1. Defining Base Pair
Biomedical Research

3. COMPETENCIES AND OBJECTIVES:
INQUIRY
1. Apply inquiry-based and problem-solving processes and skills to scientific investigations.
a. Use current technologies such as CD-ROM, DVD, Internet, and on-line data search to explore current research related to a specific topic. (DOK 3)
• Equipment – LCD and internet

6. DNA: Structure and Function
Deoxyribonucleic acid (DNA) is how the cell encodes information to make all of the macromolecules that it requires. Most of these macromolecules are proteins but some are RNA molecules. From a chemical point of view DNA is a polymer made up of a ribose and phosphate backbone with varible side groups of Adenine(A), Cytosine(C), Guanine(G), and Thymine(T).

7. DNA: Structure and Function
Note that the polymer has a directionality associated with it because on one side of the riobse backbone the phosphate is bound to the 5' position and on the other the phosphate is bound to the 3' position, as illustrated in Figure 1. By convention DNA is represented by a string of A, T, G and C written starting at the 5' end and continuing left to right to the 3'end of the molecule. For example the strand on the left hand side of Figure 1 would be written: CAGT. The strand on the right hand side of Figure 1 would be written ACTG.

8. DNA: Structure and Function
Figure One: DNA and its complementary strand. The helix has been flattened to facilitate the viewing of the chemical interactions. The ribose phosphate backbone is colored in blue and each side group is a different color. Note that the ribose makes the molecule dirctional as the phosphate in one direction is bound at the 3 prime position and in the other direction the phosphate is bound to the 5 prime position. By convention DNA is written five prime to three prime.

9. DNA: Structure and Function
DNA's most amazing characteristic is that it will bind to itself in a very specific manner, forming a helix. Figure 1 illustrates two DNA molecules binding. The variable groups of the polymer interact with each other to mediate this binding. Adenine interacts with Thymine and Cytosine interacts with Guanine. No other bonds are energetically favorable, for example Cytosine cannot bond with itself. The bonds that these variable groups
form are called base pairs and are illustrated in Figure 2.

10. DNA: Structure and Function
Thus, by knowing the sequence of bases of one strand of DNA we immediately know the sequence of the DNA strand which will bind to it, this strand is called the reverse complement or just the complementary strand. In Figure 1 the right hand strand is the reverse complement of the left hand side and vice-versa.

11. DNA: Structure and Function
Figure Two: Illustration of DNA base pairing. Thermodynamically the interactions Adenine, Guanine, Cytosine, and Thymine are driven by both the hydrophobic stacking interactions hydrogen bond interactions. The specificity of the base pairing is driven mainly by hydrogen bonding and stearic interference.

12. DNA: Structure and Function
This relationship to the complementary strand has many implications that make life as we know it possible, and allows all sorts of molecular biology techniques. In one of the greatest understatements of all time Watson and Crick said it best in their original paper on the structure of DNA: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." In the cell DNA is stored in helical form with its complementary strand. When the cell need to duplicate the DNA the strands for cell division the helix is split apart and each strand is used as a template to make a complementary strand of itself, an amazingly elegant solution.