F BICH 410 1st Edition Lecture 4 Outline of Last Lecture Enthalpy Entropy Free Energy Outline of Current Lecture Free energy can be determined at any temp as long as the equilb constant and deltaG 0 were measured at that temp too Amino Acids and the Peptide Bond o Contains amino and carboxyl group o Alpha amino acid an amino acid AA which the amino group is attached to the carbon adjacent to the carboxyl group o All proteins are composed of 20AA o At physiological conditions amino is protonated and carboxyl deprotonated o Fully protonated is found only at low pH o AA consists of amino H carboxyl and R side chain group o Side chains determine structural and physical characteristics Nonpolar Hydrophobic polar hydrophilic o All AA are hydrophilic its their side chain that could be hydrophobic o Types of AA noncharged positive charged negative charged Margret Dayhoff pioneer of bioinformatics and created 1 letter code Non polar o Will not form H bond bc need polar bond o Want to associate with hydrophobic group o Will not participate in ionic dipole interactions o All AA chiral except Gly and Gly can also be classified as polar noncharged o Pro cyclic means 2nd amine group o Ile has 2 chiral centers o Nonpolar AA Glycine Gly G side chain H Alanine Ala A side chain CH3 Proline Pro P side chain cyclic pentagon attaching amino group with 3 CH2 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 Valine Val V side chain CH with CH3 attached in shaped of V Leucine Leu L side chain CH2 CH CH3 2 Isoleucine Ile I side chain CH with Ch3 and CH2 CH3 attached Methionine Met M side chain CH2 CH2 S CH3 o Aromatic R Groups Phenylalanine Phe F side chain CH2 benzene ring Nonpolar Tyrosine Tyr Y side chain CH2 benzene ring CH Polar noncharged Tryptophan Trp W side chain CH2 CYCLIC C double bond CH NH attached to benzene ring Nonpolar Aromaticity is used for protein detection since aromatic compounds absorb UV light o Uncharged Polar R groups Don t like ionic interactions unless deprotonated since they have no charge Wont do hydrophobic bond since polar Uncharged at pH 7 4 Serine Ser S side chain CH2 OH Primary alcohol Threonine Thr T side chain CH WITH OH CH3 attached Secondary alcohol Cysteine Cys C side chain CH2 SH Asparagine Asn N side chain CH2 with NH2 and C 0 attached Amide will never change always NH2 Glutamine Gln Q CH2 CH2 C with NH2 and 0 ATTACHED o Polar Charged POSITIVE Want ionic interactions Can be Hbond donor Ionic predominated Polar charged cant be H acceptor unless deprotonated Avoid hydrophobic Lysine Lys K side chain CH2 4 NH3 Arginine Arg R CH2 3 NH C with NH2 and NH2 attached Guanidine group Histidine His H side chain CH2 with cyclic C NH CH N CH attached Protonated version has H on double bond N o Polar Charged NEGATIVE Like ionic interactions H bond acceptor bc lacking protons to donate Ionic dominated Can be H bond donor if protonated Hydrophobic interactions Aspartate Asp D side chain CH2 COO Glutamate Glu E side chain CH2 CH2 COOAmino acid 21 22 o Selenocysteine and pyrrolysine Use stop codon UAG as code but only under specific conditions Nonstandard amino acids can be important part of protein but nonstandards are always inserted into sequence firest and then altered to nonstandard there are over 300 o Most are not constituents of proteins
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