The Codon

The codon is the three letter word that spells amino acid. Each codon (three nitrogenous bases) in any order, will write for one of the 20 amino acids needed for life. For example, the codon A-A-A writes the amino acid lysine, whereas the codon G-A-A writes for the amino acid glutamine. Each of the amino acids has its own spelling words.

Each chromosome has roughly 10,000 codons! Now just imagine, if each nucleotide base measured 1 foot across, the codon would be 1 yard long. The whole chromosome would be 10,000 yards long or 1.89 miles long. So how many codons does it take to make a protein that can be used by our body? Well, it takes about 100 codons to as many as 1,000 codons to produce a protein that our body can use. Thus, 300 yards to a 1,000 yards of codons are needed to make a "gene". If each codon is read one at a time, you would have to walk down three football fields to get to the end of the message. In some cases you would have to walk down 10 football fields to get to the end of the message. In any case, a chromosome can have multiple genes along its length. Just imagine, 10,000 codons per chromosome times 46 chromosomes produces 460,000 codons. Wow, think of all those proteins. The primary function of DNA is to make proteins!

Learning the Alphabet

Amino acids are the building blocks of life. Hard to accept that we all are just a bunch of acids. What all amino acids share is our introvert nitrogen (N). It seems that when things were forming billions of years ago, nitrogen was one of the first gases. It seems to have had the advantage of being resistance to radiation. This would certainly give it a leg up on the other chemicals trying to form in a stream of electomagnetic radiation. It would seem that these nitrogen atoms pulled together some hydrogen (H) to form the amine groups NH(3) that ultimately forms the anchor for the amino acids. Each of the twenty amino acids have this introverted nitrogen groups that brings with it all sorts of other atoms, our carbon (C), oxygen (O), hydrogen (H), and sulfur (S) along with it. The earliest forming cells must have seen the advantage of having this nitrogen based group of molecules since the cell ultimately placed them incharge of everything or more likely, they took charge of everything! Now the amino acids that seem to have the most useful shapes and charges end up being "glutamate", "asparagine", and our friend "glycine". Each of these amino acids bring to the table its nitrogen atom and forms special proteins, containing two to five intorverted nitrogens. The special proteins are 1) adenine (A), 2) guanine (G), 3) thymine (T), and 4) cytosine (C). A fifth protein Uracil (U) comes in handy outside the nucles but that story is yet to come. Now each of these proteins carry at least one positive charge, and one negative charge. It is the charges that determines how good a swimmer each molecule is in the pool of salt water! The charge determines the degree of assoication with water. Uncharged parts of an amino acid chain (polypeptide) tend to coalesce, excluding water. The charged portions of the peptide chain remain in the water interface, thus a better swimmer. It is these four speical proteins adenine (A), guanine (G), thymine (T), and cytosine (C) that make up the alphabet of our genetic code.

Get the Picture: The Path of Life

For the visual learners out there I have tried to draw the Glycine amino acid. The picture to the right shows that the molecule is held together by our strong carbon atom (C) which has four carbon bonds. Up top is another carbon (C) with two oxygen atoms (O) attached written as COO- which is called the carboxyl group. This carbon atom also has four bonds, with each oxygen sharing a double bond with the carbon atom. To the left is the nitrogen (N) atom surrounded by three hydrogen atoms. Adding nitrogen to the molecule makes it an amino acid and carries the positive charge +. The other two carbon (C) bonds in the middle carbon are bound by additional hydrogen atoms. Remember, this is the simplest amino acid. There are nineteen others each more complicated. It is a good thing that over the last million or so years the human DNA has selected only four amino acids to direct the path of life.

Drop some Acid

Our four "Super Heroes": The Strong Man Carbon (C), The Extrovert Oxygen (O), The Introvert Nitrogen (N), and the flighty Hydrogen (H), with their two side kicks Phosphorus (P) and Sulfur (S) come together to fight for Truth, Justice, and the Survival of the Human Race! They do this first by making "Proteins". The way the individual atoms; carbon, oxygen, nitrogen, hydrogen, and sometimes sulfur come together will form molecules called "amino acids". The different combinations, the numbers of each atom, and the position of these atoms form 20 different kinds of amino acids. Each of these amino acids are given a name based upon the number of our introvert Nitrogen (N) and the number of our strongman Carbon (C) holding two extroverted Oxygen (O) atoms. Just think of the strength it would take for one Carbon (C) atom to hold together two Oxygen (O) atoms who would rather be any place else. The simplest amino acid is called a mono (one) amio (nitrogen with three Hydrogen (H) surround it, mono (one) carboxyclic acid. [a Carbon (C) atom with two Oxygen (O) atoms attached.] Thank goodness it is also called "glycine". Just to give you a mental picture of how this amino acid is drawn:

COO- single carboxyl
|
H(3)-N+ -C- H
|
H
single amino

The plus (+) and minus (-) signs are to show that the amion acid carries charges. This is much like a battery, with a "positive end" and a "negative end". These charges become important. Just like you have to put a battery the correct way (positive pole and negative pole)in a camera before it will operate, the cell must put together the amion acids in the correct way. These "charged" ends of the amino acids help the cell to accomplish this. Wow, enough for today. Just recognize that the these amino acids are the building blocks of proteins.

[Note: I am unable to line up the molecule the way it should be when I push "publish post". The carbon atom should have the four bonds around it, shown as (| and - ) not at the edge of the nirtogen atom as the blog shows. Sorry, the blog changes it no matter what I have tried.]

Feed Me, Feed Me

Starting to build molecules from our "Super Hero Atoms" we will began to build the three basic food groups...carbohydrates, fats, and proteins.

Carbohydrates are built teaming our strong man "carbon" with skittish "hydrogen" and our out going "oxygen". Short chains of carbon atoms, five to six in number, form the sugars. Glucose, fructose, mannose, and galactose are the "six carbon sugars". Ribose, ribulose, oxylose, and other strange names are the five carbon sugars. Approximately two-thirds of our cells energy come burning these sugars (carbohydrates). Now to build DNA our bodies use a five carbon sugar called ribose, but more will be said about this later.

Fats are built by joining long, long chains of carbon and hydrogen atoms. When linked together they form triglycerides (lipids) and fatty acids. About one-quarter of the energy produced by our bodies come from fats. However, it mainly serves as reserve to sugars for producing energy. Fats have very little to do with DNA.

Proteins are made when carbon, hydrogen, oxygen, and nitrogen are bound together. They become large molecules, and their size helps them from leaking out of cells. The bond which makes proteins special surrounds our introvert "nitrogen". When nitrogen binds with carbon it is called a "peptide bond". This nitrogen is housed in a molecule called an "amino acid" and brings this amino acid along with it as it binds to the carbon atom. Long chains of these nitrogen-carbon bonds (peptide bonds) are what make up proteins. Thus, formally, proteins are polymers (long chains) of amino acids. When long chains of proteins are created they form a structural feature called a protein "helix". Sound familiar? DNA is housed in a protein "double helix". Now you know why DNA is called a "double helix"! Were almost ready to build our DNA.