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Peptides and Proteins

Peptides and Proteins. Classification (vague). Peptides have fewer than 50 amino acids Oligopeptides (di, tri-, tetra-, etc.) up to about 10 aa Polypeptides (longer chain of aa than an oligopeptide)

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Peptides and Proteins

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  1. Peptides and Proteins

  2. Classification (vague) • Peptides have fewer than 50 amino acids • Oligopeptides (di, tri-, tetra-, etc.) up to about 10 aa • Polypeptides (longer chain of aa than an oligopeptide) • Proteins have more than 50 amino acids, and may be combined with other structure classes, such as carbohydrates, lipids, etc. • Simple…yield only amino acids upon hydrolysis • Conjugated…yield amino acids and other structure types (carbohydrate, lipid, etc.) on hydrolysis

  3. Levels of Protein Structure • Primary structure: the amino acid sequence • Secondary structure: the conformation due to rotations around C-C and C-N single bonds • Tertiary structure: the folding of the peptide chain into its characteristic 3D-shape • Quaternary structure: the aggregation of several subunits held together by other than covalent bonds (not all peptides have this feature)

  4. Primary Structure • the amino acid sequence, written from the N-terminal (on the left) to the C-terminal (on the right). Formerly abbreviated using three-letter abbreviations: Ala, Gly, Phe, Val, etc.; now we use one-letter abbreviations: A, G, F, V. Ala – Gly – Phe – Val or A-G-F-V

  5. Secondary Structure • the 3-D arrangement (conformation) of segments of a peptide/protein chain due to rotation around C-C and C-N bonds

  6. Secondary Structure • There are several named conformations due to common typical combinations of rotation angles around C-N (f) and C-C (y) bonds: f y • a-helix -58º -47º • b-pleated sheet ( -140º 135º • hairpin turns are sharp curves in the peptide chain, often due to proline residues )

  7. Problem w/ flat sheet (F and y = 180º)

  8. b-pleated sheet (F = -140º; y = 135º) 7.0 Å a-helix can be stabilized by H-bonding between adjacent peptide chains

  9. a-helix (F = -58º; y = -47º) a-helix is stabilized by H-bonding within a peptide chain

  10. Tertiary and Quaternary Structure • Tertiary structure: the coiling or folding pattern of single polypeptide chains • Many individual shapes, but generally fall into one of two categories: • Fibrous (insoluble; generally function as structural component) • Globular (soluble; coiled into compact, spherical shapes, with hydrophobic groups oriented inward and hydrophilic groups oriented outward toward the aqueous environment of the cell) • Quaternary structure: non-covalent aggregation of two or more protein molecules and possibly other structures into functional units. (examples shown in WebLab Viewer Lite)

  11. Functions of Proteins • Hemoglobin: the Oxygen-carrying molecule in the blood • Insulin: regulates glucose metabolism • HIV protease: cleaves peptide bonds of large protein to allow activation of HIV virus within host cell • Carboxypeptidase: digestive enzyme that hydrolyzes peptides into their component amino acids • Keratin: provides structure of wool, hair, fingernails, and feathers

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