Slides2 011712(2)

Slides2 011712(2) - Today! Amino acids and polypeptides...

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Today! Gibbs free energy and metabolism/catabolism Thermodynamics Spontaneity against the odds Amino acids and polypeptides Peptide bonds and peptides Features of amino acid side chains Charge and pH (Protein structure)
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Question of the day: Why for thousands of years has the goldfish been the choice for a household fish pet? From last time: swarming bees Video at: http://www.bees-on-the-net.com /honey-bee-swarms.html
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Proteins: chains of amino acids http://www.c-science.com/txt/images/1999/990406tefax.jpg
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Amino acids The α -carbon -20 common amino acids -Tetrahedral arrangement of four distinct groups (exception Glycine R=H) Lehninger
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Stereoisomers- each amino acid can exist in two conformations Lehninger Also called “enantiomers” Protiens in living organisms are almost exclusively synthesized with L- enantiomers
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Convention for naming the enantiomers (D-, L-) Lehninger Stereo chemistry influences structure: evolutionary selection for one enantiomer
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Peter Kim (when at MIT) current president of Merck Research Laboratories How would peptides made of D-amino acids behave? -Potential use as drugs as stabile in serum and cells -Strategy has identified promising candidate D-peptides for blocking HIV cell entry How to identify useful D-peptides? Kim idea: make protein from D-amino acids (used Src, a protein involved in cancer) Then screen huge collection of L-peptides for binding Mirror symmetry: make D-peptides of -Some of these D-peptides inhibit normal Src!! the L-peptides that bind “D-Src” To read the original paper: Schumacher et al. (1996) Identification of D-peptide ligands through mirror-image phage display. Science 271:1854
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Peptide bonds
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Peptides have a distinct orientation Direction of synthesis (remember, they are synthesized using mRNA template 5’ to 3’ yields amino- to carboxyl-)
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Peptide bonds restrict rotation (partial double bond characteristics) (Like a playing card)
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Figure 3-3a Molecular Biology of the Cell (© Garland Science 2008) Although proteins can fold in an enormous number of ways, there are steric interactions within the polypeptide chain that restrict the possible three-dimensional arrangements of atoms. The steric hindrance may involve the NH hydrogen atom and the CO oxygen, or it may involve adjacent R groups (see later examples of this) Proteins are flexible because the bonds of the C α carbon of amino acids can rotate
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A space filling model of peptide bonds
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Steric hindrance occurs when both psi and phi values are equal to 0
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Molecular Biology of the Cell (© Garland Science 2008) These values correspond to an β sheet These values correspond to an α helix Ramachandran plot (all angles observed in a protein) -But lots of flexibility (secondary structure defines many angles)! -There are angles that do not occur (0, 0)
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This note was uploaded on 03/07/2012 for the course BIOL 212 taught by Professor Kina during the Spring '12 term at UPenn.

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Slides2 011712(2) - Today! Amino acids and polypeptides...

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