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Primary Structure of Proteins
The primary structure of proteins refers to the specific sequence of amino acids that make up that protein. Every protein contains its own unique sequence of amino acids that determines the three-dimensional structure of that protein. The linear polymer of amino acids, which are held together by peptide bonds, has polarity. This is because one end of the polypeptide chain contains a full positive charge while the other end contains a full negative charge. By convention, the beginning of the polypeptide chain is always at the positively-charged alpha amino group while then end is at the negatively-charged alpha carboxyl group. Each amino acid in the polypeptide chain has the ability to donate a hydrogen atom to form a hydrogen bond via the N-H group and accept a hydrogen atom to form a hydrogen bond via the C=O group. This will play an important role in determining the secondary structure of proteins. The peptide bond holding each adjacent pair of amino acids is resonance stabilized, which means that it has a double bond character. Therefore the peptide bond is planar and does not rotate in space. The cis configuration of the peptide bond is typically more stable than the trans peptide because of steric hinderance. Each amino acid contains two bonds that can readily rotate - this includes the phi angle and the psi angle. The phi angle is the angle between the alpha carbon atom and the nitrogen while the psi angle is the angle between the alpha carbon and the carbon of the carbonyl group. These angles, known as the torsion angles, are responsible for rotating the entire linear polymer and ultimately transforming the linear polymer into a three-dimensional molecule.
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