F BICH 410 1st Edition Lecture 7 Outline of Last Lecture Amino Acids L vs D Peptide Bonds Outline of Current Lecture Proteins agents of bio Function o Classified by function and shape and solubility globular fibrous membrane o Levels of protein structure Primary sequence Secondary local structure Tertiary overall 3d shape Quaternary subunit a separate polypeptide chain organization Covalent bond peptide bond Noncovalent bond o NH H bond donor o COO H bond acceptor o Secondary determined predominantly by backbone H bonded o 3rd and 4th structure determined predominantly by side chain Quaternary assume no covalent interactions Noncovalent bonds H bonds form whenever possible o Ionic interactions usually occur on surface interacting w H20 bc polar o Van der waals interactions everywhere o Hydrophobic cluster interior of protein Protein structure based on amide plane o Twists can occur about either bonds linking alpha a to other atoms of peptide backbone o Dihedral angle describes conformation of entire peptide backbone o 2 angles per peptide plane Rotation around peptide bond o Phi describes rotation about N C a bond o Psi describes rotation about C a C O bond o Angles have to be between 2 planes not at a N or C terminus Favorable Phi and Psi angles o Ramachandran plot shows most of psi phi angles not accessible plot is used to determine what 2nd structure exists o Unfavorable orbital overlap precludes some combinations of phi and psi Cis and Trans conformation These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute o Normally trans conformation is favored by 8KJ mol o Proline is the exception 10 of Pro residues follow cis bond bc of binding to itself o Pro in a peptide bond doesn t have H on N no charge Secondary structure driving force for formation is H bond o Initial study of 2nd structure done by Astbury by observing unstretched stretched wool o Linus Pauling then discovered protein structure o Alpha helix Rise residue 1 5 A Pith or rise turn 5 4A 3 6 AA residues turn 5 4 1 5 Approx 10 residues helix Sidechains point out and away from helix H bond pattern in alpha heliz is right handed spiral and is stabilized by extensive H bonds C O of pep Bond is H bonded to the N H of the 4 th AA away i to the i 4 last 4 residues at either end are least stable because only 1 H bond middle section most stable w 2 H bond alpha helix has dipole moment all C O pointing up partial negative charge all N H pointing down partial positive charge often times charge HPO42 added at N terminus and charge added to C terminus Lys Arg o Beta sheet 3 A from C a to C a and 7A Form backbone H bonds to neighboring polypeptide chains interstand not intrastrand like alpha helix Parallel Backbone running in same direction causes zigzag Hbonds Antiparallel backbone running in opposite direction causes straight Hbonds H bond run perpendicular to axis B sheet could be mixed Sidechains alternate up down Antiparallel B sheet 3 5A between residue Large B sheets exhibit right hand twist Connections between strands can be simple or complex o Can be llp or can contain additional 2nd structure ie alpha helix o Beta turn Tight Turn Consist of 4 5 AA in well define structure not repetitive alpha and beta In contrast to loops and random coils which are non repetitive and no well define structure Beta turns allows pep chain to reverse direction Beta turn can connect strands of antiparallel B sheet Carbonyl C of 1 residue is H bonded to amine 3 residues away I i 3 o Glycine and proline very prevalent and allow turns very flexible Gly and can form cis Pro Amino acid location B shet tend to find lare bulky and beta branched amino acids Breakers Proline rigid structure Glycine too flexible and side chain too small to protect backbone Amino acid location more important for alpha helices can potentially form Hbonds w adjecents I to i 4 I to i 3 pseudo 7 repeat I to i 7