Proteins
Almost all amino acids in nature are L-amino acids (aside from glycine which has a H R-group).
This should form a CORN configuration where -NH2 is present on the left hand side. They are
held together by peptide bonds which have double bond characteristics through the resonance
structures which form in between the C=O and C-N bonds.
Three types of covalent bond are present: N-C, C-C=O, and C=O-to-N-H of the next amino
acid. Disulphide bonds form between the side chains of two cysteines in oxidising
conditions. The bond can be cleaved by reduction with the reducing agent B-
mercaptoethanol. The disulphide bond tends to be found in proteins present in extracellular
proteins.
The terminal residues with unused NH2 or COOH groups are called the amino (N-terminus) and
the carboxyl (C-terminus). The N-terminal residue is called residue number 1. The primary
structure is written out in terms of the sequence of the amino acid residues from left to right with
the N-terminal residue always on the left.
Peptide Bond Configurations
The majority of peptide bonds are in trans configuration meaning the two alpha carbons point in
different directions. This is thermodynamically more stable. This is because in cis configuration,
side chains of neighbouring amino acids would undergo steric hinderance. The trans
Proteins 1
, configuration allows the amino acid side chains to be spaced apart without electrostatic
repulsion. This causes the energy of the cis configuration to be higher and less stable.
The exception is the X-Proline bond where X can be any amino acid. Steric hinderance occurs in
both cis and trans configurations therefore the X-Proline bond can be present in cis-configuration
more frequently than any other peptide bond.
The peptide bond is resonance stabilised which means the actual structure is neither one. The
peptide bond therefore has double bond character so the length of the C-N bond is in between a
single bond and double bond. This means the C-N bond cannot rotate in space due to the double
bond character as single bonds can rotate but double bonds cannot. The C-N peptide bond is rigid
with other bonds being able to rotate forming the cis and trans configurations. The double bond
nature of the peptide bond means that 6 atoms lie in the same plane.
Phi (ϕ) Angle: The phi angle describes the torsion angle around the N-Cα bond in the protein
backbone.
Psi (ψ) Angle: The psi angle describes the torsion angle around the Cα-CO bond in the protein
backbone.
These angles, known as the torsion angles and are responsible for rotating the entire linear
polymer and ultimately transforming the linear polymer into a three-dimensional molecule.
Proteins 2
Almost all amino acids in nature are L-amino acids (aside from glycine which has a H R-group).
This should form a CORN configuration where -NH2 is present on the left hand side. They are
held together by peptide bonds which have double bond characteristics through the resonance
structures which form in between the C=O and C-N bonds.
Three types of covalent bond are present: N-C, C-C=O, and C=O-to-N-H of the next amino
acid. Disulphide bonds form between the side chains of two cysteines in oxidising
conditions. The bond can be cleaved by reduction with the reducing agent B-
mercaptoethanol. The disulphide bond tends to be found in proteins present in extracellular
proteins.
The terminal residues with unused NH2 or COOH groups are called the amino (N-terminus) and
the carboxyl (C-terminus). The N-terminal residue is called residue number 1. The primary
structure is written out in terms of the sequence of the amino acid residues from left to right with
the N-terminal residue always on the left.
Peptide Bond Configurations
The majority of peptide bonds are in trans configuration meaning the two alpha carbons point in
different directions. This is thermodynamically more stable. This is because in cis configuration,
side chains of neighbouring amino acids would undergo steric hinderance. The trans
Proteins 1
, configuration allows the amino acid side chains to be spaced apart without electrostatic
repulsion. This causes the energy of the cis configuration to be higher and less stable.
The exception is the X-Proline bond where X can be any amino acid. Steric hinderance occurs in
both cis and trans configurations therefore the X-Proline bond can be present in cis-configuration
more frequently than any other peptide bond.
The peptide bond is resonance stabilised which means the actual structure is neither one. The
peptide bond therefore has double bond character so the length of the C-N bond is in between a
single bond and double bond. This means the C-N bond cannot rotate in space due to the double
bond character as single bonds can rotate but double bonds cannot. The C-N peptide bond is rigid
with other bonds being able to rotate forming the cis and trans configurations. The double bond
nature of the peptide bond means that 6 atoms lie in the same plane.
Phi (ϕ) Angle: The phi angle describes the torsion angle around the N-Cα bond in the protein
backbone.
Psi (ψ) Angle: The psi angle describes the torsion angle around the Cα-CO bond in the protein
backbone.
These angles, known as the torsion angles and are responsible for rotating the entire linear
polymer and ultimately transforming the linear polymer into a three-dimensional molecule.
Proteins 2
