Putting It All Together

Now that you know the genetic alphabet (A),(C),(G),(T) and sometimes (U). And, now that you know how to spell using this alphabet three letters at a time. [called a codon] It is now time to put it all together into our DNA. So, drum roll please...
phosphate plus sugar plus nitrogenous base! Yes, that's right...phosphate + sugar + nitrogenous base. Say again...phosphate + sugar + base (nitrogenous) come together to form our DNA! So from now on, when you see the word DNA, you think, phosphate + sugar + base! Kind of rhymes "phosphate plus sugar plus base" makes us healthy, wealthy and wise. Well at least healthy, assuming all goes well at this biochemical level.

The phosphate atom is actually the little brother to the nitrogen atom so you can imagine that it is a strong fellow also. It combines with three oxygen atoms to form the backbone of the DNA helix. It then connects our sugar (called ribose) molecules, stringing them along the outside of the chain like Christmas tree lights. The ribose sugar then holds the nitrogenous base to the inside of the DNA chain. The nitrogenous base, our alphabet, flap their molecular structure toward the inside, holding out promise to its partner, asking a partner to come join me. Another nitrogenous base from the other side of the helix. A [adenine] will only combine with T [thymine], and C [cytosine] will only combine with G [guanine].

So there you have it...DNA... "deoxyribonucleic acid" = phosphate + sugar (deoxyribose)+ nucleic acid (nitrogenous base)!

Learning to Spell

Now that you have learned the genetic alphabetic A, C, G, T, and sometimes U, it is time to figure out how to spell using these letters. Like any spelling word, you have to use the letters of the alphabet to spell any word that makes sense. How many letters of our alphabet are needed to make a word? Well let's see. If each letter made a word, then you would only have four words. Certainly not nearly enough to spell 20 amino acids. Taking two letters at a time in any combination would only give 16 words. [You can try combining two letters in any order and see what you come up with.] Now if you take three letters at a time, combine them in any order, you would come up with 64 possible combinations. This would certainly give enough words to spell our 20 amino acids. As it turns out, that is exactly what our DNA figured out on its own. Taking three of our letters (nitrogenous bases) they were able to spell "amino acid". Combing these letters three at a time, in different order, spells each amino acid! What a deal. These three letters (nitrogenous bases) are now called a "codon". Thus our "Genetic Code" is made up of these "codons" lined up in sequence to tell us what to do. Each cell contains its own directions in the nuclear DNA. They tell the cell which amino acids to hook together in what order, and how many to join together in our polypeptide chain. [Remember poly=many, peptide=amine=nitrogen bound] chain. This chain becomes a protein.

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.

Superhero Comic Book

The chemicals (atoms) that join together to make us work, first come together as molecules. (one or more atoms) However, before we can discuss putting molecules together to form DNA, two additional chemicals need to be presented. They are phosphorus and sulfur.

Phosphorus is more abundant than nitrogen. Phosphorus compounds (molecules) are essential constituents of all animal and plant life. When it combines with oxygen it becomes one of the main units in helping to form DNA, which is certainly one of the most complex organic molecules. Its other function is to provide a means for storing energy in the cells. Without phosphorus, none of the ovens (mitochrondia) would work!

Sulfur is the least common chemical. It is used by the human body to help make certain molecules called proteins. Proteins are the building blocks of DNA. Sulfur is also important in forming molecules that help in the cytoplasm to help make the cell work properly.

Wow. There you have it. The building of DNA is ready. Let's see now, oxygen is the chemical extrovert, it wants to bind with everything. Nitrogen is the chemical introvert and can form triple bonds, holding everything inside. Carbon is the strong man who makes things firm. Hydrogen is the minnow, darting about between atoms, easy to make new friends. Phosphorus provides the energy. Sulfur shows up when needed. Sounds like a superhero comic book.