BIOB 380 1st Edition Lecture 8 Outline of Last Lecture I. Polypeptide chainsOutline of Current Lecture II. Structures of proteinsA. Primary, Secondary, Tertiary, Quaternary III. Ramachandran PlotIV. The alpha helixCurrent LectureStructures of proteins: - Primary- Secondary- Tertiary- QuaternaryHow are the 3D structures of proteins determined?- X-ray crystallography  protein concentrated in a crystal- Multidimensional NMR  protein concentrated in a solutionBovine Ribonuclease- Ribonuclease A is a secreted enzyme that hydrolyzes RNA during digestion- Bovine ribonuclease A NMR structure- Figure combines a set of very similar structures that satisfy the data on atomic interactions- Only the backbone of the polypeptide chain is shownResonance Structure of peptide bond- In this resonance form, the peptide bond is shown as a single C-N bond- In this resonance form, there is a double bond- The actual structure is best represented as a hybrid of the 2 resonance forms in which electrons are delocalized over the carbonyl oxygen, the carbonyl carbon, and the amide nitrogen- A peptide group consists of the N-H and the C=O groups involve in formation of the peptide bond, as well as the alpha carbon on each side of the peptide bond- Rotation around the N-C alpha and C alpha-C bonds that link peptide groups in a polypeptide chain can lead to crash b/t atomsRamachandran Plot- Plotting the rotations and when crashes b/t atoms occur- Observed phi and psi values in known structures are plottedThe Apha Helix - In the right handed helix, the backbone turns in a clockwise direction when viewed along the axis from either its N- or C- terminus- The helix is stabilized by hydrogen bonds- In an ideal alpha helix there are 3.6 amino acid residues per turn* Know alpha helix and beta sheets *Beta Sheets- Parallel Sheet- The hydrogen bonds are evenly spaced but slanted- Anti-parallel Sheet- They hydrogen bonds are essentially perpendicular to the beta strands, and the space between hydrogen-bonded pairs is alternately wide and