BioMolecular Explorer 3D: Explore the Molecules

Software for interactive molecular exploration in High School Biology courses.

Quick Links:

DNA (New resource added!)        Proteins

Carbohydrates      Lipids      Vitamins

Explore the Molecules

This table draws together the 3d resources with background information for your convenience. Each molecule is descibed briefly in a summary, which is followed by links to the 3d displays, bullet points of features of each display, and finally links to background information for lesson planning purposes.

To rotate a molecule in the 3d display, click and drag on it with the mouse. To zoom in or out, use your scroll wheel, or SHIFT-drag with the mouse. To identify an atom, let the mouse cursor rest on top of it for a few seconds. Use buttons and controls next to or below the molecule to change the display. To access more functions, click on the Jmol logo in the corner of the structure area for a pop-up menu.

All 3d resources open in a new window. Guided Tutorials and Animations are authored by Eric Martz unless otherwise noted. All Biomodel resources authored by Angel Herráez unless otherwise noted. We hope you enjoy exploring!

PLEASE tell us if you use BME3D for teaching!

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.

Format: Guided Tutorial

Opens in new window

  • Includes introductions to molecular displays for amino acids, small peptides, and disulfide bonds
  • Shows the domain structure of IgG, and details of the interactions with an antigen (lysozyme), and more.
Note: Includes some very advanced material on antibodies

View an Antibody
Format: FirstGlance in Jmol

  • 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

View the "Business End" of an Antibody
Format: FirstGlance in Jmol

  • 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

Background information on Antibodies:


Composed entirely of carbon, hydrogen, and oxygen, carbohydrates are literally hydrated carbon, as seen by their generalized formula, Cx(H2O)y. Carbohyrates range from simple sugars to complex assemblies of sugars, and have diverse functions. Their most famous functions are those of energy storage and providing cellular structure.

Format: Biomodel

en español

  • the monosaccharides glucose & fructose
  • the disaccharide sucrose
  • several polysaccharides, such as cellulose and glycogen

Background Information on Carbohydrates:

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
Format: FirstGlance in Jmol

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

Background Information on Collagen:

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.

DNA Structure
Format: Guided Tutorial

en español

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
  • For more on teaching about DNA, see "More DNA Resources"
newExploring DNA
Format: Guided Tutorial
A Guided Tour
  • Descriptive text forms the narrative for a cool tour of DNA
  • Topics: different ways of displaying DNA, the significance of DNA structure, and the flexibility of the DNA double helix
  • Includes a surface rendering of DNA (see chapter 1) and several views of a nucleosome (chapter 3)

View DNA
Format: FirstGlance in Jmol

  • Displays a DNA molecule that is 22 base pairs long.

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.

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

View Hemoglobin
Format: FirstGlance in Jmol

  • Displays a molecule of human hemoglobin
  • This molecule of hemoglobin is fully oxygenated (oxygen is bound to all four hemes)

View Hemoglobin's Interaction with Heme
Format: FirstGlance in Jmol

  • Isolates one of the four subunits of hemoglobin to enhance the view of heme, iron, and oxygen
  • To display the heme binding pocket, click FirstGlance in Jmol's "Contacts" link. The choose the "Residues/Groups" option, click on heme, and click "Show atoms contacting target".

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
Format: FirstGlance in Jmol

  • HIV Protease with the inhibitor ritonavir bound in the active site.

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
Format: FirstGlance in Jmol

  • 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

View Lactase's Interaction with Lactose
Format: FirstGlance in Jmol

  • Isolates one of the four subunits of lactase to enhance the view of lactose in the active site

Background Information on Lactase:


Lipids are the mainstays of biological membranes and efficient energy storage. Their hydrophobic nature lends itself to the creation of flexible, semi-permeable dividers of separate cells and subcellular compartments. The breakdown of fats yields more than twice as much energy per gram than that obtained from carbohydrates or protein.

Format: Biomodel

en español

  • Fatty acids
  • Triacylglycerols
  • Phospholipids
  • Steroids
  • A lipid bilayer (for an extensive tutorial on lipid bilayers, see below)

Background information on lipids :

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.

View a Channel Protein in a Thin Slice of Lipid Bilayer
Format: Guided Tutorial

Author: Eric Martz

  • Shows the gramicidin channel protein embedded in a lipid bilayer membrane
  • Shows water passing through the ion channel
  • Illustrates how water is excluded from the lipid bilayer
  • Brief tutorial good for a quick look
  • Molecular scenes can be enlarged to full screen with a popup button

Lipid Bilayers
Format: Guided Tutorial

Authors: Eric Martz & Angel Herráez

en español

  • 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

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
Format: FirstGlance in Jmol

  • 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"

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 DNA section.

View a Nucleosome
Format: FirstGlance in Jmol

  • See the DNA double helix making nearly two complete turns around the histone core of one nucleosome

Background Information on the Nucleosome:


Proteins are the most versatile of molecules, carrying out both most of the molecular functions and providing many of the molecular structures that support life. Twenty amino acids comprise the building blocks of these spectacular molecules. Each amino acid is endowed with a unique combination of size, shape, and chemical character. Amino acids are strung together in linear chains to form proteins, which then fold back on themselves to adopt a unique structure and function.

Protein Structure
Format: Biomodel

en español

  • Protein structure overview
  • Four levels of structure are explained, from the building blocks to complete, folded proteins
  • Lysozyme and hemoglobin are used as example proteins

What are Proteins?
Format: Animation

Author: Frieda Reichsman

  • Emphasizes the linear chain nature of proteins
  • Myoglobin, a DNA-binding protein, and porin (a pore-forming protein) are used as examples

Background Information on Proteins :


Vitamins act as helper molecules that enable proteins to do things they otherwise would not be able to do. For example, Vitamin A is critical for night vision. It attaches to proteins in the rod and cone cells of the eye and abosorbs a photon of light energy, which a protein alone simply cannot do. The energy absorbed by the protein-Vitamin A complex in turn causes a nerve impulse to travel to the brain, resulting in the visual perception of light. As you can imagine, vitamin deficiencies often result in serious diseases, because some important functions cannot be carried out without them.

Format: Biomodel

en español

  • Vitamins A and B2 are shown

Background Information on Vitamins:

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.

Format: Animation

Authors: Eric Martz & Angel Herráez

en español

  • Simulation of 10 water molecules forming a drop
  • Shows hydrogen bonds between water molecules

Background Information on Water:

More molecules and resources

DNA Structure Answers are available if you provide all of the following by email to

  1. State your faculty position, including, if available, evidence to verify this, such as using a school email address, or citing a school or college website listing faculty.
  2. Name of your school.
  3. City, State/Province, and Country.
  1. State that you are a student and give your grade level or age.
  2. Full name of your school.
  3. Name and EMAIL ADDRESS of your science teacher.
  4. City, State/Province, and Country.