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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, Part 3

Posted July 07, 2009 12:00 AM by Bayes

This is the third part in a four part series on DNA. The earlier two parts can be found here: The Chemistry of DNA, Part 1 and Part 2.

Up until now we have only discussed the chemical structure of DNA (What it is) We have not, as of yet, discussed the chemical interactions of DNA (what it does). I think the best way to handle this is to work from the macroscopic and work our way back to DNA, since everyone is more familiar with the macroscopic. Therefore this post will detail briefly proteins and how they are used in the body. The fourth and final post will tie the proteins back to DNA.


The Stuff That We Are Made Of

The human body is made up of water, proteins, lipids (fats), carbohydrates, apatite (mineral found in bones that gives them there hardness), DNA and RNA, dissolved inorganic ions (sodium, potassium, etc.), and dissolved gases (oxygen, etc.). These materials make up the muscle, fat, bone, organs, connective tissue (tendons, ligaments), blood, lymph, urine, etc. that are us. It should also be mentioned that there are a large number of microorganism symbionts found in and on humans as well.

Most of the above is mostly water, since most of the above are made of cells and cells are mostly water (anywhere from 60% to 90%). Muscle, besides water, is made mostly of the proteins actin, nebulin, myosin, and titin; along with some carbohydrates like glucose. Fat (adipose tissue), besides water, is made mostly of lipids and some proteins. Bone, besides water, is made mostly of apatite, calcium, and the protein callogen. What Organs are made of depends on the organ, however most, besides being mostly water, are mostly proteins. Blood besides being mostly water are mostly Hemoglobin and other proteins along with some glucose (a carbohydrate). And so on and so on, we could go much longer but lets stop here and look back.

I hope you have noticed two things from the two paragraphs above. First, that we are mostly water. Second that proteins seem to be involved in everything in a major way. The truth is that everything important about life mostly comes from proteins so let's take a closer look at them.

I'm sure you've heard the term enzymes, right? They are biomolecules that catalyze chemical reactions in the body, sometimes making those reactions millions of times faster than they'd otherwise be. Almost all chemical reactions in all cells in all life need enzymes to occur. Guess what enzymes are.......that's right, they're almost always proteins.

I'm sure you've heard of hormones too, right? Things like insulin, leptin, etc. That's the stuff that alters certain cell's metabolisms, thus the way the body can regulate it's cellular parts. Basically how the body can coordinate between it's different groups of cells. These are usually modifications of amino acids (the building blocks of proteins), proteins, or lipids. Mostly proteins. Here's a list giving some detail if you're interested.

That stuff we generically call "tissue", besides the water, is mostly proteins. Skin is mostly proteins. Bone is mostly proteins. Muscle is mostly proteins. The chemicals in our body are mostly proteins.

Besides water, we are mostly proteins.

The Spice of Life

So now that we know that proteins are very important to humans (and life in general), let's learn some things about them.

The first thing to know about proteins in the human body (and all life), is there is a lot of them. How many you ask? Well, so many that we don't know how many there are. Some estimates say 10s of thousands distinct different types of proteins in the human body, others say 100s of thousands. In fact, one of the fastest growing fields in biology today, called Proteomics, is simply the identification and characterization of proteins in the human body. The project dwarfs the Human Genome project with several databases holding the structures of thousands of proteins such as the Protein Data Bank, or the Protein Information Resource.

The structure of proteins are as diverse as they are complicated. Proteins are polymer chains made up of amino acids (actually proteins are made up of peptides which are made up of amino acids, we'll get to that later). Those chains can vary in length from a few amino acids to the 34,350 amino acids of Titin (C132983H211861N36149O40883S693.) Yikes! They tend to look like tangled ropes. Here are a few examples:

The molecule on the left is Insulin and the molecule on the right is Hemoglobin, both proteins.

Amino Acids?

Alright, we're getting close now. We know there are a huge variety of proteins found in human beings (actually in all life). The question now is why? Where are all these proteins coming from?

To answer that question we need to understand what a Protein is. A protein is a polypeptide chain, or sometimes crosslinked polypeptide chains. A polypeptide chain is a polymer made out of something called an amino acid. There are 20 amino acids used to make the proteins found in us. They are:

Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, and Valine.

Remember, that's 10's of thousands or perhaps 100's of thousands of distinct proteins that are all built by putting the above 20 amino acids together in different combinations. To give you an idea of what these amino acids look like, here are some amino acid structures.

Alanine

Histidine

In general amino acids have the following chemical structure:

On the left side of the diagram above, the nitrogen attached to two hydrogens is called the amino group. On the right side of the diagram above, the carbon along with the two oxygens attached two it and the hydrogen attached to one of those oxygens is called the carboxyl group. Carboxyl groups are acidic in nature, thus the term "Amino (Amino group) Acid (Caboxyl group)". The R in the diagram above, which stands for Radical, is a place holder for what can be an atom or atoms, and it's what makes amino acids different from one another. For instance take another look at the amino acid Alanine:

You can see that the radical (R) in the amino acid alanine above is CH3 (Methyl)

Now lets look at the amino acid Histidine again:

You can see that the radical (R) above in the amino acid Histidine is C3H4N2 (Imidazole).

Here's one more amino acid, Tryptophan:

You can see that the radical (R) above in the amino acid Tryptophan is C8H7N (Indole)*.

So those are the Amino Acids. Now, as I said earlier, Proteins are made of peptides, which themselves are polymer chains of amino acids (keep in mind that a protein can be made of just one peptide as well). If you remember, amino acids have an amino group and an carboxyl group, well these can bond to each other, resulting in a continuous chain of amino acids. To see how this bonding occurs, look at the diagram below:

Once the peptide bond is formed, the amino acids are linked, and a dipeptide has formed (di meaning two). Notice that the dipeptide bond above still has a carboxyl group on one end and an amino group on the other. Clearly you can add more amino acids, and thus polypeptides are made (poly meaning many). See for instance the polypeptide below:

These polypeptides can be proteins themselves, or sometimes it's several polypeptides crosslinked together that make the protein as in the protein Callogen:

In the diagram above, a Callogen protein is displayed on the left and right. The right side shows that the protein itself consists of three crosslinked polypeptide chains (each a different color).

The point is that amino acids strung together into polymers called polypeptides are the building blocks of proteins. Since there are 20 different types of amino acids, even a dipeptide (two amino acids linked) molecule has 202=400 possible structures! A tripeptide (three amino acids linked) molecule has 203=8000 possible structures! Remember the protein Titin I told you about? That had 34,350 Amino Acids! The fact that the body has perhaps 100s of thousands of proteins isn't remarkable because it's a lot of proteins, in a way, given all the possible combinations of the available 20 amino acids, it's remarkable that there are so few. Of course, the body doesn't just make so many proteins for varieties sake. They have functions (at least we think they all do, most probably do).

The ordering of the amino acids in the protein are what ultimately determine the function of the proteins as they are what determine the shape and chemistry of the proteins. The variety of properties a protein can have are almost overwhelming, mainly because of the diversity offered by its constituent amino acid building blocks.

In my next and final post on the chemistry of DNA, we will be getting back to DNA and explaining how it relates to the stuff regarding proteins we just discussed. However, if you are interested in learning more about Proteins, you may consider the following videos. If you're really ambitious you can try the last one (it gets into the thick of it).

Here are some excellent followup videos regarding proteins. (Short Summary Video on Protein Structure, Protein Folding Video , Detailed Lecture on Protein Formation (Long))
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Special thanks to wikipedia, my favorite website on the web.

*I originally labeled this functional group incorrectly. A big thanks to Jmueller for catching the error and letting me know.

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#1

Re: The Chemistry of DNA, Part 3

07/07/2009 11:48 PM

Thanks Roger, quite educational for us non-biochemistry types.

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#2

Re: The Chemistry of DNA, Part 3

07/08/2009 9:35 PM

Roger,

You did a lot to take a complex topic and present it in a way comprehensible to most people. You may want to check the correctness of the section on tryptophan, as I believe the radical in it is incorrectly identified. Many years (decades now) ago, I attended a lecture by a graduate chemistry student who's PhD thesis was on the structure and function of the enzyme carboxypepdidase-A. This was cutting-edge work for the early 1970's and X-ray crystallography. The presentation was with stereo slides so we could see the 3-D structure and how the peptide had tucked its own carboxy end safely inside so it couldn't self-destruct. He showed how a peptide would have its carboxy end surrounded and the enzyme could exert the stress of multiple hydrogen-bonds to break the peptide apart one amino acid at a time.

Kudo's to you--JMM

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#3
In reply to #2

Re: The Chemistry of DNA, Part 3

07/09/2009 12:26 AM

Thanks for the correction, those aromatic heterocyclic organic molecules get me every time. I think I've fixed it now.

My next post will be about how mRNA and tRNA assembles these amino acids into proteins. Ribosomes have 20 different proteins involved in the forming of the peptide bonds. Some interesting research is being done to see which of these proteins can be removed and the process still work (albeit slower). A way in a sense of reverse engineering life! Pretty cool stuff.

I'll consider a 5th part of the series that provides links to cutting edge stuff I can find since I see there is an interest in this stuff here.

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#4

Re: The Chemistry of DNA, Part 3

07/19/2009 4:47 PM

Great series Roger.. please keep going.

I'd like to know if any mechanisms have been found which might justify the case for evolution? (other than accidental crossbreeding) I've also read that DNA has been successfully copied by certain species for hundreds of millions of years, such as the Coelecanth, which can be seen live at the Musem of Nature in Ottawa.

Chris

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Re: The Chemistry of DNA, Part 3

07/19/2009 6:19 PM

Thanks Chris. Yes, the case for evolution is pretty clear as you can examine each species DNA for similarities. What is less clear is the path that evolution takes. The common misconception is that genes are gradually changed over time from generation to generation and so new species come into being, which is true somewhat, but there are many other mechanisms the produces changes in the genetic code. There is also an astonishing number of deadends in evolution. Mother nature is more persistant than she is efficient when it comes to evolution. Though that's changing as the process of evolution itself is evolving.

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