Lecture 7Outline of Last Lecture I. Formation of PeptidesA. Protein formationB. Peptide bondsII. Biological PeptidesA. Amino Acid FunctionsIII. Levels of Protein StructureIV. Primary StructureA. Definition of Amino Acid CompositionB. Definition of Amino Acid SequenceV. Secondary StructureA. Alpha HelicesOutline of Current 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 Current LectureAlpha helices can be part of a protein’s secondary structure. It has a helical shape, naturally. The R groups stick outwards from the helix. The basic peptide backbone of the alpha helix is stabilized through hydrogen bonding. The way biochemists describe the hydrogen bonding of an alpha helix is called the n+4 rule.N represents a given amino acid in the peptide backbone of the alpha helix. The +4 represents going 4 more amino acids down the backbone, towards the carboxyl terminus. This rule states that the “n” amino acid of thepeptide backboneis hydrogen bonded to the amide group of the fourth amino acid down the chain. The secondary structure of the protein can also contain beta sheets. A beta sheet lies fairly flat and is a planar arrangement. Beta sheets contain multiple peptide backbones. As with alpha helices, the structure is stabilized through hydrogen bonding. One difference between alpha helices and beta sheets is how the R groups are configured. In beta sheets, the R groups alternate sticking straight up and down on each peptide BCHM 30700 1st Editionbackbone. The hydrogen bonding in beta sheets are between the carbonyl group of an amino acid and the amide group of the adjacent peptide chain. Unlike alpha helices, there is no “rule” to predict how far away the amino acid residues are from each other. Going back to the multiple peptide chains that each beta sheet contains, the chains themselves have specific orientation. The adjacent chains can be either parallel or antiparallel. The parallel structure has the carboxyl termini all at the same end. The antiparallel structure has the carboxyl and amide termini alternating which end they are on, with each peptide chain. Within the secondary structure, the peptide backbone can have different orientations. Small areas of the peptide backbone can “turn” and form little loops. Glycine and proline amino groups often promote these turns. A protein’s tertiary structure involves interactions between the secondary structures. Specifically, it involves interactions between the R-groups of the amino acids. If an interaction of multiple antiparallel beta sheets occurs, a beta barrel can form. This is essential a tertiary structure with a pore in it. Beta barrels can also be formed by repeating units of alpha-beta
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