Wednesday, September 29, 2010

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)!

Thursday, September 23, 2010

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.

Sunday, September 19, 2010

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.

Thursday, September 16, 2010

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.

Wednesday, September 15, 2010

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
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.]

Monday, September 13, 2010

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.

Saturday, September 11, 2010

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.

Friday, September 10, 2010

Where DNA lives

The human plastic bag that holds all the chemicals and salt water is called a cell. Trillions of them come together to keep all that water and chemicals from running out all over the place. Now imagine an egg cracked onto a skillet. You will not have to imagine because the piture to the right is just the thing. What do you notice? First there is a distinct watery looking margin that takes an oval shape. All cells in the human body have this margin called a "cell membrane". The cell membrane keeps things in and other things out. It is made up of long chains of those carbon atoms forming a water tight shield. (called a lipoprotein membrane) The most dramatic object is the large round yellow thing in the middle. This is the nucleus of the cell and it has its own special membrane called a nuclear membrane. The space between the nucles and the cell membrane is called the cytoplasm. It is here that the cell carries on its intended activites, all under the direction of the DNA housed in the yellow part (nucleus). All cells in the human body have these basic parts...a nucleus, cytoplasm, and speical membranes. It is in the cytoplasm that the special ovens called mitochrondia live. These ovens produce heat and energy that the cell needs to function. The ovens are controlled by their own special DNA called mitochrondial DNA or mtDNA. This is the DNA that has received the most attention in the press since it was first used to explore our human roots. It is the DNA that is received only through the mother, and has proved a "mother load" indeed. The nuclear DNA comes from both parents and is formed at the point of conception. If male, it is the nuclear DNA that contains the Y-chromosome that is only transmitted from the male generation to generation. So there you have it, an egg in the pan, not an egg in the face.

Wednesday, September 8, 2010

Chemicals of Life

The chemicals that are included in this sack of salt water (the body is two thirds water) are really few in the number as to the types that are needed to build and maintain this body. There are only four main chemicals; hydrogen, carbon, oxygen, and nitrogen.

Hydrogen is the most abundant element in the whole universe. It powers the stars, including our own sun some 93 million miles away. It is thought to be the very first element created, and our bodies seem to need it to operate. For that matter, all plant and animal matter is composed of compounds with oxygen, carbon, nitrogen, sulfur, and a few other elements. Our bodies are approximately 10% hydrogen by mass. This hydrogen is combined with oxygen to make up the very water that we carry around with us everyday. The hydrogen atom forms special bridges between its self and other atoms called a "hydrogen bond". These hydrogen bonds are important in biological systems providing a way for chemicals such as oxygen and nitrogen to share space and to organize themselves into useful molecules know as proteins. Thus the structure and hence the properties of proteins depend on the existence of hydrogen bonds.

Carbon is the second most abundant element in the human body. (oxygen is first) Like hydrogen, it occurs in all plant and animal tissues. The joining of one carbon atom to another carbon atom produces a strong chemical bond. The uniqueness of carbon stems from the fact that these carbon to carbon bonds remain strong when carbon is also combined with other chemicals. This is the bond that really holds us together.

Oxygen is the most abundant element. It forms compounds with all other elements except some rare gases. It is by far the most abundant element in the earth's crust on the basis of both mass and number of total atoms. On a number basis, oxygen atoms are more numerous than all other kinds of atoms combined. It is a good thing since the air we breath is 20% oxygen by volume. The most import compound is the water molecule which all the other chemicals that reside in our bodies swim around. The water molecule is held together by the hydrogen bond, imagine that.

Nitrogen is about one-third as abundant as carbon. In plants and animals nitrogen is found combined in the form of proteins, which average in composition 51% carbon, 25% oxygen, 16% nitrogen, and 7% hydrogen. It has the ability if needed to form triple bonds.

So there you have it, the chemical cocktail that when combined in the right way holds us together. The blueprint for this cocktail is held in DNA.

Tuesday, September 7, 2010

A bag of salt water

In the simplest of terms, a Homo sapien is just a big bag of salt water with a whole bunch of chemicals thrown in the mix. It so happens that these chemicals are needed to be arranged in certain ways so that the bag of salt has organization and function. The control panel to all this organization lives in the center of the big house called a cell. The room that it lives is called a nucleus, and from this room the control panel directs the rest of the house. It is from this nucleus that orders are given to the cell (the rest of the house) on what it is to do, how it is to do it, and what it needs to carrying all this out. These directions are placed in special containers called a double helix and stored in boxes called a chromosomes.
The chromosomes are first brought together by specialized cells called gametocytes (more commonly called sperm and ova which only contain one half of the control panel). On first contact (union) they duplicate their own control panel and 23 maternal and 23 paternal chromosomes split into two halves. This splitting allows for the restoration of the full number of chromosomes (46) and decides the sex of the new Homo sapien. At random, this union joins the chemical materials that carry the speical messages known as DNA into a new person. What mystery it is.

Monday, September 6, 2010

DNA and Genealogy

DNA and genealogy have become an important topic.  The identification and application of the genetic code that makes us all spearate individuals, yet make us one of the human race, has added a new tool to the understanding of ancestry.  It adds a "no doubt" phenomina that often proves or disproves all the years of genealogy work that has been done on our family trees.  It is a complex topic, full of scientific terms, scientific approaches, "over my head" assumptions, and the application of new technologies to a much older field called genealogy.  How we put the two fields together will make the difference in our understand of who we are, and what is truely our lineage.  An  understand of DNA, and how it is used to aid the genealogist,  is the goal of this blog.  It is especially important for a surname like JONES whose frequency is among the most common surname in the Western World.  I will use my own JONES DNA and more that 50 years of doing genealogy to try and tie the ends together.  It also helps that I have a medical backgound so I understand most of the scientific terms.  So let's begin a journey to see if the new DNA approach and the old Genealogy approch can come to a common ground.