Stev 2055 PC lab Introduction: Although these exercises are being introduced in both PC
and Mac computer labs, the exercises are not platform
specific. You may choose to use either Netscape or Explorer
as the browser. This introduction is geared [or tries to
be] both to those with little experience using the
Internet and web browsers, and to those with a significant
amount of experience. If instructions seem to move along too fast, ask for help
from other students and from me. If instructions seem too
detailed, and you just want to get on with it, please
do. If using the IMac labs, you will need a 100 MB zip disk
to save your work. Floppy drives are being fazed out in
favor of zip drives. You also may print your work to the
printer in the lab you are working. It is strongly suggested that you keep a log of
your sessions on-line. Although you may bookmark sites while
using a lab computer, the bookmarks are removed daily. Even
if you are using your own computer, try using a log anyway.
You can add comments, store specific database sources, and
cut/paste whole pages of information for future use. A
current version of Word is quite useful for a log, because
URLs [Web addresses] can be turned into active link
sites. In other words, you can carry your bookmarks with
you, without having to retype them. You can save your log to
disk or e-mail it to yourself. [For more on logs, go to
"Computing", then "Keeping
a log".] There are summary questions at the end of each
part. Read them through before you start browsing. You can
answer them as you go, or answer them after browsing the
following sites. Points = 10. Due 2/19. The last thing to do is to begin to explore the
Interactive site on WebCT. A portion of the
discussion points will awarded for on-line
participation. 1. Getting to the edge of the pool: Log on
and open Netscape. The following web sites are to get you
started. Briefly explore each one, noting what they have to
offer locally and what links to other sites are available.
When using you own computer or one to which you have regular
access, I strongly recommend that you bookmark the sites you
like. [Bookmarks are regularly removed from school
computers, but they are still handy during a single session,
so give them a try. For now, click on "Big Picture Book of Viruses": There
are several ways to search for virus structures here. a. Try "virus families by genome type" and look
for positive sense RNA viruses. Check out the
Picornaviruses. b. Try "list of individual viruses" to search
by name. Look for Tobamoviruses. [This should be quite helpful as we go through the
different groups of viruses.] 2. Testing the water: For more on virus modeling,
go to Bock Labs. a. Click on "multimedia library"; then on
"computer visualization". Try "analgraphic stereo" &
use the 3D glasses for a cool viewing experience. b. Go back to "computer visualization" page and
click on "topographical maps" to learn how the isometric
and 3D images are generated from the topology of a single
facet or face of the particle surface. c. Go back to "multimedia library" and click on
"electron micrograph". Explore to see what they have
available. Later, try other subsites of the Bock Labs site to
become familiar with what they have to offer. 3. Going for a quick swim on your own: Some sites
may initially appear simple, but have rich collections of
other sites. They are quite useful. A single bookmark can
lead to many hallways and many doors. You'll probably want
to revisit these link sites a few times in order to get a
real feel of what all they have to offer. Make note in your
log of useful destination sites you like. These can be
shared. [Also, try going to "Links" for access to these
and other useful sites.] A useful strategy to try at this point is using
multiple windows. Go to file, and open a new browser
window. Copy/paste the URL to the new window. Now you can
explore some links in one, while you have one as an easy
home-base. You can also have one loading while you
explore the contents of another. With time, you'll find
lots of uses for multiple windows. Try to limit your answers to one typed page [12 pt
font] for this part. [You need not retype the
questions as part of your responses.] 1. [Big Picture Book] What key differences
can you identify between Picornaviruses and Tobamoviruses?
Compare the surface structure of a polio virus and a
rhinovirus. What similarities and differences can you
find? 2. Look closely at one of the isometric viruses.
What different types of repeating patterns can you detect?
What geometries do you see? 3. [Bock Labs] What additional information
did you get from the triangular maps? How does it add to
your understanding of viral structure? 4. Ultimately, what influences the "texture" of
these particles? 5. Give the URLs of two sites you liked which you
found by exploring the link sites given in #3 above. Briefly
state why you thought they were interesting or how you think
they may be of interest to others in class. [I'll
summarize these and post them on the "Links"
page.] Time to learn how to explore individual proteins, alone
and sometimes in association with other molecules. If you
have never played with molecular models, or you want to
start with some interactive instruction, begin at 1
below. If you are familiar with modeling and you want to see
some viral coat proteins, skip to 2 below. 1. As a warm-up activity to molecular
modeling, go to one of the sites below. For either the Kuby
text site or the Lodish text site below, click on "molecular
visualizations", and select a chapter. As you go through the
guided explanation, you'll see different types of displays
of the proteins. This will give you an idea of what you can
do during this exercise, and after, with proteins of your
choice. 2. Go to NCBI: a. Try 1QJY [You can type this
accession number into the search line.] It's
human rhinovirus 16 coat protein associated with an
anti-viral compound. Click on the accession number to
open the summary page. Explore this page to see what
information is available. To view the protein in
Chime/RasMol, go to the bottom of the summary page,
select "RasMol", then click on "view". Once the protein model comes up, click on the MDL
prompt in the bottom right corner of the screen to access
the command menu. If you are familiar with Chime, play.
If you want some help getting started, do the
following: 2) Drag down to "display" and click on
"ribbon". Next, try some of the other display
types. 3) Place the arrow on the protein, click and
hold down the mouse. As you move the mouse, you can
move the protein. As you move the protein around, do
you see anything that you couldn't see before? 4) Try marking individual amino acids. For
example, select cysteine to locate any disulfide bond
sites. Or try to mark amino acids which you would
predict as being found on hairpin loops. [See
"Shorthand symbols
for amino acids" for abbreviations. Chemical
characteristics of the amino acids are listed below
the symbol table. See a biochem or molecular biology
reference for amino acid structures. Or go to
"www.whfreeman.com/lodish"
for an on-line reference.] b. Return to the report page of 1QJY. Click on
1QJY to go to another data source page. Explore what is
available here. Click on "other sources" to explore
further. c. Open a new window and go to PDBsum
[by copy/pasting the URL below] or click
below to go directly there: Here you can view primary, secondary, and simple
tertiary structures of each chain of a protein. The
motifs are included in the graphical views, as well as
being summarized. d. Return to the NCBI/ Structure site. Try a
new search with either 1RMV [ribgrass mosaic
virus] or 2TMV [intact tobacco mosaic
virus]. 3. Go back to NCBI/Structure. Type in a
virus name, such as polio or another virus of interest; or a
family name, such as Leviviridae or Tobamoviridae. Select a
protein of interest and explore it as you did the others
above. [This will give you a small taste of finding
proteins of interest and exploring independently. The next
assignment will focus in part on search strategies. Try to limit your answer to one typed page [12 pt
font] for this part. [You need not retype the
questions as part of your responses.] Structure determines function. Now that you have
gone from BIG [whole virus images] to
small [single peptide chain models], write a
summary of viral capsid structure as determined by amino
acid sequences of the coat proteins involved. Keeping
molecular interactions in mind, consider and address the
following: Optional: Look at some general browser search engines, such as
Dogpile, Yahoo, and Google [among many
others]. When looking for something specific, sometimes
you don't quite know where to start; or you thought you did,
but came up empty. Sometimes, you just want to find out what
is available in a general category. The search engines can
be very useful, if you know how to use them efficiently.
Different search engines will give different results. Click on "Interactive" below to enter the WebCT portion
of this site. Log on with your ID and password. Go to
"Fora". Select either the topic "Computer problems" or "Cool
new sites" and post a comment or respond to another comment
already posted. For more on using WebCT, go to "Computing".
Take note of format when entering text. Use double returns
between paragraphs, since there is no indenting. Also check
spelling and grammar carefully. You can compose off-line in
a word processing program, then copy/paste to the text box.
This may be advisable if composing a lengthy piece.
a
Computer Exercise 1: Introduction to Virology &
Molecular Modeling
Part 1: Cool Web Sites
http://www.bocklabs.wisc.edu/
How do the maps help in understanding viral
structure? What is the basis of the surface
topography?
Part 2: Molecular modeling
http://www.clunet.edu/BioDev/omm/gallery.htm
[Online Macromolecular Museum]
http://www.whfreeman.com/kuby
http://www.whfreeman.com/lodishhttp://www.ncbi.nlm.nih.gov/Structure/
1)Drag down to "color" and
highlight "groups". How many different groups are
there in your protein?
http://www.biochem.ucl.ac.uk/bsm/pdbsum
As you explore this protein, note the
differences you see when compared to the rhinovirus
coat protein.
For those of you not used to general searching on the
web, you should try the following as a way of becoming
familiar and comfortable in digging up information and
resources of interest.
Introduction to Interactive
Virology
Updated 1/5/02 by thatcher@sonoma.edu