Amino Acids PDF
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These notes explain the properties of amino acids, including their protonation states and how they relate to pKa values, hydrophobic and hydrophilic properties, zwitterions, and classification. The document also covers protein structure and bonding forces that contribute to the three-dimensional structure of proteins.
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Amino Acids mi IE mEii eri.iis Eieiminu Protonation state and how it relates to Pka Charge and protonation state are related Hydrophobic andhydrophilic properties I free N terminus and I free...
Amino Acids mi IE mEii eri.iis Eieiminu Protonation state and how it relates to Pka Charge and protonation state are related Hydrophobic andhydrophilic properties I free N terminus and I free c terminus ftp fEb9 fffff NeutralPH deprotonated state 7 in the peptidechange O Proline Pro P 1 causes Kinks in the aminoacidchain most amino acids are chiral Except for glycine becausesidechain is a hydrogen Zwitterion A molecule that has and charge manyaminoacids are twitterions EO H3Ñ If OH Han PH7 nocharge A lowerPH LowPH Protonate charge j i ighPH deprotonate Oka The PH which 50 is protonated and 50 is deprotonated carboxylic Acid PKa 2 Aminogroup PKa 9 I IsoelectricPoint PH at which the molecule is neutral PI 5.5 neutralpH PKa.JP2a 2 1 12 Hent 0H neutralPH Han o highPH g PH PKa deprotonate PH PKa Protonate t.ii.EE PH PKa 50 Protonated and50 deprotonated Amino Acid classification non polar eg Alanine Polar Acidic eg side chain has Coo BasfR was ÑH3 neutral R has 0H Canformhydrogenbonds does notprotonate ordeprotonate Amino acids have ionizable side chains canbe charged at PH 7 9 ITEAtz TEE'a.n Atz o H3Ñ EO H3Ñ 80 on not I 0 1 2 PI pkai PKa_ 3 22 3.2 General Properties of proteins andPolymers EE EEIEi.Enims E 2 Aa dipeptide 4 20 Aa Oligo peptide 20 or more Aa Polypeptide 100 or more Aa Protein peptidessaid initiate jéÉeen2 Aminoacid connottbe Amide linkage between the carboxyl group of AA 1 and the amino group rotated of AA 2 2 resonance structures Peptide bondhas a double Ñ É It IgE o character cannot rotate Has partial charges 1 Hat Loss of water when a peptidebond isformed Its a condensation reaction monomers single chain N C Multimers several subunits TIE severalchain Cofactors Non protein components required for protein activity or function Minerals metal ion cartmgt Fe Zn't ca't Vitamins Small organic molecules MAD FAD heme Amino acid modification I Threonine Phosphatase Phosphoserine removesphosphategroup I At.it is proline hydroxyproline 3 3 Protein structure 4 Levels primary Linear arrangementof aminoacids eg M O O O C Ala Ser Trp A S W Mutations Ala Gly TrP indicatingthemutation Ser2Guy secondary connectsthe α helix Bsheet turnsandcoilloops in the structure connectsalphahelices The structure is heldtogetherbyhydrogen bonds Tertiary Overall shape of theprotein motifs combinations of secondarystructures such as 2 helicesandbetasheets Domains piecesof protein that retain their structure in the absence of the rest 0 the protein They are discretely fdff.fm tgfesinto their threedimensionalstructh Bonding forces in 3 structure hydrophobiceffect hydrophicparts of a molecule clusterto geth Hydrogen bonds London dispersionforces Cuander Waals salt bridges dipole dipoles Cation x̅ interaction Disulfide bond covalent Quartenarysee How multiple subunits cometogether can have Quartenary structure mfgf monodimersdonot have quartenarystructures tetramer Homodimer 2 identical chains Heterodimer 2 different chains Alphahelices sidechains are Pointingtothe outside AngstromsCA 1 10nm residues 504A width ofalphahelixstructure 6A Its PartialPositiveandPartialnegativecharge Betasheets Parallel N to C Antiparalle C to N
