FBICH 410 1st Edition Lecture 7Outline of Last Lecture - Amino Acids L vs.D- Peptide BondsOutline of Current Lecture - Proteins agents of bio. Functiono 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 bondo NH = H bond donoro COO- = H bond acceptoro Secondary- determined predominantly by backbone H-bondedo 3rd and 4th structure determined predominantly by side chain Quaternary assume no covalent interactions- Noncovalent bonds: H bonds form whenever possibleo Ionic interactions- usually occur on surface – interacting w/ H20 bc polaro Van der waals interactions everywhereo Hydrophobic- cluster interior of protein- Protein structure based on amide planeo Twists can occur about either bonds linking alpha a to other atoms of peptide backboneo Dihedral angle describes conformation of entire peptide backboneo 2 angles per peptide plane- Rotation around peptide bondo Phi- describes rotation about N-C(a) bondo Psi- describes rotation about C(a)- C(O) bondo Angles have to be between 2 planes not at a N or C terminus- Favorable Phi and Psi angleso Ramachandran plot shows most of psi/phi angles not accessible- plot is used to determine what 2nd structure existso Unfavorable orbital overlap precludes some combinations of phi and psi- Cis and Trans conformationThese 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/molo Proline is the exception 10% of Pro residues follow cis bond bc of binding to itselfo Pro in a peptide bond doesn’t have H on N (no + charge)\- Secondary structure- driving force for formation is H bondo Initial study of 2nd structure done by Astbury by observing unstretched/stretched woolo Linus Pauling then discovered protein structureo 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 4th 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 helixo 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 Glycine and proline very prevalent and allow turns-very flexible (Gly )and can form cis (Pro) o 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 H-bonds w/ adjecents, I to i+4, I to i+3, pseudo 7 repeat I to