Question

RNA is believed to be a more primitive molecule than DNA because

Answer 1

1. It is more flexible in structure
2. it uses a less complex base pairing system
3. it lacks the base pairing system used by DNA
4. It can have catalytic properties.
5. it is always a much shorter molecule than DNA

Answer 2

Would like this to be a discussion, rationale behind why the other answers are wrong.

Answer 3

thats an interesting topic there
what are your thoughts tho?

Answer 4

1. I don't see why one would be less flexible they're almost identical in chemical structure (although DNA more commonly exists in nature as a two stranded duplex, while RNA is mostly single stranded - in which case RNA would obviously be more flexible). RNA also forms more complex structures because of self-association into loops and whatnot, so maybe that's what they're getting at.

2. Both can base pair in watson-crick and hoogsteen forms.

3. no

4. Both can have catalytic properties.

5. Don't know if RNA it's "always" shorter, but the functional forms are relatively short in comparison to say a human chromosome.. but not entirely sure if you compare them to bacterial genomes.

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I don't see how any of these can be indicative of one preceding the other.

Answer 5

1. Yeah, in terms of flexibility that didn't make much sense to me
2. They use virtually the same basepairing system except for the fact that T becomes U uracil.
3. I think both can have catalytic ability.
4. their BP system is virtually the same.
5. Yeah RNA molecules are relatively short compared to DNA i think about RNA as just a page copied out of a Book that's DNA. I was thinking that this choice made the most sense.

Answer 6

I would love to say that it is #4 due to finding of ribozymes (RNA enzymes) which is basically RNA taking a superstructure able to perform catalyze reactions in a similar manner as enzymes. I am almost fairly sure nothing similar has been found in DNA, as the protein system then was developed simultaneously (don't quote me on that as I am fairly unsure about that).

The super critical point in all of this is the finding of important thing:
Ribozymes is able to catalyze the produce new RNA, you could say an "RNA polymerase ribozyme" With this in mind you have evidence that RNA very much could exists independently of DNA and from a evolutionary perspective it would also seem reasonable that DNA then came later, as a more stable alternative to RNA, as RNA would be able to create a 2',3'-cyclic phosphodiester those breaking the backbone (propose mechanism linked attached)

Answer 7

Sorry I got to write so fast, I made multiple mistakes in the typing.

Answer 8

The question is asking which is more primitive molecule, and to determine this there are some criteria that are to be met. These criteria are those that are vital to life, of all listed properties
1. It is more flexible in structure (just as aaron said)
2. it uses a less complex base pairing system (again just as aaron explained)
3. it lacks the base pairing system used by DNA - the system is next to exactly same except T that is replaced by U as you all know
""4. It can have catalytic properties.""
5. it is always a much shorter molecule than DNA - this is out of question, cause length doesn't exactly determine its primitiveness

Now coming back to 4th point, as we all know one of critical things our cells need to survive are proteins/enzymes, without these Genetic info is pretty much nothing but a bunch of molecules/atoms put together
so our biological catalysts are enzymes, and back to your topic, we have enzymes that are RNA based a.k.a Ribozyme, so here as you can see RNA is playing a role of an enzyme which is an important factor for survival of cell as it deals with translation of mrna to proteins and its function is not limited to just that. From here i can say that RNA seems to be more primitive than DNA because it has the properties it takes to survive, and considering evolution and RNA's unstable structure then you can say at some point DNA took over as more stable information storage bank or whatever you want to call it
Now about DNA, i have never heard a DNA acting as an enzyme, @Frostbite have you?

Answer 9

I've not yet seen an example of catalytic DNA with similar functionally as ribozymes no.

Answer 10

alright i did some searching and it seems there is some data on DNA acting as an enzyme (in lab)
but the problem is that the DNA that can have a potential to act as an enzyme has to be single stranded which doesnt usually happen in living cell or i have never heard of it as we have all these DNA repairing mechanisms that just won't let the DNA strand to be alone on its own

Answer 11

@aaronq is there something more to it?

Answer 12

Yeah woudln't a singe stranded dna molecule be unstable? wouldn't it just want to hybridize with whatever it can? @Somy

Answer 13

I guess maybe we're supposed to think of this in context of the cell

Answer 14

it could be more stable stable than RNA but still unstable ofc
thats precisely why i said in lab
coz they add up other molecules that would let it act as a catalyst

Answer 15

in lab they are basically trying to create an environment in which single stranded DNA would act as a catalyst, so to me it doesnt seem like DNA does any catalytic work under natural conditions of our body

Answer 16

that's interesting.. well for me the key words were "more primitive" I was thinking that naturally RNA is much shorter than DNA.

What's interesting also is that double stranded RNA can exist too, as a virus though. I didn't know this lol.

"Rouble-stranded (ds) RNA viruses are a diverse group of viruses that vary widely in host range (humans, animals, plants, fungi, and bacteria), genome segment number (one to twelve) and virion organization (T-number, capsid layers or turrets)."

i'm going to read up on how these structures form.

Answer 17

yeah they do exist

Answer 18

in terms of stability DNA, is more stable than RNA but it's interesting how it cant really exist as single stranded in the cell. Like I know that mRNA is modified with a 5 prime cap and poly A tail befure going out into the cytoplasm and that can protect it from being degraded by RNAses. I've never heard about DNA being further modified, maybe the fact that single stranded DNA can't exist in the cell is for that reason not sure.

Answer 19

have you heard of epigenetics?

Answer 20

yeah but I haven't looked into that very much

Answer 21

isn't that like DNA/grene can be modified when the organism is alive?

Answer 22

DNA is 98% non coding
only 2% is coding, so we are the result of that 2%

Answer 23

now epigenetics about is basically switching system of DNA

Answer 24

what is to be switched on and what is to be switched off
so generally speaking you have a lot of info in DNA
and there is a lot of things that can change your DNA
e.g. mutations that happen naturally, sometimes they are fixed and sometimes they are missed
sometimes there are more major mutations in which you lose a bigger piece of DNA, could be one strand or both
this also creates changes and diversity
next is our daily life, such as diet
or exposure to microorganisms
everything has at least some effect on DNA actually

Answer 25

thats how we are so different from each other
so its not like DNA is fully protected and so is untouchable and all

Answer 26

I see

Answer 27

but our cells do try to protect the DNA thats why i think our cells just dont let a single stranded DNA to be there for too long, probably it could be harmful of the rest of the DNA
i mean single stranded pieces that are there now because of DNA breakage

Answer 28

So I would assume that certain say stimuli trigger parts of the noncoding portion to be expressed, or can maybe turn off expression of genes already expressed?

Answer 29

non coding portion being expressed is no big deal since it doesnt code for anything

Answer 30

more like
if that certain trigger causes a mutation say in a sequence that is a ' switch' of the other coding sequence which is next to it
that can cause a problem depending on, " is this coding gene supposed to be off " or " is it supposed to be on"

Answer 31

so in simple terms: the stimuli can influence gene expression of the coding region of DNA

Answer 32

yes

Answer 33

or ofc if mutation is in coding section then there will be a problem with the resulting protein it was coding for

Answer 34

but it also depends on where on the coding region is the mutation lol
so there are a looot of stuff to consider :D

Answer 35

Thanks for the explanation this really helped

Answer 36

no problem :)

Answer 37

one last thing,

Answer 38

m?

Answer 39

For a single strand to exist like by itself, wouldn't there be a problem with say the machinery involved in replicating DNA or maybe something went wrong in replicating that particular strand. I should have touched on this before. So if a single strand of DNA is harmful to the rest of the DNA, it would just be degraded by nucleases, etc?

Answer 40

okay, do you know about DNA repair mechanisms?

Answer 41

no actually
can u tell why can cell repair DNA to begin with?

Answer 42

Here's my attempt to answer this

well there are enzymes that are involved in proofreading I believe during DNA replication, but sometimes DNA polymerase adds in the wrong nucleotides but I think this is rare. I think that it has to do with the cell cycle too and the certain check points to ensure that the DNA is intact before replication can begin. I guess from my level of knowledge it doesn't seem possible that a single un-replicated strand would exist in the cell. then again it's complimentary so if there's something wrong with one strand there's definitely something wrong with the other. and it's possible that if the DNA didn't make it past the check points it might be degraded.

Answer 43

" Complementary "
thats the answer
when there is a mistake in one, the other strand can be used as reference to fix the issue with a correct set of nucleiotide additions
now if it existed as single stranded, we'd face constant mutations that would not be fixed just because of the fact that there is no info on what was the correct sequence there
but our cells want to store info in a way that its unharmed/safe/and accurate at least to some point

Answer 44

So with that said, i'm guessing that if the mistake was severe then it would even pass the check point to be replicated

Answer 45

but it also depends on how bad was the damage, and how much of the sequence is to be lost as a result

Answer 46

Well, I guess there would have to be some flexibility, unless there would never be any mutations.

Answer 47

yeah

Answer 48

thats how cancer happens

Answer 49

This is coming together now

Answer 50

i mean, there is no perfectness
once a mutation, even if it is mild, is missed, and is not corrected, then thats it, it'll stay there in new generations

Answer 51

thats how evolution happens at molecular level

Answer 52

interesting

so from your previous point that to me seems why scientists are trying to find ways to make single strands of DNA in the lab that can act as catalysts because they just wont exist for long in the cell given

Answer 53

"""what we discussed

Answer 54

i assume so, i just read a little on it :)

Answer 55

hey man thanks for your help I appreciate it.

Answer 56

no problem :) im a female tho lol

Answer 57

LOL sorry

Answer 58

its okay :D

Answer 59

I know you guys already discussed about this, but DNAzymes do exist - they can now be "discovered" through the various varieties of SELEX, and are mostly used for analytical assays, and not so much for therapeutic endeavours - so it wont really matter how long they last inside a cell before they are degraded.

...more importantly, to me it doesn't seem to fair to make the assumption that because we don't observe them (DNAzymes) in nature \(now\), it automatically asserts that RNA precedes DNA. It could also be argued (from a functional evolutionary standpoint) that RNAzymes \(\sf replaced\) DNAzymes because of their shorter lifetimes (due to their higher chemical instability) and their biological functions are on a shorter timescale. (e.g. say you only wanna build 10 molecules not 100, a RNAzyme would be degraded after those 10, a DNAzyme after 100).

Overall I think that what @Somy is saying is logically sound, but not necessarily the whole truth - something we possibly won't ever know, but merely just speculate on. Its like asking how did the first cell every come to be? We won't ever find the answer to that and talking about it borders on philosophical thinking and is inspiring but not necessarily useful.

Answer 60

you are right there, and i was not saying that im sure thats how it is, i said that i've never heard of those and also that 'i think...'
im not necessarily putting a period there since science is advancing day by day
but if we take the knowledge that we currently have, we are for now assuming that RNA is more primitive than DNA, it could be right and it could be totally wrong in near future :D

Answer 61

Again I appreciate your time @somy @aaronq

Answer 62

np :)