Forming a peptide bond
Fig. 6 Formation of a peptide bond
Two amino acids can combine in a condensation reaction (where a molecule of water is formed). The resulting bond between the amino acids is called a peptide bond.
Image by Alejandro Proto CC BY-SA 3.0 from Wikimedia Commons modified by text translation and cropping
Fig. 7. Sharing of electons among adjacent p orbitals creates resonance structures that give partial double bond character to the peptide bond.
Because of the delocalization of electons from the double-bonded oxygen to the peptide bond (Fig. 7), the peptide bond has partial double bond character that prevents free rotation around the bond. Thus the atoms in the vicinity of the bond (the carbon and nitrogens forming the bond, the oxygen connected to the carbon, and the hydrogen connected to the nitrogen) have fixed positions in the plane that is formed by the bonds between them (rectangle on the right of Fig. 7). This is significant because the non-rotatibility of the peptide bond ensures that the oxygen and hydrogens are always oriented in opposite directions relative to the peptide bond.
Fig. 8 Using the keyed linker in a peptide bond.
In order to prevent free rotation in the CPK models, a special keyed gray linker is used to connect the nitrogen and carbons of adjacent amino acids. The keyed linker fits into slots in the two atoms.
Fig. 9. Formation of a dipeptide using a CPK model
The animation above shows the steps in forming a dipeptide using CPK models.
Pushfit models
Although space filling models illustrate molecular packing very well, skeletal ("ball and stick") models are easier to work with for most other applications.Their principal advantage is that the positions of the atoms and bonds can easily be seen. The atoms can therefore be positioned accurately to correspond to atomic coordinates calculated from geometric considerations or deduced from x-ray crystallographic analysis.When a model has been constructed, interatomic distance can easily be measured. We will use a ball and stick modeling system called "pushfit". The scale for the pushfit models is 1 cm = 1 Å.C, N and O atoms are represented by 0.5 cm diameter balls. H atomic positions are represented as the ends of short rods coming from the other atoms.
The color code used in the pushfit model does not differentiate between different types of atoms. Rather, it uses color to code for different parts of the polypeptide. The backbone chain is formed out of white pieces, while side chains (R groups) are formed out of gray pieces. For simplicity, only one kind of side chain is represented (CH3 for alanine).
Fig. 10 Structure of pushfit piece representing the peptide bond.
Because pushfit models are typically used to construct protein secondary and tertiary structures, it is important that they accurately portray the non-rotatable peptide bond. For this reason, the peptide bond is part of a single piece that contains parts of two adjacent amino acids. The practical implication of this is that when you build a polypeptide, you will always have parts of incomplete amino acids at both ends of the chain. Confusion about this piece is the most common source of problems with building pushfit models.
Image by Alejandro Proto CC BY-SA 3.0 from Wikimedia Commons modified by cropping
Fig. 11. Rotatible and non-rotatible bonds in a polypeptide. The backbone chain bonds on either side of the alpha carbon (designated by phi and psi) can freely rotate, while the peptide bonds (on which the blue planes are centered) cannot rotate.
Fig. 11 shows the behavior that pushfit models are designed to imitate. The rigid pushfit piece that includes the peptide bond is designed to model the blue planes. Regardless of the rotations labeled phi and psi, the oxygen atoms in the planar unit will always be on the opposite side of the chain from the hydrogen atoms attached to the adjacent nitrogen.
