Sinh học - Chapter 3: Amino acids, peptides, and proteins

Chapter 3Amino acids, peptides, and proteinsProperties of Amino Acidscapacity to polymerizenovel acid-base propertiesvaried structure and chemical functionalitychiralityBasic Amino Acid Structure a-carbon is chiral (except for glycine) at pH 7.0 uncharged amino acids are zwitterions amino acids have a tetrahedral structureside chaincarboxyl groupamino groupa-carbonAmino Acid EnantiomersSteroisomers / enantiomersBiological system only synthesize and use L-amino-acidsAmino Acid ClassificationAliphaticAromaticSulfur containingPolar/unchargedbasic/acidicHydrophobicHydrophillicAliphatic (alkane) Amino AcidsProline (pro, P)- cyclic “imino acid” Glycine(gly, G)-only non-chiral amino acid, not hydrophobicAlanine (ala, A) – R-group = methyl-groupValine (Val, V) –Think V! Leucine (Leu, L) – Isoleucine (Ile, I) -2 chiral carbons HydrophobicityAromatic Amino AcidsAll very hydrophobicAll contain aromatic groupAbsorb UV at 280 nmPhenylalanine (Phe, F) Tyrosine (Tyr, Y) – -OH ionizable (pKa = 10.5), H-BondingTryptophan (Trp, W) – bicyclic indole ring, H-BondingSulfur Containing Amino AcidsMethionine (Met, M) – “start” amino acid, very hydrophobicCysteine (Cys, C) – sulfur in form of sulfhydroyl, important in disulfide linkages, weak acid, can form hydrogen bonds.Contain carboxyl groups (weaker acids than a-carboxyl-group)Negatively charged at physiological pH, present as conjugate bases (therefore –ate not –ic acids)Carboxyl groups function as nucleophiles in some enzymatic reactionsAspartate – Glutamate – Acidic Amino AcidsBasic Amino AcidsHydrophillic nitrogenous basesPositively charged at physiological pHHistidine – imidazole ring protonated/ionized, only amino acid that functions as buffer in physiol range.Lysine - diamino acid, protonated at pH 7.0 Arginine - guianidinium ion always protonated, most basic amino acidPolar side groups, hydrophillic in nature, can form hydrogen bondsHydroxyls of Ser and Thr weakly ionizableSerine (Ser, S) – looks like Ala w/ -OHThreonine (Thr, T) – 2 chiral carbonsAsparagine (Asn, N) – amide of aspartic acidGlutamine (Gln, Q) – amide of glutamic acidPolar Uncharged Amino AcidsEssential/Non-Essential Amino AcidsEssential –histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valineNon-essential – alanine, arginine*, aspartate, asparagine, cysteine*, glutamate, glutamine, glycine*, proline*, serine, tyrosine*Titration Curve for AlaninepI (isoelectric point) = the pH at which the number of positive and negative charges on a population of molecules is equal (i.e. no net charge). pK1 carboxylic acid = 2pK2 amino group = 10pI = (pK1+ pK2)/2Titration Curve for Glutamic AcidpK1 carboxylic acid = 2.2pK2 R group = 4.3pK3 amino group = 9.7pI = (pK1+ pK2)/2pI = (2.2+4.3)/2pI = 3.25pK1 carboxylic acid = 2.2pK2 amino group = 9.0pK3 R group = 10.5pI = (pK2+ pK3)/2pI = (9+10.5)/2pI = 9.75Titration Curve for LysinepKa’s of charged amino acids R-groupsAspartate/Glutamate = 4.0Histidine = 6.0Cysteine = 8.4Tyrosine = 10.5Lysine = 10.5Arginine = 12.5 Protein NomenclaturePeptides 2 – 50 amino acids Proteins >50 amino acidsAmino acid with free a-amino group is the amino-terminal or N-terminal residueAmino acid with free a-carboxyl group is the carboxyl-terminal or C-terminal residueThree letter code – Met-Gly-Glu-Thr-Arg-HisSingle letter code – M-G-E-T-R-HPeptide Bond FormationPartial double bond nature of peptide bondStability and Formation of the Peptide BondHydrolysis of peptide bond favored energetically, but uncatalyzed reaction very slow.Strong mineral acid, such as 6 M HCl, good catalyst for hydrolysisAmino acids must be "activated" by ATP-driven reaction to be incorporated into proteinsEnzymatic and Chemical Cleavage of Peptide LinkageTitration Curve of a Tetrapeptide +H3N-Glu-Gly-Ala-Lys-COO-Proteins have pIsAla-Cys-Glu-Tyr-Trp-Lys-Arg-His-Pro-GlyAssigmentDraw the decapeptide at pH 1, 7, and 12. (pay attention to the form the N- and C- terminal and each R-group takes on at each pH)Calculate the overall charge at each pH.Write out the one letter code for the decapeptide