BIOL 302 1st Edition Lecture 4 Outline of Last Lecture I. Antioxidant and redox regulation of gene transcription Outline of Current Lecture II. Tertiary StructureIII. Quaternary Structure Current LectureIV. ICiicker question: Two residues have the following combination of torsion angles: Ψ= 180 φ= -180. Which secondary structure do these residues likely have?A. α-HelixB. β-SheetC. OtherD. Outside the allowed regionsV. ICiicker question: Two residues have the following combination of torsion angles: Ψ= -60φ= 60. Which secondary structure do these residues likely have?A. α-HelixB. β-SheetC. OtherD. Outside the allowed regionsVI. iCLicker question: How is the α- helix oriented here?A. N-terminus at the topB. C-terminus at the topVII. Right handed alpha helixThese 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.A. 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 arrayVIII. Tertiary StructureA. Refers to the overall 3-dimensional structure of an entire polypeptide. B. Specific structures result from short and long-range interactions1. Electrostatic (charged) interactions2. Hydrogen bonds 3. Hydrophobic interactions van der WaalsC. Soluble proteins have an inside (core) and outside1. Folding driven by water- hydrophilic/phobic2. Side chain properties specify core/exterior3. Some interactions inside, others outsideIX. Electrostatic interactionsA. Form between 2 charged side chains: B. 1 Negative – Glu,Asp 1 Positive – Lys,Arg,His C. Also called “salt bridges”.D. Ionic interactions are pH-dependent (pKa) and salt dependent.E. Typical "salt bridges" have lengths of around 3.0 Angstroms. F. Bonding energy is 5.9 to 12 kJoule/mol.X. 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.L. pH dependent.XI. Van der Waals interactionA. When the electron orbitals of two atoms approach closely, there is attraction due to induction of complementary dipoles in the electron density of these atoms.B. Strongly dependent on distance, otherwise non-specific geometry.C. Bond lengths range beteen 2.5 and 4.6 Angstroms, averaging 3.6 Angstroms.D. Typical bonding energies are small, (2 to 4 kJoule/mol).XII. 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.D. Surface complementarity is key.XIII. Disulfide bonds can provide another covalent link in a polypeptideXIV.iClicker question: Where are proteins with disulfide bonds usually found?CytosolExtracellular proteinsIn bacteria: proteins in the periplasmIn eukaryotes: endoplasmatic reticulum and golgiThe cytosol is a reductive environment, whereas the extracellular space, the periplasm in bacteria and the endoplasmatic reticulum and the golgi in eukaryotes are oxidative environments.XV. C-α trace representation of a proteinUseful to overlay structures. The trace connects the C-α atoms.XVI. Protein tertiary structures are diverseXVII. The protein data baseA. 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 C ATOM 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 20 CD2 TYR A 457 -4.119 -13.289 -21.490 1.00109.06 C ATOM 21 CE1 TYR A 457 -2.302 -11.314 -22.209 1.00109.10 C ATOM 22 CE2 TYR A 457 -4.273 -12.610 -22.698 1.00109.42 C ATOM 23 CZ TYR A 457 -3.360 -11.622 -23.048 1.00109.66 C ATOM 24 OH TYR A 457 -3.514 -10.929 -24.227 1.00109.88 O ATOM 25 N ILE A 458 -4.013 -16.335 -19.478 1.00104.53 N