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Amino Acids, Peptides, and Proteins. Monomer Unit: Α-Amino Acids H NH2 R = Sidechain R CO2H

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Amino Acids, Peptides, and Proteins. Monomer Unit: Α-Amino Acids H NH2 R = Sidechain R CO2H Chapter 27: Amino Acids, Peptides, and Proteins. monomer unit: α-amino acids H NH2 R = sidechain R CO2H !- Amino Acid Biopolymer: the monomeric amino acids are linked through an amide bond (the carboxylic acids of one AA with the α-amino group of a second) R R1 R 1 H + 2 - H2O N CO2 H3N CO2 H3N H3N CO2 C-terminus O R N-terminus 2 O R O R O R O H 2 H 4 H 6 H N N N N N N N N H H H H R1 O R3 O R5 O R7 Peptide or protein (polypeptide) peptide (< 50 amino acids) protein (> 50 amino acids) 307 27.1: Classification of Amino Acids. AA’s are classified according to the location of the amino group. H H H H H H H2N C CO2H H2N C C CO2H H2N C C C CO2H H H H H H H !-amino acid "-amino acid #-amino acid (2-amino carboxylic acid) (3-amino carboxylic acid) (4-amino carboxylic acid) There are 20 genetically encoded α-amino acids found in peptides and proteins 19 are primary amines, 1 (proline) is a secondary amine 19 are “chiral”, 1 (glycine) is achiral; the natural configuration of the α-carbon is L. CHO CHO CO2H CO2H H OH HO H H2N H H2N H CH OH CH OH 2 2 CH3 R D-glyceraldehyde L-glyceraldehyde L-alanine CHO CHO CO2H CO2H HO H H OH H2N H H2N H H OH HO H H OH H3C H CH2OH CH2OH CH3 CH2CH3 308 D-erythrose L-erythrose L-theronine L-isoleucine (2S,3R) (2S,3S) 157 α-Amino acids are classified by the properties of their sidechains. Nonpolar: – COO COO– COO– NH 3 NH3 NH3 Glycine (Gly, G) (S)-(+)-Alanine (Ala, A) (S)-(+)-Valine (Val, V) – S COO– COO COO– NH3 NH3 NH3 (S)-(–)-Leucine (Leu, L) (2S,3S)-(+)-Isoleucine (Ile, I) (S)-(–)-Methionine (Met, M) COO– COO– N COO– NH H H 3 N NH3 H (S)-(–)-Proline (Pro, P) (S)-(–)-Phenylalanine (Phe, F) (S)-(–)-Tryptophan (Trp, W) Polar but non-ionizable: OH COO– COO– HO COO– NH3 NH3 HO NH3 (S)-(–)-Serine (Ser, S) (2S,3R)-(–)-Threonine (Thr, T) (S)-(–)-Tyrosine (Tyr, Y) pKa ~ 13 pKa ~ 13 pKa ~ 10.1 – COO H N COO– O HS 2 COO– NH3 O NH3 H2N NH3 (R)-(–)-Cysteine (Cys, C) (S)-(–)-Asparagine (Asn, N) 309 (S)-(+)-Glutamine (Gln, Q) pKa ~ 8.2 O Acidic: - – O COO COO– -O O NH3 NH3 (S)-(+)-Aspartic Acid (Asp, D) (S)-(+)-Glutamic Acid (Glu, E) pKa ~ 3.6 pKa ~ 4.2 Basic: N H H – – N H3N COO H COO COO– NH H N N NH3 N 3 2 H NH H 3 (S)-(+)-Lysine (Lys, K) (S)-(–)-Histidine (His, H) (S)-(+)-Arginine (Arg, R) pKa ~ 10.5 pKa ~ 6.0 pKa ~ 12.5 27.2: Stereochemistry of Amino Acids: The natural configuration of the α-carbon is L. D-Amino acids are found in the cell walls of bacteria. The D-amino acids are not genetically encoded, but derived from the epimerization of L-isomers 310 158 27.3: Acid-Base Behavior of Amino Acids. Amino acids exist as a zwitterion: a dipolar ion having both a formal positive and formal negative charge (overall charge neutral). R R + _ H2N CO2H H3N CO2 H H pKa ~ 5 pKa ~ 9 Amino acids are amphoteric: they can react as either an acid or a base. Ammonium ion acts as an acid, the carboxylate as a base. Isoelectric point (pI): The pH at which the amino acid exists largely in a neutral, zwitterionic form (influenced by the nature of the sidechain) _ R + R + H3O R HO _ H N CO H + _ H N CO 3 2 H N CO 2 2 3 2 H H pKa 1 H pKa2 low pH high pH Table 27.2 (p. 1115) & 27.2 (p. 1116) 311 pKa + pKa pI = x y 2 CH CH + 3 + CH3 3 H3N CO2H H3N CO2 H2N CO2 pKa H H 1 H pKa2 (2.3) (9.7) low pH high pH CO H 2 CO2H CO2 CO2 CH 2 CH2 CH2 CH2 H3N CO2H H N CO H3N CO2 H N CO pKa1 3 2 pKa pKa 2 2 H 3 H 2 (1.9) H (3.6) (9.6) H low pH high pH NH3 NH NH3 NH3 2 (CH2)4 (CH ) (CH2)4 (CH2)4 2 4 H3N CO2H H N CO H N CO H2N CO2 pKa1 3 2 pKa 2 2 pKa3 2 H H (2.2) H (9.0) H (10.5) low pH high pH 312 159 Electrophoresis: separation of polar compounds based on their mobility through a solid support. The separation is based on charge (pI) or molecular mass. + _ + _ _ _ _ _ + + + + 313 27.5: Synthesis of Amino Acids: Br NH2 Br2, PBr3 NH3 R-CH2-CO2H R C CO2H R C CO2H Ch. 19.16 H H Strecker Synthesis: recall reductive amination NaB(CN)H3 NH2 O NH3 NH2 R C CO2H R C CO2H R C CO2H H H NH NH O NaC!N 2 H O+ 2 NH3 NH2 3 R C C!N R C CO2H R C H R C H -or- H NaOH, H2O H N!C: Amidomalonate Synthesis: recall the malonic acid synthesis O O H O H2N H HN CO Et EtO Na HN CO Et 3 2 2 C C C - CO2 RCH CO H RCH2X 2 2 H CO2Et RCH2 CO2Et 314 160 27.5: Reactions of Amino Acids. Amino acids will undergo reactions characteristic of the amino (amide formation) and carboxylic acid (ester formation) groups. H3C O O O H2N H H N HN HOCH2CH3 3 H H3C O CH3 H R CO CH CH + base 2 2 3 H R CO2 R CO2H 27.6: Some Biochemical Reactions of Amino Acids. Many enzymes involved in amino acid biosynthesis, metabolism and catabolism are pyridoxal phosphate (vitamin B6) dependent (please read) - R CO2 O H racemase, - H CO2 R - N R CO2 epimerase H 2- OH + O3PO NH OH NH3 3 PO N N D-amino acid L-amino acid pyridoxal H decarboxylase phosphate (PLP) R H transaminase H - H3N R CO2 315 O 27.7: Peptides. Proteins and peptides are polymers made up of amino acid units (residues) that are linked together through the formation of amide bonds (peptide bonds) from the amino group of one residue and the carboxylate of a second residue HO H + - H2O N CO2H H2N CO2H H2N H2N CO2H C-terminus O N-terminus Alanine Serine OH Ala - Ser - H2O (A - S) HO H C-terminus By convention, peptide sequences N CO H H N 2 N-terminus 2 are written left to right from the O Ser - Ala N-terminus to the C-terminus (S - A) O R O R O R O H 2 H 4 H 6 H N N N N N N N N backbone H H H H R1 O R3 O R5 O R7 316 161 The amide (peptide) bond has C=N double bond character due to resonance resulting in a planar geometry _ O R2 O R H H H 2 H restricts rotations N N N + N N N resistant to hydrolysis R H O 1 R1 H O amide bond The N-H bond of one amide linkage can form a hydrogen bond with the C=O of another. O H N N-O distance 2.85 - 3.20 Å R N H O N H O N H O optimal N-H-O angle is 180 ° R R H N H N O O Disulfide bonds: the thiol groups of cysteine can be oxidized to form disulfides (Cys-S-S-Cys) NH2 1/2 O2 H2O NH2 S CO H 2 2 SH HO2C S HO2C NH H2 2 317 R9 O R11 O R13 R6 O R8 O R10 H H H H H H N N N N N N N N N N N N H H H H H H O O R12 O O O R9 O S HS 1/2 O2 SH S R O O R H R1 O O R5 1 H H 5 H 2 H H H N N N N N N N N N N N N H H H H H H O R O R O O R2 O R4 O 2 4 Epidermal Growth Factor (EGF): the miracle of mother’s spit 53 amino acid, 3 disulfide linkages 1986 Nobel Prize in Medicine: Stanley Cohen 318 Rita Levi-Montalcini 162 27.8: Introduction to Peptide Structure Determination. Protein Structure: primary (1°) structure: the amino acid sequence secondary (2°): frequently occurring substructures or folds tertiary (3°): three-dimensional arrangement of all atoms in a single polypeptide chain quaternary (4°): overall organization of non-covalently linked subunits of a functional protein. 1. Determine the amino acids present and their relative ratios 2. Cleave the peptide or protein into smaller peptide fragments and determine their sequences 3. Cleave the peptide or protein by another method and determine their sequences. Align the sequences of the peptide fragments from the two methods 319 E-A-Y-L-V-C-G-E-R F-V-N-Q-H-L-F F-V-N-Q-H-L-F-S-H-L-K S-H-L-K-E-A-Y G-C-F-L-P-K L-V-C-G-E-R-G-C-F L-G-A L-P-K-L-G-A F-V-N-Q-H-L-F F-V-N-Q-H-L-F-S-H-L-K S-H-L-K-E-A-Y E-A-Y-L-V-C-G-E-R L-V-C-G-E-R-G-C-F G-C-F-L-P-K L-P-K-L-G-A L-G-A F-V-N-Q-H-L-F-S-H-L-K-E-A-Y-L-V-C-G-E-R-G-C-F-L-P-K-L-G-A 320 163 27.9: Amino Acid Analysis.
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