From Proteopedia
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- In this we can see a short fragment of a polypeptide chain in order to analyze some features of its primary structure. Atoms forming the chain backbone are disposed in zig-zag, as required by geometry of its bonding orbitals. Side chains of amino acid residues (or R groups) protrude outwards either side of backbone.
- Let's go now to a between two amino acid residues. Because phenomenon of resonance, peptide bond shows some features of a double bond, which prevents free rotation of atoms on either bond side. So, six atoms marked in on model window are always confined to the same rigid flat. We can test it by .
- Polypeptide chain backbone consist in a monotonous succession in wich the following sequenze repeats: , , . Minding the restrictions to free rotation in peptide bond, we can visualize the polypeptide chain as a succession of . Each of these rigid flats can freely rotate respect each other.
- Secondary structure.- In most proteins there are two main types of secondary structure.
- .- It is a helical structure with a thread pitch of 0.56 nm. Let's go to a . Now let's . The polypeptide chain backbone is coiled and placed at the center of structure, while amino acid side chains protrude outward from this backbone. Let's for a better understanding. Now, let's back to a . A highlights the helical folding of the backbone. Using again a we recover , now highlighted with a spectral color series. Alfa helix structure becomes stabilized by many . All peptide groups in the chain are involved in these hydrogen bonds. to a better understanding.
- Primary structure specifies secondary structure, i.e., is the amino acid sequence which determines that a polypeptide chain folds resulting a alfa helix or other secondary structure. Let's consider the effects of of either sign and the .
- .- Polypeptide chain is folded in zigzag arrangement. Let's and for a better understanding. Notice that a polypeptide chain can have several linear fragments separated by curvatures called beta turns. Now let's recover and highlight the between different linear sections of the chain. This hydrogen bonds give stability to the structure. Let's look now the polypeptide chain represented by a .
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