Biomolecule Library
Chemistry Department - CSB/SJU
Welcome to the Biomolecule Library of the Chemistry Department.
The library contains interactive graphical images of interesting biological
molecules. The x, y, and z coordinates of many of these molecules come from the
Protein Data Bank of the Brookhaven National Lab. A list of interesting biomolecules
are given below. Click on any and you will be taken to a new web page with three frames:
This web site consists of a number of frames:
The top frame - molecule.html - displays the
molecule. You can use the mouse buttons to manipulate the molecules, using the
commands shown below:
Mouse Commands
When you click on any of the molecules listed below, a black window
containing the molecule will appear in your browser. You should be able to see and
rotate your molecule by placing the mouse cursor in the black window and using the
commands given below:
- Hold down the left mouse button and move the mouse around to rotate
the molecule
- Hold down both the shift key and the left mouse button, then move the
mouse up to zoom out or down to zoom = in
- Hold down both the control button and the right mouse button, then
move the mouse to translate the molecule on the xy axes
In addition, you can change the rendering of the molecule by moving
the mouse cursor within the area of the molecule. Click and hold the right mouse
button, and a new menu will appear that will allow additional manipulation of the
molecule. Experiment with these commands. More detail instructions are given at the
end of this page.
The right frame - commands.html - gives a list of
commands which will alter the display of the structure and properties of the molecule.
Click on the different command buttons and watch the changes!
The bottom frame - page1.html - displays the text
associated with each molecule displayed in the top frame. The text in this frame
will describe the structure and function of the displayed molecule, and prompt you to
change the view of the molecule by selecting different commands in the right frame.
BIOMOLECULE LIBRARY
Select from the list below to visualize a variety of biomolecules!
PROTEINS
| structure |
students |
|
alpha
helix |
an alphja helix from an
antifreeze protein |
|
twisted
beta sheet |
a twisted beta sheet from the
arabinose binding protein |
|
beta
barrel |
a beta barrel from triose
phosphate isomerase |
| Supersecondary Structure:
helix-loop-helix |
EF Hand: Ca binding motiff
of calmodulin |
| Supersecondary Structure:
helix-loop-helix |
helix-turn-helix binding motiff from the
lambd repressor |
| Supersecondary Structure:
beta-hairpin |
from bovine pancreatic trypsin
inhibitor |
| Supersecondary Structure:
beta-helix-beta |
from triose phosphate isomerase |
| alpha helical protein:
cytochrome B562; |
Cyto b562 with heme in oxidized
state |
| alpha helical protein:
met-myoglobin; |
Met-Mb contains a heme with Fe3+ |
| beta protein:
superoxide dismutase; |
SOD with 8 antiparallel beta
strands forming a barrel |
| beta protein: retinol
binding protein; |
RBP with beta strands forming an
up-down barrel |
| alpha/beta:
triose phosphate isomerase |
TPI has 8 parallel beta strands
forming a barrel with strands connected by alpha helices |
| alpha/beta:
hexokinase |
HK has open twisted beta sheet
structure |
STUDENT PROJECTS - CH331 - SPRING 1999
| structure |
students |
| Green Fluorescent Protein |
by Annelise and Jeremy - A protein
that makes it's own fluorophore |
| Trp Repressor |
by Laura and Jessie - A protein-DNA
complex involved in regulation of Trp synthesis. |
| HIV-1 NEF-SH3/SRC |
by Shawn Alderman, Matt Rose, and
Kim Switlick - An HIV proteins meets a domain of a cell protein involved in signal
transduction |
| Acetylcholinesterase |
by Steve Aldrich, Grant Seeger, and
Jason Bartos - The enzyme that degrades acetylcholine at synaptic junctions |
| BAPP-Trypsin |
by Patty Hunt, Lisa Jungbauer, and
Laura Melohn - A protein involved in Alzheimers interacts with a well known protease |
| Lysozyme |
by Kathy Thorson and John Geissler -
A glycosidase with newly discovered properties |
| Barnase-Barstar |
by Josh Casey, liz Nesset, Marne
O'Neill |
| Glutamine Synthase |
by Matt Nugent and Melissa Illies - |
| Glu-tRNA Sythase |
by Dan Ferraro, Ryan Fey, and Deb
Wentz |
| Alcohol Dehydrogenase |
by Ryan Olson, Matt Tinguely, and
Martin Klinkhammer |
| 434 Repressor |
by Timothy Providence, Leonard
Arthur and Francis Insaidoo |
| Hemoglobin Dimer |
by Brian Zachau and Kaarin Fossum |
STUDENT PROJECTS - CH331 - SPRING 2000
STUDENT PROJECTS - CH331 - SPRING 2001
STUDENT PROJECTS - CH331 - SPRING
2002
STUDENT PROJECTS - BCHEM 321 - FALL 2002
STUDENT PROJECTS - BCHEM 321 - FALL 2003
STUDENT PROJECTS - BCHEM 321 - 2005
GREAT SITES USING CHIME
