Alanine in the pushfit model
Fig. 12. First step
Because the single piece that represents the peptide bond always includes part of an adjacent amino acid, one can never build only a single amino acid using the pushfit model kit. So simply ignore the incomplete part of the adjacent amino acid (Fig. 12 left). When the alpha chiral (alpha) carbon is fit onto the peg of the peptide unit, it can undergo the "phi" rotation shown in Fig 11.
Fig. 13. Second step
The chiral carbon atom has two long prongs onto which other pieces can be attached. If the methyl group is attached to the wrong one, the D isomer will be formed instead of the desired L isomer.
Fig. 14. Third step
The alanine molecule is completed by attaching another one of the rigid polypeptide units to the unoccupied chiral carbon prong.
Polypeptide in the pushfit model
Fig. 15. First amino acid in a polypeptide.
A polypeptide can be constructed using the pushfit model kits by continuing the process used to build a single alanine. Beginning with nitrogen of the incomplete amino acid attached to the alanine, add a chiral carbon followed by other pieces as described in the instructions for building alanine. Note: a common mistake is to build two of the units shown in Fig. 15, then attach them together. This results in two adjacent peptide bonds, rather than a peptide bond followed by an alpha carbon.
Fig. 16. Two amino acids in a polypeptide.
This image shows a correctly constructed dipeptide. The process can be continued by adding an alpha carbon to the prong of amino acid #2 and then attaching the pieces to it that are needed for amino acid #3.
Fig. 17. Polypeptide in extended conformation ("side" view).
Fig. 17 shows a "side" view of a pushfit model polypeptide in "extended conformation". In extended conformation, the oxygen atoms (white balls) alternate up, then down, then up, then down, etc. Because the rigid peptide bond holds the amino nitrogens in the opposite direction, they also alternate up and down in adjacent amino acids.
Fig. 18. Polypeptide in extended conformation ("top" view).
Fig. 18 shows the same model viewed from the "top". In this view, you can see that the backbone chain falls in a single plane and that the R groups are slightly offset to alternate sides of that plane. The video below show you how to check your polypeptide for "bad" D isomers.
