Why does DNA form a spiral shap and not just straight rods?
coffeee Thurs 17/08/06 14:50
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I did learn this in my Biology A-level but cant think of the correct reason now. I know that it is something to do with the spiral structure allowing the DNA to interact with the amino acids.
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There is more than one form of DNA as Dawkins has stated, but clearly you wish to know about the most common form known as right-handed B-DNA, with the usual double helical structure.
The "backbone" of DNA consists of two polynucleotide strands twisted around each other to create a periodic structure. The backbone has sugar and phosphate components and in itself, it is quite soluble in water.
The bases between these strands in the centre of the helix consist of Adenine, Cytosine, Guanine and Thymine in the case of normal B-DNA. Now these bases are what is termed hydrophobic, which means that they are water-repellent and virtually insoluble in water itself.
To illustrate this, one litre of water will dissolve up to around 530g of the deoxyribose sugar that makes up the backbone of DNA and the same volume will dissolve over 100g of the phosphate. However, taking Adenine as an example, only something like 0.5g of Adenine will dissolve in one litre of water. Cytosine, Guanine and Thymine have similar solubilities.
This insolubility promotes what is known as "base pairs” between the strands where the flat bases stack on top of each other in order to "hide" from the water in their own little environment.
Now you might expect that a ladder-like structure would suffice to hide the bases. The problem with such a structure is that it leaves many gaps between the atoms of the molecule and in the cell, these are likely to fill with water. The gaps can be reduced if the ladder is skewed or twisted to maximise the hydrophobic interactions between the bases by bringing the bases closer together. As a result of this twisting, a spiral is formed.
So basically DNA is a helix because the bases hate water.
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Despite dawkin's gallant attempts to bring an evolution event into the discussion, it's important to understand that DNA is completely an information system. An article in Science Today states "...we now know that the DNA molecule is an intricate message system. To claim that DNA arose by random material forces is to say that information can arise by random material forces. Many scientists argue that the chemical building blocks of the DNA molecule can be explained by natural evolutionary processes. However, they must realize that the material base of a message is completely independent of the information transmitted..." Further "...Thus, the chemical building blocks have nothing to do with the origin of the complex message. As a simple illustration, the information content of the clause "nature was designed" has nothing to do with the writing material used, whether ink, paint, chalk or crayon. In fact, the clause can be written in binary code, Morse code or smoke signals, but the message remains the same, independent of the medium. There is obviously no relationship between the information and the material base used to transmit it." Current evoluionary theories must hold to the illogical conclusion that the material used to transmit the information also produced the information itself. (I apolgize for the partial hijack of the thread, but couldn't let that one go by). Thanks...
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It's a fascinating concept Clanad but I'm afraid it's not one that's been universally adopted amongst scientists. Try looking for the articles refuting the proposals.
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dawkins:
Like Clanad, I'm rather mystified as to why you saw the need to bring evolution into your attempt to answer the question. Evolution does not provide the answer required and I don't consider that evolution per se is responsible for the structure of DNA for complex reasons that I could not begin to convey on AB - being a professor of biochemistry does have its disadvantages.
The term "Natural Selection" is one of the ambiguous and indeterminate phrases ever encountered by the layman as it conveys absolutely nothing when used in answering a question of this nature simply because not everyone has had the benefit of reading the works of Charles Darwin et al. The phrase only serves to make the layman think that scientists are putting themselves on a pedestal above the hoi polloi of society.
This was a straightforward question regarding a molecule that has been studied in more depth than any other I can think of offhand for over fifty years. The answer to the question has been confirmed incontrovertibly for the same length of time.
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With all due respect theprof, universality of opinion is not a hall mark of scientific inquiry, no? I find a great deal of empathy for this particular view in many peer reviewed publications, but as you say, and as I point out elsewhere, alternate views abound...
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Can you give provide me with a link to this theory Clanad? I'd like to look into it further.
I respect your views Clanad and they have been noted. These scientists are entitled to a fair hearing regarding their theories after all in the same way as the rest of us.
Nevertheless, the opinion of the majority of scientists remain with the status quo and I remain unaware of any efforts whatsoever to adjust the thinking of scientists regarding these issues.
As you imply, there will always be a minority of scientists with contradictory views. The interesting thing about science Clanad is that the views of the majority tend to prevail at least until the day substantive objections and evidence come to light from the minority. We're not there yet with these theories.
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Gladly, theprof...
This article deals with the problems encountered in exploring protein folding and its implications for protein evolution (highly technical, but appropriately footnoted):
http://www.cs.unc.edu/~plaisted/ce/blocked.htm l
And this is the article from which I excerpted:
http://www.allaboutscience.org/dna-double-heli x.htm
There are numerous others...
The tenor of your inquiry is appreciated, by the way. I, in no way, interpret the interest you display as other than an attempt at scientific balance...
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What's the olde English saying dawkins? 'In for a penny, in for a pound'? As long as we've completely hijacked coffeee's thread, I'm really glad you pointed that out. As usual, you have very little, if nothing at all, to say concerning the validity or accuracy of the contents of the quote... only that the author has the audacity, or in your belief system, the stupidity, to deduce an alternative thought process to 'classic', i.e., Darwinian evolution. (And yes, I've read Darwin's Second edition, in it's entirety).
I greatly appreciate an article writtent by Phillip E. Johnson, Jefferson E. Peyser Professor of Law, emeritus School of Law, University of California, Berkeley: "The problem with scientific naturalism as a worldview is that it takes a sound methodological premise of natural science and transforms it into a dogmatic? statement about the nature of the universe. Science is committed by definition to empiricism, by which I mean that scientists seek to find truth by observation, experiment, and calculation rather than by studying sacred books or achieving mystical states of mind. It may well be, however, that there are certain questions-important questions, ones to which we desperately want to know the answers-that cannot be answered by the methods available to our science. These may include not only broad philosophical issues such as whether the universe has a purpose, but also questions we have become accustomed to think of as empirical, such as how life first began or how complex biological systems were put together.
Contd.
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Contd.
Suppose, however, that some people find it intolerable either to be without answers to these questions or to allow the answers to come from anyone but scientists. In that case science must provide answers, but to do this, it must invoke scientism, a philosophical doctrine which asserts arbitrarily that knowledge comes only through the methods of investigation available to the natural sciences..."
"...Belief is inherently subjective, and includes elements such as fantasy and preference. Knowledge is in principle objective, and includes elements such as facts and laws. If science does not investigate the purpose of the universe, then the universe effectively has no purpose, because a purpose of which we can have no knowledge is meaningless to us. On the other hand, the universe does exist, and all its features must be explicable in terms of forces and causes accessible to scientific investigation. It follows that the best naturalistic explanation available is effectively true, with the proviso that it may eventually be supplanted by a better or more inclusive theory. Thus naturalistic evolution is a fact, and the fact implies a critical guiding role for natural selection."
In my opinion...
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Thanks for the links Clanad
I've always considered that we have to be open-minded as scientists and give everyone's theories a fair hearing be they a schoolchild or an emeritus professor.
Thank you for your indulgence.
Now to dawkins:
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Thank you for your comments dawkins. It is pleasing to see a reply from someone with some fascinating arguments regarding DNA development. I trust you will allow me to cover the issues you have raised seriatim.
Firstly dawkins, I think I need to convey to you the methodology I use in replying to questions on AB. The first thing I do is to read the posted question carefully and attempt to gauge the likely age of the poster. I then formulate an opinion as to the likely knowledge of the poster regarding the question using age as a basis along with the way the question has been phrased and any preconceived ideas that are present in the question. This provides me with a reasonable idea of how much detail I need to go into in my reply. I have found that this method works well and gains me a certain degree of respect on AB from at least some of the people that post here.
Now I’ll move on to me. I’m a don holding the academic chair in biochemistry in one of the UK’s most prestigious universities. I am also a dean at the same university, a government consultant/advisor and lately, much against my wishes, a tv personality. Now I’ve blown enough of my own trumpet so I’ll move on.
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The fifth paragraph of your reply states that my answer was not totally complete. Well, dawkins I will hold my hands up and admit that you are correct. I omitted to discuss genomes, denaturation, topoisomerases, sugar pucker rearrangements, torsion angles, supercoiled DNA and a myriad others that we discuss, lecture on, read and write on daily at university. Believe it or not, I even write textbooks on these matters. Nevertheless, dawkins, I need you to be aware that I could have discussed these matters in my reply, but I did not do so for one reason and one reason alone: I did not consider that the questioner would understand.
To summarise, I provided a concise reply that adhered to the nature of the original question and in my view, fell within the bounds of understanding of the questioner. The last thing we scientists need is to be considered bigheaded and vain by the general public - wouldn’t you agree?
I am indebted to you regarding the content of the penultimate paragraph of your reply. You have removed the salient facts I stated and summarised them in one paragraph albeit at a more simplistic level. It is to be noted that the paragraph contains no other information. Somehow, I don’t think that the questioner would have been satisfied with such a reply. Incidentally, stating that something is “inevitable” does not provide us with an explanation of the mechanics involved – personally I tend to stray away from such irrational words.
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The first sentence of your final paragraph is largely correct. However, although there are other types of DNA other than the B-DNA form and most forms are indeed helical, I cannot see how that information proves that there are other ways to resolve replication per se. Natural selection has indeed chosen an advantageously designed model for replication. However, it is not “unbeatable” – in recent years computer modelling has designed molecules that might be termed, more “efficient” than the present DNA model. It’s a difficult matter to go into here without at least a couple of years studying biochemistry at university. To the sceptics, I would only add that there is some evidence that DNA is evolving further and certain changes in the molecule are becoming more prevalent in the community.
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Mitochondrial DNA (mtDNA) is not widely regarded as having been evolved via symbiotic relationships because of certain complex properties of the molecule. Much revision of the original proposals has occurred. It is incorrect to describe mtDNA as circular in “shape”. Whilst the molecular form of types Hs, Sc and Ra are indeed circular, type At is in the form of a master circle, whilst types Cr and Pf are linear.
The mtDNA of fungi are largely circular, but linear forms do exist . Telomere sequences ensure DNA replication in the linear molecules.
By contrast, animal mtDNA is always circular, has a uniform size and a standard informational content, which includes the same proteins found in fungal genomes plus seven subunits of the NADH dehydrogenase complex. The genes are always tightly packed.
In higher plants, the size and complexity of mtDNA have important variations even in closely related species. The number of mitochondrial genes is greater than in fungal or animal genomes. DNA organisation is not clear in higher plants as both linear and circular molecules have been found bearing repeated sequences that might originate multiple recombination events.
Your knowledge obviously surpasses that of the original questioner dawkins. If you wish me to expand on any of these issues, please don't hesitate to ask.
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Oops, I forgot to discuss my own fascinating favourites, protozoan and yeast mtDNA.
Let me know if you want me to discuss them.
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Finally, you may wish to read this fairly brief interview with Dr. Robin Connor, Dean Emeritus of Physics and Astronomy at the University of Manitoba.
http://umanitoba.ca/manitoban/2001-2002/1128/f eatures_11.shtml
It's one of but many from scientists of all persuasions who either consider or fully believe evolution has a defined, guided end purpose... unique concept, no?
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Question Author
Ta, it amazes me you guys have time to give such long ans. I'll probably end up with more Qs now.
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Fire away. That's what we are here for.
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Just thought I'd put my humble 2 pence worth in, if we evolved from apes why are there still apes ?
Also if we are constantly evolving, surely buy studying the past evolutionary sates we could put an accurate depiction of what we we will look like in 50,000 years from now...or do we have to get an artist in to do an artist's impression,like we do when we need to know what dinosaurs etc etc look like :)
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