I. GENERAL INFORMATION
This course web page will be used for study aids (animations, web sites, etc), announcements and for posting of exam keys (see very end of this web page for exam keys).
REMEMBER TO BUY THE SOLUTIONS MANUAL FOR "THE WORLD OF THE CELL"QUESTIONS FROM END OF CHAPTERS (with answers in the SOL'N MANUAL) WILL BE ON EXAMS!
Click here to view the pdf file on derivation of the Gibb's Free Energy equation for chemical reactions (we will also discuss the ΔG for movement into the cell later). This equation for work done by or for a chemical reaction is derived in the text, but here is help understanding the equation (just reading through this will help you use of the equation on exams- know the assumptions).
I have posted a past exam that you can use for studying:
CLICK HERE (note a little bit of material
has changed since this exam so some questions are no longer pertinent).
Click here to view student question from an old exam
and
Click here to view other student questions
To be announced...
COURSE DETAILS
There is a copy of the Course Packet on the CD for the course. Note that I cannot include newspaper articles or book illustrations in this copy-- you need to purchase the hardcopy of the course packet from the bookstore ..
SAMPLE CALCULATION OF YOUR FINAL GRADE:
EXAM 1 -- 57 PTS OUT OF 100- drop this lowest grade for the exams
EXAM 2 -- 78 PTS OUT OF 100
EXAM 3 -- 79 PTS OUT OF 100
FINAL -- 77 PTS OUT OF 100 (cannot be dropped)
DROP LOWEST OF EXAMS 1-3 (DROP 57)
ADD IN EXTRA CREDIT homework questions (MAX OF about 10-13 PTS)- say you earned
10 pts.
TOTAL: 78+79+77 + 10 pts extra credit= 244 OUT OF 300 POSSIBLE; THIS IS 81% OR A "B"---You can screw
up one lecture exam and still recover and end up with a good grade! NOTE HOW THE
extra credit homework helped raise the grade from C to a B. However,
many students simply don't hand in the extra credit homework. Some do not show up for an exam (earning a "zero" for the exam)
as the student plans on dropping this exam score. However, then the student
cannot show up for another exam or does poorly on a
second exam- the student then ends up with a poor grade because you can only
drop one exam grade.
To view the many animations or videos on cell biology topics that we discuss in lecture, you may have to have a plug in (like "Shockwave") for your internet browser (either Netscape or Internet Explorer). To obtain plug ins, CLICK HERE.
Remember that you can access this site from any University of Colorado-Denver computer lab, from work or home.
The University of Colorado Health Sciences Center has a great series of animations that cover: protein, DNA, transcription, translation, cell cycle, cell signaling, and cancer genes. There is also some clinical info (emergency room, etc.). CLICK HERE.
The textbook Cells has a large number of great illustrations...see http://bioscience.jbpub.com/cells/Default.aspx and ESPECIALLY ALL THE ANIMATIONS OF CELL BIO PRINCIPLES (GREAT TO STUDY FOR EXAMS); SEE http://bioscience.jbpub.com/cells/Media.aspx
Our textbook web site has animations and other info(click here).
Here is a web site that covers many aspects of cells: www.cellsalive.com (click here)
Here is Medical School web site for cell biology:
cellbio.utmb.edu/cellbio
VERY IMPORTANT: TO INCREASE YOUR UNDERSTANDING (EVERY REVIEW HELPS!!), TO GET A BETTER GRADE, GO THROUGH THESE ANIMATIONS OVER LECTURE TOPICS.
(1) Chapter 1 and Chapter 7 of the text; Electron microscopy technique to study
membranes: click here for animation of Freeze Fracture.
Arthur Lam, a UCD student in Multimedia Studies (lam_arthur@yahoo.com) animated this process.Click here for Shockwave Plug in Required to View the Animation.
(2) Chapter 2: H20: Since the chemical properties of water are important for cell processes, take a look at this site for an interactive learning exercise on water.
(3)Chapters 2-3:
For a copy of the article on GLUCOSE AND AGING,
CLICK HERE (it is in pdf format, so you
need the pdf reader). Remember that glucose is often high in the blood
stream of a diabetic, so glucose often attaches to hemoglobin...physicians use
the amount of sugar bound hemoglobin to see whether glucose levels have been
maintained at a proper, low level. For more information about how sugar
bound hemoglobin is used with diabetics;
click here.
(4)Protein Structure Sites: Protein Folding (Chapt. 3) and Enzymes (Chapt. 6):
How a protein folds in 3D space is important for protein function. If a
protein does not fold properly, it can lead to disease such as Alzheimer's
disease, cystic fibrosis, Mad Cow disease, certain form of emphysema, even many
cancers: take a look at
www.faseb.org/opar/protfold/protein.htm.
See article on Protein Structure and Cancer: click here
Also see this web page for info on protein folding and human disease: http://www.nature.com/horizon/proteinfolding/background.html
We put all our info on weak bonding, levels of protein structure, R group structure, functional groups, and our understanding of rickety protein structure into HOW AN ENZYME WORKS. We will study the enzyme carboxypeptidase A (see our text book Figures 6.2 and 6.3). Here is a Flash animation showing the first steps of the enzyme mechanism of carbarboxypeptidase A: CLICK HERE. It shows the overall reaction and the initial binding of the substrate to the protein and requires the "Flash player/plug in" for your internet browser. To download free player, click here.
Next, let's view the active site of "carb A" and see the motion of the R groups as they bind to the substrate. We can use programs called KINEMAGE or MAGE programs (see below), to animate, view and rotate (with your mouse) the active site of carb A in addition to alpha helices, beta pleated sheets, and tertiary and quaternary level protein structure. It is a good way to review for the exam.
Click here to go to a site that animates the movement of amino acids in carboxypeptidase A (the enzyme whose mechanism we study in class) as the substrate binds to the active site. No program is required. At this web site, click on the "King" box located below the image of the protein (or "JavaMage" box to the upper right of the image). Make sure that java is enabled on your browser (see site for info). Then click on the "animate" button (lower right) to see the 3 amino acids that move as the substrate binds (this is the induced fit model) and use your mouse to rotate the image. Identify Try 248 (and other amino acids) by clicking on the check mark for the amino acid (this will erase the tyr R group from the image). GlyTry is in red and it represents a very short substrate. Find the zinc atom (what role does it play?).
To get a larger view of the active site of carb A, first, download the program MAGE (also called Kinemage; short for "kinetic image") by clicking click here. then you can dowload these files for the beta pleated sheet water pore called porin (right click here and "save target as" to get the porin kin file) or to get the barbel shaped calmodulin file (see how it folds in half upon binding a protein; use the animate button) (click here for calmodulin file, use right click procedure above)
Once you have downloaded the program MAGE/KINEMAGE and expanded the files (you will get an icon), you need to downloaded another file to that contains text and the info for the active site of carboxypeptidase A. To get the carboxypeptidase file, download the 100 kB file (right click here and "save target as" to put the carboxypeptidase "kin" file on your hard drive), you then need to start the MAGE/KINEMAGE program and click on the upper right bar and "OPEN." Then open the 100 kB file on carb A: in addition to explanatory text, you will see the active site of carb A and you can study and rotate the R groups and substrate. To get a complete list of all kinemage files that you can download, click here.
Remember: take a look at the UCHSC web site noted above (CLICK HERE)
(5) MEMBRANE TRANSPORT CHAPTERS: MEMBRANE POTENTIAL (CH. 7, 8 13)
Membrane fluidity and composition are discussed in this University of California -San Francisco Medical School web site (try it! it is interactive). CLICK HERE to go to the med school site on membrane structure.
Membrane Potential is tough to understand!! Here are some animations that should help--they
illustrate how the membrane potential develops (typically, reaching -60 to -80 mV).
In this first animation, note that as the K channel allows K to move down its concentration gradient, a membrane potential is generated (see + side where positive K moves to). Then the developing membrane potential fights further K movement. At the end of the animation, K is in equilibrium (chemical and electrical forces are equal and opposite). Click here for the animated gif (100 KB).
A second animation (by Matt Flagg, Dr. Robert Butera of Georgia Institute of
Technology; http://www.neuro.gatech.edu/~rbutera/online.html) shows essentially the same info but they note that the Nernst equation describes the equilibrium situation. Click here for the Quicktime movie (2 MB). Later in this movie, they show the membrane potential on the left side. At membrane potentials less than Ena, the chemical gradient is stronger than the electrical gradient and K ions are pushed through the K channel into the upper area. At Ena, the two forces are in equilibrium (no ions move), and at higher values, the electrical force is greater and pushes ions "downward."
Here is a link to an interactive web site that actually calculates the membrane potential values (with the Nernst equation) while you put in ion concentrations!! It also calculates
ΔGinward.Click here to link to the site on the Nernst equation (you have to have java).
LIGAND GATED ION CHANNEL: This animation (CLICK HERE) shows how the nicotinic acetylcholine receptor binds acetycholine. Note that the nerve releases acetylcholine which then moves over and binds to its receptor on the muscle cell. Once the receptor is bound, the alpha helices of the receptor move to open the channel located within the receptor. Sodium ions then flow across the membrane into the cell (note that every so often, a potassium ion leaves the cell through the channel). The large number of positive sodium ions that enter the cell leads to a depolarization of the membrane potential (the positive sodium ions negate the net negative charge found on the inside of the plasma membrane). Due to the opening of the sodium channel, sodium becomes more permeant than any other ion and the membrane potential then goes from -60 mV toward the equilibrium potential for sodium (a positive number). Without acetylcholine, K is the most permeable ion and the membrane potential is around the equilibrium potential for K (about -60 mV). See page 247-249 and Fig. 9-25 of Fifth Edition of World of the Cell by Becker, Kleinsmith and Hardin. “The structures are from acetylcholine binding protein in the extracellular domain (α subunit, aqua; ε subunit, gold) and represent the M4 (straight) and M2 (kinked) segments of the acetylcholine receptor α subunit (left) and δ subunit (right) in the membrane domain (red). The moving elements switch from closed (gray) to open (yellow)… The orientation is such that the extracellular side is above the membrane and the intracellular side is below the membrane.” From: A. Auerbach, Life at the top: The transition state of AChR gating. Sci. STKE 2003, re11 (2003). This is adapted by Cameron Slayden from an animation by R. Foxenberg.
ONLY If you are mathematically inclined; take a look at this article on the mathematics of transport. This is optional; I will not test you on this article. Click here to view (and download) the membrane transport article by A. Koch. Do not read all the detail of this article but use it for increased understanding of the Nernst equation. The Goldman equation is discussed in the textbook and this article, but we will not emphasize it. You will need the FREE "pdf" reader which can be downloaded here
Remember: take a look at the UCHSC web site noted above-look under "PROTEINS'
ON LEFT SIDE OF WEB PAGE; then click on transport proteins:(CLICK HERE)
For a discussion of peroxisomes , lipids and the smooth ER: see Dr. Stith's write up on adrenoleukodystrophy (ALD) and the movie "Lorenzo's Oil" (click here).
Here is a good site on lysosomes
Mitochondrial function (Ch. 14):Click here to view the Quicktime animation on chemiosmosis (VERY large file; 14 MB).
Why learn about mitochondria? Bad mitochondrial function may lead to diabetes; click here for the link to the article
Due to the 1974 Nobel Prize on cell organelles, the Nobel Prize web site has a game to play on cell organelles, the ultracentrifuge (used to separate organelles for study), and the TEM (used to observe cell parts); click here to play the game.
This new web site (Virtual Cell Animation Collection) has one of the best
animations of electron transport and another on ATP synthase (the flow of
electrons turns the synthase like a turbine to make ATP-- cool!) --
CLICK HERE
Here are other web sites with a great animation of the electron transport chain and chemiosmosis. Click here
and
HERE and HERE.
Although it is set up more for researchers than students, the journal Nature has a web site devoted to Cell Signaling (or signal transduction): www.signaling-gateway.org
Take a look at a very good animation of how the heterotrimeric G protein is
regulated by GTP and subunit disassociation. Note the protein structure of the
receptor involved.
click here. Also, there is another site devoted to G proteins; take a
look:
Click here.
Click here to view the Quicktime animation on G proteins and the cAMP system (VERY large file; 14 MB).
Click here to view the Quicktime animation on receptor tyrosine kinases (VERY large file; 14 MB).
See article on Protein Structure of Receptor Tyrosine Kinases and Cancer:
click here
Click here to view animation on how receptor tyrosine kinases activate phospholipase C to release calcium (VERY large file; 14 MB).
Here is another animation on the IP 3 path: click here.
Dr. Donald Slish (SUNY Plattsburgh) has animated the receptor tyrosine kinase-map kinase path;
click here to go to the web site.
Here is another web site that has an animation of the receptor tyrosine
kinase/map kinase path. This site also has the NOTCH pathway (which I discuss in Devel Biol or Cell
Signaling but typically not in Cell Biology 3611).
Click here to go the web site of "Biocreations" --a company that makes science animations.
There is a site on receptor tyrosine kinases that is sponsored by a drug company. This drug company site centers in on the epidermal growth factor (EGF) receptor and they note that drugs that inhibit this receptor kinase will stop cancer. For example, AstraZeneca has a drug called Iressa, Novartis has Gleevec and Genentech has Herceptin. Click here.
Mutations in Fibroblast Growth Factor (FGF) receptor tyrosine kinases and the map kinase path have been associated with dwarfism,
Pfeiffer syndrome (a malformation syndrome characterized by limb defects and by
the premature fusion of the cranial sutures -craniosynostosis- that results in
abnormal skull and facial shape), Crouzon Syndrome (have craniosynostosis, but
have normal limbs), Jackson-Weiss syndrome (a syndrome of craniofacial
malformation and foot abnormalities: enlarged great toes and the coalescence of
the tarsals and metatarsals), and Apert Syndrome (a set of malformations
involving craniosynostosis and severe syndactyly or fusion of digits)(Click here to view
the site).
View the animation on APOPTOSIS (another really big file at 6 mb): CLICK HERE.
Click here for a web site from Journal of Cell Science; this site has review articles on many cell signaling areas.
Remember: take a look at the UCHSC web site noted above--LOOK UNDER MODULES
ON LEFT; CELL SIGNALING:
(CLICK HERE)
(9) EXTRACELLULAR MATRIX,
CELL JUNCTIONS (ch. 17):
To view a site on collagen and human disease,
click here.
For biochemistry of cadherins,click
here. NOTE HOW WHEN YOU BLOCK CADHERIN, CELLS DO NOT ADHERE (AND THE EMBRYO
FALLS APART INTO A PILE OF CELLS)
For a site on connexins and human diseases,click
here. NOTE THAT MUTATIONS IN THE CONNEXIN GENE (PROTEIN MAKES UP GAP
JUNCTIONS) CAN CAUSE DEAFNESS, HEART AND NERVE PROBLEMS.
(10) CYTOSKELETON: microfilaments and microtubules (Ch. 15-16)
To view an animation of a vesicle moving along a microtubule (using dynein as the motor molecule), click here.
Here is an animation of treadmilling (in this case, for a microfilament). Click here.
THE MOVEMENT OF CILIA OR FLAGELLA: The molecular mechanism for the flexing is complex. CLICK HERE to view A MUST SEE, BEST animation of what causes a cilium or flagellum to move back and forth (from Northland Community and Technical College). Click here to view another animation of the bending movement. TEST YOURSELF: when the cilium/flagellum flexes downward, which outer doublets are trying to move toward you out of the plane of your computer monitor screen (i.e., those outer doublets at the top or the bottom of the cilium/flagellum)?
CELL CRAWLING: Cell Crawling begins with extension of a thin layer of cytoplasm; take a look at this really cool cell (note movement at the leading edge of this cell- this occurs just before the cell uses the clutch model to move forward); CLICK HERE.
To view the video of a leukocyte chasing a bacterium; click on this link: neutrophil.mov. Note the side of the cell that is moving forward (the leading edge) is very flat; this is where the lamellipodium (flat part) and filopodia (spikes) are located. The lamellipodium and filopodia at the leading edge is where the "clutch model" (see below) takes place--this is where the cell EXTENDS (and then crawls).
I have developed a new animation showing cell crawling and the CLUTCH MODEL; it is based on our
text books illustration
FIG. 16-27. VIEW THIS A COUPLE OF TIMES: Click here to
view the Flash animation (you will need the shockwave or flash plug in for
Internet Explorer).
Due to the 2001 Nobel prize in research on the cell cycle, the Nobel Prize web site has a game that reviews the cell cycle; click here.
To view a brief animation on the phases of mitosis, click here.
Here is another web site that has a great brief animation of mitosis. It is from "The Biology Project" and has other good animations on other topics. Click here.
Dr. Donald Slish (SUNY Plattsburgh) has developed a super animation of anpahase A and B, complete with molecular motors! Click here to go to the web site.
Dr. Slish also has a great animation of how MPF is activated (showing cyclin increasing during cell cycle); click here.
Take a look at this web site that animates the rise and fall of cyclin during the cell cycle. Select "Cyclin B" for M phase (or "mitosis"). This animation is located near the bottom of the web page and is from "Biocreations;"
click here to go to this web site to view this animation.
Our textbook web site has a lot of animations that we will use in lecture - animations show mitosis, cytokinesis, there are even movies on EACH of the phases of mitosis, etc.). Let me know if you have trouble using our text web site.
Remember: take a look at the UCHSC web site noted above--ON THE LEFT, UNDER
"MODULES," CLICK ON "CELL CYCLE," AND SEE THE CYCLIN, CDKS AND
P53! NOTE THAT P53 NOT ONLY LEADS TO A STOP IN THE CELL CYCLE, BUT THEN INDUCES
APOPTOSIS (CELL DEATH FROM CHAPTER 10).(CLICK HERE)
