F BICH 410 1st Edition Lecture 4Outline of Last Lecture - Enthalpy- Entropy- Free EnergyOutline of Current Lecture - Free energy can be determined at any temp as long as the equilb constant and deltaG0 were measured at that temp too- Amino Acids and the Peptide Bondo Contains amino and carboxyl groupo Alpha amino acid- an amino acid (AA) which the amino group is attached to thecarbon adjacent to the carboxyl groupo All proteins are composed of 20AAo At physiological conditions amino is protonated and carboxyl deprotonatedo Fully protonated is found only at low pHo AA consists of amino, H, carboxyl, and R (side chain group)o Side chains determine structural and physical characteristics Nonpolar=Hydrophobic polar=hydrophilico All AA are hydrophilic its their side chain that could be hydrophobico 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 bondo Want to associate with hydrophobic groupo Will not participate in ionic/dipole interactionso All AA chiral except Gly and Gly can also be classified as polar-nonchargedo Pro cyclic means 2nd amine groupo Ile has 2 chiral centerso 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 3CH2These 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-CH3o 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 lighto 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 ATTACHEDo 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 No 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-COO-- Amino acid 21&22o 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
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