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Select Molecule options

These options may allow selection of the entire molecule, subcomponent molecules (for example protein vs nucleic acid), or smaller molecular components (cofactors, carbohydrates, specific nitrogenous bases or amino acids, etc) of the model presented in the Jmol window.

Selecting a molecule so that it’s name heads the menu allows alteration of its appearance in the model.

A molecule can be hidden or revealed using the adjoining checkbox. Hiding a molecule will hide all components (atoms, bonds, ribbon, etc.) of the model associated with that molecule.

Display options

Display options determine how the selected molecule will be rendered in the model. The model may include atoms, bonds, a ribbon, trace, etc, which can be individually sized using the ‘Size’ buttons. The adjoining checkboxes can be used to hide or make visible different model components.

Atoms: Atoms can be rendered as solid spheres with a uniform radius in Angstroms, which together with bonds comprise a traditional ‘ball and stick’ projection. This is normally the default view. Note about hydrogen atoms: some models show hydrogen atoms but others do not.

vdW checkbox: toggles rendering of atoms between uniform diameters and percentage of the van der Waals radius of each element. The van der Waals Radius of an atom is the calculated radius when it is adjacent to but not bonded to another atom. Since the van der Waals radius of an element is related to the size of its electron cloud, elements with greater mass will have larger van der Waals radii.

Dots: This projects an array of small dots around the surface of atoms. Dots are a useful way to show a molecular surface while not obscuring other aspects of the molecular structure, such as a ball and stick rendering. If vdW is checked, the dots are drawn as a percent of the van der Waals radius.

Bonds: Covalent bonds are generally drawn as rods between the atoms. In some models single, double and triple bonds are distinguished (but this does not occur in all models).

H-bonds: The position of hydrogen bonds is calculated by the Jmol applet. This is performed between N-H and C-O groups of proteins and between nitrogenous bases of nucleic acids. Thus, not all hydrogen bonds may be rendered in a model.

Ribbon: A ribbon-like feature that follows the backbone of DNA and proteins. For nucleic acids, a ribbon will follow the sugar-phosphate linkages, and for proteins it follows the path of peptide bonds and alpha carbons. The flattened appearance of the ribbon highlights secondary structural features, such as the alpha-helices and beta-sheets of a protein.

Trace: Like a ribbon, a Trace follows the molecular backbone, but is rope-like in appearance. A Trace shows the path of the backbone while allowing other structural features to be emphasized.

IsoSurface: IsoSurface projects a surface to a molecule as it would appear to water molecules rolling along the perimeter. This is also referred to as the Sovent-excluded or Connolly surface. Follow this link for a more complete description of the rendering of molecular surfaces.

Color by options

Atoms, Ribbons and Traces can be colored to highlight structural features. Follow this link for a more complete description of colors.

Element: Atoms will be colored according to element type. The colors of the most common elements are:

H C N O P S Fe

1o Structure: different types of amino acids and nucleotides are given a unique color (according to the Jmol ‘shapely’ color scheme).

2o Structure: This differentiates regions of protein secondary structure:

α-helix β-sheet

4o Structure: This gives a different color to each peptide subunit of a multi-subunit protein and to each strand of a nucleic acid.



Structure of Nucleotides and Nucleic Acids

Examine the following models to explore the structure of nucleotides, DNA and RNA.

1. Nucleosides. The first models show several nucleotides so that their shared and uniques features can be compared.

All nucleotides possess a 5-carbon carbohydrate (ribose or deoxyribose) linked to a phosophate via the #5 carbon and to a nitrogenous base via the #1 carbon. The nitrogenous base is either a single-ringed pyrimidine or a double-ringed purine. In nucleic acids, complementary base pairing always occurs between a purine and pyrimidine base. Notice that the nucleotides with deoxyribose (found in DNA) lack an -OH at the #2 carbon.

Select a nucleoside to examine its structural components.
Deoxy-Adenosine-5-phosphate. This purine possesses the nitrogenous base adenine, which occurs in both DNA and RNA. This is the DNA form of the nucleotide.
Guanosine-5-phosphate This purine possesses the nitrogenous base guanine, which occurs in both DNA and RNA. This is the RNA form of the nucleotide.
Cytidine-5-phosphate. This pyrimidine possesses the nitrogenous base cytosine, which occurs in both DNA and RNA. This is the RNA form of the nucleotide.
Deoxy-Thymidine-5-phosphate. This pyrimidine possesses the nitrogenous base thymine, which occurs only in DNA, and the nucleotide contains deoxyribose.
Uridine-5-phosphate. This pyrimidine possesses the nitrogenous base uracyl, which occurs only in RNA, and the nucleotide contains ribose.

Nitrogenous base Phosphate Carbohydrate Show carbon numbers

2. Base pairs. The following models show base-pairing between nucleotides.

Specificiy of the base pairing results from matching size and geometry of the nucleotides and the ability of the bases to form either 2 or 3 hydrogen bonds. In DNA base-pairing occurs between Adenine and Thymine, and between Guanine and Cytosine.
Adenine - Thymine base pair. This model shows the base-pairing between deoxy-Adenosine-5-Phosphate and deoxy-Thymine-5-Phosphate.
Guanine - Cytosine base pair. This model shows the base-pairing between deoxy-Guanosine-5-Phosphate and deoxy-Cytidine-5-Phosphate.
Uracil - Adenosine base pair. This model shows the base-pairing between Uridine-5-Phosphate and Adenosine-5-Phosphate, which may occur within a folded RNA Molecule.

3. The sugar-phosphate backbone. Covalent linkages between nucleotides create the sugar-phosphate backbone of a nucleic acid strand.

The bond between nucleotides is called a phosphodiester linkage.Click here to show the phosophodiester linkage between two deoxyribo-nucleotides. As each new nucleotide is added, the phosphate it carries is attached to the #3 carbon of the previous nucleotide of the strand. Thus, the phosphates couple nucleotides between the #3 and #5 deoxyribose carbons.

Click here to add more nucleotides. The phosphodiester linkages form the 'sugar-phosphate backbone' of the nucleic acid strand.

Click here to add the other strand of the DNA molecule. The two strands are linked by the hydrogen bonds between the complementary base pairs, creating the double helix structure.

RNA also consists of a polymer of nucleotides linked by phosphodiester linkages, although in this case between ribo-nucleotides. Click here to examine a short RNA molecule. RNA molecules do not exist as a double helix, but can fold into a 3-dimensional shape.

Click here to examine a much larger tRNA molecule, which carries an amino acid to ribosomes for protein synthesis. Although it consists of a single RNA strand, there are several regions where it folds back upon itself to allow complementary base pairing. These regions help to stabilize the 3-dimensional structure of the molecule. (The hydrogen bonds are not displayed in this model.)

4. 3' to 5' orientation. Nucleic acids have a polarity determined by the orientation of the sugar phosphate backbone.

The alternate linking of #5 and #3 carbons of the sugars imposes a polarity upon the nucleic acid strand. The diagram below shows a short, three-nucleotide strand. At one end of the strand there is a uncoupled #5 carbon -- this is called the 5' (5-prime) end of the strand. The phosphodiester linkages alternate #3,#5,#3,#5,#3, etc. to the other end of the strand, where a free #3 carbon will be found -- this is called the 3' (3-prime) end of the strand. Click here to examine the orientation in a three dimensional model.

In the double helix, the two strands have opposite (antiparallel) orientations. Click here to show the complementary trinucleotide strand; notice the orientation of the 3' and 5' ends are reversed. Carefully rotate the model to convince yourself that the two strands have antiparallel orientations.

No matter how long the double helix (even for an entire chromosome) the strands have anitparallel orientations, as shown here for this longer length of DNA. This antiparallel orientation has important implications for the mechanism by which the double helix is replicated.

5. Major and Minor Grooves. The DNA molecule is asymmetrical, and the sugar-phosphate backbone of the two strands are not located on direct opposite sides of the double helix.

The distance between the backbones of the strands is not equal on either side of the double helix, giving rise to a wider major groove and a narrower minor groove.Click here to show the major and minor grooves of the double helix.

Major and minor grooves reflect the assymetry of the sugar-phosphate backbone across the nucleotide pair.Click here to examine this assymmetry. Notice that the identify of the bases is most exposed within the major groove

Proteins that interact with DNA can recognize and bind to specific base sequences exposed in the grooves, and the major groove is particularly important for this purpose. Click here to show a gene regulatory protein bound to DNA. In order for binding to occur, amino acids of the protein must recognize and bind to a specific base sequence of the DNA. In this projection the backbone of the double helix is shown as a trace.

The next model shows another gene regulatory protein bound to DNA.Click here to show a 'leucine-zipper' type regulatory protein, which has two subunits that straddle the major groove of the DNA.

6. Mutations. A mutation is a change to the genetic code carried by the DNA molecule and may be beneficial or (more likely) harmful to the organism.

While major lesions to the genetic code can occur (e.g., deletions of long segments), most common are 'point mutations'--changes to single base pair. Point mutations can originate from errors during DNA replication or from a chemical modification that later causes the base-pair identify to be changed.

Click here to show a DNA strand with a Thymine-Cytosine mismatch -- can you find it?. If not,Click here to show it. This type of error might occur during DNA replication when the wrong base is inserted into the new DNA strand. Although DNA polymerase has error-checking functions, mistakes can still occur.

Sometimes the nitrogenous base may be removed from a nucleotide. Click here to show a DNA strand altered by 'depurination' -- removal of a purine-type base. Look for the nucleotide missing a base. By looking at the complementary base you can tell which base was deleted; and in a similar way, DNA repair proteins can detect and repair this type of mutation.

Exposure to UV light causes a chemical change called a thymine dimer, in which two adjacent thymine bases become covalently linked. Click here to show a DNA strand containing a thymine dimer. Notice how the dimer perturbs the symmetry of the sugar-phosphate backbone, as reflected in the ribbon. Look carefullyfor the aberrant bond linking the two bases. Cells possess special enzymes that can detect and repair thymine dimers; however, many can go unrepaired following excessive exposure to sunlight, and a cancerous condition may result.

Dept of Biology & Environmental Science

Steven R. Spilatro
© 2008

Test Your Knowledge of Nucleotides and Nucleic Acid Structure

Answer the following questions and perform the following activities. Change the appearance of the models as you wish to facilitate answering questions.

Name: _______________________

Date: _______________________

Results for Nucleic Acids Inquiry Activities

1. The first models show several nucleotides. After selecting each nucleotide, identify its structural parts.

Nucleotide #1 Nucleotide #2 Nucleotide #3 Nucleotide #4

a.Click here and then on the nitrogenous base.

b.Click here and then on the phosphate group.

c.Click here and then on the carbohydrate.

d. Select here and then click on the 1' carbon 3' carbon 5' carbon

e. Click all of the following that apply to this nucleotide:

Pyrimidine Deoxyribose-containing

Attempts: Correct:

2. The next models show several nucleotide base pairs. Working with each model, perform the activities and answer the questions.

Base Pair #1 Base Pair #2 Base Pair #3 Base Pair #4

a. Click Here and then on the purine-type base of the pair.

b. For the selected base pair, select all of the following that are true.

Purine contains: ribose deoxy-ribose
Pyrimidine contains: ribose deoxy-ribose
Molecule is from: DNA RNA DNA/RNA hybrid

c. Click Here and then on each pair of atoms that will form a hydrogen bond between the two bases.

d. This base pair will form 23 hydrogen bonds.

e. Is this a G-C or A-T or A-U base pair?

Attempts: Correct:

3. Use the next models to investigate the orientation of nucleic acids.

Working with each of the models and changing its appearance as necessary, find the 5' and 3' ends.

A short DNA strand A DNA double helix

a. Click here and then on the deoxyribose at the 5' end(s).

b. Click here and then on the deoxyribose at the 3' end(s).

Attempts: Correct:

4. It's time to play the newest game sensation:
"Find the Mutation!"

Select each of these DNA models and then identify the type of mutation that is present. Change the appearance of the model as necessary to help reveal the aberration.

Mutation #1 Mutation #2 Mutation #3 Mutation #4

Which type of mutation is present?
Base mismatch Thymine dimer
Depurination Depyridination
Which base(s) are affected by the mutation?
Attempts: Correct: