Polypeptides, amino acid sequence ribbon

For the sake of convenience, the different aspects of protein structure have been divided into four categories primary, secondary, tertiary, and quaternary structures. When we speak of the primary structure of a protein, we are concerned with the amino acid sequence of its component polypeptide chains. A protein may have a single polypeptide chain with one N and one C terminus, or it may have two or more polypeptide chains, often termed subunits, with multiple N and C termini. Secondary structure problems address themselves to whether the polypeptide chains of a protein exhibit any sort of periodicity of structure in three dimensions that is, is the polypeptide chain simply an extended ribbon, or is it present in the form of a spring or a folded structure Secondary structure has also been referred to as conformation. Tertiary structure is concerned with the overall three-dimensional appearance of the protein for example, is the shape of the protein molecule best approximated by a sphere or by a disk Last, quaternary structure refers to the number, size, and shape of component polypeptide chains in a protein. 

The simplest way to create a local ordered structure within a polypeptide chain made up of amide linkages would be to form hydrogen bonds between residues which are close to one another in the amino acid sequence. As seen from Figure 3.9, this would involve either the second, third, fourth, or fifth NH group from the C=0 of the first amino acid residue. In the 2.2y ribbon description, 2.2 refers to the number of residues per turn and the subscript 7 to the number of atoms between the main chain carbonyl oxygen and the amide... 

Another feature of peptide structure must be considered. The overall structure of a long polypeptide is determined by its amino acid sequence (primary structure) and whether it forms an a-helix or a P-pleated sheet (secondary structure). It is also possible to fold or coil the peptide chain into a complex, globular structure that is known as its tertiary structure. This is illustrated by the ribbon diagram for ribonuclease A, 131. The peptide chain folds and coils into a very complex structure in 131. This is the tertiary structure of the peptide. 

Proteins are high molecular mass polypeptides with complex structures. The sequence of amino acids gives the primaiy structure of the protein, while the secondary and tertiary structures reveal the spatial properties of the peptide chain. The secrurdary structure takes into account the folding of polypeptide chains into domains called a-helices, jd-sheets, turns and coils, hr the ribbon representations of the protein structures illustrated in this chapter, the same colour coding is used to differentiate between... 

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