BioMolecular Explorer 3D: Explore the Molecules

Software for interactive molecular exploration in High School Biology courses.

 

BME3D Contents

Welcome
The Software and How to Install It
A Guide to These Resources
Explore the Molecules
Frequently Asked Questions
Contact Us/Credits

Quick Links:

Antibody
Collagen
DNA
Hemoglobin
HIV Protease
Lactase

 
 

Explore the Molecules

Before viewing the resources in this table you must install software.
Note- Background Information links may require a more modern browser than Netscape 4.8.


Guided Tutorials and Animations are authored by Eric Martz unless otherwise noted.

Antibody: Immune System

Antibody production is one part of a complex response mounted by the immune systems of vertebrates to an unwelcome molecular guest. Antibodies, also called immunoglobulins, are soluble proteins secreted by specialized cells called B lymphocytes. Antibodies can recognize and bind very specifically to foreign molecules, such as toxins or parts of invading microbes. Toxins are neutralized when antibodies bind. Microbes marked with bound antibodies are killed by white blood cells. People who lack antibodies get recurrent, severe infections, and are treated by injecting antibodies from healthy donors.

Antibodies
Format: Guided Tutorial

Opens in new window

  • Advanced subject matter
  • Includes introductions to molecular displays for amino acids, small peptides, and disulfide bonds
Cannot be used with Internet Explorer

View an Antibody in Protein Explorer

Opens in new window

  • View a model of a complete human antibody
  • This is a partially idealized (computer modeled) structure, making it easier to show the different protein chains that make up an antibody
  • This structure is also simplified: it contains only the alpha carbons of the protein backbone, due to technical factors
  • This is the same structure used in the Antibodies Guided Tutorial listed immediately above, 'Whole IgG1, Carbohydrate' section
Windows: Internet Explorer OK

View the "Business End" of an Antibody in Protein Explorer

Opens in new window

  • The "business end" is the part of an antibody that binds to a foreign molecule (antigen) to alert the immune system
  • The antigen bound to this antibody is a small protein, lysozyme
Windows: Internet Explorer OK

Background information on Antibodies:

Collagen: Connective Tissue

Collagen literally holds us together. Collagen is a relatively simple protein, made of three separate chains of amino acids that twist together. Just as strong rope is made of small strands twisted together, collagen is strong, yet flexible. Collagen provides flexible strength to our skin, tendons, and internal organs, and underlying structure for bones and teeth. Rare genetic diseases and scurvy (from vitamin C deficiency) are due to defects in collagen.

View Collagen in Protein Explorer

Opens in new window

  • The three protein chains in this collagen molecule are 29 amino acids long. Natural collagen is more than 1400 amino acids in length.
Windows: Internet Explorer OK

Background Information on Collagen (requires an Internet connection):

DNA: Genetic Inheritance

The DNA double helix carries genetic information in the sequence of the nucleotide building blocks of which it is composed. DNA holds the genes for all life on Earth. The structure of DNA is uniquely suited to its purpose as an information-carrying molecule capable of faithful duplication. Although the structure of DNA was proposed by Watson and Crick in 1953, it was not directly observed as you will see here until over 25 years later (by X-ray crystallography). Also see The Nucleosome.

Exploring DNA
Format: Guided Tutorial

Author:
Andrew Carter

Opens in new window

Highly recommended for novices to 3D structures or DNA
  • Basics of DNA structure, replication, and genetic information
  • How molecules in general are colored and displayed in different ways by scientists
  • How DNA bends and twists for gene expression and packaging into chromosomes
Windows: Internet Explorer OK

DNA Structure
Format: Guided Tutorial

(Note that text is on pages separate from the animations)

Opens in new window

Basics of DNA structure
  • Addresses replication, transcription, and translation
  • Includes lesson plan
  • Includes questions to guide students' exploration - answers are provided for teachers on request
  • "Intelligent" buttons affect structures differently depending on what "path" the student has taken through the tutorial
  • See the link on the opener page to "More DNA Resources" for further information on teaching about DNA (requires Internet connection)
Windows: Internet Explorer OK

View DNA in Protein Explorer

Opens in new window

  • Displays a DNA molecule that is 22 base pairs long.
Windows: Internet Explorer OK

Background information on DNA:

Hemoglobin: Respiration

Respiration depends on the presence of the protein hemoglobin in red blood cells. Hemoglobin picks up oxygen in the lungs, where oxygen concentration is highest, and releases the oxygen at the tissues, where, due to the continual use of oxygen, the oxygen concentration is lowest. When oxygen is bound, the heme adopts a bright red color. Inherited mutations in hemoglobin may cause diseases, such as sickle cell anemia. Breathing carbon monoxide is fatal because it binds tightly to the iron in heme and is never released, thereby blocking the transport of oxygen.

Hemoglobin
Format: Guided Tutorial

Opens in new window

 

  • Includes introductions to molecular displays for amino acids, small peptides, and disulfide bonds
  • Shows the four protein subunits of hemoglobin
  • Highlights the hemes within hemoglobin subunits
    • oxygen bound to heme
    • ferrous iron of heme
  • Explains sickle cell disease hemoglobin structure
Cannot be used with Internet Explorer

View Hemoglobin in Protein Explorer

Opens in new window

  • Displays a molecule of human hemoglobin
  • This molecule of hemoglobin is fully oxygenated (oxygen is bound to all four hemes)
Windows: Internet Explorer OK

View Hemoglobin's Interaction with Heme in Protein Explorer

Opens in new window

  • Isolates one of the four subunits of hemoglobin to enhance the view of heme, iron, and oxygen
  • In Protein Explorer, click on "Explore More at Features" link, then click on "Substructures of Interest" and then "Go To Sites." Use links there, and in "Ligands" immediately below "Sites," to highlight the features.
Windows: Internet Explorer OK

Background information on Hemoglobin:

HIV Protease: Infectious Diseases - AIDS Virus

A protease is a protein enzyme that can break a bond in another protein at a specific point. The AIDS virus builds copies of itself by getting a human cell to synthesize a very long protein chain coded for by genes in HIV. This long pre-protein is then cut by the HIV protease into pieces which assemble to make new HIV. Without the function of this protease, the AIDS virus cannot spread. HIV protease inhibitor molecules were designed from a detailed knowledge of the HIV protease structure. The addition of HIV protease inhibitor to two previous anti-HIV drugs has enabled HIV-positive people to live much longer and healthier lives. This is because it is too difficult for HIV to develop resistance mutations to all three drugs at once.

View the HIV Protease in Protein Explorer

Opens in new window

  • HIV Protease with the inhibitor ritonavir bound in the active site.
  • To see the active site, in Protein Explorer click on "Explore More at Features" link, then click on "Substructures of Interest" and then "Go To Sites." Use links there to highlight the features.
Windows: Internet Explorer OK

Background information on HIV Protease:

Lactase: Digestion

The sugar found in milk, lactose, is a compound sugar which is made from two simple sugars, glucose and galactose. Lactase is the enzyme that initiates digestion of lactose by breaking it down into the two simple sugars. A deficiency of the enzyme lactase causes lactose intolerance, which is now recognized as a common condition. Lactose intolerance generally develops after childhood.

View Lactase in Protein Explorer

Opens in new window

  • Lactose has four subunits (four separate protein chains interact to make one enzyme)
  • Lactose is bound in the active site of each of the four subunits
Windows: Internet Explorer OK

View Lactase's Interaction with Lactose in Protein Explorer

Opens in new window

  • Isolates one of the four subunits of lactase to enhance the view of lactose in the active site
  • In Protein Explorer, click on "Explore More at Features" link, then click on "Substructures of Interest" and then "Go To Sites." Use links there, and in "Ligands" immediately below "Sites," to highlight the features.
Windows: Internet Explorer OK

Background Information on Lactase:

Lactose Operon Repressor Protein (Lac Repressor): Regulation of gene expression

The lac repressor is a protein that can bind loosely to virtually any segment of DNA. However, when it finds its target sequence on a DNA double helix, it changes the way it interacts with DNA, binds tightly, and turns off the expression of genes for metabolism of the sugar lactose.

Lac Repressor Binding to Target DNA
Format: Animation

Opens in new window

Advanced material. Four animations of increasing detail.

  • Animates the lac repressor protein bending DNA sharply when it binds to its target DNA sequence
  • Emphasizes the molecular means of binding to DNA at a target sequence of nucleotides (specific binding) vs. binding to any sequence of DNA (non-specific binding)
Windows: Internet Explorer OK

Background Information on Lac Repressor:

Lipid Bilayers: Cell Structure

Biological membranes serve as selective barriers that keep water, ions, and and other polar molecules from passing indiscriminately in and out of cells and cell compartments. Membranes are largely composed of double layers of phospholipids (lipid bilayers) studded with proteins and cholesterol. This tutorial explores the structure of cholesterol, phospholipids, a lipid bilayer, and a small protein that can form a channel allowing water and small ions to cross a membrane.

Lipid Bilayers
Format: Guided Tutorial

Author: Eric Martz and Angel Herráez

Opens in new window

  • Starts with cholesterol, an important component of cell membranes
  • Identifies all parts of a single phospholipid molecule
  • Adds phospholipids gradually to build a lipid bilayer
  • Explores polar and non-polar regions of phospholipids
  • Shows how gramicidin, a small protein, forms a channel for water and ions to traverse a membrane
Cannot be used with Internet Explorer

View a Channel Protein in a Lipid Bilayer in Protein Explorer

Opens in new window

  • To show membrane and channel without water, click on the "Hide/Show Water" button
  • To show water and channel without membrane, first show water with "Hide/Show Water" button, then click on "Explore More at Features" link, then scroll down and click the "Ligand" button
Windows: Internet Explorer OK

Background Information on Lipid Bilayers:

Myosin: A Molecular Motor - Movements of Cells and Muscles

Myosin is actually a family of proteins—they are molecular motors that move along filaments composed of the protein actin. The amazing thing is that this family mediates movement in some of the tiniest contexts- for example, one type of myosin is involved in amoeboid movement of single cells, yet also in the largest contexts that we know- myosin makes skeletal muscles contract in humans and all other animals. To provide the energy for its movement, myosin breaks down ATP to ADP + Pi (inorganic phosphate).

View Myosin in Protein Explorer

Opens in new window

  • View the motor domain of a molecule of myosin II, the type found in skeletal muscle
  • This myosin motor has ADP bound, leftover from the ATP that provided the energy for the myosin head "power stroke"
Windows: Internet Explorer OK

Background Information on Myosin:

The Nucleosome: Chromosomes

During cell division, the DNA must be compacted into chromosomes so that each daughter cell receives a complete copy. Even during interphase, most of the DNA is not actively used, and needs to be in a compact storage mode. The DNA in each cell is 1.8 meters long, and is compacted nearly 10,000-fold in order to fit in the nucleus. To accomplish this, the negatively charged DNA is wrapped around positively charged proteins called histones. Each "spool" of DNA wrapped around histones is called a nucleosome. The DNA for appropriate genes must be "unwrapped" in order for those genes to be expressed by transcription of mRNA. See also the guided tutorial, Exploring DNA.

View a Nucleosome in Protein Explorer

Opens in new window

  • See the DNA double helix making nearly two complete turns around the histone core of one nucleosome
Windows: Internet Explorer OK

Background Information on the Nucleosome:

Water: The Medium of Life's Chemistry

The nature of water molecules profoundly influences all of biology. For example, the polar character of water drives proteins to fold with their nonpolar amino acids at their core and their polar amino acids at the surface. Furthermore, hydrogen bonding between molecules, which is critical to DNA and protein structures, can be seen in its most elemental form in the behavior of water molecules.

Water - Simulation of 10 Water Molecules Forming a Drop
Format: Animations

Opens in new window

  • Opening page explains methods used to simulate
  • Opening page shows animated gif movie (does not require Chime, but structure not rotatable)
Cannot be used with Internet Explorer

Background Information on Water:


 

More molecules and resources


DNA Structure Answers are available to teaching faculty who inquire with an email to emartz@microbio.umass.edu providing evidence of their faculty positions, such as by reference to a school or college Web site listing faculty. Please specify "Answers for DNA Structure" in your email.