Bioinformatics

Biological Basics

1. Amino acids I 2. Peptide bond I 3. Proteins I 4. DNA I 5. Miscellaneous

2. Peptide bond

2a.) Formation

• joins amino acids together (covalent bonds)
• chemical linkage -CO–NH- formed by the head-to-tail condensation of the α-amino group (-NH₂) of one amino acid and the α-carboxyl group (-COOH) of another amino acid (endothermic reaction)
• 1 mol water per 1 mol peptide bond was formed during the reaction
  • resulting C-N bond called "peptide bond"
  • resulting molecule called "amide"
• peptide bonds can be broken by hydrolysis (adding of water)

2b.) Properties

"partial" double bond character electronegative oxygen can accept electrons from the nitrogen double bound character has marked effect on the the rigidity of the polypeptide chain and consequently also on the folding of the polypeptide chain C-N bond length (1.33 Å) is shorter than the Cα-N bond (1.45 Å) C=O bond is actually longer (1.23 Å) than normal carbonyl bonds
peptide bond N–C–O atoms and atoms attached to them lie all in the same plane peptide bond is planar !
very rigid that means only 2 bonds can freely rotate Cα–N bond and Cα–C(O) bond
limit amount of free rotations possible (high torsion barriers) specified by the torsion angles Φ (phi, Cα–N bond) and Ψ (psi, Cα–C(O) bond) possible Φ and Ψ values are constrained by the structure of adjacent amino acid residues
Φ angle angle between the C α –N bond viewing along the C α –N bond (axis) the next bonds, the CO attached to the N and the CO attached to the C α define the angle Ψ angle angle between the C α –CO bond viewing along the C α –N bond (axis) the next bonds the next bonds to the N attached to the CO and the N attached to the C α define the angle
common defined secondary structures characterized by there Φ and Ψ angles α-helices Φ between - 40° and ~ - 100° Ψ between - 40° and - 65° Φ between - 80° and - 120° β-sheets Ψ between 120° and 170°
carbonyl oxygen and amide hydrogen are in a trans configuration (energetically more favorable), because of the steric hindrance (steric clashes) between the functional groups attached to the C α atoms almost all peptide bonds in proteins are in trans configuration !
cis configuration is sometimes found to occur with proline residues (cyclic nature of the proline side chain)
Ramachandran Plot shows allowed Φ and Ψ angles white areas = sterically disallowed conformations protein structures all fall within allowed regions Source: Stryer, figure 3.28

2c.) Peptides

• any number of amino acids can be joined together in chains:
  • dipeptide contains two amino acids,
  • tripepetide contains three amino acids etc.
    • in general, these structures are called "oligopeptides"
• after 20 or longer amino acids, they called "polypeptides"
  • long polypeptides (over 100 amino acids) are "proteins" (molecular weights [M_w] ≥ 10.000)
  • many proteins have 400 - 500 amino acid residues (M_w of 40.000 to 50.000)
  • one of the largest proteins is myosin from muscle with 1.750 amino acid residues (M_w = 192.500)

Additional information

• LIFE - The Science of Biology (7th edition) (by W.K. Purves, D. Sadava, G.H. Orians, H. Craig Heller)
• Hansen, J.L.; Schmeing, T.M.; Moore, P.B.; Steitz, T.A.; Proc. Natl. Acad. Sci. USA 2002, 99(18), 11670-11675. Structural insights into peptide bond formation. [PDF I PubMed]

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