Gentilucci, Amino Acids, Peptides, and Proteins. Peptides and proteins are polymers of amino acids linked together by amide bonds CH 3

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1 Amino Acids Peptides and proteins are polymers of amino acids linked together by amide bonds Aliphatic Side-Chain Amino Acids - - H CH glycine alanine 3 proline valine CH CH 3 - leucine - isoleucine CH CH 3 - CH CH 3 CH 3 CH 3 CH 3 Hydroxy- Containing Amino Acids 2 stereocenters - - CH H H 2 stereocenters CH 3 serine threonine 1

2 Sulfur-Containing Amino Acids - - cysteine SH methionine S CH 3 Acidic Amino Acids - aspartatic acid - glutamic acid C C - - Amides of Acidic Amino Acids - - asparagine C glutamine NH 2 C NH 2 - Basic Amino Acids - lysine arginine NH NH 3 + C NH 2 NH 2 + 2

3 Benzene- Containing Amino Acids - - phenylalanine tyrosine H Heterocyclic Amino Acids C H 2 N N HN NH proline histidine tryptophan Configuration of Amino Acids 3

4 Acid Base Properties of Amino Acids An amino acid can never exist as an uncharged compound The isoelectric point (pi) of an amino acid is the ph at which it has no net charge 4

5 Some amino acids have ionizable hydrogens on their side chains The pi of an amino acid that has an ionizable side chain is the average of the pk a values of the similarly ionizing groups A mixture of amino acids can be separated by electrophoresis on the basis of their pi values A mixture of amino acids can also be separated on the basis of polarity 5

6 Ninhydrin is used to detect the individual amino acids Synthesis Gabriel synthesis with phtalimide Malonic synthesis + Gabriel reaction 6

7 Strecker Reaction Resolution of racemic mixtures Enzymatic synthesis Non chiral 2-oxopentanedioic gives optically pure glutamic acid 7

8 Formation of a Peptide Peptide Bond Formation of Disulfide Bonds Disulfides can be reduced to thiols 8

9 Peptides Angiotensin II: blood pressure regulating hormone Asp-Arg-Val-Tyr-Ile-His-Pro-Phe Vasopressin: diuretic hormone excitatory neurotransmitter inhibitory neurotransmitter Tyroid hormones 9

10 Antibiotic peptides Vancomycin is a very large, aminoglycoside antibiotic produced by the fermentation of the actinomycete bacteriaamycolatopsisorientalis. The main target of this antibiotic is the D-alanyl-D-alanine terminal dipeptide of peptidoglycan precursors, used by bacteria for constructing their cell walls. Vancomycin binds with the substrate, not the enzyme: this is in contrast to the way penicillin inhibits peptidoglycan synthesis. pioid peptides Peptide hormones The disulfide bridge in proteins contributes to the overall shape of a protein 10

11 A problem arises when one attempts to make a particular peptide Strategy for making a specific peptide: Gly-Ala and ot Ala-Gly, Ala-Ala, etc Protection of N-terminus + 11

12 Activation of CH terminus 12

13 Protecting group removal Merrifield automated SPPS Etc, etc 13

14 Determination of protein sequence 1. Cleavage and identification of disulfide bridges 2. Acidic hydrolysis and identification of a.a. composition protein 6 N HCl 100 C 24 h amino acids 14

15 3. Determination N-terminal amino acid by Edman degradation The particular PTH-amino acid can be identified by chromatography using known standards 15

16 4. Cyanogen bromide causes the hydrolysis of the amide bond on the C-side of a methionine residue 5. The C-terminal amino acid can be identified by treating the protein with peptidases (eg carboxypeptidases) Proteins Secondary structure Describe the conformation of segments of the backbone chain of a peptide or protein Three factors determine the choice of secondary structure: the regional planarity about each peptide bond maximization of the number of peptide groups that engage in hydrogen bonding adequate separation between nearby R groups The tertiary structure It is defined by the primary structure The stabilizing interactions include covalent bonds, hydrogen bonds, electrostatic attractions, and hydrophobic interactions Disulfide bonds are the only covalent bonds that can form when a protein folds Proteins that have more than one peptide chain are called oligomers 16

17 The α-helix Is Stabilized by Hydrogen Bonds (prolines are helix breakers) Two Types of β-pleated Sheets 17

18 The tertiary structure is the three-dimensional arrangement of all the atoms in the protein Most globular proteins have coil conformations 18