Amino acids and the Peptide Bond Dr Mullins 1 Amino Acids Amino Acid a compound that contains both an amino group and a carboxyl group Amino acid an amino acid in which the amino group is on the carbon adjacent to the carboxyl group All proteins are composed of 20 standard amino acids 2 Draw in the fully protonated form This form is only found at low pH not under physiological conditions You will be drawing either at pH 7 or at an another specific pH Figure 4 3 p80 Classification of Amino acids All amino acids contain an amino group and a carboxyl group What is different between them all is the R group or side chain The side chain determines the structural range and general physical characteristics of the amino acids The amino acids are generally grouped according to the various characteristics of their R groups Non polar amino acids hydrophobic Polar amino acids hydrophilic Non charged no charge at physiological pH 7 4 charged charge at physiological pH 7 4 charged charge at physiological pH 7 4 4 Non Polar R group Form hydrophobic interaction Want to associate with other hydrophobic groups Will NOT form hydrogen bonds participate in ionic or dipole interactions 5 Aromatic R Group Phenylalanine and Tryptophan are also classified as non polar Tyrosine can be also be classified as polar non charged The aromaticity is most important in protein detection since aromatic compounds absorb UV light 6 Uncharged Polar R Groups Hydroxyl Amide and Thiol Groups Uncharged at pH 7 4 These side chains like to participate in hydrogen bonds However will NOT from ionic interactions unless deprotonated since they have no charge Hydrophobic interactions since bonds are polar 7 Polar Charged R Groups Positively at pH 7 4 These side chains like to participate in ionic interactions Can be hydrogen bonds donors However will NOT Be hydrogen bond acceptors unless deprotonated since they have no free electron lone pair Hydrophobic interactions since bonds are polar 8 H Polar Charged R Groups Negatively charged at pH 7 4 These side chains like to participate in ionic interactions Can be hydrogen bonds acceptors However will NOT Be hydrogen bond donors unless protonated since they have proton on the carboxyl group Hydrophobic interactions since bonds are polar D Asp E Glu 9 Amino Acids 21 22 Selenocysteine 1 pyrrolysine Use stop codon UAG as code but only under specific conditions 10 Non Standard Amino Acids Unusual amino acids can be important components of proteins and peptides or play a metabolic role The non standard amino acids in proteins generally results from a specific modification of an amino acid residue after it is incorporated into the polypeptide strand Approx 300 non standard amino acids have been found in cells Most are not constituents of proteins 11 Biologically Active Amino Acids Amino acids and their derivatives sometimes function in non protein roles in cells The most common example are some neurotransmitters and chemical messengers 12 Unique Characteristics Glycine non chiral too flexible Proline Cyclic not primary amine rigid not flexible Isoleucine and threonine two chiral centers Cysteine two can oxidize to form cystine Asn and Gln Amide forms of Asp and Glu Asn and Gln are easily hydrolyzed to Asp and Glu 13 Nomenclature The atoms of the side chain are assigned sequential letters in the Greek alphabet beginning with the carbon next to the carboxyl group 14 Stereochemistry of amino acids Except for glycine the carbon is attached to four different groups chiral center The configuration about the C atom is generally described by the Fisher convention L amino acids predominate in nature All amino acids derived from proteins have the L stereochemical configuration left O O right 15 R S vs D L all L amino acids are S except Cys which is R Two amino acids have more than one stereocenter Ile and Thr Problem with D L system is how to distinguish between the two stereocenters 16 Chirality of Life Biosynthetic processes produce pure stereoisomers Chemical processes generally produce racemic mixtures Most active biological compounds are chiral i e only one enantiomer imparts biological activity 17 Thalidomide Used to treat multiple myeloma Leprosy Possible uses HIV related mouth and throat ulcers Inflammatory Diseases Lupus and Rheumatoid Arthritis cancer 18 Spectroscopic Properties All amino acids absorb in infrared region Only Phe Tyr and Trp absorb UV Absorbance at 280 nm is a good diagnostic device for proteins 19