What exactly is
DNA abbreviates DeoxyriboNucleicAcid, and its fundamental building block is the nucleotide. This nucleotide consists of three components:
|A phosphate group that acts as a bridge between adjacent deoxyribose sugars||A nitrogen-containing
pyrimidine, or purine base.
|A deoxyribose sugar.
Refer to diagram on the right:
The top level shows the phosphate group.
The middle level shows the sugars.
The bottom level shows the different bases in DNA and RNA.
Now, each deoxyribose sugar unit contains five carbon atoms joined in a ring structure together with an oxygen atom.
The carbon atoms in the deoxyribose sugar are designated by numbering them sequentially from one to five.
The first carbon atom, numbered 1, is defined as the one attached to one of four organic bases:
|1. Guanine (G)|
|2. Adenine (A)|
3. Thymine (T)
4. Cytosine (C)
Remember the purine base and pyrimidine of DNA mentioned earlier? Well, Adenine and Guanine are purines, while Cytosine and Thymine are pyrimidines. Phosphate groups are attached to the third (3) and fifth (5) carbon atoms.
Now, with all thats been gathered so far, you should be able to conclude that in DNA, a nucleotide refers to the complete assemblage of a nitrogenous base (A, G, C or T), a five-carbon deoxyribose sugar, and a phosphate group. So far so good?
Lets go into DNA
Do you know that the diameter of the DNA helix (its "spiral") is 2 nm, and the vertical rise of each base pair is 0.34 nm? Note: It's not millimetre but nanometre!
A DNA molecule consists of two unbranched polynucleotide chains (the strands you commonly see as DNA) that wind about each other into a structure called a Double Helix. Each polynucleotide is a linear polymer in which the monomers (deoxynucleotides) are linked together by means of phosphodiester bridges, or bonds. These bonds link the 3' carbon in the ribose of one deoxynucleotide to the 5' carbon in the ribose of the adjacent deoxynucleotide. Note: If the aforementioned paragraph is a wee bit blur to you, please refer to the section on sugars just below. If it is very blur to you, please read this whole page again, from the top, slowly!
The structure of the DNAs helix is stabilized by hydrogen bonds between complementary organic bases (a base pair), and hydrophobic (leading to the aversion of water) interactions between the nitrogenous bases and the surrounding sheath of water.
The alternating sugar-phosphate groups in each DNA strand form the "backbone" of DNA, and they also confer a directionality. As mentioned earlier, Adenine and Guanine are purines, while Thymine and Cytosine are pyrimidines. (A) pairs with (T), and (G) pairs with (C). Therefore, in a complete helix, the As always line up with the Ts and the Gs with the Cs. Note: It is recommended that you read the last line of this paragraph again.
The hydrogen bonding between complementary base pairs is such that the most energetically stable DNA configuration is achieved when Adenine pairs with Thymine and Guanine pairs with Cytosine. Thus hydrogen bonding between base pairs contributes to the stability of the DNA double helix and the base sequence affects the stability of the DNA.
There are other DNA conformations (configurations) that use the same nucleotides and molecular bonds, but the three-dimensional structure of their helixes are different. At least six different DNA conformations (designated A, B, C, D, E and Z) have been identified (so far). Only the A, B and Z conformations are found in natural biology, that is: animals and plants. The B-DNA turns out to be the most common form of DNA found in living organisms, and has an average diameter of about 2 nm.
Note: Base pairs are often referred to as A-T or G-C base pairs (or BPS). Rarely do people or textbook publishers use the full names of the nucleotides (e.g. Adenosine-Thymidine).
Do you know that Repetitive DNA actually makes up between 20% to 50% of a Human Genome?
Despite its majority, scientists still do not know much about these "junk" DNA. All we know is that they are necessary and important to DNA synthesis. These repetitive DNA can exists anywhere along a DNA strand. They could exist in the DNA linkages (introns), before a DNA strand (with the promoters), after a DNA strand, and anywhere else along the DNA strand.
figure shows the different "boxes" (in number of base-pairs)
of repetitive DNA before a transcription point.
In repetitive DNA, certain base sequences are repeated many times in a haploid chromosome (sometimes up to a million copies can exists for one particular repetition).
In humans, repetitive DNA can be classified into two main groups:
(Long Interspersed Nuclear Element)
2) SINE (Short Interspersed Nuclear Element)
LINE repetitive DNA has an average length of 6500 base-pairs and are dispersed throughout the Human Genome.
SINE repetitive DNA are much shorter in length, and are only 150 to 300 base-pairs in length. These are widely spread on all Human Chromosomes, and make up 5% of the Human DNA. These SINE repetitive DNA have been known to cause several genetic diseases. Transposition, rearrangements and recombinations of these sequences can produce mutant phenotypes. For example, an extra insertion of a set of repetitive DNA would cause either acholinesterasemia or neurofibromatosis. If it is a rearrangement, either hypercholesterolemia or thalassemia might result.
What are DNA sugars like?
The atoms of a sugar, whether it is a deoxyribose like in DNA or a ribose like in RNA, are numbered 1', 2', 5'. Atoms in the sugar component of a nucleotide provide the link between the base and the phosphate group. For example, the 1' carbon is attached to the 9 nitrogen of a purine, or the 1 nitrogen of a pyrimidine. A bond to the phosphate group (ester bond) replaces the OH (hydroxyl) group on the 5 carbon.
To understand DNA sugars, there are three main points to remember.
1.There are four basic sugars:
2. These sugars are important metabolically. They are the major energy storage molecules for living organisms. Their carbon rings contain large amounts of energy.
3. There are two ways for sugars to polymerize (the process of forming compounds of molecules from repeated units of smaller molecules).
1) One way is through Alpha Linkages.
2) Another is through Beta Linkages.
To distinguish between the Alpha and Beta Linkages, one can examine the position of the hydrogen on the first carbon molecule (remember the 1 molecule?). In an Alpha Linkage, the hydrogen is pointing up, but it points down in a Beta Linkage.Sucrose and lactose are composed of two sugars, thus, they are termed disaccharides. Amylose and cellulose, composed of long chains of glucose molecules, are examples of polysaccharides. The only structural difference between them is the linkage between the glucose molecules, yet the compounds have very different properties. Cellulose is a tough material found in plant cell walls, whereas amylose (a form of starch) is water soluble and used by plants as a carbon storage compound.
When you write a letter, you put together words using different letters of the alphabet. With 26 letters you can say anything you want. However, it is important that the letters go in the right order. The sentence stops making sense when the letters are not arranged in the right order (to form a word).
Similarly, when you make new cells, your body is putting together different letters of the DNA alphabet. Even with just 4 letters, the DNA alphabet spells out all the information you need to create new cells and to stay healthy. The order of the DNA bases is called the sequence. The sequence of the bases in DNA can spell out all the instructions for your entire bodyyes, with just 4 letters.
Right now, scientists are trying to sequence every base in a human cell. They're trying to create a complete map of the human genome. With this information they hope to cure diseases (Gene Therapy).