1Amino acids and the Peptide BondDr. Mullins2Amino Acids• Amino Acid - a compound that contains both an amino group and a carboxyl group! α-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 acidsFigure 4-3 p80Draw 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!4Classification of Amino acids• All amino acids contain an α amino group and a αcarboxyl 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-polaramino acids (hydrophobic)•Polaramino 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)5Non-Polar R group•Form hydrophobic interaction• Want to associate with other hydrophobic groups•Will NOT–form hydrogen bonds–participate in ionic or dipole interactions6Aromatic R Group•Phenylalanine and Tryptophan are also classified as non-polar•Tyrosine can be also be classified as polar non-charged•The aromaticityis most important in protein detection since aromatic compounds absorb UV light7Uncharged 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 polar8Polar 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–Behydrogen bond acceptors (unless deprotonated) since they have no free electron lone pair– Hydrophobic interactionssince bonds are polar+H9Polar 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–Behydrogen bond donors (unless protonated) since they have proton on the carboxyl group–Hydrophobic interactionssince bonds are polarDEAsp Glu10Amino Acids 21 &22•Selenocysteine & 1 pyrrolysine•Use stop codon (UAG) as code but only under specific conditions11Non-Standard Amino Acids•Unusual amino acidscan 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 proteins12Biologically 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 messengers13Unique CharacteristicsGlycine – non chiral, too flexibleProline – Cyclic (not primary amine), rigid, not flexibleIsoleucine and threonine – two chiral centersCysteine – two can oxidize to form cystine Asn and Gln – Amide forms of Asp and Glu- Asn and Gln are easily hydrolyzed to Asp and Glu14Nomenclature•The atoms of the side chain are assigned sequential letters in the Greek alphabet beginning with the carbon next to the carboxyl group15Stereochemistry of amino acids•Except for glycine, the α-carbon is attached to four different groups - chiral center•The configuration about the Cα atom is generally described by the Fisher convention•L-amino acids predominate in nature. All amino acids derived from proteins have the L – stereochemical configurationO rightleft O16R 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 stereocenters17Chirality 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 activityThalidomide•Used to treat –multiple myeloma–Leprosy•Possible uses–HIV related mouth and throat ulcers–Inflammatory Diseases – Lupus and Rheumatoid Arthritis–cancer1819Spectroscopic Properties•All amino acids absorb in infraredregion•Only Phe, Tyr, and Trp absorb UV•Absorbance at 280 nm is a good diagnostic device for