Recitation 3:Protein polymerization, structure, and conventional depictions in biologyGoals: 1. Review in-class concepts of protein structure and folding2. Learn the multiple ways that proteins are depicted in scientific literature (and your textbook)You have probably heard of prion proteins, the culprits behind the Mad Cow disease scare of the mid-90's. Prion proteins are convenient for discussion of protein structure and folding because they are relatively small, for proteins. Also, the diseases they cause are unusual in that they are infectious, yet not caused by the usual suspects (viruses, bacteria, fungi, or parasites).Introduction:Prion proteins (PrP), in their noninfectious form (referred to as PrPC, for "cellular form"), are useful members of cellular society. We're not entirely sure what function they perform, but the latest thought is that they aid in the health and connectivity of neuronsin the brain, and the maintenance and repair of the myelin sheaths that insulate neurons.Disease arises when the victim eats the infectious form of the protein (called PrPSc). It's the same protein, but it has been somehow warped into a zombie version of itself. Like a zombie, it no longer serves any cellular function. Worse, it shuffles around finding others of its kind, latching onto them and turning them into misfolded zombies like itself.And like zombies, it's hard to kill-- the normal cellular machinery that degrades misfolded, damaged, ormalformed proteins cannotdestroy it. The victim's brainfills with big clumps of theuseless prions, and ultimatelybig, spongy holes (see imageon right). Prions are not destroyed by the heat of cooking or by the low pH of gastric juices. Kuru is one example of a prion disease (unsteady gait, slurred speech, muscle tremors, uncontrollable laughter and eventually, death). Ironically, the "zombie protein" is passed on primarily through the consumption of diseased brain tissue.Let's take a look at the prion protein, and how such proteins are presented in the literature. Read the document, and answer the questions about prion proteins on the attached workskeet. You only need to turn in one worksheet per group.Prion Primary structureThe primary sequence1 of the full prion protein is 253 amino acids long. Amino acid numbering begins at the N-terminal end. Primary sequences are always depicted using single-letter abbreviations, so I require students to memorize the letters. If you print out the full color version of this document, you will see that the colors correspond to the four groups of amino acids (green for nonpolar, aqua for polar, red for acidic, and purple for basic).Primary sequence alignmentOften, it is useful to compare sequences of the same protein between species. (There are online tools to do this.) Below is a comparison between five vertebrate species2. The highlighted regions (amino acids #98 -157) show stretches of amino acids that are mostly identical between all of them. The prion protein was present in the common ancestor of all of these vertebrates, and the important regions have not changed much over the millenia.Protein functional domain diagramIt's also common to see the primary structure depicted as a diagram depicting information about the functions of the protein, and areas of particular interest. The diagram below3 shows several relevant features that you don't have to know, but I want to draw your attention to two of them: The disulfide bond between amino acids #179 and #214, and the "HC" (hydrophobic core) region between #111 - 134.1 http://www.diseasemotifs.co.uk/prion/prprotein.html2 Pietropaolo et al. (2009), ChemPhysChem 10(9-10):1500-10.3 Aguzzi & Heikenwalder, 2006, Nat. Rev. Microbio 4:765-775Prion secondary and tertiary structureRibbon DiagramThe diagram below is a very common way to illustrate the three-dimensional shape of a protein. Such diagrams are often foundonline as an animation, toallow the viewer to rotate themolecule. If you refer to thefull-color version of thisdocument, you can see thatthe alpha helices are renderedin green, the beta sheets inred, and the single disulfidebond in yellow.This diagram also illustratesthe distinction between thePrpC form (normal, left) andthe PrPSc form (zombifiedabnormal form, right). Youmight not be able to infer the functions tehy perform, but they are very clearly different 3D stuctures, and we all know that structure relates to function.Process/Model diagramsMany of the diagrams in your book are simple depictions of a process or order of events. The diagram below4 depicts how the abnormal prion proteins interact with normal (endogenous= already present in body) PrPC proteins. Note that in these types of diagrams, the proteins are just depicted as simple blobs. I threw this diagram to make the point that you will be seeing many different kinds of diagrams in this class that depict blobs and arrows. Make sure you can distinguish between a model diagram like this one, a metabolic pathway diagram, an electron transport chain, and a signal processing diagram. It's not entirely clear in the literature yet (1) where the misfolded PrPSc proteins originally came from, and (2) how they convert PrPC to a misfolded form.4 http://www.vce.bioninja.com.au/aos-2-detecting-and-respond/defence-against-disease/pathogens.htmlChart of Amino Acids, organized by