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Amino acids Amino acids •Tetrahedral alpha () carbon (C) with H, amino group, carboxyl group, and side chain (so-called R group). •Neutral solution (pH 7): The Carboxyl group –COO- and the amino group – NH3+. A neutral molecule called a zwitterion. Peptide bond •Amino acids in proteins joined by peptide bonds. •Head-to-tail fashion •Eliminating a water molecule •Forming a covalent amide linkage •Polypeptides and proteins 20 amino acids •Nonpolar or hydrophobic amino acids •Neutral (uncharged) but polar amino acids •Acidic amino acids (which have a net negative charge at pH 7.0) •Basic amino acids (which have a net positive charge at neutral pH) 1 Nonpolar amino acids (a) Nonpolar (hydrophobic) • With alkyl (烷基) chain R groups (alanine, valine, leucine, and isoleucine). • With its unusual cyclic structure (proline). • One of the two sulfur-containing amino acids (methionine). • Two aromatic (芳香基) amino acids (phenylalanine and tryptophan). (a) Nonpolar (hydrophobic) Polar amino acids •These amino acids are usually more soluble in water than the nonpolar amino acids. Glycine contain R group that can form hydrogen (H) bonds with water. •Tyrosine displays the lowest solubility in water of the 20 common amino acids. •Proline is very soluble in water. •Alanine and valine are about as soluble as arginine and serine. Polar amino acids (b) Polar, uncharged •The amide groups of asparagine and glutamine; the hydroxyl groups of tyrosine, threonine, and serine; and the sulfhydryl group of cysteine are all good hydrogen bond-forming moieties. •Glycine, the simplest amino acid, has only a single hydrogen for an R group, and this hydrogen is not a good hydrogen bond former. The solubility properties are mainly influenced by its polar amino and carboxyl groups, and it is best considered a member of the polar, uncharged group. 2 (b) Polar, uncharged Acidic amino acids •Aspartic acid and glutanic acid. •R group contain a carboxyl group. •Have a net negative charge at pH 7. •Play several important roles in proteins. Basic amino acids •Histidine, arginine, and lysine. (c) Acidic •Side chains with net positive charges at neutral pH. •Histidine side chains play important roles as proton donors and acceptors in many enzyme reaction. •Histidine-containing peptides are important biological buffers. •Arginine and lysine side chains, which are protonated under physiological conditions, participate in electrostatic interactions in proteins. (d) Basic 3 Uncommon amino acids •Several amino acids occur only rarely in proteins. Some amino acids are not found in proteins collagen and gelatin protein Iodinated amino acids;thyroglobuline a protein produced by thyroid gland In protein isolated from corn In several proteins involved in blood clotting In a unique lightdriven protonpumping protein called bacteriorhodopsin Certain muscle proteins contain methylated amino acids •Certain amino acids and their derivatives, although nor found in proteins, nonetheless are biochemically important. Certain protein involved in cell growth and regulation In histone proteins associated with chromosomes Acid-base properties of amino acids A part of coenzyme A neurotransmitter •The common amino acids are all weak polyportic acids. •All the amino acids contain at least two dissociable hydrogens. Neurotransmitters and regulators 4 Glycine Glycine Amino acids undergo typical reactions •Carboxyl group reaction (COOH) •Amino group reaction (NH3+) Glutamic acid Lysine 5 Amino acids side chains undergo specific reaction •A number of reactions of amino acids are noteworthy because they are essential to the degradation, sequencing, and chemical synthesis of peptides and proteins. Green fluorescent Protein (GFP) & Aequorin • Serine • Tyrosine • Glycine Amino acids are chiral molecules •Asymmetric (不對稱的 ) or chiral (對掌 性) (from Greek cheir, meaning “ hand” ) •Mirror-image isomer or enantiomers (鏡 像異構物) •Optical activity: dextrorotatory (+) (右旋) and levorotatory (-) (左旋) 6 Chiral molecules are described by two systems •D,L system -- Mirror-image isomer or enantiomers •R,S system -- Non-image isomer or diastereomers (非 鏡像異構物) R,S system •The configuration of molecules with more than one chiral center can be more easily, completely, and unambiguously. •Several amino acids have two chiral centers: isoleucine, threonine, hydroxyproline, and hydroxylsine. •R-right; S-left •Higher atomic numbers having higher priorities. -- SH > OH > NH2 > COOH > CHO > CH2OH > CH3 7 Spectroscopic properties of amino acids 分光光譜 •Spectroscopic methods -- measure the absorption and emission of energy of different frequencies by molecules and atoms. •Phenylalanine, thyrosine and tryptophan exhibit significant ultraviolet (UV) absorption above 250 nm. Nuclear Magnetic Resonance (NMR) 核磁共振 •A spectroscopic technique that involves the absorption of radio frequency energy by certain nuclei in the presence of a magnetic field, played an important part in the chemical characterization of amino acids and proteins. Chromatography 層析 •Partition properties •Electrical charge •Ion exchange chromatography, gas chromatography (GC), and high-performance liquid chromatography (HPLC). 8 9