Tertiary structure

The secondary structure of Proteins

There are two main forms of protein secondary structure, the alpha helix and the beta sheet, however other forms such as the beta turn and the omega loop are known to exist (Berg et al., 2007:40).
The structure of the alpha helix, first predicted by Pauling and Corey in 1951, consists of a coiled helical structure held together by hydrogen bonds (Berg et al,. 2007:40). The helix can be left or right handed, coiling in an anticlockwise or clockwise direction respectively; however the right handed configuration is more energetically favourable due the fact that the side chains of the peptide backbone do not interfere with each other as much (Berg et al,. 2007: 41). The hydrogen bonds that stabilise the structure are formed between the carbonyl oxygen (CO group) of the nth residue and the amide hydrogen (NH group) of the n+4th residue (Berg et al., 2007: 40). A turn of the helix consists of 3.6 amino acid residues and the rise from one residue to the next is approximately 1.5A (Berg et al., 2007: 40).
The beta sheet is the other main secondary structure of proteins, beta sheets are made up of two or more peptide chains called beta strands( Berg et al., 2007:42). Hydrogen bonds are formed between two adjacent beta strands(Berg et al., 2007: 42). The side chains of the amino acid residues point out perpendicularly in opposite directions (up and down) to the plain of the peptide backbone of the beta strands(Berg et al., 2007: 42).
There are two types of beta sheets, anti-parallel and parallel. Anti parallel beta sheets are formed from adjacent beta strands running in an alternating configurations, if beta strand n runs from the N terminus to the C terminus the beta strand n+1 runs from the C terminus to the N terminus and the strands of the beta sheet alternate in that manner (Berg et al., 2007:42). The hydrogen bonds are formed between the amide hydrogen (NH group) and the carbonyl oxygen (CO group) of one beta strand and the carbonyl oxygen (CO group) and the amide hydrogen (NH group) of the adjacent strand respectively (Berg et al., 2007: 42). The hydrogen bonds in an anti-parallel beta sheet are short and straight making them strong (Berg et al., 2007: 42).
The parallel beta sheets are formed from adjacent beta strands running in the same configuration, if beta strand n runs from the N terminus to the C terminus then beta strand n+1 also runs from the N terminus to the C terminus (Berg et al., 2007:40). The hydrogen bonds are formed between the amide hydrogen (NH group) of an amino acid residue on beta strand n and the carbonyl oxygen (CO group) of the adjacent strand beta strand, n+1 (Berg et al., 2007:42) The carbonyl oxygen (CO group) of beta strand n forms hydrogen bonds with the amide hydrogen (NH group) of the amino acid residue two residues further down on the adjacent strand (Berg et al., 2007:43). The hydrogen bonds in parallel beta strands are long and angled making them weaker than those found in anti-parallel beta sheet (Berg et al.,2007: 40).

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