Friday, December 12, 2008

Advent 2008: Week Two Tuesday

Let's continue with just a little more, about Carbon before we proceed to the larger issues of our study. I want to give you some technical comments from a reference work, not to overwhelm you with science, but to hint at larger topics, to be addressed when I or someone else has more time:
Carbon is unique among the elements in the number and variety of the compounds which it can form. Over a quarter of a million have already been isolated and described [1950] but this gives a very imperfect idea of its powers, since it is the basis of all forms of living matter. Moreover, it is the only element which could occupy such a position. We know enough now to be sure that the idea of a world in which silicon should take the place of carbon as the basis of life is impossible; the silicon compounds have not the stability of those of carbon, and in particular it is not possible to form stable compounds with long chains of silicon atoms. If our theory of the relation of atomic structure to properties is sound, it must give reasons for the unique position which carbon occupies.
These reasons are essentially two. In the first place, the typical 4-covalent state of the carbon atom is one in which all the formal elements of stability are combined. It has an octet, a fully shared octet, an inert gas number, and in addition, unlike all the other elements in the group [below it in the Periodic Table] an octet which cannot increase beyond 8, since 4 is the maximum covalency possible for carbon. Hence the saturated carbon atom cannot co-ordinate either as donor or as acceptor, and since by far the commonest method of reaction is through co-ordination, carbon is necessarily very slow to react, and even in a thermodynamically unstable molecule may actually persist for a long time unchanged. More than 50 years ago Victor Meyer drew attention to the characteristic "inertness" (Tr├Ągheit) of carbon in its compounds, and there can be no doubt that this is its main cause.
There is, however, another reason for the multiplicity of carbon compounds, and this is that the affinity of carbon for the most diverse elements, and especially for itself, for hydrogen, nitrogen, oxygen, and the halogens, does not differ very greatly: so that even the most diverse derivatives need not vary much in energy content, that is, thermodynamic stability.
[Sidgwick, The Chemical Elements and Their Compounds, 490]
It would seem that the word "catholic" or "universal" applies to carbon in some strange sense, just as it applies to water.

Now, as I mentioned last time, there are several important classes of compounds which are studied in the "interdiscipline" known as "biochemistry" , sitting halfway between biology and chemistry and having its own sub-speicializations like molecular biology and so forth - but having practical branches in medicine and phamacology, and also in food and cooking.

Chief among these important classes of compounds are the proteins. But before you start to feel overwhelmed with the gigantic numbers of possible organic compounds alluded to above, I must point out that proteins are actually quite simple, at least when they are formed. Much as Maria Von Trapp taught the "Do-Re-Mi" of music, you will only need to learn "alphabet" of proteins in order to sing along.

For proteins are polymers - chains or strings of simple compounds, just as words are strings of letters, and melodies are chains of notes. There are other polymers we shall meet later, and you may already know of plastics with names like polystyrene or polyethylene (which are polymers of all one thing, like styrene or ethylene) but for proteins, the simple "mer" (Greek for "part") the building block is an amino acid, of which there are 20. And unlike those plastics, the proteins are made of what will appear as arbitrary sequences of these amino acids - as arbitrary as the letters of a word, or words of a sentence. But before we can talk about proteins, we need to talk about amino acids, and in doing so we shall see the central importance of carbon!

An amino acid has one central carbon, and all four of its bonds are connected to different things. One is just the lowly hydrogen. The second connects to something written as -NH2, which is called an "amine" group - this is why they are amino acids. The third connects to a something written as -COOH, which is called a "carboxylic acid" group - this is why they are amino acids. The fourth is connected to something else - 20 different something elses - which give us the 20 different amino acids. (Actually there are others, but these 20 are the primary ones.)
The something can be as simple as one more hydrogen - this one is called glycine:

Or it could be as complex as the phenyl group as in tyrosine:

For convenience, chemists call this "different" part (the thing on the fourth carbon bond) the "R" group: it's the one that makes the specific amino acid. If you want to see all twenty, you can use my index.

Next you need to know how these amino acids join together. It works rather like railroad cars, with a coupler at either end. I have to digress a little, but it is quite relevant. Here is one of those elegant facts (which very few people ever notice) about letters, unless one is a computer scientist, or has studied other languages like Chinese or ancient Egyptian that use pictograms of various kinds. A letter (like an amino acid in a protein, or like a railroad car) actually has two couplers: it connects on the left and on the right. (Unless one is playing Scrabble or doing crosswords or such gmaes, then we pretend.) Now for an amino acid, the "left connector" is the amino group, and the "right connector" is the carboxylic acid group. They are joined by taking off one of the hydrogens from the amino group, and the -OH from the acid group, and linking the nitrogen in the amino group to the carbon in the acid group. This new bond is called a peptide bond.

How is that done? There's a vast piece of machinery called the "ribosome" - it's so big we can see it in a microscope. It builds the protein, one amino acid at a time, like the conveyor belt in a little factory. (In a future post I will tell you about how it knows which one to add next!)

Why are there proteins? Since the are rather like words, and words have all kinds of differnt uses, the same is true for proteins. Proteins do most of the work - the machinery - of the living cell, in particular the special kinds called enzymes, which are able to convert one chemical into another. But they are important in larger organisms too: proteins are the main components of muscles. And remember that I said the machine called the ribosome is what makes proteins? The ribosome contains several dozen proteins. (Yes, if this sounds complicated, it is. That is another one of the great examples of why biology and computer science are so intimately related! It's like using a copier to run off copies of the design plans for that copier!)

But here we have to stop for today.

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