4.Amino Acids

  • Structure
    • Central to this structure is the tetrahedral 四面体 alpha carbon (Cα)
    • Cα covalently bonded to
      • the amino group
      • the carboxyl group
      • a hydrogen
      • a variable side chain R
    • In neutral solution (pH 7), the carboxyl group exists as –COO- and the amino group as –NH3+.
    • Peptide Bonds
      • The amino and carboxyl groups of amino acids can react in a head-to-tail fashion, eliminating a water molecule and forming a covalent amide酰胺 linkage, a peptide bond
      • The equilibrium for this reaction in aqueous solution favors peptide bond hydrolysis.
  • 分类
    • Nonpolar Amino Acids
      • contains
        • Alanine 丙氨酸,R=methyl group, -CH3
        • Valine 缬氨酸, R=isopropyl group, (CH3)2CH-
        • Leucine 亮氨酸, R=butyl group
        • Isoleucine 异亮氨酸,
        • Methionine 蛋氨酸,甲硫氨酸 (oneof the two sulfur-containing amino acids),
        • Proline 脯氨酸 (with its unusual cyclic structure)
        • Two aromatic芳香族 amino acids
          • Phenylalanine 苯丙氨酸 abenzene ring after alanine
          • Tryptophan 色氨酸
        • 图
    • Polar, Uncharged Amino Acids
      • contains
        • Serine 丝氨酸R=methyl alcohol
        • Threonine 苏氨酸R=ethyl alcohol
        • Glycine 甘氨酸,氨基乙酸 R=H
        • Cysteine 半胱氨酸 sulfhydryl group 巯基, another sulfur-containing amino acid
        • Tyrosine 酪氨酸 aromatic amino with hydroxyl group
        • contain extra amide groups 酰胺(–CO-NH2)
          • Asparagine 天冬酰胺
          • Glutamine 谷氨酰胺
        • 图
      • The polar, uncharged amino acids (except for glycine) contain R groups that can form hydrogen bonds with water.
        • the amide groups of asparagine and glutamine
        • the hydroxyl groups of serine, threonine, and tyrosine
        • the sulfhydryl group of cysteine
    • Acidic Amino Acids
      • contains
        • Aspartic acid 天冬氨酸
        • glutamic acid 谷氨酸
      • R groups contain a carboxyl group.
      • They have a net negative charge at pH 7
      • Many proteins that bind metal ions for structural or functional purposes possess metal binding sites containing one or more aspartate and glutamate side chains
    • Basic Amino Acids
      • contains
        • Histidine 组氨酸
        • Arginine精氨酸
        • Lysine赖氨酸
      • Three of the common amino acids have side chains with net positive charges at neutral pH
      • The side chains of Arginine and Lysine are fully protonated at pH 7
        Arginine and lysine side chains, which are protonated under physiological conditions, participate in electrostatic interactions in proteins.
      • Histidine, with a side chain pKa of 6.0, is only 10% protonated at pH 7
        Histidine-containing peptides are important biological buffers.
    • Uncommon Amino Acids
      • contains
        • 图
      • Several amino acids occur only rarely in proteins
      • hydroxylysine and hydroxyproline are found in connective tissue proteins
      • 羟基赖氨酸和羟基脯氨酸存在于结缔组织蛋白中
      • pyroglutamic acid is found in bacteriorhodopsin (a protein in Halobacterium halobium)
        焦谷氨酸存在于嗜盐杆菌（一种来自盐生盐杆菌的蛋白质）的细菌视紫红质中
      • aminoadipic acid is found in proteins isolated from corn
        氨基己二酸存在于从玉米中分离出的蛋白质中
  • electric properties
    • Amino Acids Are Weak Polyprotic Acids 多质子酸
      • The common amino acids are all weak polyprotic acids.
      • The ionizable 可电离的 groups are not strongly dissociating ones, and the degree of dissociation thus depends on the pH of the medium.
      • All the amino acids contain at least two dissociable hydrogens.
    • Dissociation of Electrolytes 电解质
      • Ka ionization constant
        • states the extent to which a substance forms ions in water
        • pKa =-log Ka
      • titration curve 滴定曲线
        以acetic acid醋酸举例
        • At the point where half of the HAc has been neutralized, that is, where 0.5 equivalent of OH has been added, the concentrations of HAc and Ac are equal and pH=pKa for HAc.
        • Thus, we have an experimental method for determining the pKa values of weak electrolytes.
        • These pKa values lie at the midpoint of their respective titration curves.
        • Note that the titration curve is relatively flat at pH values near the pKa, in other words, the pH changes relatively little as OH is added in this region of the titration curve.
        • 图
        • A biologically important point is revealed by the basic shape of the titration curves of weak electrolytes, in the region of the pKa, pH remains relatively unaffected as increments of OH- (or H+) are added. The weak acid and its conjugate base are acting as a buffer.
          弱电解质滴定曲线的基本形态揭示了一个重要的生物学现象, 在pKa附近区域，即使持续加入OH⁻（或H⁺），pH值仍能保持相对稳定，此时弱酸及其共轭碱正发挥着缓冲作用
    • Histidine 组氨酸 System
      • Histidine is one of the 20 naturally occurring amino acids commonly found in proteins.
      • It possesses as part of its structure, an imidazole 咪唑 group, a five-membered heterocyclic ring possessing two nitrogen atoms.
      • The pKa for dissociation of the imidazole hydrogen of histidine is 6.04.
    • 氨基酸的两次电离
      • The cationic 阳离子 form is the low pH form, and the titration of the cationic species with base yields the zwitterion两性离子 and finally the anionic 阴离子 form

        • 阳离子形式存在于低pH环境，用碱滴定阳离子物质会依次生成两性离子，最终得到阴离子形式
      • 例子
        • Titrations of glutamic acid and lysine.谷氨酸和赖氨酸的滴定
        • 氨基酸的pK1, pK2
      • isoelectric point 等电点
        • the pH where the molecule has a net charge of 0, is defined as (pK1+pK2)/2
        • Titration of glycine, a simple amino acid
  • rections
    • Carboxyl and Amino Group Reactions 羧基和氨基的反应
      • 每个氨基酸的-COOH与-NH2性质相似, it is the characteristic behavior of the side chain that governs the reactivity of amino acids incorporated into proteins
      • -COOH
      • -NH2
      • peptide bond
        • The Peptide Bond Has Partial Double Bond Character
        • Peptide Classification
          • Dipeptides
          • oligopeptides
          • polypeptide
            Proteins Are Composed of One or More Polypeptide Chains
    • 特殊R表现出独特性质
      • Aspartic and glutamic acids contain an additional carboxyl function
      • arginine carries a guanidinium 胍 function
      • histidine contains an ionizable imidazolium proton
      • lysine possesses an aliphatic 脂肪族 amino function
    • The Ninhydrin 茚三酮 Reaction
      • Amino acids can be readily detected and quantified by reaction with ninhydrin
      • produces a colored product called “Ruhemann’s Purple” that absorbs light at 570 nm
      • 探案时候可以显示指纹
      • ninhydrin
  • Optical Activity 旋光性 and Stereochemistry 立体化学
    • Chiral 手性
      • Except for glycine, all of the amino acids isolated from proteins have four different groups attached to the α-carbon atom.
      • In such a case, the α-carbon is said to be asymmetric or chiral
      • the two possible configurations for the α-carbon constitute nonsuperimposable mirror image isomers, or enantiomers 旋光对映体
        围绕α-碳原子的两种可能构型会形成无法完全重叠的镜像异构体，即旋光对映体
    • 旋光性
      • Enantiomeric molecules display a special property called optical activity—the ability to rotate the plane of polarization of plane-polarized light.
        旋光对映体分子显示一个特殊的属性，称为光学活性—可以旋转平面偏振光的偏振平面的能力。
      • Clockwise rotation of incident light is referred to as dextrorotatory behavior 右旋性 (+), and counterclockwise rotation is called levorotatory behavior 左旋的 (-).
        入射光顺时针旋转称为右旋性（+），逆时针旋转称为左旋性（-）
    • Nomenclature 命名 for Chiral Molecules
      • It is found that nearly all of the amino acids derived from natural proteins are of the L configuration.
        天然蛋白质来源的氨基酸几乎均为 L 型构型
      • Amino acids of the D configuration are nonetheless found in nature, especially as components of certain peptide antibiotics, such as valinomycin 缬氨霉素，gramicidin 短杆菌肽，and actinomycin D 放射菌素 D, and in the cell walls of certain microorganisms.
        D 型氨基酸在自然界中也存在，尤其作为某些肽类抗生素（如缬氨霉素、短杆菌肽、放射菌素 D）的组分，及某些微生物的细胞壁成分
      • 例
  • Spectroscopic Properties 光谱性质
    • Ultraviolet Spectra 紫外光谱
    • Only the aromatic amino acids phenylalanine, tyrosine, and tryptophan exhibit significant ultraviolet absorption above 250 nm.
      仅芳香族氨基酸（苯丙氨酸、酪氨酸、色氨酸）在 250 nm 以上有显著紫外吸收
  • Separation and Analysis of Amino Acid Mixtures
    • 基于Mass
      • Centrifugation 离心法
    • 基于Electrical charge
      • Electrophoresis 电泳法
    • 基于Partition properties 分配性质
      the tendency to associate with one solvent or phase over another
      • Chromatography 层析法，色谱法
      • chromatography techniques depends on the repeated microscopic partitioning of a solute mixture between the available phases.
        层析技术基于溶质混合物在两相间的反复微观分配
      • Two phases—solid–liquid, liquid–liquid, or gas–liquid
        两相包括固 - 液、液 - 液或气 - 液
      • 流程
          1. 将氨基酸混合液加至阳离子交换柱
          1. 通过改变洗脱液条件，使不同氨基酸依次流出
          1. 分部收集流出液并检测，最终得到按时间分离的洗脱图谱
        • 图
      • HPLC chromatogram of amino acids, x-保留时间, y-响应度, 信号越强, 代表该氨基酸的浓度越高
  • Key takeaways from this class
    • Structure of a Typical Amino Acid
    • Typical properties of 4 types of Common Amino Acids
    • Ionization of Amino Acid, pKa, pH and isoelectric point, pI
    • The Ninhydrin (茚三酮) Reaction
    • Enantiomers, the amino acids derived from natural proteins are of the L configuration
    • Peptide Bond（肽键）