Amino Acids, Peptides and Proteins
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1 Amino Acids, Peptides and Proteins 1. α-amino Acids C (S) or L amino acids a) dipolar nature (isoelectric points) b) synthesis (racemic) i) from α-bromoacids ii) Strecker synthesis from aldehydes iii) reductive amination of α-ketoacids iv) amidomalonate synthesis 2. Peptides (up to 50 amino acids) -terminal " C-terminal a) amino acid analysis b) sequencing i) Edman degradation (-terminal) ii) carboxypeptidase (C-terminal) c) peptide synthesis (step-by-step and solid-phase) 3. Proteins (large peptides, occasionally with something else attached) a) structure (primary, secondary, tertiary and quaternary) b) classifications 64
2 α-amino Acids = side chain Examples: ~ 500 known in nature 20 in humans 10 of them essential glycine smallest, not chiral valine neutral, bulky, hydrophobic proline 2 o cyclic, bending in the peptide chain 2 C 2 S lysine basic, nucleophilic, used in catalysis aspartic acid acidic, carboxylate available, used in catalysis cysteine crosslinking, catalysis histidine basic, catalytic side chain 65
3 Peptide Structure Determination 1. Amino acid analysis: a) hydrolysis with Cl/ 2 b) column chromatography c) detection with ninhydrin a/ 2 + C C 2 (purple) 66
4 Peptide Structure Determination 2. The Edman degradation: a) treatment with phenyl isothiocyanate (-=C=S) b) mild acid hydrolysis c) the resulting phenylthiohydantoin is identified by chromatography S C Peptide S Peptide S Peptide S Peptide + ext cycle S 67
5 Peptide Structure Determination 3. C-terminal residue determination a) enzyme (carboxypeptidase) used to hydrolyze one amino acid at the C-terminus b) identifaction of the amino acid c) further hydrolysis 4. Putting together peptide (protein) structure from fragments Asp-Arg-Val Arg-Val-Tyr Val-Tyr-Ile Ile-is-Pro Pro-e Asp-Arg-Val-Tyr-Ile-is-Pro-e (angiotensin II) 68
6 (Di)Peptide Synthesis a) protect the amino group of amino acid 1 1 BC 1 1 b) protect the carboxyl group of amino acid 2 C 2 /Cl C c) couple the two amino acids using DCC BC C 2 DCC BC 1 2 C 2 d) remove the protective groups BC 1 2 C 2 CF 3 C 2 1 C 2 2 /Pd or a ote: side-groups of same amino acids require extra protectiondeprotection!
7 Peptide Synthesis Solid-ase Technique 1. BC-protected amino acid is linked to the polystyrene beads (S 2 ester bond formation) 2. The beads are washed (to remove excess reagents) and treated with CF 3 C to remove BC group 3. A second BC-protected amino acid is coupled to the first one using DCC. The beads are washed. 4. The cycle of deprotection, coupling and washing is repeated asmany times as desired to add amino acid units to the growing chain. 5. After the desired peptide has been made, the treatment with anhydrous F removes the final BC group and cleaves the ester bond to the polymer 6. The peptide is purified The yields of the reactions are critical! For a dodecapeptide (20 aa) it requires 40 chemical steps (not counting special treatment for some side groups). If the yield is 90% per step the overall yield is only ( ) 1.5% If the yield is 99% per step the overall yield is only ( ) 67% If the yield is 99.9% per step the overall yield is only ( ) 96% 70
8 1. Primary structure Protein Structure and Function sequence of amino acids 2. Secondary structure three-dimensional structure of segments (α-helical, β-pleated sheets) 3. Tertiary structure three-dimensional arrangements of segments 4. Quaternary structure three-dimensional shape of several proteins in a protein complex Protein denaturation Fibrous proteins (insoluble) Simple proteins Globular proteins (soluble) Conjugated proteins (carbohydrates, nucleic acids) Enzymes: holoenzymes = apoenzyme + cofactor (vitamin) 71
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