Peptides and proteins
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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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Classification vague l.jpg
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


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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)


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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


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Secondary Structure

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


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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

)


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Problem w/ flat sheet

(F and y = 180º)


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b-pleated sheet

(F = -140º; y = 135º)

7.0 Å

a-helix can be stabilized by H-bonding

between adjacent peptide chains


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a-helix

(F = -58º; y = -47º)

a-helix is stabilized by H-bonding

within a peptide chain


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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)


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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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