Friday 9 30 05

9/30/2005 Lecture
• {Review from Wed: alpha helix structure has stabilizing bond between nitrogen and carboxyl. The alpha-carbon holds them in a plane. Figure 4-2. Each H bond form has stability to the structure. }
• Figure 4-7 Beta structure formed when 2 chains are superimposed and each hydrogen is in a bond. Beta structure gives a long range of interactions. Give large two dimensional chains.
• Alpha-carbon is not in the plain, gives a pleat, ripple look.
• R-group not involved. Alternate from the plane, in and out of the plane. R-group charges do interact with each other, so they are adjacent to each other in the beta-sheet.
• Antiparallel has a chain running in an opposite form, because of opposite polarity. The hydrogen bonds are also aligned. Most common beta-conformation. More stabilizing energy because of the H bond alignment.
• Parallel has all strands running in the same direction. Has an enteric difference because the strength of the H bond is lowered. The H bonds are no collinear which makes them not stable.
• Gamma turns are very rare; it is a U-turn (180 degrees) with only three residues.
• Beta turns are U-turns with 4 residues, which have less strain. There is only 1 hydrogen bond between alpha-carbon 1 and alpha-carbon 4.
• Figure 4-8a There are two types of turns. Type I is on surface of proteins, where the hydrogen from alpha-carbon 2 and alpha-carbon 3 form with water, forms water soluble proteins. Type II is less frequent. The alpha-carbon 3 is always glycine so that steric crowding is minimized.
• Figure 4-8b Proline isomers- are the “weirdo” amino acid. There is a cis and trans form, the cis form, which happens 5-10%, the chain breaks or the helix of beta-structure makes a wrong turn.
• Figure 4-9 Stric interference the plot validated by the structures found.
• Figure 4-10 There are no rules for protein in structure there are only tendencies of how they will fold. Proteins are context dependent.
• Figure 4-11 Fibrous proteins, keratin alpha helix in a right hand helix. Form two chain coiled given strength; both strains running in the same direction inter-weaving in a left hand helix form. The two strains are compressed to make it more stable. Then protofilaments can combine to make protofibril, which is a higher level structure of mammal hair.
• Box 4-2 Disulfide bonds keep hair stable so to perm hair, you use chemicals to break those bonds which allow you to shape hair.
• Figure 4-15 Beta conformation is longer than alpha helix. The globular form is smallest. Spiders use Ala and Gly to form a beta structure that can bond closer together.
• Figure 4-16 Myoglobin in sperm whales. To see this structure, you need to go to the class web site and download Ras or Chime so that you can look up and view 3D pictures of proteins. Instructions are on the website. We will use these programs for some homework problems.
• Figure 4-17 The structure of heme. Do not need to know the structure, but it is a great example of evolution. The electron carrying citron in the middle moved just enough for Oxygen to fit but not for carbonmonxide to stick.