Peptide Bonds Biochem 4511 Figures Essentials of Biochemistry 3rd Ed OSU Custom Edition Principles of Biochemistry 5th Ed Moran et al Lehninger Principles of Biochemistry 5th Ed Nelson Cox Fundamentals of Biochemistry 2nd Ed Voet Voet Pratt Proteins as Macromolecules 1780s Substances isolated from natural sources that seemed to contain nothing but carbon hydrogen nitrogen and oxygen and sometimes phosphorus and sulfur Protein chemistry until mid 1800s elemental analysis to try to figure out what these things all had in common Gerrit Mulder analyzes albumins from several sources declares them to contain as a minimal unit C400H620N100O120 8600 Da in today s units plus assorted other groups Meaning of this Proteins are very very big Proteins as Macromolecules 1840s earthworm blood on a slide forms crystals Crystals of hemoglobin were grown from several hundred species and had different properties Results proteins are relatively pure substances with a distinct shape Different species are measurably chemical distinct Peptide Bond Formation Peptide amide bond formed by the condensation of two amino acids and the release of a water molecule When drawing peptides using Fischer projections use the AC linear format to maintain proper stereochemistry R1 O H N H3N O OR2 Peptide Bond Formation Practice drawing the peptide TEST using the amino acid line structure drawing rules you have learned Peptide Bond Resonance Partial double bond character maintains planarity of peptide amide bonds Peptide Bond Planarity Partial double bond character maintains planarity of peptide amide bonds As a result protein backbone rotations are similar to sheets of paper Amides Planarity In extended linear form side chains are on alternating sides due to stereochemistry This is the most convenient way to draw peptides but this structure is not extensively found in folded proteins Amides cis vs trans Trans is energetically favored due to steric clash of side chains in cis conformation The severity of this effect will depend on the side chain Do you think glycine may commonly be found in the 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 Always written N to C If one letter codes all capital letters If three letter codes first letter capitalized Termini are sometimes specified PEPTIDE H2N PEPTIDE COOH ProGluProThrIleAspGlu H2N Pro Glu Pro Thr Ile Asp Glu OH Proline Glutamic Acid Proline Threonine Isoleucine Aspartic Acid Glutamic Acid Peptide Bond Formation Practice drawing the peptide PEPTIDE using the line structure rules you have learned Why L amino acids Many important macromolecules and metabolites are chiral Proteins DNA sugars Evolutionarily speaking Once chirality is established it is necessarily maintained L amino acids were selected as the building blocks for proteins in the distant past and that choice has lead to the 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 Is Chirality Important Nick Vujicic Check youtube com for inspirational video 1960s given as anti nausea to pregnant women One of the stereoisomers is a drug another teratogen Structures with small chirality mistakes are WRONG In vivo Peptide Bond Formation Ribosomal protein synthesis Translation proceeds N to C Carried out by massive ribosome complexes Non ribosomal protein peptide synthesis e g antibiotics Forms complex structures incorporating standard and modified amino acids including D amino acids cyclic products etc Utilizes modular enzyme architecture Levels of Protein Structure Levels of Protein Structure Primary Structure Linear sequence of amino acids linked by peptide bonds Secondary Structure Defined by local interactions of the primary sequence helices sheets loops turns Tertiary Structure Protein domains defined by long range interactions between secondary structural units Quaternary Structure Associations between protein domains Central Dogma of Molecular Biology Protein primary sequence is determined by DNA and encodes all required information for protein to fold properly and function As always in biology there are some exceptions A a sequence primary structure Sequence of amino acids from N to Cterminus May include disulfide bonds Defining polypeptides Oligopeptide a few amino acids linked Polypeptide 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 Thought Questions Peptide Characteristics Why is a peptide bond planar Draw the relevant structures to demonstrate Draw a cis peptide bond Draw a trans peptide bond Which is more common Why 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 Restraints on Local Protein Structure Phi Psi C CO NH C CO NH C In this figure 180 extended conformation Free rotation is limited to the NH C and C CO bonds The angles around these bonds are known as dihedral or torsion angles Extended Conformation 180 Side chains extend on opposite sides of the backbone Full extended conformation is rare in real protein structures Easiest semi realistic geometry on the plane of the paper The way we are drawing peptides Ramachandran Plot Amino acid side chain determines allowed conformations The allowed or favored green regions also correspond to the main types of secondary structure Ramachandran Plot Glycine Glycine is allowed across more of dihedral space than other amino acids D space opposite chirality is reflected in and Gly has access since no side chain Problems 12 14 17 19