The building blocks of DNA

Genetic information is stored within the nucleotide subunits of the DNA molecule. In this activity, you will learn about the different subunits and their distinctive structures.

Worksheets:

The building blocks of DNA and the double-strand DNA drawing

1. Open the structure file 1NAJ.cn3

2. Open File > Preferences. Make sure that the Preferences are set on Low quality.

3. Open the Style menu. Select Rendering Shortcuts > Ball and Stick.

4. Look at the menu at the top of the screen. Click the pointer in the structure Sequence/Alignment Viewer window - Notice that the menu options change. There will be different menu options depending upon which window is active.

5. In the Sequence/Alignment Viewer window, select a "g" from the middle of either DNA strand, by clicking it with the mouse. The g is an abbreviation for the nucleotide, guanine. Both the letter "g" and the guanine in the DNA will appear yellow once they've been selected.

6. Click the pointer in the Structure window to see the Select menu. Choose Show Selected Residues

7. Open the Style menu. Select Coloring Shortcuts > Element. Note: the color will remain yellow until the g in the Sequence/Alignment window is deselected.

8. Deselect the g by clicking once inside the Sequence/Alignment Viewer window and clicking any other base. Now the g will be colored according to the elements it contains. It may be helpful to enlarge the structure for better viewing.

In the next steps, you will identify the elements that make up guanine and build a color key, for future reference, matching each element with the color assigned by Cn3D. When Cn3D assigns colors by element, each element is drawn with a distinctive color. The colors used are standard for all structure viewing programs and will be the same in all structures.

9. Begin by comparing the drawing of deoxyguanosine monophosphate, shown on the next page, with 1NAJ, the structure presented in Cn3D. There will be some differences since the drawing is flat and two-dimensional and Cn3D shows a three-dimensional structure. Also note that many of the hydrogens are missing from the drawing and that one or two solid lines are used to represent covalent bonds.

a. Examine the phosphorus in 1NAJ and the atoms that are attached. What color is used to represent oxygen?

b. Look at the oxygens in the drawing above. What charge is shown on two of the oxygens? Do you see any other atoms, in addition to the oxygens, that indicate a charge? What overall charge is DNA likely to have?

c Examine the drawing of double-stranded DNA (in your worksheet handout). Find, circle, and label: an oxygen, a phosphorus, and a phosphate group.

11. Turn 1NAJ around and look at the ring with four carbons and one oxygen. This is deoxyribose, the sugar component of the nucleotide. The hydrogens are shown in light grey.

a. What color is used to represent carbon?

b. Look at the numbering scheme in the drawing above. Find where the 1' carbon of the deoxyribose is attached to the base. Locate each of the deoxyribose carbons in 1NAJ, from the 1' carbon to the 5' carbon. Label these carbons on your worksheet.

c. Refer to the drawing of double-stranded DNA. Circle and label the deoxyribose groups at both ends of both chains. Add the numbers (1'-5') for the carbons

12. Examine the base component of guanine in 1NAJ and compare it to the drawing.

a. What color is used to represent nitrogen?

b. Locate and label all the guanines, on the diagram of double-stranded DNA, by comparing it to the structure in 1NAJ and the drawing above.