CHIME is an application which allows you to view an organic chemical or biochemical in 3-dimensions, from any angle.  It also allows you to display it in various ways and in different color schemes.
 

In order to make the best use of this tutorial, keep two windows open on your Desktop! In the first window, view this tutorial. Even though you may have a hard copy, you can't follow the links unless you have this page open in your browser. In the second window, run Protein Explorer with the DNA model.

To see what CHIME can do, first open a new window. In the new window, go to: " MolViZ.Org.  Molecular Visualization Resources"  (hosted on the San Diego Supercomputer) .

Then click on the link to  " DNA".

The index page for the DNA tutorial should appear. Scroll down this page until you see a set of images which looks like this.

The Sugar-Phosphate backbone

1. Click on the "trace" button to identify the two sugar-phosphate chains. Click on the "off" button.
2. Click on the "phosphorus" button. This emphasizes how the dexoxyribose sugars are linked together by phosphate molecules. Click on the "off" button.
3. Click on "X spin" button.
4. Click on the "sugars" button to erase the sugars, and view the nitrogenous base pairs.
• A-T base pairs are held together by two H-bonds.
• G-C base pairs are held together by three H-bonds.
5. Click on the "Reset" button to restore the original view. Click on the "trace" button. Click on the "Y spin" button to rotate the molecule around the Y axis. As you look down through the molecule from the top, note how the 2 strands twist around each other to form a hollow tube, with all the base pairs are to the inside of the helix.
6. Click on the "Reset" button to restore the original view. Click on the "H bonds" button to erase the H-bond depictions. erase the dark brown strand with the appropriate button. Hold down the left button and use the mouse to move the molecule around.
• Note how the phosphates connect to the 5' and 3' carbons in the deoxyribose sugars of each nucleotide.
• Note how the nitrogenous bases connect to the 1' carbons in the deoxyribose sugars of each nucleotide.

The Nucleotides.

• Click on the "5' end" button. Hold down the left button and drag the mouse to show the 5' end of this DNA in different orientations.
• Identify where each nucleotide. begins and where it ends.
• Identify the 5' carbons in each of the first 3 nucleotides.
• Identify the 3' carbons in each of the first 3 nucleotides.
• Identify the 1' carbons in each of the first 3 nucleotides.
• What is the name of the base in the first nucleotide?
• Why is this called the 5' end of the strand?

• Click on the "Reset" button to restore the original view. Click on the "3' end" button. Hold down the left button and drag the mouse to show the 3' end of this DNA in different orientations.
• Identify where each nucleotide. begins and where it ends.
• Identify the 5' carbons in each of the last 3 nucleotides.
• Identify the 3' carbons in each of the last 3 nucleotides.
• Identify the 1' carbons in each of the last 3 nucleotides.
• What is the name of the base in the last nucleotide?
• Why is this called the 3' end of the strand?

The Nitrogenous Base Pairs.

1. Click on the "1/2" button. Click on the "Spacefill" button. Then click on the "X spin" button to rotate the molecule around the X axis. Locate the major groove and the minor groove. Click on the "Reset" button to restore the original view.
2. DNA contains 4 nitrogenous bases:  Adenine; Guanine; Thymine; Cytosine. Why are they called nitrogenous bases?
3. Click on the "AT" button. Adenine pairs with Thymine to form A_T base pairs with 2 H-bonds. Move it around so you can get a good idea of what the base pairs look like.
• How can you tell which one of the base pairs is the pyrimidine?
• How can you tell which one of the base pairs is the purine?
• Identify the 1', 3' and 5' carbons on both deoxyribose molecules.
4. Click on the "GC" button. Guanine pairs with Cytosine to form G-C base pairs with 3 H-bonds.
• How can you tell which one of the base pairs is the pyrimidine?
• How can you tell which one of the base pairs is the purine?
• Identify the 1', 3' and 5' carbons on both deoxyribose molecules.
5. Click on the "Replication" button to see an animation of DNA Replication.
6. Click on the "Codons" button to see an animated explanation of how DNA sequence codes for protein primary structure.

Length of Double Stranded  DNA

In living organisms, DNA is a very long molecule.

• The bacterium Escherichia coli, which lives in our guts, has a chromosome 4,000,000 base pairs long (4 megabases).  Here is a scanning electron micrograph of a burst bacterium with its DNA spilling out !
• An average human chromosome has 150,000,000 base pairs (and there are 46 chromosomes in each one of our cells!).

Watson and Crick

The B-form of DNA is a right handed helix.  It is the classical structure first described by James Watson and Francis Crick.