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Scott Napper Lecture Notes
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The Three-Dimensional Structure of ProteinPeptide Bonds
Covalent linkages between carboxyl group of one amino acid and amino group of
another. (Side chains don’t matter, that’s why they have been R’ed out)
Peptide bonds form by condensation reactions involving the generation and releasing
of a water molecule
Formation of peptide bonds eliminates the charged alpha-carboxyl and alpha-amino
charged groups.
o For water to make you’ll need 1 O and 2 H. 1 O will come from one of the amino
acids (here the left one) and two H will come from the amino acids (the right one
here)
Constant portions in the chain of amino acids are called the main chain (everything except the side c
Repeating pattern within the main chain: NCCNCC…
Partial Double Bond Characteristics
, resonance structure (a double bond that can be shared)
So, the double bond will spend half of its time between C=O and the other half
between C=N. This gives it partial double-bond characteristics.
Since double bonds are rigid (cannot fold) and single bonds are flexible (freedom
of rotation), rotation around C=N peptide bond is restricted due to the partial db.
Configuration
The partial double bonds of the peptide bond create cis-trans isomers.
Oxygen of the carbonyl group and the hydrogen of the amide nitrogen are usually trans
(opposite) to each other.
Peptide bonds (95%) tend to be in trans configuration
o Since steric interference (cant have cis)
Four Levels of Protein Structures
Primary Structure: linear sequence of amino acids
Secondary Structure: localized interactions within a polypeptide
Tertiary Structure: final folding pattern of a single polypeptide
Quaternary Structure: folding pattern when multiple polypeptides are involved.
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