Protein structure notes PDF

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L1-8...

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BS1032

February 24, 2020

Primary structure: the sequence of amino acids, these are linked together by ribosomes. This sequence forms the 3D structure of a protein in turn its function. -

Protein are made from L-amino acids (the S enantiomers) this determines the 3D structure of the protein. Amino acids cannot rotate around the peptide bond formed between proteins. -

The amino acids can rotate on other bonds just not the peptide bond. These are measured as phi and psi angles. These are torsion angles.

Phi is the angle between successive carbonyl carbons.  Psi is the angle between successive backbone nitrogen’s. Some values of  and  are more stable than others. Some combinations are favoured by hydrogen-bonding interactions with the backbone. Ramachandran plot- A plot of  against  for a particular polypeptide. 

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Secondary Structure:  sheet is an extended structure; the angle is near 180°, 3.5 Å (an angstrom unit of measurement) between residues. -helix 1.5 Å between residues residues. There are Hairpin () turns between helices. It is clockwise therefore a righthand protein. - Proline distributes into both -helices and -sheet. - Glyceine and Proline commonly cause -turns, but can adopt  and  angles. - Hydrophobic chains favour -sheet. - Small hydrogen bonding sidechains distribute into -helices. Tertiary Structure (refers to 3D structure): -

Tertiary structure is stabilised by: o Non covalent interaction: hydrophobic effect, ion dipole, hydrogen bonds, salt bridges, dispersion forces. o Dilsufide bridges

BS1032

February 24, 2020

Loops “random coils” are binding sites in proteins. Antibodies can bind antigens strongly at loop regions....