AA s are the building blocks of proteins
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1 Chamras Chemistry 106 Lecture otes Chapter 24: Amino Acids, Peptides, and Proteins General Formula: () n (') α-amino Acids: (n = 1) Example: Amino Acids and Proteins: Glycine Alanine Valine AA s are the building blocks of proteins 1
2 Chirality of α-amino Acids: Example: C C 2 L-amino acid (S) (S) ***L-amino acids are usually what is found in the nature. Standard Amino Acids: 20 amino acids found in nearly all proteins Types of Standard Amino Acids: (Based on the nature of the side chain [the group]) The side chain (the group): (For more details please see Table 24-2) 1. is a non-polar or alkyl group: (7) Gly, Ala, Val*, Leu*, Ile*, Phe*, Pro 2. contains an : (3) Ser, Thr*, Tyr 3. contains S: (2) Cys, Met* 4. contains non-basic : (3) Asn, Gln, Trp* 5. is acidic: (2) Asp, Glu 6. is basic: (3) Lys*, Arg*, is* Essential Amino Acids: C 2 L-glyceraldehyde Incomplete Proteins: 2
3 Acid-Base Properties of Amino Acids: Summary of Physical Properties: Amino acids 1. ave high MP (MP>200 o C) 2. Are 2 soluble 3. Are more polar than simple amines and carboxylic acids. 4. Are less acidic than most carboxylic acids and less basic than most amines. Acidic part = protonated amino group Basic part = deprotonated carboxylic group Carboxylic functional group: Avg. p = 2 Amino functional group: Avg. p =
4 Titration curve for simple amino acids (lacking acidic or basic side chains): 9 p 2 Equivalents of added Electrophoresis: A technique for separation, based on the net charges of amino acids. 4
5 Syntheses of Amino Acids: 1. eductive Amination: (α-keto acid α-amino acid) General Equation:!-ketoacid 3 (excess) imine 4 2 Pd!-amino acid 4 Example: 1. 3 (xs) 2. 2, Pd 2. Amination of α-halo acid: (α-bromo acid α-amino acid) General Equation: (VZ) carboxylic acid *Stereochemistry: 1. Br 2, PBr Br 3 (xs)!-amino acid 4 Example: (VZ) 1. Br 2, PBr 3 3 (xs)
6 3. The Gabriel-malonic ester synthesis: 1. Cl Last Step: ydrolysis of: esters & phthalimide, followed by protonation of amine. Phthalimide operates as a protected amine until it gets hydrolyzed. 4. The Strecker synthesis: Aldehyde + ammonia + C Amino acid (in acidic medium) + + C 3 + 6
7 Mechanism: 1. Imine formation by acetaldehyde and ammonia 2. Addition of cyanide 3. ydrolysis of nitrile into carboxylic acid 7
8 eactions of Amino Acids: 1. Esterification of the carboxyl group: Amino acid Amino ester (Similar to Fischer Esterification) Product = Amino ester 2. Acylation of the amino group: Amino Acid Amide eacts with acid anhydride or acid chloride 3. eaction with ninhydrin: (uhemann s Purple) + 2 8
9 4. Formation of Peptide bonds: 9
10 10
11 Peptide Structure and omenclature: Structure: Peptide bond (linkage): -Terminus: C-Terminus: esidue: Types of Peptides; Dipeptide: (2) ligopeptide: (5-10) Polypeptide: (MW <5000g.mol 1 ) Protein: (6000 < MW < 40,000,000) g.mol 1 11
12 omenclature: Template: { ( yl) n ine} Examples: 12
13 Protein Structure Determination: General Approach: breaking down the protein into residues. 1. Breaking the disulfide bonds: esults in breaking the cross-links between chains containing cysteines. Agent: Peroxyformic acid S S 3 S S 3 2. Separation and purification into individual chains. 3. ydrolysis of individual chain: esults in separation of all residues present in the individual chain. Agent: Boiling 6M Cl(aq), 24 rs. 4. Passing the hydrolyzed mixture through an analyzer: esults in identification of the amino acids present. 3. Terminal esidue Analysis: Alternatively, in order to identify the sequence of amino acids in the chain, one residue at a time could be hydrolyzed and identified. a) -Terminus Analysis: Edman Degradation & Sanger Method Agent: Phenyl isothiocyanate C S 13
14 Mechanism: (Edman) Mechanism: (Sanger) 14
15 b) C-Terminus Analysis: esults in cleavage of the C-terminal amino acid. Agent: Carboxypeptidase, 2 c) Partial ydrolysis: Agents: i) Dilute acid: ii) Trypsin: Cleaves at the carboxyl groups of basic amino acids (lysine and arginine) iii) Chymotrypsin: Cleaves at the carboxyl groups of aromatic amino acids (phenylalanine, tyrosine, and, tryptophan) Examples: 15
16 Solution Phase Peptide Synthesis: Based on the following reaction: Cl ' ' Starts at the -terminus (left to right): Cl (Z Cl) Cl 2, Pd 16
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Name: 5.5.# BCHS 3304/ Exam I September 26, 2002............... Instructions: 1. There are 13 pages to this exam. Count pages prior to beginning exam. You may use the back pages of the exam as scratch