lecture2 - Course Subsection Outline 1. Amino Acids (AAs)...

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Copyright 2002 University of Florida. All Rights Reserved Course Subsection Outline 1. Amino Acids (AA’s) 2. Peptides and Peptide Bonds 3. Three-dimensional Structure of Proteins 4. Protein Dynamics and Protein Folding 5. Protein Function, Myoglobin and Hemoglobin 6. Protein Function, Contractile and Motile Systems
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Copyright 2002 University of Florida. All Rights Reserved Peptides and the Peptide Bond • Amino acids can be covalently bonded together into a polymer by the formation of a amide bond (the peptide bond ) between the α - carboxyl group of one AA and the α -amino of the next AA. A molecule of water is eliminated for each peptide bond formed and the product is called a peptide (e.g. dipeptide below). The portion of the AA left in the peptide is termed an amino acid residue . Note: the N-terminal amino and C-terminal carboxyl groups are available for further reaction + + Glycine Alanine Glycylalanine water Planar peptide bond PDB File
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Copyright 2002 University of Florida. All Rights Reserved Structure of the Peptide Bond Peptide bond is a resonance hybrid of two structures so that O=C-N-H are co-planar Peptide bond is nearly always in a trans configuration since the steric hindrance of side chains is greater for a cis configuration Figure 6.2, p. 162: Lehninger Principles of Biochemistry
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Copyright 2002 University of Florida. All Rights Reserved Formation and Stability of the Peptide Bond • A molecule of water is eliminated for each peptide bond formed. • The energy for peptide bond formation is provided by hydrolysis of high- energy phosphate bonds during the process of translation of the genetic code by the machinery of the cell (more on this machinery later). • In an aqueous environment, the formation of a peptide bond is not favored thermodynamically (G ~ +10 kJ/mol at room temperature). Instead, the reverse reaction, hydrolysis of the peptide bond, is favored. O N H 3 + O - O N H 3 + C H 3 O - O N H 3 + O NH C H 3 O - + + H 2 O G = - 1 0 K J / m o l G = + 1 0 K J / m o l
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Copyright 2002 University of Florida. All Rights Reserved Polypeptides • The convention is always to represent the N-terminus on the left and the C- terminus on the right. • Short peptides of a few residues (e.g. the pentapeptide below) are called oligopeptides, Longer chain peptides are call polypeptides and proteins are very long chair polypeptides (>10,000 daltons). Figure 5-14, p. 126: Lehninger Principles of Biochemistry Ser Gly Tyr Ala Leu • Also the difference between a polypeptide and a protein is that the term polypeptide refers simply to a chain of amino acids while the term protein refers to the chain of amino acids after it folds properly and is (in some cases) modified. Also proteins may consist of more than one polypeptide chain.
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Copyright 2002 University of Florida. All Rights Reserved Properties of Amino Acids Found in Proteins Amino Acid M pK pK pK pI Hydropathy Occurrence in (-COOH) (-NH3) (R-group) Index proteins (%) Nonpolar, aliphatic Glycine 75 2.34 9.60 5.97 -0.4 7.2 Alanine Ala 89 2.34 9.69 6.01 1.8 7.8 Proline 115 1.99 10.96 6.48 1.6 5.2 Valine Val 117 2.32 9.62 5.97 4.2 6.6 Leucine 131 2.36 9.60 5.98 3.8 9.1 Isoleucine Ile 131 2.36
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lecture2 - Course Subsection Outline 1. Amino Acids (AAs)...

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