelavent.

...In RNA, the opposite occurs, with the O and N having less electron density to share, this lowers the potential with the hydrogen bonding hydrogen.


Why less electron density ? What's the difference between the bases involved in DNA and RNA hybridisation (e.g. deoxyribothymidine (DNA) and ribothymine (RNA) differs by one hydroxyl group on the ribose sugar). I'm not being sarcastic, this is a genuine question.
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#11 Nashyboyo

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Posted 21 March 2006 - 02:02 PM

It does? I must have miss-understoood the informaiton given in my textbook then.
Probably was that because of the way it was listed - in the groups not of the type RNA and DNA) but of another method I am not even shure of.

Thats probably why my teacher did not understand, it was because I asked him a question that was not correct (Maybe he thought I meant why is Uraciil present instead of Thymine :-)

Thanks for the help but I wonder if you could help me with an altered version of my quesiton on that case, why is Uracil present and not Thymine?

Cheers,

Ryan Jones



RNA polymerase does not use thymine as a substrate only uracil. Therefore RNA molecules are generated in transcription.
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#12 Nashyboyo

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Posted 21 March 2006 - 02:05 PM

That wasn't so hard.
Here is another example of the cell going to a great deal of trouble to put a methyl group on the C-5 of uracil. It is a major energy-requiring process that needs a very special enzyme and vitamin cofactors in order to occur (thymidylate synthetase). The reason is not, however, all that obvious unless you step back and look at the chemical reactivity of the bases. The amino group on cytosine is somewhat vulnerable; under even physiological conditions, cytosine residues will undergo a small but finite deamination reaction. The result, of course, is to convert C to U. This means that a measurable population of RNA molecules have defects; but since several RNA molecules can be made from one template and the probability that a large fraction will have that defect is very small, the net effect is negligible. But if that happened in DNA, it would result in a permanent, heritable change in the genome, since there is but one copy of it. Indeed, the cell takes this seriously enough to have evolved a repair system that hunts out any uracil in the DNA and replaces it with the base dictated by the complementary strand. Pretty neat!

Taken from http://uhura.rpc.mso...w/sec4/4-20.htm



This is simply a repair mechanism. The reason RNA is RNA is because the recruitment of uracil as a complementary base during transcription is thermodynamically favorable when catalysed by RNA polymerase. Sidenote: There is evidence to suggest that RNA was around before DNA.
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#13 sunspot

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Posted 22 March 2006 - 12:48 AM

The RNA coming first is probably true since its single helix nature would make transcription easier by requiring less prep steps, such as separating the DNA double helix. Duplication of of a single strand of RNA would also be easier than duplicating two strands of DNA.

#14 tejaswini

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Posted 5 October 2006 - 04:02 PM

DNA and RNA also differ by the pentose sugars. RNA's pentose sugar is more oxidized (extra -OH group) and the DNA's pentose sugar is more reduced (-H instead). The same is also true of thymine and uracil. The extra -CH3 group on thymine of DNA is more reduced than the -H group on uracil of RNA. Two big differences between DNA and RNA that appear to reflect thse differences in reduction potential, are that the DNA always forms the double helix, while the RNA has more options. Secondly, the DNA is much larger than the RNA. Amazing what a little extra reduction or oxidation potential can do.


DNA occurs as a single strand as well . for example in parvovirus etc.
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#15 thedarkshade

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Posted 24 December 2007 - 04:58 PM

Once I had a project that had to do with nucleic acids, and came across an info that states that there are some cases when RNA contains thymine! Right next to my door lives a person who's got a PhD on genetics, and I asked him about this, he told me that there are some specific cases when thymine is located in RNA, and he said that in these cases RNA can me called "single-chain DNA" or "double chain RNA".
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#16 Dak

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Posted 24 December 2007 - 06:14 PM

umm... if it's RNA, why would it be called scDNA?

RNA = riboneucleic acid, DNA = deoxyribonucleic acid.

the deoxigination is significant: it stabalises the chain and (iirc) is the difference that several enzymes capitalise on to only work on either DNA or RNA (not entirely sure on that), so i'd be skepticle of something actually being RNA with thymine in it being called scDNA.
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#17 thedarkshade

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Posted 24 December 2007 - 06:57 PM

umm... if it's RNA, why would it be called scDNA?

RNA = riboneucleic acid, DNA = deoxyribonucleic acid.

the deoxigination is significant: it stabalises the chain and (iirc) is the difference that several enzymes capitalise on to only work on either DNA or RNA (not entirely sure on that), so i'd be skepticle of something actually being RNA with thymine in it being called scDNA.

I'm telling you, he told me they're called that way! The guy has a PhD on genetics, and he's currently on of the top 10 european scientists working in cancer, so I guess he knows more things then must of us here about genetics. I'm just using the words that he told me!
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#18 iNow

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Posted 24 December 2007 - 07:42 PM

It's also possible that you've misheard or misquoted him...
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#19 thedarkshade

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Posted 24 December 2007 - 07:47 PM

It's also possible that you've misheard or misquoted him...

You want me to bring you a clip where you can see him saying that? Jesus:doh: !!!!
I'm 100% sure he said that! I just asked him again 30mins ago!
And I'm not saying that this is the scientific name, but I'm just saying what he told me to when it comes to that!
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#20 DrDNA

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Posted 26 December 2007 - 08:01 PM

One point to keep in mind is that, compared to DNA, RNA is much less stable and does not hang around long. You usually don't hear about RNA being extracted from mesquitoes in fossilized amber or old samples in forensics testing, for example.
Why? It is MUCH less stable than DNA; especially in biological fluids or even muck from fingers that contain nucleases/RNAases. RNAases chew it up immediately.
This fact is important in the formation of proteins and cellular metabolism. So, what do you think might happen it translation wasn't halted quickly and efficiently?

The guy has a PhD on genetics, and he's currently on of the top 10 european scientists working in cancer, so I guess he knows more things then must of us here about genetics. I'm just using the words that he told me!


Impressive. Top 10 by what measure?
USA Today Poll,
BCS Poll,
or the AP Coaches Poll?
Paper championships cause so much confusion. I wish that they would just battle it out in a tournament........
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