The Organic Chemistry of Amino Acids, Peptides, and Proteins

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1 Essential rganic Chemistry Chapter 16 The rganic Chemistry of Amino Acids, Peptides, and Proteins

2 Amino Acids a-amino carboxylic acids. The building blocks from which proteins are made. H 2 N C 2 H Note: except for glycine (R = H), a-amino acids are chiral molecules. * C R H

3 Amino Acids Peptides and proteins are polymers of amino acids. The amino acids are linked together by amide bonds: A + B A-B + H 2

4 Peptides Dipeptide: contains 2 amino residues Tripeptide: contains 3 amino residues ligopeptide: contains 4-10 amino residues Polypeptide: contains 10 > amino residues Proteins: polypeptides contain amino acids

5 The classification of proteins Proteins can be divided roughly into two classes: 1. Fibrous proteins: long chain of polypeptides arranged in bundles. They are usually insoluble in water and function as structual proteins such as collagen and keratin. 2. Globular proteins: have roughly spherical shapes and are soluble in water. They usually functions as catalysts (enzymes).

6 The biological functions of proteins

7 The classification of Amino Acids In organisms, proteins are usually composed of 20 amino acids. These amino acids differ only in the (side chain) substituents (R) attached to the α-carbons. C 2 H H 2 N The wide variation in these substituents (side chain) gives proteins the great structural and functional diversity. The amino acids are always called by their common names. C R H

8 The common names of amino acids The common name of amino acids tell us some information about the amino acids: Ex. Glycine: because of its sweet taste (glykos is Greek for sweet ) Asparagine: firstly found in asparagus ( 白 蘆 筍 ) Tyrosine: firstly isolated from cheese (tyros is Greek for cheese ) Glumate: 味 素 的 主 要 成 分 Abbreviation: amino acids have both three-letter abbreviation or single-letter abbreviation.

9 The common names of amino acids 10 of these 20 amino acids are essential amino acids: (Valine, leucine, isoleucine), threonine, methionine, (lysine, arginine), phenylalaine, (histidine, and tryptophen). Humans must obtain these 10 essential amino acids from the diets because either we cannot synthesized them at all or in enough amounts. Ex. We cannot synthesize bezene rings, thus we cannot produce phenylalanine. Arginine cannot be produced in enough amount in human body.

10 Proteins and nutrition Dietary proteins are hydrolyzed in human body to individual amino acids. Their fate in human body will be: 1. Used to synthesize proteins need by the body. 2. Broken down further to supply energy for the body. 3. As starting materials for the synthesis of non-protein compounds Most proteins from meat contain all essential amino acids. However, most proteins from vegetables are incomplete proteins, and they contain too little of one or more essential proteins. Ex. 大 豆 蛋 白 缺 乏 methionine; 小 麥 蛋 白 缺 乏 lysine.

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14 The configuration of amino acids The α-carbon of amino acids except glycine is an asymmetric center. Most amino acids found in nature have L configuration! H 3 N C - CH 3 H 1 = (S)-alanine

15 The acid-base properties of amino acids

16 The acid-base properties of amino acids At neutral ph (ph 7): Carboxylic groups: pka < ph, in basic form (-C - ) Amino group: pka > ph, in acidic (protonated) form (-NH 3+ ) Zwiterion: a compound has a negative charge on one atom and a positive charge on another atom.

17 The isoelectric point of amino acids The isoelectric point (pi, 等 電 點 ) of an amino acid is the ph at which it net charge is zero. 1. When the amino acid does not have an ionizable side chain: its pi is midway between two pka values.

18 Separation of amino acids 1. Electrophoresis ( 電 泳 )

19 Separation of amino acids 2. Ion-exchange chromatography ( 離 子 交 換 層 析 法 ) 當 胺 基 酸 的 靜 電 荷 不 為 0 時, 會 以 正 離 子 或 負 離 子 的 狀 態 存 在 此 時 可 以 與 帶 有 相 反 電 核 的 層 析 基 質 作 ionic interaction Ex: 可 與 帶 正 電 荷 的 胺 基 酸 或 蛋 白 質 結 合 的 層 析 基 質 (cation-exchanger)

20 Separation of amino acids 2. Ion-exchange chromatography ( 離 子 交 換 層 析 法 ) Cation-exchange chromatography: A. A negatively charged amino acid (glutamate): travel down the column rapidly! B. A positively charged amino acid (lysine): bind to the negatively charged resin tightly!

21 Separation of amino acids How to elute the amino acids or proteins from the cationexchange resin? S3 -.. AA + A. Increasing the ph in the buffer The amino acid will gradually become negative charged! B. Increaing the salt concentration in the buffer The ionic interaction between resin and amino acids will be destroyed

22 Separation of amino acids 2. Ion-exchange chromatography ( 離 子 交 換 層 析 法 ) If ninhydrin is added to each fraction, the relative amount of amino acids in each fraction can be determined using UV-Vis spectroscopy.

23 Peptide bonds and disulfide bonds Peptide bonds and disulfide bonds are the only covalent bonds that join amino acids together in a protein! 1. Peptide bonds The amide bonds that link amino acids. Proteins are written with the free amino group on the left and the free carboxylic group on the right.

24 Peptide bonds When the sequence is unknown: Represents the composition of amino acids When the sequence is known: Represents the sequence of a peptide or protein A peptide bond has partial double-bond

25 Partial double bonded peptide bonds is in a plane 平 面 的 轉 折 處 在 α-carbons

26 Peptides Peptides are amino acid polymers containing 2 50 individual units. Peptides with >50 units are called proteins. By convention, peptide structures are written with the N-terminal amino acid on the left and the C-terminal amino acid on the right. H 3 N CH 2 C NH CH C 2 CH 3 glycylalanine = gly-ala

27 Peptides Peptides are amino acid polymers containing 2 50 individual units. Peptides with >50 units are called proteins. By convention, peptide structures are written with the N-terminal amino acid on the left and the C-terminal amino acid on the right. glycine amino-terminal amino acid H 3 N CH 2 C NH CH C 2 CH 3 glycylalanine = gly-ala

28 Peptides Peptides are amino acid polymers containing 2 50 individual units. Peptides with >50 units are called proteins. By convention, peptide structures are written with the N-terminal amino acid on the left and the C-terminal amino acid on the right. alanine carboxy-terminal amino acid H 3 N CH 2 C NH CH C 2 CH 3 glycylalanine = gly-ala

29 Peptides Peptides are amino acid polymers containing 2 50 individual units. Peptides with >50 units are called proteins. By convention, peptide structures are written with the N-terminal amino acid on the left and the C-terminal amino acid on the right. H 3 N CH 2 C NH CH C 2 CH 3 the peptide bond glycylalanine = gly-ala

30 A tetrapeptide: Peptides H 3 N CH 2 C NH CH C CH 2 H NH CH C NH CH 2 C 2 CH 2 C 6 H 5 glycylserylphenylalanylglycine gly-ser-phe-gly

31 A tetrapeptide: Peptides H 3 N CH 2 C NH CH C CH 2 H NH CH C NH CH 2 C 2 CH 2 C 6 H 5 gly-ser-phe-gly

32 A tetrapeptide: Peptides H 3 N CH 2 C NH CH C CH 2 H NH CH C NH CH 2 C 2 CH 2 C 6 H 5 N-terminus gly-ser-phe-gly

33 A tetrapeptide: Peptides H 3 N CH 2 C NH CH C CH 2 H NH CH C NH CH 2 C 2 CH 2 C 6 H 5 C-terminus gly-ser-phe-gly

34 A tetrapeptide: Peptides H 3 N CH 2 C NH CH C NH CH C NH CH 2 C 2 glycine CH 2 H CH 2 C 6 H 5 gly-ser-phe-gly

35 A tetrapeptide: Peptides H 3 N CH 2 C NH CH C NH CH C NH CH 2 C 2 CH 2 H serine CH 2 C 6 H 5 gly-ser-phe-gly

36 Peptides A tetrapeptide: H 3 N CH 2 C NH CH C CH 2 H NH CH C NH CH 2 C 2 CH 2 C 6 H 5 phenylalanine gly-ser-phe-gly

37 A tetrapeptide: Peptides H 3 N CH 2 C NH CH C NH CH C NH CH 2 C 2 CH 2 H CH 2 C 6 H 5 glycine gly-ser-phe-gly

38 Structure Determination of Peptides Partial Hydrolysis (enzymatic) Hydrolyze the peptide into smaller fragments. Trypsin Cleaves at lys and arg. Chymotrypsin Cleaves at phe, tyr, and trp. Pepsin Cleaves at phe, tyr, trp, leu, asp, glu. Cyanogen bromide (not enzymatic) Cleaves at met. Determine the sequence of the fragments. Successive Edman degradations.

39 Sample Problem 20 amino acid polypeptide Amino acid analysis: gly 2 ala 4 leu 4 phe 3 trp 1 lys 2 met 2 ser 1 arg 1 Terminal residue analysis: N-terminus = ala C-terminus = phe

40 Sample Problem Trypsin hydrolysis (cleaves at lys and arg) gave four fragments: I. trp phe arg II. ala leu gly met lys III. leu gly leu leu phe IV. ala ala ser met ala phe lys

41 Sample Problem Cyanogen bromide cleavage gave three fragments: 1. ala leu gly met 2. ala phe lys leu gly leu leu phe 3. lys trp phe arg ala ala ser met

42 Sample Problem We can now assemble the peptide: BrCNtrypsin trypsin ala-leu-gly-met-lys-trp-phe-arg-ala-ala ser-met-ala-phe-lys-leu-gly-leu-leu-phe BrCN trypsin

43 Sample Problem We can now assemble the peptide: BrCNtrypsin trypsin ala-leu-gly-met-lys-trp-phe-arg-ala-ala ser-met-ala-phe-lys-leu-gly-leu-leu-phe BrCN trypsin

44 Sample Problem We can now assemble the peptide: BrCNtrypsin trypsin ala-leu-gly-met-lys-trp-phe-arg-ala-ala ser-met-ala-phe-lys-leu-gly-leu-leu-phe BrCN trypsin

45 Disulfide bonds Peptide bonds and disulfide bonds are the only covalent bonds that join amino acids together in a protein! Disulfide bonds When two thiol groups (-SH) of are oxidized, a disulfide bond is formed.

46 Peptides The only other type of covalent bond between amino acids in proteins and peptides is the disulfide linkage between two cysteine units: NH C CH HN HN C CH 2 S S CH 2 CH NH

47 Peptide bonds and disulfide bonds Peptide bonds and disulfide bonds are the only covalent bonds that join amino acids together in a protein! 1. Disulfide bonds When two thiol groups (-SH) of are oxidized, a disulfide bond is formed. Cysteine is the only amino acid that contains a thiol group

48 Disulfide bonds Disulfide bonds contribute to the overall shape of a protein. 1. Disulfide bond in a polypeptide 2. Disulfide bonds between two polypeptides

49 The structure of proteins Primary structure: the sequence of amino acids linked by peptide bonds. Secondary structure: The repetitive conformations of segments of a polypeptide. Two major types are α-helix and β-pleated sheet. Tertiary structure: three dimensional arrangement of all the atoms in a polypeptide. Quaternary structure: Some proteins have more than one polypeptide chain. Quaternary structure of a protein described the way the polypeptides are arranged in space.

50 Proteins Secondary Structure: The local hydrogen-bonding scheme. a-helix

51 Proteins Secondary Structure: The local hydrogen-bonding scheme. a-helix C H N R C H H C R C H N H N R C C H

52 Proteins Secondary Structure: The local hydrogen-bonding scheme. Hydrogen bonds a-helix C H N R C H H C R C H N H N R C C H

53 Proteins Secondary Structure: The local hydrogen-bonding scheme. a-helix

54 Proteins Secondary Structure: The local hydrogen-bonding scheme. b-sheet

55 Proteins Secondary Structure: The local hydrogen-bonding scheme. b-sheet R H CH C N CH C N CH C N R H R H H R N C CH N C CH N C H R H

56 Proteins Secondary Structure: The local hydrogen-bonding scheme. b-sheet R H CH C N CH C N CH C N R H R H H R N C CH N C CH N C H R H Interchain hydrogen bonds

57 The secondary structure of proteins 1. α-helix Ex. 羊 毛 可 沿 著 軸 展 延 取 代 基 向 外, 減 少 空 間 拒 斥

58 The secondary structure of proteins 1. β-pleated sheet Ex. 蠶 絲 蜘 蛛 絲 較 無 法 展 延 由 於 無 空 間 可 伸 展,R 基 必 須 較 小 ( 多 glycine alanine)

59 Generally, less than half of the protein s backbone is arranged in a defined secondary structure! Most of the rest of a protein is difficult to described.

60 The tertiary structure of proteins In solution, protein fold spontaneously to maximize their stability. The stabilizing interactions in a protein include: 1. Disulfide bond (a covalent bond) 2. Hydrogen bonds 3. Electrostatic attractions (between opposite charges) 4. Hydrophobic interaction (between nonpolar groups) Interactions can occur between: 1. Backbone backbone (hydrogen bond) 2. Side chain side chain (electrostatic or hydrophobic interactions) 3. Backbone-side chain

61 The tertiary structure of proteins

62 Proteins Tertiary Structure: How the protein, with all of its regions of secondary structure (ahelix, b-sheet) has folded over upon itself.

63 Proteins Tertiary Structure: How the protein, with all of its regions of secondary structure (ahelix, b-sheet) has folded over upon itself. a-helix regions

64 Proteins Tertiary Structure: How the protein, with all of its regions of secondary structure (ahelix, b-sheet) has folded over upon itself. b-sheet regions

65 The quaternary structure of proteins Four subunits of a hemoglobin

66 Proteins Quaternary Structure: How protein subunits aggregate into a larger functional unit. Hemoglobin has two a and two b subunits that fit together to form the whole hemoglobin molecule with four hemes and their associated irons to transport 2 and C 2.

67 Protein denaturation The methods to destroy the high order of conformation of a protein: 1. Changing the ph (disrupts electrostatic interactions and H bonds) 2. High concentration of salts (disrupts electrostatic interactions and H bonds) 3. Urea (disrupts H bonds in a protein) 4. rganic solvent (disrupt hydrophobic interaction) 5. Heat (disrupt the attractive forces)

68 Which of the following amino acids is polar? 1) Valine 2) Serine 3) Phenylalanine 4) Leucine 5) Alanine

69 In which form does glutamic acid exist at ph 7.4 (physiological ph)? H 2 N CH CH H 3 N CH CH H 3 N CH C 1) 2) 3) CH 2 CH 2 CH CH 2 CH 2 CH CH 2 CH 2 CH H 3 N CH C H 2 N CH C 4) 5) CH 2 CH 2 C CH 2 CH 2 C

70 Indicate the peptides that would result from the cleavage of the following peptide by the peptidase trypsin. His-Lys-Leu-Val-Glu-Pro-Arg-Ala-Gly-Ala 1) His-Lys Leu-Val-Glu-Pro-Arg Ala-Gly-Ala 2) His-Lys-Leu-Val-Glu-Pro-Arg Ala-Gly-Ala 3) His Lys-Leu-Val-Glu-Pro Arg-Ala-Gly-Ala 4) His-Lys-Leu-Val-Glu Pro-Arg-Ala-Gly-Ala 5) His-Lys Leu-Val-Glu-Pro-Arg-Ala-Gly-Ala

71 What type of stabilizing interactions occur between the side chains of phenylalanine and leucine? 1) Hydrogen bonding 2) Disulfide bridges 3) Hydrophobic interactions 4) Polar (dipole dipole) 5) Electrostatic attractions

72 What type of intermolecular forces are responsible for stabilizing the a-helix secondary structure? 1) Intermolecular H-Bonding between C= and NH of backbone 2) Intramolecular H-Bonding between C= and NH of backbone 3) Electrostatic attractions 4) Dipole Dipole 5) Hydrophobic

73 Which amino acid is the only one that is achiral? 1) Glycine 2) Leucine 3) Tyrosine 4) Proline 5) Aspartic Acid

74 Which of the following amino acids has a sulfur in the R group? 1) Serine 2) Cysteine 3) Asparagine 4) Tyrosine 5) Leucine

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