 It refers to the amino acid content (type and number),and sequence in the polypeptide chain and the location of the disulfide bonds if present.  It is stabilized by the covalent peptide bond.  It is the simplest level of protein structure.  It is present in all proteins.  It is not affected by the denaturation factors.  It is the most stable structure of proteins.  The primary structure of a protein is determined by the specific gene coding for that protein.  It is the specific number, type and sequence of the amino acids in the polypeptide chain that determine its primary structure, and it is the primary structure of the protein that determines the proteins three dimensional structure and finally it is the structure of the protein that dictates its function.

 Sickle cell anemia is an example that shows how the amino acid composition (primary structure) of a protein affects the protein structure and consequently its biological function. Sickle cell anemia is a disease that results from the substitution(caused by a mutation) of polar glutamate by nonpolar valine in the β -subunit of hemoglobin. Normal RBC Sickled cells

 Secondary structure refers to the spatial arrangement of amino acids that are near one another in their linear sequence.(or the regular recurring arrangement in space of adjacent amino acid residues in the polypeptide chain).  Α-helix. ; the backbone of the polypeptide chain is tightly coiled around a long axis while the R-groups extend outwards.  The α-heilx is stabilized by Hydrogen bonds which is formed between the peptide –CO group of one amino acid and the peptide –NH group of another amino acid that is situated four amino acid residues ahead in the linear sequence.  All the peptide –CO and –NH groups are involved in the Hydrogen bonding except those at terminal ends of the polypeptide chain.  Each turn in the α-heilx contains 3.6 amino acid residues.  Each amino acid in the α-heilx is 1.5 A˚ apart from the next amino acid.

 The screw sense or direction of the α-heilx can be right handed or left handed, in proteins the right handed α-heilx prevails.  The Hydrogen bonds run parallel to the long axis of the α-heilx.  The α-heilx is stabilized by;  Clusters of amino acids carrying the same charge such as Asp, Glu or Lys,Arg,due to the disruptive action of the repulsion forces between the similar charges.  Amino acids with bulky side chains e.g Leu.  The occurrence of proline breaks the α-heilx because its α-amino group is involved in a ring structure which makes it bulky and difficult to be accommodated in the tight α-heilx structure and also due to the fact that it has no H atom at its α-amino group thus it cannot participate in the Hydrogen bond formation.  The helical content of proteins ranges from almost 0-100%  α-heilx structures can wind around each other to form a superhelix.

Β-pleated sheet;  Here the backbone of the polypeptide chain is almost fully extended (rather than being tightly coiled) into a zigzag structure.  The distance between adjacent amino acids is approximately 3.5 A˚ (reflecting an extended backbone compared to the α-heilical structure).  The side chain of the amino acid residues point in opposite directions, above or below the backbone plane.  It is stabilized by a large number of hydrogen bonds that are formed between the peptide –CO group of one amino acid on one strand and the peptide –NH group of another amino acid on a different adjacent strand.  These linked β-strands can run in opposite directions antiparallel Or in the same direction parallel.

α-heilxΒ-pleated sheet It has a helical rod shapeIt has a zigzag sheet shape The polypeptide chain is tightly coiled. The polypeptide chain is almost fully extended. The hydrogen bonds occur between amino acids within the same strand. The hydrogen bonds occur between amino acids in the different adjacent strands. The hydrogen bonds occur between amino acids near to each other. The hydrogen bonds occur between amino acids further apart.