Tuesday, October 26, 2010

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.

Thursday, October 21, 2010

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.

Monday, October 18, 2010

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.

Saturday, October 16, 2010

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.

Thursday, October 14, 2010

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.

Sunday, October 10, 2010

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.

Thursday, October 7, 2010

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!

Sunday, October 3, 2010

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.