Everything about Peptide Bond totally explained
A
peptide bond is a
chemical bond formed between two
molecules when the
carboxyl group of one molecule reacts with the
amino group of the other molecule, releasing a molecule of
water (H
2O). This is a
dehydration synthesis reaction
(also known as a
condensation reaction), and usually occurs
between
amino acids. The resulting CO-NH bond is called a
peptide bond, and the resulting molecule is an
amide. The four-atom functional group -C(=O)NH- is called an
amide group or (in the context of proteins) a
peptide group.
Polypeptides and
proteins are chains of
amino acids held together by peptide bonds, as is the backbone of
PNA.
Polyamides, such as
nylons and
aramids, are synthetic molecules (
polymers) that possess peptide bonds.
A peptide bond can be broken by
amide hydrolysis (the adding of water). The peptide bonds in proteins are
metastable, meaning that in the presence of water that'll break spontaneously, releasing about 10
kJ/
mol of
free energy, but this process is extremely slow. In living organisms, the process is facilitated by
enzymes. Living organisms also employ enzymes to form peptide bonds; this process requires free energy. The
wavelength of
absorbance for a peptide bond is 190-230nm.
Resonance forms of the peptide group
The amide group has two
resonance forms, which confer several important properties. First, it stabilizes the group by roughly 20 kcal/mol, making it less reactive than many similar groups (such as
esters). The resonance suggests that the amide group has a partial
double bond character, estimated at 40% under typical conditions. The peptide group is uncharged at all normal pH values, but its double-bonded resonance form gives it an unusually large dipole moment, roughly 3.5 Debye (0.7 electron-angstrom). These dipole moments can line up in certain
secondary structures (such as the α-helix), producing a large net dipole.
The partial double bond character can be strengthened or weakened by modifications that favor one resonance form over another. For example, the double-bonded form is disfavored in
hydrophobic environments, because of its charge. Conversely, donating a
hydrogen bond to the amide
oxygen or accepting a hydrogen bond from the amide
nitrogen should favor the double-bonded form, because the hydrogen bond should be stronger to the charged form than to the uncharged, single-bonded form. By contrast, donating a hydrogen bond to an amide
nitrogen in an X-
Pro peptide bond should favor the single-bonded form; donating it to the double-bonded form would give the nitrogen five quasi-covalent bonds! (See Figure 3.) Similarly, a strongly
electronegative substituent (such as
fluorine) near the amide nitrogen favors the single-bonded form, by competing with the amide
oxygen to "steal" an electron from the amide
nitrogen (See Figure 4.)
Cis/trans isomers of the peptide group
The partial double bond renders the amide group planar, occurring in either the
cis or
trans isomers. In the unfolded state of proteins, the peptide groups are free to isomerize and adopt both isomers; however, in the folded state, only a single isomer is adopted at each position (with rare exceptions). The trans form is preferred overwhelmingly in most peptide bonds (roughly 1000:1 ratio in trans:cis populations). However, X-Pro peptide groups tend to have a roughly 3:1 ratio, presumably because the symmetry between the
requires that the partial double bond be broken, so that the activation energy is roughly 20 kcal/mol (See Figure below). However, the
activation energy can be lowered (and the isomerization
catalyzed) by changes that favor the single-bonded form, such as placing the peptide group in a hydrophobic environment or donating a hydrogen bond to the nitrogen atom of an X-Pro peptide group. Both of these mechanisms for lowering the activation energy have been observed in
peptidyl prolyl isomerases (PPIases), which are naturally occurring enzymes that catalyze the cis-trans isomerization of X-Pro peptide bonds.
Conformational
protein folding is usually much faster (typically 10-100 ms) than cis-trans isomerization (10-100 s). A nonnative isomer of some peptide groups can disrupt the conformational folding significantly, either slowing it or preventing it from even occurring until the native isomer is reached. However, not all peptide groups have the same effect on folding; nonnative isomers of other peptide groups may not affect folding at all.
Chemical reactions
Owing to its resonance stabilization, the peptide bond is relatively unreactive under physiological conditions, even less than similar compounds such as
esters. Nevertheless, peptide bonds can undergo chemical reactions, usually through an attack of an
electronegative atom on the
carbonyl carbon, breaking the carbonyl double bond and forming a tetrahedral intermediate. This is the pathway followed in
proteolysis and, more generally, in N-O acyl exchange reactions such as those of
inteins. When the functional group attacking the peptide bond is a
thiol,
hydroxyl or
amine, the resulting molecule may be called a
cyclol or, more specifically, a thiacyclol, an oxacyclol or an azacyclol, respectively.
Further Information
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