BIOL 302 1st Edition Lecture 3Outline of Last Lecture I. Protein Composition and Structure Outline of Current Lecture II. Primary StructuresIII. Secondary StructuresIV. Protein Hierarchy Summary Current LectureV. Protein Structure is HierarchicalA. Primary Structure1. Proteins are linear polymers of amino acids whose sequence is referred to as its primary structure 2. Incorporated into a peptide or poly peptide, amino acids are referred to as residues3. Amino acid residues4. Read a polypeptide chain from N terminus to C terminus (amino terminal residue to carbonyl-terminal residue)5. Two amino acids join by forming a peptide bonda. Reaction is a condensation reaction: one oxygen molecule is removed from the carbonyl group of one amino acid and 2 hydrogen atoms from the amine group are removed the proceeding amino acid and water is therefore removedb. Once peptide bonds are formed they are extremely stablec. Half times for reverse reactions in the enzymes approaches 1000 yearsd. iClicker question: alanlylglutamylglycylalanylleucine has:4 peptide bondse. iClicker question: an octapeptide composed of four repeating glycylalanyl units has:one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue 6. Peptide bonda. Peptide-bond resonance structures causes a partial double bond which manifests in a shortened N-C bond length b. Both cis and trans conformations support resonace interactions BUT most peptides are in the TRANS conformation because the cis conformation causestoo much steric strainc. Partial double bond restricts mobility: polypeptide chain can be pictured as a set of rigid planes with consecutive planes sharing a common point of rotation at the alpha carboni. The polypeptide chain can thus be pictured as a set of rigid planes with consecutive planes sharing a common point of rotation at C alphad. Torsion angles define peptide backbone structurei. Although there is little to no rotation around the peptide bond, there can be rotation around the nitrogen and the C and between the C and the carbonyl carbon atome. Torsion angles phi and psi7. Ramachandran Plot for L-Alanine Residuesa. Ramachandran plotted combinations of  and , noticed that many combinations were not possible due to steric interactions. The allowable combinations seemed to fall into only a few major groupings. B. Secondary structure1. α –helixa. Right handedb. Except at the ends, all –C=O are hydrogen bonded to an H-N- c. The hydrogen bonds are parallel to the axis of the helixd. The polypeptide backbone forms the core, the side chains project outward in helical arraye. α helix is stabilized by intrachain backbone bondsi. Hydrogen bonding scheme of an alpha-helix (i with i+4)ii. Only polypeptide backbone –C=O and H-N- involved. -The idealized alpha helix has 3.6 residues per turn and a rise of 5.4 Å per turn. Thus the rise for each amino acidis 1.5 Å.f. Knowing your right from left handed helices2. Helix breakersa. T, V, and I, tend to disrupt alpha helices because of steric clashesb. S, D, N disrupt helices because their R groups compete for H-bonding with the backbone atomsc. Proline disrupts helices because of H-bonding and conformational preference3. Stable, spatial arrangement of a polypeptide segment without regard to the conformations of their side chains. 4. Stabilized by hydrogen bonds between amides in the backbone.5. A few types of secondary structure are particularly stable and occur widely in proteins6. The most prominent are the α helix and β sheet7. Allowed conformations correspond to secondary structures1. The Ramachandran plot reveals that both the right-handed and the left-handed helices are among allowed conformations.C. The β strand1. Unlike the alpha helix, the polypeptide backbone is stretched. 2. Several of these form into β sheets. There are two kinds:a. Parallel: backbones orientated in opposite directionb. Antiparallel: backbones oriented in same direction3. In β sheets, the polypeptide backbones form a zig-zag pattern with hydrogen bonds forming between –C=O and H-N- of the polypeptide backbones of strands that are adjacent in space to one another4. The hydrogen bonds are perpendicular to the axis of the polypeptide backbones of the strands. AntiparallelParallel5. To reverse the direction, a polypeptide chain can also have specific structures such as:Left: the reverse turn or the beta turn – Pro and GlyRight: the omega loop (red) D. Elements without secondary structure: loops1. Torsion angles must still be in favorable regions of Ramachandran plot.2. Conformation may be defined or flexibleE. Common secondary structures have characteristic bond anglesF. Side chains engage in noncovalent interactions1. The types and strength of these interactions dictate structure and function of all folded proteinsVI. Structural hierarchy in proteins1. Primary structure (1º structure)-for a protein is the amino acid sequence of its polypeptide chain(s). 2. Secondary structure (2º structure)-the local spatial arrangement of a polypeptide’s backboneatoms. Stabilized by hydrogen bonds between amides in the backbone.3. Tertiary structure (3º structure)-refers to the overall 3-dimensional structure of an entire polypeptide. Stabilized by all four types of non-covalent interactions4. Quaternary structure (4º structure)-The spatial arrangement of two or more polypeptide chains (subunits) bound by noncovalent