How does rna polymerase read dna ?

[ARAVIND113122]

How does rna polymerase "read" dna ??

How does RNA polymerase "read" DNA? What i mean is ,after all,the polymerase is just a molecular complex,not an intelligent organism?how does it "know" that it has to combine 'A' to 'U' and 'G' to'C'. What is the exact mechanism involved??

 

[Ygggdrasil]

RNA polymerase reads DNA through the hydrogen bonding of the bases (A hydrogen bonds optimally with U and G hydrogen bonds optimally with C) and through the shape of the base pair formed. In some way, you can think of this process like a toddler randomly putting differently shaped pegs into differently shaped holes. The square peg will not fit into a round, triangular or star-shaped hole, but will only fit into the square hole. Similarly, if GTP goes into the RNA polymerase active site opposite an adenine base, the GTP will not be able to bind stably (because it does not form hydrogen bonds with the adenine very well) and it will not bind with the correct geometry (the bound GTP will prevent the enzyme from clamping its active site closed to perform the reaction). Only UTP will be able to form stable hydrogen bonds with the adenine and bind opposite the adenine in such a way to allow the enzyme to close its active site and efficiently perform the reaction that will add the UTP to the growing RNA chain.

 

[Ryan_m_b]

How does RNA polymerase "read" DNA? What i mean is ,after all,the polymerase is just a molecular complex,not an intelligent organism?how does it "know" that it has to combine 'A' to 'U' and 'G' to'C'. What is the exact mechanism involved??

Ygggdrasil has already provided a thorough answer so I have nothing to add on that. However I will just share a bit of advice: when we use terms like "read" we are using them with the caveat that this is not "reading" as we use the term in everyday life. When it comes to chemistry there is no "knowing", all the processes are simply mechanical. RNA polymerase no more "knows" what it has to do than a lock "knows" to unlock when a key is in it.

 

[Ken Natton]

Nature, so the saying goes, abhors a vacuum. Of course nature doesn’t abhor anything, but the nature of physical laws is such that pressures, like temperatures and electrical charges, tend to equalise. When he describes fire, Feynman talks about how ‘carbon and oxygen atoms like to be together’. Of course carbon and oxygen atoms don’t like or dislike anything. Their tendency to make molecules of carbon dioxide rely on this phenomenon called ‘ground state’. Even that sometimes is described as electrons ‘preferring’ to find their lowest energy state. But electrons too are only obeying the laws of physics. All of these biological processes – meiosis, mitosis, transcription, whatever, are essentially chemical reactions – what is the term ‘self catalysing reactions’ – that are also ultimately explained by physical phenomena. We tend to anthropomorphise as we analogise. It shouldn’t be taken too literally.

 

[jerrsy]

Hi,
DNA sequence is read by RNA polymerase, which produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement.DNA is read from 3' → 5' during transcription.If you want to find the suppliers of DNA & RNA please click the link below http://www.biosciregister.com/find/...=RNA+DNA&SearchKe=AllKey&SearchLo=ALL&x=0&y=0

 

[Pythagorean]

Just a reminder: we're only obeying the laws of physics, too :)

 

[Ken Natton]

Just a reminder: we're only obeying the laws of physics, too :)

Huh. Yes. Back to the determinism question again. I still don't believe it, but at least I recognise that I have no scientific evidence whatever to support that belief.

 

[Pythagorean]

well, determinism argument can be held independent. Laws of physics aren't necissarily deterministic, especially when a lot of dissipation is involved (see Prigogine).

 

[ARAVIND113122]

If the molecules "lock in",then there must be no error during transcription.Then how and why do mutations occur??

 

[Ygggdrasil]

The system is not perfect, and I probably made the process seem a bit more accurate than it is. A mispaired base does not completely prevent the "locking in" step (i.e. the active site closure that allows for the chemical reaction to occur). Rather, this step occurs much more slowly for a mispaired nucleotide than for a correctly paired nucleotide.

 

[ARAVIND113122]

Could you please elaborate.where exactly do the mistakes occur?what are the steps?

 

[Ygggdrasil]

I might not have time to pen a more thorough response in the next few days, but here is a paper that discusses this issue with DNA polymerases (which are the relevant enzymes to consider when thinking about mutations to the genome):

Johnson KA (2010) The kinetic and chemical mechanism of high-fidelity DNA polymerases Biochim Biophys Acta. 1804[i/]:1041-8. http://dx.doi.org/10.1016/j.bbapap.2010.01.006

(if you can't access the paper through the 1st link, it is freely available through the second link)

 

[That Neuron]

Huh. Yes. Back to the determinism question again. I still don't believe it, but at least I recognise that I have no scientific evidence whatever to support that belief.

Well, There is scientific evidence supporting that we operate randomly, not deterministically... quantum theory. But as for free will, or any other sentient evasion of determinism, I don't see much evidence. But even though the events of quantum mechanics seem completely dependent upon probability, Intuition tells me that there is some underlying deterministic law... but then again maybe that's just my Newtonian mind failing to grasp a foreign concept.

 

[Ryan_m_b]

Well, There is scientific evidence supporting that we operate randomly, not deterministically... quantum theory. But as for free will, or any other sentient evasion of determinism, I don't see much evidence. But even though the events of quantum mechanics seem completely dependent upon probability, Intuition tells me that there is some underlying deterministic law... but then again maybe that's just my Newtonian mind failing to grasp a foreign concept.

Just because quantum mechanics exist doesn't mean we throw out the classical rulebook. The table in front of me doesn't pop in and out of existence for example, whilst individual quanta behave randomly large populations of them act deterministically rather than probably. Also as I understand it there is definitely no http://en.wikipedia.org/wiki/Hidden_variable_theory" .

 

[That Neuron]

Just because quantum mechanics exist doesn't mean we throw out the classical rulebook. The table in front of me doesn't pop in and out of existence for example, whilst individual quanta behave randomly large populations of them act deterministically rather than probably. Also as I understand it there is definitely no http://en.wikipedia.org/wiki/Hidden_variable_theory" .

No I completely agree, Its far too common for people to dismiss the role statistical mechanics plays in averaging out of minute differences created by randomness. And yes my rational mind tells me that randomness is just as fundamental a law of nature as QM tells us it is, but something just doesn't "feel" right about it, lol. Of course that's because my mind perceives reality, not as it is, but in a way that is evolutionarily useful to me. And the best way to do this is by looking at things from an instinctive classical perspective, for example... It is more efficient for a caveman looking up at a falling boulder to assume it should fall on him, even though there is a 1/10^10^10^10^10 etc it wont.