The Gene Tree, Haplogroups

Haplogroups are defined by their single nucleotide substitution called a SNP (snip). [single nucleotide polymorphism] Those in the know [researchers who have established the system of naming [nomenclature] have assigned an English alphabetical system starting with the letter A. This haplogroup is felt to be the oldest genome surviving since our earliest days. The figure to the right is my attempt at showing a "big picture" of this classification system. The dates generally believed to be starting points for each branch of this gene tree are given along the top ridge for each haplogroup. More than 60,000 years ago the human race is believed to have shared a common genetic message. At around 50,000 years ago the human genome started to branch, giving rise to several new DNA messages. Down through the ages, each branch developed a new haplogroup, passing its single nucleotide polymorphism down to the next generations. As time passed, these branches became the roots of our ethnic and cultural family groups. My JONES DNA is haplogroup R1b, believed to have branched from haplogroup R1 some 25,000 years ago. It was around this time that the earliest human burial has been described on the island that was to become my family's home. [The "Red Lady of Paviland" on the Gower Peninsula.] What a deal!

Terms, Terms, and more Terms

By now the poor brain should be spinning around the terms that are used to communicate information about DNA. This is especially true when ordering a DNA test, and the results are given in a bunch of different terms. Having some idea how all these terms fit together is a helpful thing. My own DNA testing results state:

"We provide the actual scientific Allele values and DYS #'s for your results unless the markers were discovered at the University...."

My results were given as "Panel 1 (1-12)", "Panel 2 (13-25)", and "Panel 3 (26-37). Under each panel the results were given as "Locus", "DYS#", and "Alleles". Wow! Terms, terms, and more terms...what is one to do?

To begin, a "Panel" is how the DNA testing is organized and actually carried out in a testing laboratory. Panel 1 is the first group of 12 genetic markers that have been accepted as the standard among all testing labs. The "Locus" is the assigned panel number that each marker has received beginning with number 1 to number 12 for Panel 1.[number 13-25 for Panel 2, and number 26-37 for panel 3] Each "Locus" number corresponds to a DYS# and Allele value. The DYS# and Allele values had already been described in separate research labs which would of course cause a great deal more confusion if each lab reported their results under different labels!

Now the term DYS# is an abbreviation for D = DNA, Y = Y-Chromosome, and S = (unique) Segment.
A unique segment is the part of the DNA molecule [in this case the Y-chromosome] that has undergone changes (mutation) among several nucleotides in a row. Remember that a change at only one nucleotide is called a SNPs (single nucleotide polymorphism). Changes that have occurred at more than one site in a row (segment) have been termed a "Short Tandem Repeat" or STR. These short, tandem (next to one another) repeats are identified along the DNA molecule at the address called "Allele Value". [The allele was the earliest concept of genetic addresses for the codons that produced a protein.]

Here is the key issue and perhaps the most confusing. A single nucleotide change (SNP) is a very rare occurrence. This change (SNP) is past down generation to generation among a family, thus an ethic group. The SNP is used to characterize a "Haplogroup". The STR (Short Tandem Repeat) happens all along the DNA molecule, and when analyzed together produce the genetic finger print that is called the "Haplotype". Haplogroup (SNP) - Haplotype (STR). Using the Y-chromosome, the haplotype should be the same or very close to all males in the family. It is the STRs that are used to match our ancestors. More to come.

Baby Blue Eyes

Eye color is one of those things that everyone recognizes. What color is his/her eyes? Blue eyes, green eyes, hazel eyes, brown eyes, and perhaps some shades in between are the basic colors. Your eye color is given to you by your parents. Mom and Dad transmit half of the information needed to make this determination. Once these halves are joined together in your DNA, they will determine which color comes shinning through.

As you now know, this determination is made by the message you carry on your DNA. A series of codons, which make up the "gene" for eye color, is strung along one of those chromosomes (DNA molecule). It has two sides...the one from Mom, and the one from Dad. Remember your dinning rooms? The one you stood in to image 3-D space is one side of this gene. Your bucket truck reaches out to the other side. If you are standing in your mother's dinning room, your father's dinning room would be on the other side. [the gene is the whole series of dinning rooms on both sides, stacked upon one another, running in opposite directions]

If Dad has blue eyes, and mom has brown eyes, brown eyes will win out every time if Mon only carries the brown eye message on both sides of her DNA. [Brown eyes are called dominate.] If Mom carries a brown eye/blue eye gene, then it is possible to transmit blue eyes to a child. [one blue side from Dad, one blue eye from Mom] The blue eye color has been called recessive. Each side of this genetic message is now called an "allele". This term is important to know as we continue in our understanding of using DNA for genealogy. The "allele value" is the number giving to one half of the genetic marker along the codon (genome). It is like spray painting your side of dinning rooms, and spray painting the other side a different color. Thus each side of the gene can be classified by an address (allele number). The side for "brown eyes" and "blue eyes" will be labeled by a number. When you order a DNA test today, you will be given a series of "allele values" as results. These are the places along your genes that have been tested. The results of a 12 marker test is given by a series of numbers which identify the "alleles" that were examined by the laboratory doing the test. Baby blue eyes any one?

Mapping and Markers

Mapping the human genome was a daunting task. Starting in the early 1980s, The Human Genome Project began depositing enormous amounts of known DNA sequence information in very large computer databases. Over the next 20 years, the "big picture" became clearer. Most, if not all, of the human genome was successfully map around 2002. Since that time, this mapping has been used to help explore the "genetic" history of our human race. It became clear that the genes are DNA segments that encode information about an individual's heritable traits. Mutations are the original source of variation among these heritable traits. It ended up that most of these "mutations" (changes) are substitutions of one base pair (a single nucleotide, remember standing in your dinning room), for another. Once a mutation (SNP)is established, it is past down from one generation to the next. It has been estimated that about 10 million of these SNPs have occured in our human population. [see National Center For Biotechnology Information (NCBI)] Each SNPs is thought to have arose during the passage of time since our human history began.

Basic concepts have been developed that believe the greatest genetic diiversity of the human species is found in the the geographic area which it orginated. [known as Valilov's Concept] A mutation (change) found in the Y-DNA/mtDNA of a large number of people in various parts of the world most likely happened in a common ancestor. These changes can be "marked" and followed as "genetic markers". These genetic markers can be used to place that population group into a "haplogroup". More to come.

Easy way to Remember

You now know that the smallest unit of our genetic information is the triplet of nucleotides called a codon. To help our understanding, these have been represented using the first letter of each nucleotide's spelling. A is for Adenine, C is for Cytosine, G is for Guanine, and T is for Thymine. I seem to always have trouble remembering which nucleotide goes with what partner. To help me remember I use their alphabetical order A, C, G, T...then I remember that the ends meet. Thus A goes with T which leaves C to go with G. Easy way to remember.

A Review

By way of review, the unit of genetic information that makes one workable protein chain is called a gene. This gene has two sides that come together to make its home along the DNA molecule. A gene determines the amino acid sequence of a larger protein called a peptide, which in turn fixes the properties (function) of this peptide in the organism. A change in the nucleotide sequence (codon) at one position of a DNA molecule (a SNP=snip) can alter the codon, thus its message, and create a change (mutation) in a gene. This change (mutation) can then be transmitted to the next generation, and the next, and the next, and so on, until this mutation ( a SNP=snip) becomes a marker for this genetic group. A haplogroup is born, and all members of this group that share this mutation (SNP=snip) become tagged with this marker to become a haplogroup. These SNPs = snips have been marked along the DNA, the Y-chromosome for the male, and the mitrochrondial DNA (mtDNA) for the females. These markers become the message board for that DNA's genetic history, and serves as a way to classifiy all human ethic groups. A generalized system of organization has been adopted for these markers, and a series of laboratory procedures have been developed to analysis these DNA markers. These test are widely available on the market today, and serve as an avenue to analysis the genetic history of your own DNA. Y-chromosome analysis for the males, and mtDNA for the female. The more markers you have analyzed, the more cost. Understanding how these markers work is the next stage.

Two Pictures SNPs (snips)

The pictures shown are those of the "dinning room" [phosphate + sugar} and the "bucket truck" [nucleotide base]. Remember, you are standing on the five sided dinning room table which is the five sided sugar. The bucket truck is attached to the 1st dinning room chair (carbon one). To extend the bucket out the window is to place the nucleotide base into the world of the helix that is seeking its partner. It is a change in a single bucket that defines the SNPs (snips).

Our Address Book

Over the years our DNA has undergone multiple mutations. The longer the DNA has been active in our environment, the more time it has been exposed to the causes of mutation. A population group that has many of these changes would indicate that it has been around a lot longer that a population group that has few. This simple logic has been used to figure out which population group has been around the longest, even since the beginning of the human experience. Today, these changes, snips (SNPs), have been identified. Each single nucleotide change that has been found, has been coded and grouped. In essence, each mutation that has been found, has been given a genetic address that can be tested repeatedly. When enough of a population group shares a mutation, this mutation (SNPs) help define that part of the DNA that has been transmitted from one generation to the next. This change (SNPs) then becomes the "label" (haplogroup) for that family group. Today there are around 20 haplogroups know to exist. They are given the simple coding of the alphabet, beginning with the letter A, going to the letter T. It is believed that haplogroup A is the oldest.

Understanding the concept of the "snip" is the bases of moving on in the understanding of how DNA has been examined and these gene addresses have been used. Knowing where the "snips" occur along the DNA chain of codons (three nucleotide bases), and the type of "snips" present, tell the history of this DNA. It might be helpful to go back and review the blogs that discuss the dinning room and bucket trucks. A snip is a change in only one dinning room. The bucket at the end of the truck has been changed. This change will of course produce a change in the other side of the nucleotide pair (base pair). Go back and run through this mental concept until you have a clear understanding of the SNPs! This becomes our DNA address book.

Causes of Mutation

DNA has to be changed (a mutation) before the individual carrying that DNA is changed. The individual is changed before the population (cultural group) is changed. If a constant rate of mutation is assumed (not sure this can be assumed), then there has been 1 mutation per 25,000 - 50,000 years that has survived to be past down to us today! It is a good thing that most mutations do not seem to affect the functioning of the individual!

The causes of mutations fall into several categories. The most ancient was probably radiation since the nitrogen molecule is the most resistant to radiation. Also the double helix hold the codons (genes) in their matrix that is most resistant to radiation.

The second most likely is the errors that occur during the duplication (replication) of the DNA. You can imagine that each cell replicates hundreds of times, and some probably thousands of times. Somewhere along the line, there is bound to be an error made.

The third cause seems to be viruses. Some viruses have only a protein coat and a single strand of DNA/RNA inside. If this virus gets control of the cell (which it does when it invades the cell), then it can induce changes by its very action.

Chemicals in the environment called "mutagenic chemicals" have been shown to change the DNA pattern. This is especially true if the embryo is exposed at a very early date.

A last category is called "transposions". This describes the changes that happen when one nucleotide is shifted (transposed) with another. It being "moved around" in the codon line so to speak.

When these mutations occur, and they are pasted on to the next generation, and enough of the next generations carry these changes, the changes probably happened in a common ancestor. Bingo...a halogroup.

Today, these changes (mutations) have been identified for the various cultural groups in the land. The changes have been labeled on the Y-DNA (passed down through the males), and mtDNA (mitochrondial DNA) passed down through the female. When enough of a single population group carried a mutation, this become their halogroup marker. Having your DNA done, will provide you with a halogroup marker. This is the first step in using DNA for genealogy research.

A little SNIP here

Over time, the changes that occur to our DNA are called mutations. These changes can happen at the active part of the DNA (about 10% of the DNA), or at the inactive segments (some call the variable part). The changes are actually substitutions of one base pair (the bucket chair that you put out the window) for another. In essence, you change one letter for another. This can happen in three ways. First, one base pair can have a "substitution" made for it. The letter A can be substituted for the letter G. This would mean that the opposite side would also be changed since G would only go with C whereas, A only goes with T. Secondly, there can be an "insertion" of a nucleotide base between two existing bases. This would change the codon sequence thus changing the code for this segment. Thirdly, there can a "deletion" of a nucleotide base thus changing the sequent of the code for this segment of DNA. Once a mutation is established, it is past on down the line to each new generation.

Now here is where all the terminology comes. When only a single nucleotide base is substituted, it is called a "Single Nucleotide Polymorphisms" or SNP (pronounced snip). You can now visualize this in your 3-D dinning room since you would only be replacing one bucket truck. The inactive segments are much more likely to undergo mutations which can occur up and down these segments at multiple locations. [Remember that this is also about 90% of your DNA!] The changes are grouped together (in tandem) and occur at variable places along the codon. They can be of variable lengths. The short length changes are called "short tandem repeats" (STRs). The longer series of changes have been called "variable number tandem repeats"(VNTRs). These are the terms which are thrown about in all the literature regarding DNA and genetics. They are also used in describing the test which can be ordered for your own DNA.

It might now be helpful to go back and reread the previous blogs that present the DNA strutcture. More to come.

Basic Principles

1) Genes encode proteins. (Remember that a gene is a string of Codons that work.)

2)Proteins govern the development of inherited traits. (What makes us...us!)

3)A variation in the DNA sequence of a gene will often express itself as a variation in the proteins that it controls. This in turn, causes variation in the traits contolled by those genes and proteins.

If you will, this becomes the three basic principles to the understanding of mutation:...DNA...to protein...to inherited trait. Simple, yes?

Where Our Genealogy Begins

The biochemical world of our DNA takes up its own 3-D space. As long as it has sugar (food) and oxygen (fuel), it goes merrily about its two tasks of life, making proteins and a copy of itself. Protein synthesis is the day in and day out activity that keeps us going. Duplication is the "as needed" process by which a cell divides under the direction of its own control center. Some cells divide every twenty-four hours or so, and some cells rarely if ever divide. Imagine keeping more than a trillion cells in order! The DNA molecule keeps us going and defines our characteristics. These are our chromosomes, which are the coiled up molecules of DNA. There are also some extra proteins thrown in that help to stabilize the DNA such as the handle that it uses to help it make a copy (called replication or duplication). This "handle" is located at different places along each chromosome giving a distinctive shape to each of the 46 chromosomes. Called a "centromere", its position along the DNA coil helps the folks who know what their doing arrange a picture of the chromosomes. At the ends of each chromosome are special proteins called "telemeres" which break away and release the tips of the DNA molecule. Thankfully this happens and keeps the DNA molecule from becoming too fat and sassy!

A basic premise of life is that all organisms replicate their DNA and pass it on. DNA contains the segments that work (called genes) encoding the information about our heritable traits. Our heritable traits come from mom and dad where our genealogy begins.

Pass it On

You are in the middle of it...this DNA! Three nucleotides in sequence make a word that spells amino acid. Piecing together a bunch of amino acids makes a protein molecule that when working correctly with other protein molecules makes us work.

Now just imagine trying to make this all come together. Let's see...three codons C.A.T. spells G.T.A. on the other side. A.C.T. spells T.G.A. on the other side. Well, what if that doesn't work? Throw them out? Over billions and billions of years the genetic code had to be figured out. What did the chemicals do if they made a chain of codons that did not make anything? It would seem that the DNA molecules (chromosomes) have tried a lot of combinations that did not work. They moved all this none helpful stuff out into never, never, land which accounts for almost 90% of the DNA molecule. I guess they just did not have trash collection at that time. Just think, this would suggest that for every working gene, it took nine tries to get it right.

That's right, only about 10% of our DNA is active and working on our behalf! For many years those who first recognize this fact called this non-working DNA segments as junk. It just hangs around and is known as the "variable" part of the DNA. This part of the DNA is much more likely to undergo changes called "mutations". [Much more will be said about this.] At any rate the basic fact is that all organisms replicate their DNA and pass it on, including the junk.

A single nucleotide base

The idea of a bucket truck may be foreign to some readers. The image to the right shows a picture of a similar type of equipment. This is used in any high, or difficult to reach area. I suspect that some of the codons have their problems reaching out in the biochemical space they must negotiate. Anyway, this should give you a visual image to place in your mind, and now it is up to you to imagine locking the base of this monster to your first chair and extend the bucket into space. Remember, it will take three "buckets" (nitrogenous bases to make a codon. Each three "buckets" spell one amino acid. You will be standing in the room of a single nucleotide base.

What a way to go

You are now living in the 3-D space you have created. Stand in the bucket, and as you hold hands with the matching letter of our alphabet, A=T, C=G, you are in the middle of our double helix. Looking up, the buckets go on and on into to space. Looking down, the buckets go on and on into space. You are at the business end of the DNA molecule. You are at the end of a "single" nucleotide. Keep this in mind as we continue our adventure. At any time you can move about your bucket arm (nucleotide base), into the five sided table (ribose sugar), or reach up or down to the phosphate group that holds the table (sugar) to the next phosphate group at the floor above, or below, depending on which direction you choose to look. Now just think, after the billion of years that it took to figure all this out, DNA has the task of keeping us going. From one generation to the next, DNA is passed down, 1/2 from the moms, and 1/2 from the dads. This requires the DNA to do two things. The first is to duplicate itself when needed. The second is to direct the making of proteins so that our bodies can form and function correctly. Seems pretty simple if you put into these terms, but has you can see the miracle of life is far from simple. The basic premise is that the more stable the molecule, the more likely it is to survive the test of time. Nitrogen is the most resistant to radiation, and when the nitrogenous base is tucked inside it's double helix, it is most resistant to ultraviolet radiation. How neat that these very facts help keep the messages that DNA carry most stable.

Now standing inside your bucket, you are at the center of one cell's universe. Trillions and trillions of cells carry out their daily activities under the directions contained in this DNA. When you let your hands go, (release the hydrogen bond) the bucket on the other side is released and the double helix can begin to "unzip". It unzips along the codons reading each codon (three buckets in a row) until it gets the entire message it needs to make the protein it is directed to make. This entire message is called a gene! Only one side of the double helix is used to give directions for making proteins (called protein synthesis), and the other side is use to duplicate itself. (called replication) Read one side, duplicate one side. What a way to go.

The Ultimate Bucket List

You should have a good feel for the 3-D space about you as you stand on the table in your dinning room. What fun! Didn't you always want to get away with something like this as a child. I guess that most kids spend their time under the table instead of on top, so you get a little advantage.

Now move to the first chair position [carbon 1 atom] and get ready to extend your bucket arm out the window. Remember that it is at this first chair position that the nitrogen [N] atom connects to your table. It is this nitrogen [N] - carbon [C] connection that gives the name to this nitrogenous base that you are about to extend out the window. You have certainly seen one of these bucket trucks with its arm extended. Now take control and place your bucket out the window. If your bucket contains an "A" letter [adenine], you will have to find a "T" bucket [thymine] on the other side. If your bucket contains a "C" [cytosine], you will have to find a "G" [guanine] bucket on the other side. Amazing that after billions of years, the "A" to "T" and the "C" to "G" connection seems to be the best way to transmit our genetic information.

As you look out the window to extend your bucket you will notice something strange about the floors across from you. They are stacked in the opposite direction. The fellow extending his bucket out his window directly across from you will appear to be upside down. What in the biochemical world is this? Well, the opposite series of rooms are arranged exactly like your dinning room except they are heading the opposite direction. In the world of rooms stacked opposite, their world is right side up, and you are upside down. In this 3-D space, it will depend on where you are standing to determine which direction is up! At any rate, the rooms across from your set of parallel rooms run in the opposite direction. I guess this utilizes biochemical space to the maximum, and allows the buckets to be place between each series of floors.

Anyway, you have to find your match as you extend your bucket out the window. Once you find your mate, you hold hands with your partner. Now if you climb into the bucket yourself, you will see a whole world of buckets holding hands up and down between the two sides of rooms. As far as the eyes can see, bucket after bucket holding hands with its partner. What a sight. The holding of hands represent the hydrogen [H] bonds that keep the buckets connected when they are not being used. The buckets take a twist as they hook up giving the form of the double helix, which is the final structure that houses out destiny. What a bucket list.

DNA in 3-D

Three dimensional space is often difficult for many to mentally visualize. Starting with what you know, then moving to what you don't, is always a good plan. [It also works well in doing genealogy.] So let's try to visualize the phosphate + sugar + nitrogen base using the dinning room picture shown to the right.

Get a good look. There is a dinning room table with chairs placed about. Pictures are on the walls, windows letting light invade the room. A floor and ceiling with the walls complete the picture. Now place yourself into this three dimensional space standing next to the table. It would come about waist high and you could sit yourself down. But no time to rest. Get a good feel for the space about you. Floor is down, ceiling is up, table is in the middle, and you are standing in this room.

Now imagine that the table beside you is a five sided table. It would be shaped like the Pentagon building. Place one point of this five sided table pointing toward the picture on the wall. Next, place a chair at each point along this table except for the point facing the picture. Chair one to the right of the point, chair two at the bottom right, chair three at the bottom left, and chair four at the the upper left. Then stand up in chair four with a fifth chair held about your head. It should just about reach the ceiling with your arms reaching upward. Looking down, you would see the top of the table with the first chair almost directly across from your position standing in chair number four. You can rest a little bit now, for I know holding up a chair to the ceiling would get old fast! Look around the room. Space above the table, under the table, to the right and to the left. Three dimensional space! You have it.

The five sided table is the ribose sugar of our DNA. Each chair is a carbon atom place equally about the points of the table. A oxygen atom is at the point facing the picture. You are holding the fifth carbon atom in your hands as you raise it to the ceiling. Now each chair has a number just as the carbon atoms are given numbers around the sugar table. Chair one (1) is where the nitrogen base attaches and reaches out to the window to the upper right. Chair three (3) is where the phosphate molecule attaches, but under the table, at the legs of carbon (3). Another phosphate molecule attaches to the chair you are holding above your head, but you have to push the chair through the ceiling to make this connection. In the same way, a person in the room below you is holding their chair (5) up to the ceiling, only you see it as the floor below chair (3). A person in the room above you would look down and see your ceiling as their floor! And so it goes. Floor, after floor, after floor, of phosphate + sugar + base streaches for hundreds of floors! The phosphate holds the chair (3) from the bottom, and you hold chair (5) to the top. A (3) chair to a (5) chair hook-up. The nitrogenous base connects at the (1) chair by its nitrogen atom extending its molecular structure out into the room toward the window much like one of those bucket trucks extending its arm into space. You are standing in a single nucleotide's 3-D space. Way to go!

Now go back to the previous blog that shows the drawing of the phosphate + sugar + base. Look at it through your 3-D eyes.

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!

Let's Summarize

You now know that atoms : [H]ydrogen, [C]arbon, [N]itrogen, [O]xygen, and their two side kicks [P]hosphorus, and [S]ulfur come together in various combinations to form:

molecules that contain a variety of chemical bonds to form:

our substances: fats {long strings of [C] atoms}, sugars {short strings of [C] atoms, and proteins, [C] atoms combined with [N] atoms.

The proteins then pull together several of their protein buddies forming the nucleotide bases. These nucleotide bases become the alphabet for our DNA. The alphabet consisting only of four letters, A, C, G, T. [In the cytoplasm U is sometimes used.]

Two of these substances, a 5[C]arbon sugar, and the nucleotide bases join up together using a phosphate molecule to form long chains of a helix shaped substance which we now know is "deoxyribosenucleic acid" or DNA! [phosphate + sugar + nitrogenous base].

Words are written three letters at a time which form a "codon". Enough codons lined up in a row that tell the cell what to make is called a "gene". Wow, there you have it, the secret to life.

The drawing to the right is my attempt to represent the basic structure of DNA for those visual learners. Three "ribose" sugars are drawn with their "phospate" backbone. To the right, which would be the inside of the poly(many)nucleotide(nitrogenous bases), shows how the bases attach to the sugars and flap their arms and legs to invite their matching base. More to come.

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.

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.

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.

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.

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.