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This 19 page Class Notes was uploaded by Amalachi Notetaker on Sunday September 18, 2016. The Class Notes belongs to CHEM3510 at University of Toledo taught by Bellizzi,J in Fall 2016. Since its upload, it has received 5 views. For similar materials see Biochemistry I in Natural Sciences and Mathematics at University of Toledo.
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Lecture 6 Amino Acids CHEM 3510 Biochemistry I Dr. John Bellizzi Fall 2016 Lecture 6 - 2016 2 Proteins • Linear macromolecular polymers formed from amino acids. • Peptide bond – amide linkages connecting amino acid residues. • A polypeptide chain has a backbone (main chain) and side chains. • Backbone – peptide links between amino acids • Amino acid side chains project out from the backbone and bear different functional groups • Synthesized in cells on ribosomes – large nucleoprotein particles which translate information from mRNA into protein • Linear polypeptide chain folds up into 3D shapes due to interactions between different parts of the chain w/each other and w/water. • Proteins play many diverse functional roles in biochemistry • Enzymes that catalyze chemical reactions • Receptors/transporters for small molecules and ions • Structural proteins which provide mechanical stability/integrity • Transcription factors that control the expression of genes • Antibodies that recognize foreign biomolecules Lecture 6 - 2016 3 Amino Acids • α-amino acids • Carboxylic acids with amino group attached to α- carbon • Other 2 substituents on α-carbon are H and side chain (R) • Different side chain = different amino acid • 20 different amino acids found in proteins • α-carbon is chiral (unless R=H) • Most important role of amino acids = building blocks for proteins. • However, many of them play other roles on their own as well. Lecture 6 - 2016 4 L-Amino Acids • All amino acids except glycine are chiral. • Configuration of amino acids described as L or D • (by comparison to L, D-glyceraldehyde): • Line up COO and H of amino acid with CHO and H of glyceraldehyde • All amino acids in proteins are L-amino acids. Lecture 6 - 2016 5 Structural representations of L and D alanine Lecture 6 - 2016 6 Amino Acids have two ionizablegroups Lecture 6 - 2016 7 The 20 Amino Acids of Proteins – Part 1 Lecture 6 - 2016 8 The 20 Amino Acids of Proteins – Part 2 Lecture 6 - 2016 9 The 20 Amino Acids of Proteins – Part 3 Lecture 6 - 2016 10 The 20 Amino Acids of Proteins – Part 4 pK aalues: Aspartate 3.65 Glutamate 4.25 Histidine 6.00 Other ionizable side chains: Lysine 10.53 Cysteine (pK 8.18), Tyrosine (pK 10.07) Arginine 12.48 a a Lecture 6 - 2016 11 Atom nomenclature in amino acids Lecture 6 - 2016 12 Ionization of amino acids • Isoelectric Point (equivalence point, pI) is the midpoint of titration • Amino acid has net charge of 0 at its pI. Lecture 6 - 2016 13 Chemical Environment affects pK Values a Lecture 6 - 2016 14 Ionizable side chains Lecture 6 - 2016 15 Isoelectric Point • Isoelectric Point (equivalence point, pI) is pK + pK pI = 1 2 2 • At this point, the net charge is zero • AA is least soluble in water • AA does not migrate in electric field • For amino acids without ionizable side chains, the two pK values are for the carboxylate and the amino group. What if you have an ionizable side chain? • Identify species that carries a net zero charge • Identify pK far the +1 charge species losing a proton • Identify pK of the net zero charge species losing a proton a • Take the average of these two pK valaes • Ex: pI of Histidine Lecture 6 - 2016 16 Modified Amino Acids in Proteins Lecture 6 - 2016 17 Important amino acid derivatives and non- protein amino acids Lecture 6 - 2016 18 Learning Objectives – Amino Acids • Structures of the 20 standard proteogenic amino acids • α-carbon with amino, carboxylate, H and R group with proper stereochemistry and protonation state/formal charge at pH 7. • Side chain structures • Names, one and three letter abbreviations • Atom number/letter nomenclature • Chemical classification (nonpolar aliphatic, aromatic, polar, positively charged, negatively charged). • Also know which amino acids absorb UV light and which forms disulfide bonds. • Approximate pK of amiao and carboxylate group, ionizable side chains • (You will be given exact values if you need to do pI calculations). • You should also know the names/structures of the following modified amino acids: • 4-hydroxyproline, phosphoserine, phosphotyrosine, 6-N-acetyllysine Lecture 6 - 2016 19 Summary • Proteins are linear heteropolymers (macromolecules) built from amino acids • Amino acids • Amino groups attached to the α-carbon of a carboxylic acid • 20 amino acids (with different side chain groups attached to α- carbon) that make up proteins • Have one and three letter abbreviations • Can be divided into groups based on the chemical and physical properties of their side chains. • Amino acids have different charges at different pH values because of ionizable groups.