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
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
levels of protein structure
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)
primary structure
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

secondary structure
Secondary Structure
  • the 3-D arrangement (conformation) of segments of a peptide/protein chain due to rotation around C-C and C-N bonds
secondary structure6
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

)

problem w flat sheet
Problem w/ flat sheet

(F and y = 180º)

b pleated sheet
b-pleated sheet

(F = -140º; y = 135º)

7.0 Å

a-helix can be stabilized by H-bonding

between adjacent peptide chains

a helix
a-helix

(F = -58º; y = -47º)

a-helix is stabilized by H-bonding

within a peptide chain

tertiary and quaternary structure
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)

functions of proteins
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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