Lecture 8Outline of Last Lecture I. Alpha HelicesA. The N+4 RuleII. Beta SheetsA. Hydrogen BondingB. R-Group OrientationIII. Orientation of the Peptide BackboneA. Parallel vs. AntiparallelIV. Turns and LoopsV. Tertiary StructureA. Beta Barrels Outline of Current Lecture I. Tertiary StructureII. Favorable ResiduesA. Secondary StructureB. Tertiary StructureIII. Protein FoldingA. Protein DenaturingB. Denaturing AgentsCurrent LectureThe backbone of a polypeptide chain is made up of covalent peptide bonds. The interactions between different regions of polypeptide chains are stabilized through hydrogen bonding. The tertiary structure of a protein is a combination of all the secondary structure of that protein. This means that the tertiary structure could include both alpha helices and beta sheets.The secondary structure of a protein is determined by the primary structure. Certain structures are more favored than others for the secondary. In an alpha helix, charged or bulky amino acid residues are not favored. For both alpha helices and beta sheets, the amino acid proline is unfavorable. In the case of turns, though, proline is favored, as is glycine. In turn, the secondary structure dictates the tertiary structure. The exterior of a protein does not favor amino acid groups that are hydrophobic. This is due to the inability to make H-bonds with water. The interior ofa protein does not favor charged amino acids, unless they are paired with the opposite charge. The tertiary structure is covalently stabilized by disulfide bridges.Proteins tend to fold up into to their lowest energy state, because of the factors listed above. When they are unfolded, the proteins are in their highest energy state. The proteins are also extremely flexible when unfolded. Even when the proteins are folded, they are not completely rigid. BCHM 30700 1st EditionProteins can also be denatured, or unfolded, in which they lose all their structure except for the primary. The protein takes on a random coil conformation when it is denatured. These requires an energy input to happen. The denatured protein loses its function, including enzymatic activity. Certain chemical agentscan interfere with protein folding stabilization and cause denaturing of the proteins. Agitation can target the H-bonds and hydrophobic interactions by making air bubbles. Changes in pH can disrupt salt bridges. Detergents can coat the outside of a protein with a charge. This disrupts the hydrophobic interactions and causes the protein to unfold. The Nobel prize was won by Anfinsen through the process of showing that the denaturation process can be reversed. His experiment focused on ribonuclease proteins. His experiment proved that all the information needed for a protein to fold properly is contained within the primary structure. Therefore, it is the primary structure that dictates function. He discovered that when the denatured protein was slowly cooled and chaperones proteins were added, the protein refolded. This is extremely difficult to do in reality, though it is possible in
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