Peptide Bonds Biochem 4511 Figures from Essentials of Biochemistry 3rd Ed OSU Custom Edition Lehninger Principles of Biochemistry 4th 5th Ed Voet Voet Biochemistry 3E Voet Voet Pratt Fundamentals of Biochemistry 2E Levels of Protein Structure Levels of Protein Structure Primary Sequence Primary Sequence Depending on definition may include disulfide bonds Defining polypeptides Oligopeptide is a few amino acids linked Polypeptide is many amino acids linked Protein is a large polypeptide typically with a MW 10 000 Da g mole cutoff In reality these terms are amorphous ish Peptide Bond Peptide amide bond condensation of two amino acids with release of water Note appropriate selection of Fischer projection to maintain stereochemistry H R H 3 N C O O the line structure S S Peptide Bond Peptide Bond Planarity Delocalization creates partial double bond character Amide bond is planar like paper Peptide Bond Planarity Peptide Bond Dipole Peptide Bond cis vs trans Two isomers around the amide bond with its partially double character Trans is energetically favored due to steric clash of side chains in cis conformation Proline cis vs trans Due to the ring structure of proline cis and trans are energetically similar for X Pro often 30 cis Peptide Drawing Rules If one letter codes all capital letters If three letter codes first letter capitalized Always written N to C Termini are sometimes specified PEPTIDE H2N PEPTIDE COOH ProGluProThrIleAspGlu H2N Pro Glu Pro Thr Ile Asp Glu OH Proline Glutamate Proline Threonine Isoleucine Aspartate Glutamate Peptide Drawing Practice Practice drawing the peptide PEPTIDE using the line structure rules you have learned Extended structure Ionization charge state L amino acid H3NCOO RH Peptide Charge States pH lower than pKa protonated pH higher than pKa deprotonated Physiological Acidic groups C terminus Basic side chains N terminus His 10 but predominantly neutral Cys Oxidation state Note Microenvironment affects pKa Problem What is the formal charge for the peptide CHARGED at pH 7 R N terminus 2 E D C terminus 3 0 C below pKa H above pKa A G Formal charge 2 3 1 What is the net charge for the peptide CHARGED at pH 7 R N terminus 0 1 His His HisH 10 at pH 7 2 1 E D C terminus Cys A HA 0 04 so negligible 3 0 A G Net charge 2 1 3 0 9 Note Microenvironment affects pKa A HA 10pH pKa Problem What is the net charge for the peptide CHARGED at pH 6 R N terminus 0 5 His His HisH 1 at pH 6 2 5 E D C terminus 3 0 C A G Net charge 2 5 3 0 5 Note Microenvironment affects pKa Why L amino acids Many important macromolecules and metabolites are chiral Proteins DNA sugars Evolutionarily speaking Once chirality is established it is necessarily maintained The establishment of L amino acids as the building blocks for proteins in the distant past has lead to chiral requirements of many metabolites Is there a special requirement for L amino acids or is it possible to prepare fully functioning proteins from D amino acids HIV Protease Ligation Extra Preparing synthetic protein Synthesize two peptides of 50 aa each Ligate together the two peptides to yield full length HIV protease Note In this scheme a sulfur has replaced the amide nitrogen at the ligation site Don t memorize just concept Dawson P E and Kent S B H Annu Rev Biochem 69 923 960 2000 Mirror Image HIV Protease Extra Dawson P E and Kent S B H Annu Rev Biochem 69 923 960 2000 Questions Amino Acids Peptides Why is a peptide bond planar Draw the relevant structures to demonstrate Be able to draw the chemical structure of any peptide sequence provided Practice by drawing peptide sequences think about how the side chain ionization would change under different pH conditions based on pKa values Book Chapter 4 1 Odd problems 1 through 19 10 12 26