Objectives

1. To be able to utilize molecular modeling software tools to visualize and explore molecules in 3D.

2. To be able to describe how nucleic acids and proteins are formed.

3. To be able to explain how the chemical composition of nucleotides and amino acids affects the structure of nucleic acids and proteins, respectively.

4. To be able to describe how the structure of nucleic acids and proteins relates to their function.

 

Introduction

The program that is used to visualize the examples below is Chime. If you go to the links below and the structures do not appear, you will be directed to install the Chime plug-in. To download the plug-in you will need to register which is free.

  1. You be asked to agree to the terms for registration. Scroll down and accept.
  2. Then fill out the registration.
  3. Once you have completed the registration, you will be brought to a new screen. Choose Download under the heading of Download.
  4. You will need to accept the terms and click on Next>>.
  5. Be sure to follow the stepwise instructions to install the plug-in.
  6. Finally, be sure that you are using Netscape version 4.5-4.76 for best results.


The following links will provide you with several different views of molecules. In all instances, you can click directly on the molecules to reorient them in space. The tutorials provided below have either boxes with "X's" in them or balls which will be linked to either commands for manipulating the molecules or movies depending upon the tutorial. (FYI: You might find that sometimes the square is missing, slow to appear, or appears as a small bar. Go ahead and click where it should be).

You can manipulate a molecule on the computer screen using the right mouse button in Windows to generate a menu of options. To see the menus and other keyboard shortcuts for visualizing molecules as well as some examples, visit Chime: How to Use It. The ability to manipulate the models with the mouse menu holds true for some of the tutorials, but in others there is a special control panel instead for more specific manipulations, for which directions are included in the text of the tutorial.

 

Nucleic Acids

Begin by viewing this molecule of DNA and others that emphasize:

Once you feel comfortable with manipulating these structures try this more in-depth tutorial Nucleotides: Building Blocks of Nucleic Acids which explores the structural differences between DNA and RNA. Be sure to focus upon the parts of the tutorial in parentheses:

  • Overview of Nucleotide Structure (1-5)
  • The Base Determines Nucleotide Identity (6-7)
  • The Pentose Ring Is Nonplanar With Several Functional Groups (12)
  • The Phosphate Group Is Key to Nucleic Acid Chain Formation (15-17)
  • Noncovalent Interactions Drive the Formation of Double-Stranded Nucleic Acid Structures (18-19)

 

Proteins

Protein Architecture is a comprehensive tutorial of amino acids and protein structure. Be sure to cover the topics bolded. If you have time, you can explore the other tutorials.

  • Amino Acids
  • Sequence and Primary Structure (I. Introduction, II. Forming a Dipeptide, & III. The Peptide Bond)
  • Secondary Structure (Alpha Helix, Beta Sheet, & Turn)
  • Tertiary Structure
    • Introduction
    • Fibrous Proteins (III. Collagen & IV. Silk Fibroin)
    • Small Globular Proteins (I. Introduction & II. Myoglobin)
    • Large Globular Proteins-Supersecondary structures with examples of Beta-structures, Alpha-beta structures
  • Quaternary Structure (I. Introduction & II. How Chains are Organized-Hemoglobin )

Another excellent, but very short tutorial focuses upon on the hydrogen bonding and placement of hydrophilic and hydrophobic residues in alpha-helix and beta-sheet structures of proteins.

 

Additional Notes and Resources

Though Nucleotides: Building Blocks of Nucleic Acids and Protein Architecture are excellent resources, the server for these tutorials may sometimes be down, so you might need to try again later or try some of the following links:

  
 
Copyright ©2000-2001, Susanne Bockholt, Ph.D.