BCH4024 - Mareci Lecture 4

BCH4024 - Mareci Lecture 4 - Lecture 4 Course Subsection...

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Lecture 4 Course Subsection Outline L-3. Amino Acids (AA’s) L-4. Peptides and Peptide Bonds ept des a d ept de o ds L-5. Three-dimensional Structure of Proteins L-6. Protein Dynamics and Protein Folding L-7. Protein Function; Hemoglobin L-8. Protein Function, Contractile and Motile Systems Copyright University of Florida. All Rights Reserved 1
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Lecture 4 Peptides and the Peptide Bond • Amino acids can be covalently bonded together into a polymer by the formation of an amide bond (the peptide bond ) between the - carboxyl group of one AA and the -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 . + + Glycine Alanine Glycylalanine water Note: the N-terminal amino and C-terminal carboxyl groups are available for further reaction Copyright University of Florida. All Rights Reserved 2 Planar peptide bond
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Lecture 4 Structure of the Peptide Bond Peptide bond is a resonance-hybrid of two structures so the O=C-N-H bonds are co-planar is rans isomerization is defined by the C=0 Figure 5.12, p. 138: Biochemistry; Mathews, Van Holde, Ahern Cis-Trans isomerization is defined by the C=0 to NH orientation. The peptide bond is nearly always in a trans onfiguration since the steric hindrance of side Copyright University of Florida. All Rights Reserved 3 configuration since the steric hindrance of side chains is greater for a cis configuration.
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Lecture 4 Formation and Stability of the Peptide Bond • A molecule of water is eliminated for each peptide bond formed. + + Glycine Alanine Glycylalanine water AA Residue i+1 AA Residue i+3 • In an aqueous environment, the formation of a peptide bond is not favored AA Residue i AA Residue i+2 • The energy for peptide bond formation is provided by hydrolysis of high- thermodynamically (G ~ +10 kJ/mol at room temperature). Instead, the reverse reaction, hydrolysis of the peptide bond, is favored. Copyright University of Florida. All Rights Reserved 4 energy phosphate bonds during the process of translation of the genetic code by the machinery of the cell (more on this machinery later).
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Lecture 4 Polypeptides • The convention is always to represent the N-terminus on the left and the C- terminus on the right. The peptide naming convention lists the individual AA’s in order starting at the N-terminus with the name of every AA ending in –yl, except for the C-terminal AA, which takes its full name. • Short peptides of a few residues (e.g. the tetrapeptide below) are called oligopeptides, Longer chain peptides are call polypeptides and proteins are very long chair polypeptides (>10,000 daltons). Glu Ala Gly Lys • Also the term polypeptide refers simply to a chain of amino acids while the term Figure 5.9, p. 136: Biochemistry; Mathews, Van Holde, Ahern Copyright University of Florida. All Rights Reserved 5 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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This note was uploaded on 03/15/2010 for the course BCH 4024 taught by Professor Allison during the Spring '08 term at University of Florida.

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BCH4024 - Mareci Lecture 4 - Lecture 4 Course Subsection...

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