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!
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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 |
- 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
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Background information on Antibodies:
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Carbohydrates
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. |
Carbohydrates
Format: Biomodel
en español |
- the monosaccharides glucose & fructose
- the disaccharide sucrose
- several polysaccharides, such as cellulose and glycogen
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Background Information on Carbohydrates:
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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.
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Background Information on Collagen:
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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"
|
Exploring 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.
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Background information on DNA:
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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
|
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:
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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.
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Background information on HIV Protease:
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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:
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Lipids
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. |
Lipids
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:
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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
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
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. |
Vitamins
Format: Biomodel
en español
|
- Vitamins A and B2 are shown
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Background Information on Vitamins:
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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
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:
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