Exam 2 biochem - Average packing density of 0.74 for...

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Average packing density of 0.74 for protein Definitions for orders of protein structure, including supersecondary and domains 1. Primary: sequence of amino acids by peptide bonds to form polymer 2. Secondary: Regular recurring arrangements of primary protein, which is polymer a) The helices formed by the polymer backbone b) Example: Alpha helix and Beta Sheet Supersecondary-motif, short range associations of secondary structural elements, often through side chain interactions Domain- associations of lower order structure to form a 3-D unit 3. Tertiary: folding of all helical units, which is secondary, to produce the complete 3-D polypeptide structure. (Actual protein) 4. Quaternary: interaction between protein monomers to form multiple proteins. Planar structure and cis/trans configuration of peptide bond unit; reason for and consequences of - Usually found in trans configuration because the true electron density is intermediate - Cis peptides are energetically extremely unfavorable because of steric clashes between neighboring C atoms - Double bond character causes the six atoms of the peptide bond group to always be planar Definition of φ and ψ angles; φ angle of pro is fixed Φ phi controls the C'-N distance, apprx 15 degrees pucker out of planarity due to partial double bond nature, doesn’t change ψ psi controls the C’-C’ distance, can rotate around the bond φ angle of pro is fixed at 60 degrees because it contains a five membered ring helix breaker( because of fixed structure What a Ramachandran plot shows; why glycine can be located anywhere on the plot shows the sterically reasonable values of the angles φ & ψ. pg 138 for picture Glycine is excluded because it has a wide range of angles permitted because of lack of side chain, often found in flexible regions with unusual backbone conformations If number on plot is negative, left handed, positive=right handed Plot is surface of a sphere that’s been sliced so 2D Why α helix and β conformation predominate (i.e., because they represent minimum free energy states) - Proteins adopt most stable tertiary structures possible (those of lowest free energy) - Fold as so to bury hydrophobic side chains and leave charged groups on surface a. Since sidechains of hydrophobic residues are located in the hydrophobic core, the mainchain atoms of the same residues in most cases are also within the hydrophobic core b. Since the presence of polar groups in hydrophobic environment is very unfavourable, the main chain N- and O- atoms have to be neutralized by formation of hydrogen bonds c. The two most efficient ways of hydrogen bond formation is to build an alpha helix or a beta sheet Why parallel β sheets are in the interior of proteins and are less stable than antiparallel sheets (viz., less favorable skewed H-bonds can’t compete with H-bonding to water) -Antiparallel sheets are usually arranged with all their hydrophobic residues on one side of the sheet. This requires an alternation of hydrophilic and hydrophobic residues in the primary structure of peptides involved
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This note was uploaded on 02/08/2012 for the course CHEM 3361 taught by Professor Marsh during the Spring '11 term at University of Texas at Dallas, Richardson.

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Exam 2 biochem - Average packing density of 0.74 for...

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