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This blog is all about science and technology (with occasional math thrown in for fun). The goal of this blog is to try and pass on the sense of excitement and wonder I feel when I read about these topics. I hope you enjoy the posts.

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The Chemistry of DNA

Posted August 25, 2008 10:01 AM by Bayes

Deoxyribonucleic Acid (DNA) consists of two polymers with backbones consisting of sugars and phosphate groups. These two polymers are connected to each other through hydrogen bonds between nucleobases attached to the sugar group on the backbone. Please see the diagram below:

There are four types of nucleobases found in DNA, they are Cytosine, Guanine, Adenine, and Thymine. The four bases are complimentary, meaning that when DNA is formed and the nucleobases hydrogen bond, Cytosine can only pair with Guanine and Adenine can only pair with Thymine. The diagram above is a bit vague, so lets view the molecular components of DNA one by one.

First the sugar group from the DNA backbone is Deoxyribose. Deoxyribose (actually 2-Deoxyribose) is basically a Ribose minus an oxygen (thus Deoxy). Technically it replaces the hydroxyl group (OH) with a hydrogen at the second carbon (thus 2-Deoxy). Please see image below:

The Phosphate group (see below) connects to the sugar group to form a polymer.

Finally there are the 4 nucleobases which connect to the sugar group and "stick out" so that they can hydrogen bond:

Put them together and you form single stranded DNA:

Now if you take two single stranded DNA and line them up with complimentary base pairs hydrogen bonding, you get double stranded DNA

You can see above that the reason that DNA nucleobases are complimentary has to do with the hydrogen bonding, like two puzzle pieces that fit together.

DNA is so large that pieces of it can be chemically interesting. One often hears about DNA sequences. These are the order in which the nucleobases are found in the DNA. Next time we will discuss DNA sequencing and the chemical origins of inherited traits.

http://www.albany.edu/~rp858838/

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#1

Re: The Chemistry of DNA

08/26/2008 9:50 AM

Roger, nicely done with very nice illustrations! Kudos.

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#2

Re: The Chemistry of DNA

05/29/2010 11:19 PM

Hi Roger. I have one or two questions about things i seem to remember reading about a long time ago and while reading your marvelous description of dna i think you can clear these up for me. If someone was able to take one of these dna molecules and unwind it while not breaking it would it be a circle? Are the constituents of comets in any way similar to the consltituents of dna or what preceeded dna? Depending on what your thoughts on these questions are, i have a few other questions but they would only follow according to your answers. regards - rabbit16

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#3
In reply to #2

Re: The Chemistry of DNA

05/31/2010 2:49 PM

The shape of the DNA, whether it is split into single strands or remain a double helix depends most upon the local enviroment. For instance DNA in slightly acidic water has a different shape than DNA in slightly basic water. DNA in oil is different from DNA in water. Off the top of my head, I don't know if there are situations where DNA or single strand DNA form spheres or circles, but I wouldn't be surprised if such situations existed. Polymers, and that's what DNA is essentially, tend to form many shapes depending on the situation.

If you're question is whether life came from comets, I think it is far more likely life developed in water on earth when a bunch of organic (carbon backbone molecules) got together with some RNA at the right time. What people seem to miss about the origin of life is, the 5 or 10 chemicals that were probably necessary to form the first self replicating reaction (life) only had to come together once in order for life to happen. Once they are together they multiply and the reaction becomes robust (life perseveres and evolves).

One might say, yes, but what are the odds of those 5 or 10 right polymers/chemicals coming together? The answer is, probably not great, but if you wait a 100 million years, I'm sure it happens at least once. Meaning that if you have all the ingredients, and you are constantly sloshing the ingredients about, they are bound to come together in the right combination given enough time.

And if it can happen here, given the vastness of the universe and the multitude of Earth like planets that probably exist, then it can happen anywhere and probably does. We tend to think of life as something extraordinary, but really, it probably is no more extraordinary chemically than a star's nuclear fusion. Just a chemical reaction that happens given enough time. Just like star and planet formation.

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#4
In reply to #3

Re: The Chemistry of DNA

05/31/2010 3:22 PM

Hi Roger. I thank you very much for paying attention to my questions. The reason I asked about the possible circularity of a dna molecule is because that would make it able to have a path or circuit of electrical or otherwise information moving around in it. I link this to something called the frequency of base perception on a molecular scale because the moving information could i think have a sort of perception of its own as it travels around and "sees" a gradiated or changing vista that gives a past - present - future perspective. I hope this is not to much gibberish as this is certainly not my most familiar subject.

About the comets - As a comet orbits around the sun and then sweeps back out past the farthest planets it recieves a much more varied input than a planet. The radiation from the sun to the cold reaches of the outer solar system offer quite a variety of energy both qualitative and quantitative. If some precursor molecule was able to exist in theenvironment of a comet could it not flourish in the greener pastures of a planet like earth if it ever made its way to earth? As you know when you are traversing a path around an ellipse you are in four quarters either getting nearer to or farther from the middle area. This is another difference that i think has lent itself to the varieties that an elliptical path can convey to the molecules within the comet.

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#5
In reply to #4

Re: The Chemistry of DNA

06/01/2010 9:46 AM

I think you're making it more magical than it is. DNA is just a molecule, that when you put it into the right chemical conditions is able provide a template for constructing proteins. There's not much more to it than that.

A water molecule carries in its chemistry the different crystal structures of ice. In the similar, but more complicated way, DNA carries in its chemistry the different structures of proteins used in the human body. DNA is just a complicated molecule, that's it. Where people get lost is their inability to comprehend what a billion years really means. Because it's several billion years of evolution that got cells to the complexity that they have achieved. It's also several billion years that has allowed DNA to get so complicated as a molecule, but it's still just a molecule.

As for life coming from comets, it's not likely at all, and not even remotely necessary to explain life on Earth. Is it possible? Sure in the sense of me winning the lottery 10 times in a row is possible. Likely? Not so much.

Hope that helps.

Hope that helps.

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#6
In reply to #5

Re: The Chemistry of DNA

06/01/2010 11:21 AM

Oh allright. I will think of something else. Thank you very much for the reply.

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#8
In reply to #6

Re: The Chemistry of DNA

08/03/2011 1:31 PM

First of all - what an awesome blog, I only just joined - found it by accident when I was googling. To add to what Roger already said, DNA in and of itself is merely a molecule. The information stored in it is merely code - a sequence of nucleotides has meaning in the same sense that a sequence of 1's and 0's in computer code has meaning. Think of the information in DNA as simply a recipe - like a recipe in a cookbook, this information by itself doesn't do anything, it needs something to read it, interpret it, and follow its instructions. In this case, specialized enzymes glide along the DNA, "reading" it and reinterpreting it into a form (messenger-RNA) that can be utilized to make the protein specified in the DNA's sequence. Good questions!

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#9
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Re: The Chemistry of DNA

08/04/2011 1:20 AM

well i just noticed some interest in this subject from such a long time ago and have to state that my thoughts about a body of information passing thru space/time in a circular path within the confines of dna or other circular molecules still seems plausible to me in the way of "well why not" . i believe that a dna molecule has an intrinsic perception because of the interactions of the field that the circuit of information traveling thru the dna circuit creates and reacts. thats all - lately i have been pretty busy figuring out how to make the best use of the wood pernambuco in acoustic guitars. cheers

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#13
In reply to #5

Re: The Chemistry of DNA

05/21/2013 5:53 PM

Roger

And if you do it a repeatedly (x) times a day for several billion years, do you shorten your odds. your hypothesis is circular counteracted by your own statement, the possibility exists, I wish you luck with your lottery winnings though you may be too old to enjoy them..

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#14
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Re: The Chemistry of DNA

05/21/2013 7:44 PM

m-RNA does loop sometimes.

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#7

Re: The Chemistry of DNA

11/28/2010 2:03 PM

Just a quick 2 cents, there does exist circular DNA in nature, as in bacterial genomes and plasmids, cosmids, etc. And while in the past we thought of DNA as only a roadmap by which to make proteins, there are many uses for this molecule only currently coming to light. There is a lab I believe at UToronto using DNA and gold nanoparticles to produce highly ordered structures on the nanoscale, very cool stuff. Below is a citation for similar work done by a group at AZ State. Lots of cool applications in biosensors. Also, there is work going on right now to try to figure out how to use DNA as the basis for a computer... this is very far outside my area of expertise and I have no inkling of how you would go about doing that. Anyway, hope this helped somehow.

"Periodic Square-Like Gold Nanoparticle Arrays Templated by Self-Assembled 2D DNA Nanogrids on a Surface," Nano Lett., Vol. 6, No. 2, 248-251 (2006)

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#10

Re: The Chemistry of DNA

05/04/2013 7:30 PM

You might want to catch up on things before proceeding...

http://www.sciencedaily.com/releases/2013/01/130120150033.htm

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#11

Re: The Chemistry of DNA

05/04/2013 9:40 PM

Also, it has been recently discovered that -CN molecules which can bond in place of Oxygen molecules are what allowed the phosphate groups to bind together creating short ribonucleic chains.

Weird but what doesn't kill you makes you stronger!

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#12

Re: The Chemistry of DNA

05/12/2013 6:59 PM
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