Biology 137

Cell and Molecular Biology

http://www.uq.oz.au/nanoworld/virtual.html

Announcements

• NEW! Summer research opportunities across the country:
  • National Institutes of Health (NIH) summer programs(many, many sites - go here to start)
  • National Institute of Environmental Health Sciences summer research (NIEHS)
  • National Science Foundation research experiences for undergraduates (REUs)(many, many sites - go here to start)
  • Cold Spring Harbor Laboratories (Feb 1 application deadline)
  • Brookhaven National Laboratory summer program (here on the Island, April 1 deadline)
  • Summer opportunities at all National Laboratories operated by the Dept. of Energy (included a lot of genome and environmental research!)
  • Grice Marine Lab, Chareleson, S.C. Physiology, cell and molecular biology of marine organisms, March 3 applicaiton deadline)
• The review sheet for final is here (PDF, Word, Wordperfect). See you Thursday at 10:30 in our usual classroom!
• The Scientist is a free online magazine covering major topics in science, especially biology and medicine. Click here to read their new supplement on Cancer. This is a great review of the field if you're interested. This magazine is also a good place in general for career advice, job postings, keeping up with what's new, etc.
• Outlines for the cell signaling (Word, Wordperfect, PDF) and apoptosis / cancer (Word, Wordperfect, PDF) lectures available.
• Here's the discussion board contents, as of Sunday, November 9th (PDF, Word, Wordperfect).
• YOUR SECOND TEST HAS BEEN MOVED TO NOVEMBER 11TH! Read chapter 12 for Thursday's lecture.
• New York Biotech job fair, Wednesday, November 5th (click here for info)
• Here's the extra credit assignment on gene expression (PDF, Word, Wordperfect).
• The review sheet for Nov. 6th test is here (PDF, Word, Wordperfect).
• Here's the second quiz, in case you didn't get a hard copy (PDF, Wordperfect).
• Please read the Drug Pumps article by October 14th (in same password protected folder as your notes or on our Blackboard site).
• Here's the review sheet for your first test (held Thursday, October 2nd) (Wordperfect , Word, or PDF)
• Energetics problems can be found here (Wordperfect , Word, or PDF)
• The energetics lecture outline is here (Wordperfect , Word, or PDF), as is the extra handout (Wordperfect , Word, or PDF) that helps (I hope) explain fundamental energetics principles.
• Macromolecules assignment on the web: Check out this link from Lycoming College . You are STRONGLY encouraged to download the viewer and try the assignment yourself. Your textbook CD is a great help here, too.
• Please read the articles"Gut Check" and "Ocean Life" (in password protected folder here or on the Blackboard page) by end of next week (September 11th).
• A copy of the syllabus in Wordperfect , Word, or PDF is a click away.
• Don't have Adobe Acrobat reader on your computer? Click here to download this plug-in.

Hot Links for lecture

General information

• Home page for Cell and Molecular Biology (textbook web site)
• Cells Alive!
• The Virtual Cell Web Page
• The WWW Cell Biology Book
• MIT hypertextbook, Cell Biology Chapter
• Cell and Molecular Biology Online
• What the heck is a virus, which should explain why we are NOT studying them in cell biology.

Chapter / topic specific links: great for review!

Cell structure

• Organization of a cell
• Another review of cellular organization
• Introduction to the Archaea from UC Berkeley
• Virtual cell: an interactive site where you can zoom in on a plant cell and see its structures. The EM photos are fantastic

Biomolecules

• Chemistry Review: You know if you need it!
• Chemistry in the Cell parts I and II. Again, this is good review material if you've forgotten your basic chemistry.
• Image library of biological macromolecules
• A collection of links to review all sorts of basic structures

Energy basics

• ATP and biological energy
• A bioenergetics lecture from RPI: good review of free energy concepts
• Another review from a Mathews and Van Holde's biochemistry textbook
• A collection of links, some of which review basic energy conversions in the cell

Proteins

• Amino acids and peptide bonds
• Conversion of NADP+ to NADPH
• A detailed introduction to coenzymes and the vitamins from which they are derived.
• Enzyme introduction. Click on subtopics for detailed review information
• How enzymes work
• A graphic-intense introduction to protein structure. Warning: requires the Chime plug-in, which allows you to manipulate molecules in 3-D.
• Prions(Proteinaceous infectious particles) Altered conformation is associated with Mad-Cow disease, Kuru, and Creutzfieldt-Jakob Disease.
  • About.com's brief introdction to the topic
  • A timely review by Stanley Prusiner, whose research on prions won him a Nobel prize
  • How-Now Mad Cow: A very thorough introduction into the history of Mad-Cow disease in Great Britain
  • The Official Mad Cow Disease Home Page

Membranes

• Fluid model of lipid bilayer
• structural models of the lipid bilayer and membrane proteins.
• More membrane structure and composition: great review
• Transport of molecules in and out of cells: excellent review material
• Graphic of lipid bilayer that is a good educational tool. The browser can manipulate the structure of the lipid bilayer by rotating, slicing, etc. This image and its manipulation gives the browser a realistic, physical grasp of the biological membrane.
• The structure of well-documented integral membrane proteins
• Membrane function
• Here's that great animation of the Na+ K+ ATPase pump I mentioned in class.
• Animation of calcium pump
• Animation of ion channels

Metabolism

• An excellent web lecture on catabolism in cells by Dr. Thomas Terry from UConn, complete with links and animations. Go here to review glycolysis, Krebs cycle, fermentation, and oxidative phosphorylation.
• An animation of the electron transport chain in mitochondria, and one of ATP synthesis, also from Dr. Terry
• Here's an animation of glycolysis (Requires the Shockwave Plug-In)
• Here's a fantastic introduction to biological oxidations and cellular energy from Washington University, St. Louis. Included are the structures of important coenzymes, including Coenzyme A, NADH, and FADH2. Highly recommended for review!
• Yet one more site including several fun animations to help you understand biological oxidations.
• Here's one animated version of glycolysis. Watch the box on the right as glucose turns into pyruvate.
• A nice overview of cellular energy metabolism from the Univ. of Virginia.
• Here's an animated Krebs cycle (also from UVA), and an interactive Krebs Cycle from Kent State.
• A somewhat detailed explanation of the glyoxylate cycle, which occurs in glyoxysomes within plant cells.
• Here's an excellent site that explains photosynthesis, complete with diagrams and clear descriptions of important steps in the light dependent and light-independent reactions.
• The MIT hypertextbook has an excellent overview of photosynthesis.
• Inside the virtual cell, take a tour of a chloroplast.
• Here's a good set of links if you'd like to explore photosynthesis in even greater detail.
• "Mitochondrial Mysteries Demystified", A multimedia demonstration of the dynamic processes of Cell Respiration that occur in the Mitochondria: Electron Transport, Proton Translocation, ATP Synthesis, Krebs Cycle (TCA Cycle). Requires shockwave plug-in. Highly recommended.

DNA structure, replication, and repair. Transcription and translation, too!

• Didn't understand telomerase? Check out the telomerase demo by Dr. Slish from SUNY Plattsburgh. Highly recommended.
• Here's a nice overview of DNA structure, replication, transcription and translation from George Mason University. Included is this animation of prokaryotic replication that reviews key enzymes and steps.
• Here's the Eukaryotic replication movie shown in class.
• Here's an in-depth look at DNA repair mechanisms (far greater depth than that covered in class)
• Here's an excellent animation of RNA translation (shown in class), as well as access to many other DNA graphics and animations.

Gene expression

• Here's a graphics-rich introduction to control of gene expression. Skip the last half on topics not covered in our class.
• A thorough introduction to control of eukaryotic gene expression can be found here.

Cell signaling

• Here is a page that contains some dynamite animations. Scroll down the page and select the animation of the trimeric G-protein signal cascade.
• Here's another animation, this time of an enzyme-linked receptor and a MAP kinase transduction pathway. Really nice and highly recommended.
• This is your brain on cocaine.... (really an animation of synapse with and without cocaine)
• This is your brain on alcohol .... (same as above, but with ethanol)
• These are neurons in a person with Alzheimers
• Here's an excellent web lecture on synapses
• Here's a clip from Synapse, The Movie (might need Shockwave for this one)
• The Nobel Prize in physiology or medicine in 1994 went to these two scientist who discovered the secrets of G-proteins. This site includes a highly recommended general introduction to G proteins and their action (click on arrows >> once you're in the site).
• If you're interested, here's a thorough introduction to the sense of smell, including a discussion of G-proteins, the role of calcium in signaling, and olfactory receptors.
• To see just one example of a signal transduction pathway, check out this site which describes Wnt, a signal protein that binds to receptors and ultimately activates a variety of genes involved in development. Here's a map of the signal pathway, a static view of the pathway, and an animation of Wnt signaling.(Flash movie).

Cytoskeleton

• This animation of myosin / actin interaction and filament movement is very nice because it shows calcium's role in the process.
• This site includes movies of granules being transported on the axonal cytoskeleton. Cool stuff.

Cell cycle control, Apoptosis, and Cancer

• One review of the phases of the cell cycle
• National Center for Biotechnology's introduction to cancer and links to information about specific types of cancer, specific tumor suppressor genes and oncogenes. Click on the numbers along the top to see which oncogenes and tumor suppressor genes are located on each human chromosome.
• The Cell Cycle & Mitosis Tutorial from the Biology Project, University of Arizona
• Cancer Research Institute introduction to cancer and the immune system
• Here's that great review of apoptosis from the H.M.S. Beagle, a web-based biomedical newsletter. To see the article, click on "HMS Beagle" or "magazine". Go to the "Table of contents" and then scroll down to "Feature 1", the actual article!

Developmental Biology of the Cell

• An overview of segmentation genes in Drosophila. Nice, succinct summary.
• The Virtual World of Development is a gateway to a plethora of detail information and tutorials regarding develpment.

Links for Supplemental Readings

From the American Scientist:

• Regulating cell volume, Florian Lang and Siegfried Waldegger, September - October 1997, Volume 85(5)
• Maturation of a cell, Gary S. Stein, Janet L. Stein, André J. van Wignen and Jane B. Lian, January-February 1996, Volume 84(1)
• Testing a muscle's design, Lawrence C. Rome, July-August 1997, Volume 85(4)
• Metastasis, Cornelis J. Van Noorden, Linda C. Mead-Tollin and Fred R. Bosman, March - April 1998, Volume Volume 86(2)

From Scientific American:

• Cell Communication: The inside story, John D. Scott and Tony Pawson, June 2000.
• The Architecture of Life, Donld Ingber, January, 1998.