Introduction to DNA

This web page is intended as a brief introduction to DNA for High School-level students. We will see what it is, how it works, and we will learn how DNA is studied. It is assumed that the student has taken some basic high-school level chemistry.

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Introduction
DNA is basically a long molecule that contains coded instructions for the cells. Everything the cells do is coded somehow in DNA - which cells should grow and when, which cells should die and when, which cells should make hair and what color it should be. Our DNA is inherited from our parents. We resemble our parents simply because our bodies were formed using DNA to guide the process - the DNA we inherited from them.
We may resemble our parents, but we are never exactly like them. This is because each child gets only some of the DNA each parent carries. About half our DNA comes from our mother, and half comes from our father. Which pieces we get is basically random, and each child gets a different subset of the parents' DNA. Thus, siblings may have the same parents, but they usually do not have exactly the same DNA (except for identical twins).

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    What is DNA, and how does it determine our physical characteristics? 

To answer this question, first we must learn how DNA is structured.
DNA is a long molecule, like a chain, where the links of the chain are pieces called nucleotides (sometimes also called 'bases'). There are four different types of nucleotides in DNA which we'll call 'A', 'G', 'C' and 'T'. These four are all that's necessary to write a code that describes our entire body plan. Sounds too simple? Keep in mind that Morse Code uses only four symbols (dot, dash, short spaces and long spaces), and you could spell out entire encyclopedias of knowlege with that simple code!

The four nucleotides look a little bit alike. They all have a ring of carbons called, in chemist's terminology, a 'sugar' (not the same as 'table sugar', however). Each nucleotide also has another type of ring structure, and this is where the four types of nucleotide are different. These rings are organic bases, much like the more familiar mineral acids and bases like NaOH or HCl, except these bases are composed of carbon, nitrogen and oxygen.

I'll try to use the term 'base' or 'basic group' to refer to just the nitrogen/carbon rings, and the term 'nucleotides' to refer to the entire structure.

Now ordinarily the atoms in a nucleotide form a three-dimensional structure. To help you visualize the structure, here's what a 'T' (T stands for Thymidine) would look like if flattened onto paper:

DNA chains are made by connecting those nucleotides together via chemical bonds. At right is a diagram showing four nucleotides connected to form an oligonucleotide, in this case an RNA oligo (note that it has '-OH' at the lower right corner of each nucleotide, as opposed to the '-H' in DNA). I've left off the bases, for simplicity's sake. You can see the sugar rings linked together with phosphate bridges. This is a "single-stranded" nucleic acid. Below is the double-stranded form:   

 Double-stranded DNA is simply two chains of single- stranded DNA, positioned so their "bases" can interact with each other. At left is a cartoon depiction of double-stranded DNA. The sugar-and-phosphate 'backbone' is depicted in red, and the bases are depicted in blue.
Importantly, the two strands travel in opposite directions; hence the structure is said to be "anti-parallel".

The bases in the middle "pair up" with bases on the opposite strand, so that a type 'A' nucleotide is always opposite a type 'T', and 'G' is opposite 'C'. The attraction between the paired nucleotides is fairly weak, but when there is a whole string of them, it adds up to enough strength to hold the strands together.

One more thing holds the strands together - an interaction called "base stacking". We don't need to consider it here.
 

 
This figure was created using 'RasMol V2.6' for the Macintosh (thanks to Roger Sayle,
BioMolecular Structures Group Glaxo Research & Development Greenford, Middlesex, UK.)
The file 3cro.pdb was modified to remove the protein components, then a series of rotating
views was screen-captured to construct this moving gif.  At right is an animated drawing of a DNA molecule. There are two strands of DNA in this picture, wound around each other to form the famous "double helix". 
Down each edge is the backbone, where the nucleotides are linked together to form the chain. In this drawing, you can spot the backbone most easily by looking for the red balls, the oxygen atoms. Also look for the phosphorus atoms in the backbone. These are colored yellow. Together the phosphorus and oxygen atoms form the phosphate groups that interlink the nucleotides, as described earlier. You may be able to see the sugar rings just inside the phosphate groups, visible as grey atoms - carbon. (Note that hydrogen atoms are purposely omitted from this drawing in order to simplify it). 
Look for the rungs of the 'ladder'. These are the basic groups that point inward and hold the two chains in position against each other. They are most easily spotted by looking for the blue color of the nitrogen atoms, which are alternating with the carbon atoms of the base groups. 

DNA The recent ability of scientists to determine the structure of human DNA has created an explosion of research involving genetics, disease, evolution, and the origins of human population groups. The study of human origins is facilitated by analysis of DNA that is spared the complexity of the recombination. While most genes can come from either parent, such that the DNA from the parents is recombined in the child, some parts of human DNA are free from recombination. The mitochondria, small energy-producing structures in our cells, contain special DNA that is inherited only from the mother, without recombination with the DNA of the father. Analysis of mitochondrial DNA (mtDNA) shows DNA structures that have been passed along purely maternal lines, from mother to daughter over the generations. Such analysis has proven to be a useful tool for many purposes (Richards and Macaulay, 2001). Likewise, the Y chromosome in men is passed along paternal lines only. Analysis of Y chromosomes can be used to link modern humans to male ancestors. Both mtDNA and Y chromosomes are subject to mutations that occur rarely but with presumably constant rates (the rates depend on what portion of the DNA is being examined--some portions mutate frequently, others remain very steady over time). Groups that share many common mutations can be presumed to be closely related. Groups that have very few common mutations may be presumed to come from family lines that diverged long ago. The typical human mtDNA molecule is a circular molecule comprising 16569 nucleotides in a specific order. These nucleotides, adenine, guanine, cytosine, and thymine are labeled A, G, C, and T, respectively. An arbitrary position has been defined as nucleotide 1. A standard mtDNA sequence, known as the Cambridge Reference, was the first published human mtDNA sequence (S. Anderson et al., 1981). Mutations can result in a variety of changes, such as a substitution of one nucleotide for another, a deletion of a part of the sequence, or the addition of one or more nucleotides. Several tools are used in DNA studies. Restriction Fragment Length Polymorphism (RFLP) classified DNA by analysis of patterns in DNA that has been cleaved into chunks by enzymes (restriction endonuclease). If two organisms differ in the distance between sites of cleavage achieved with a particular enzyme, the length of the fragments produced by enzymatic attack will differ. The similarity of the patterns generated can be used to distinguish species. Recent studies employ up to 14 different enzymes that can provide high resolution of differences in portions of human DNA. RFLP is often applied to a highly variable portion of non-coding DNA in the mitochondria called either the control region (CR) or the D-loop. Direct sequencing of portions of human DNA yields series of nucleotides that allow direct comparison of various genes with those of different individuals. The extensive sequence information can be used to map groups of related individuals into clusters or clades. Genetic analysis can also be done looking at proteins in the blood, the presence of certain genetic diseases or other genetic traits, and so forth. Evidence for Asian Origins and Arguments against the Book of Mormon Studies in the 1980s based on analysis of linguistic, dental, and genetic evidence resulted in the hypothesis that there were three genetic groups in the Americas, the Amerinds, the Na-Denes, and the Aleut-Eskimos, apparently due to three separate migrations of ancestral Asian populations across the Bering Strait. Greenberg et al. (1986) suggested that the first migration (beginning 12,000 years ago) eventually resulted in the spread of Amerind-speakers throughout North, Central, and South America, followed by additional migrations that brought the ancestors of the NaDene-speakers and Aleut-Eskimo speakers into the northern part of the continent. Other early genetic studies supported the three-wave model, while mtDNA studies have pointed to as many as four major waves of migration. But in 1995, a commonly-cited study by Merriwether et al. (1995) argued for a single migration from Mongolia or northern China, based on their review of mtDNA evidence. (See also Kolman et al., 1996.)