BIOL 302 1st Edition Lecture 5 Protein Composition and StructureOutline of Last Lecture I. Protein Composition and StructureOutline of Current Lecture II. Secondary Structures, Tertiary Structures, Quaternary Structures, Bonding Types in Secondary and Tertiary Structures, Protein FoldingCurrent LectureIII. iClicker Question: Two residues have the following combination of torsion angles: Ψ= 180 φ= -180?:β- sheetIV. iCLicker Question: Two residues have the following combination of torsion angles: Ψ= -60 φ= 60?:Outside the allowed regionV. iClicker Question: How is the α- helix oriented here?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.N-terminus at the topVI. The right handed α –helixA. Except at the ends, all –C=O are hydrogen bonded to an H-N- B. The hydrogen bonds are parallel to the axis of the helixC. The polypeptide backbone forms the core, the side chains project outward in helical arrayVII. iClicker Question: Which one is the anti-parallel beta-sheet?^ Antiparallel β sheetBackbones oriented in opposite direction^ Parallel β sheetBackbones oriented in same directionVIII. Side chains engage in non-covalent interactionsIX. Tertiary Structure1. Polypeptide Chain2. Nonpolar hydrophobic side chains are attracted to one another while repelling water3. What induces tertiary structurea. In aqueous environment: nonpolar side chains move away from water, move towards the inside of the protein, bury themselves in the center causing it to foldin on itselfi. This pairs all of the NH and CO groups by hydrogen bondingb. Van der Waals interactions occur between hydrocarbon side chainsc. Interior consists almost entirely of non-polar residues such as:i. Leucineii. Valineiii. Methionineiv. Phenylalanined. Polar or ionic side chains on the outside such as:i. Aspartateii. Glutamateiii. Lysineiv. Argininee. Similar structure to a micellei. an electrically charged particle formed by an aggregate of molecules and occurring in certain colloidal electrolyte solutions, as those of soaps and detergents.; composed of amphipathic (pertains to a molecule containing both polar (water-soluble) and nonpolar (not water-soluble) portions in its structure )molecules with their hydrophilic heads pointing out4. 3D shapeX. Electrostatic interactionsA. Form between 2 charged side chains:1. 1 Negative- Glu, Asp and 1 Positive-Lys, Arg, His2. Aka “salt bridges”3. Ionic interactions are pH dependent (pKa) and salt dependent 4. Typical salt bridges have lengths of around 3.0 Angstroms5. Bonding energy is 5.9-12 kJoule/mol6. Shorter bond length=stronger interactionsXI. Hydrogen bondsA. Forms between side chains/backbone/water: B. Charged side chains: Glu,Asp,His,Lys,ArgC. Polar chains: Ser,Thr,Cys,Asn,Gln, TyrD. Occurs inside, at the exterior, and with water.E. A “donor” donates its covalently bonded hydrogen atom to an electronegative “acceptor”. F. Donors: -OH (Ser, Thr, Tyr), and -NH3+ (Lys, Arg) or -NH- (backbone, Trp, His, Arg).G. Acceptors: The lone electron pairs on these donors, as well as lone electron pairs on carbonyl oxygens C=O (backbone) or nitrogens with three covalent bonds =N- (His, Trp). Lacking hydrogens, these latter cannot serve as donors.H. Hydrogen bonds can also be bridged by tightly bound water molecules (HOH).I. Bond lengths range from 2.6 and 3.5 Angstroms between the non-hydrogen atoms.J. Furthermore, the angle between the donor and acceptor has to allow hydrogen bond formation, placing specific restrains on the geometry. K. Typical energies for hydrogen bonds range between 4 to 13 kJoule/mol.pH dependent.XII. Van der Waals interactionA. When the electron orbitals of two atoms approach closely, there is attraction due to inductionof complementary dipoles in the electron density of these atoms.B. Strongly dependent on distance, otherwise non-specific geometry.C. Bond lengths range between 2.5 and 4.6 Angstroms, averaging 3.6 Angstroms.D. Typical bonding energies are small, (2 to 4 kJoule/mol).XIII. Hydrophobic effect – solvent exclusionA. When two nonpolar residues approach each other, the surface area exposed to solvent is reduced, increasing the entropy of all the water present and decreasing the entropy of the residues. B. Temperature dependent.C. The hydrophobic energy is roughly 5 kCal for every 100 Angstroms**2 of contact surface area that was formerly exposed to water.Surface complementarity is key.XIV. Disulfide bonds provide another covalent link in a polypeptideXV. iClicker question: Where are proteins with disulfide bonds usually found? A. CytosolB. Extracellular proteinsC. In bacteria: in the periplasmD. In eukaryotes: endoplasmatic reticulum and golgiXVI. Protein tertiary structures are diverseXVII. The Protein data base: Coordinates of protein structures can be downloaded from the protein data base www.pdb.orgATOM 1 N TYR A 456 2.178 -15.381 -21.511 1.00115.37 N ATOM 2 CA TYR A 456 1.478 -14.190 -20.955 1.00114.70 C ATOM 3 C TYR A 456 0.396 -14.542 -19.925 1.00113.54 C ATOM 4 O TYR A 456 0.699 -14.712 -18.739 1.00113.81 O ATOM 5 CB TYR A 456 0.898 -13.338 -22.102 1.00116.08 C ATOM 6 CG TYR A 456 0.459 -14.117 -23.338 1.00117.73 C ATOM 7 CD1 TYR A 456 -0.729 -14.858 -23.346 1.00118.30 CATOM 8 CD2 TYR A 456 1.236 -14.113 -24.500 1.00118.39 C ATOM 9 CE1 TYR A 456 -1.131 -15.573 -24.478 1.00118.32 C ATOM 10 CE2 TYR A 456 0.845 -14.827 -25.639 1.00118.40 C ATOM 11 CZ TYR A 456 -0.339 -15.554 -25.618 1.00118.68 C ATOM 12 OH TYR A 456 -0.730 -16.266 -26.728 1.00119.03 O ATOM 13 N TYR A 457 -0.851 -14.669 -20.380 1.00111.35 N ATOM 14 CA TYR A 457 -1.988 -14.992 -19.509 1.00108.34 C ATOM 15 C TYR A 457 -2.833 -16.144 -20.063 1.00106.56 C ATOM 16 O TYR A 457 -2.433 -16.829 -21.006 1.00106.08 O ATOM 17 CB TYR A 457 -2.877 -13.758 -19.340 1.00108.21 C ATOM 18 CG TYR A 457 -3.062 -12.995 -20.627 1.00108.76 C ATOM 19 CD1 TYR A 457 -2.158 -12.001 -21.004 1.00108.75 C ATOM