Secondary structure peptide bonds affecting

The aromatic rings in the protein absorb ultraviolet light at an absorbance maximum of 280 nm, whereas the peptide bonds absorb at around 205 nm. The unique absorbance property of proteins could be used to estimate the level of proteins. These methods are fairly accurate with the ranges from 20 p,g to 3 mg for absorbance at 280 nm, as compared with 1 to 100 p,g for 205 nm. The assay is non-destructive as the protein in most cases is not consumed and can be recovered. Secondary, tertiary and quaternary structures all affect absorbance therefore, factors such as pH, ionic strength, etc can alter the absorbance spectrum. This assay depends on the presence of a mino acids which absorb UV light (mainly tryptophan, but to a lesser extent also tyrosine). Small peptides that do not contain such a mino acids cannot be measured easily by UV. 

In RPC separation of peptides, the fundamental structural properties of the amino adds within the sequence and the relative accessibility of the nonpolar amino add residues to a large measure determine the overall selectivity that can be achieved with a defined RPC systemJ20-23 As a consequence, peptides typically elute from RPC sorbents in the order of their relative hydrophobicities, for a pre-selected mobile-phase composition, pH, and temperature. However, the relative hydrophobicities of different peptides are also conditional on the solvation environment in which they are placed. The exposure or greater accessibility of previously sequestered polar or hydrophobic amino acid side chains in polypeptides with well-developed secondary structures will thus significantly affect the relative binding affinities of these peptides to hydrocarbonaceous-bonded phase surfaces. 

Two features that affect secondary protein structure (molecular shape) include the rigid, planar geometry and restricted rotation of the peptide bond, and interchain or intrachain hydrogen bonding of the type C=0-H-N. The a helix and the pleated sheet are common protein shapes. 

Give the general formula for an amino acid. Some amino acids are labeled hydrophilic and some are labeled hydrophobic. What do these terms refer to Aqueous solutions of amino acids are buffered solutions. Explain. Most of the amino acids in Fig. 22.18 are optically active. Explain. What is a peptide bond Show how glycine, serine, and alanine react to form a tripeptide. What is a protein, and what are the monomers in proteins Distinguish between the primary, secondary, and tertiary structures of a protein. Give examples of the types of forces that maintain each type of structure. Describe how denaturation affects the function of a protein. 

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