Chapter 3 Amino Acids Peptides and Proteins 3 1 Amino Acids Amino Acids Share Common Structural Features All 20 of the common amino acids are amino acids o They have a carboxyl group and an amino group bonded to the o They differ from each other in their side chains or R groups o There are many less common amino acids in addition to the 20 carbon common ones o The carbon is a chiral center and amino acids have two possible stereoisomers which are enantiomers o This makes amino acids optically active The D L system of nomenclature for different configurations of sugars and amino acids refers only to the absolute configuration of the four substituents around the chiral carbon not to optical properties of the molecule The Amino Acid Residues in Proteins Are L Stereoisomers The amino acid residues in proteins are exclusively L stereoisomers Amino Acids Can Be Classified by R Group Amino acids can be grouped into five classes based on the properties of their R groups in particular their polarity or tendency to react with water at biological pH o Nonpolar Aliphatic R Groups Nonpolar hydrophobic Alanine valine leucine and isoleucine tend to cluster together in proteins stabilizing structure through hydrophobic interactions Glycine is the simplest and hardly contributes to hydrophobic interactions Methionine has a nonpolar thioether group in its side chain Proline has an aliphatic side chain with a cyclic structure and reduces the structural flexibility of polypeptides o Aromatic R Groups Phenylalanine tyrosine and tryptophan have aromatic side chains and are relatively nonpolar and hydrophobic They all participate in hydrophobic interactions o Polar Uncharged R Groups More soluble in water more hydrophilic because of side groups capable of hydrogen bonding Serine threonine cysteine asparagine glutamine o Positively Charged Basic R Groups Some of the most hydrophilic R groups Lysine arginine histidine o Negatively Charged Acidic R Groups Aspartate and glutamate Uncommon Amino Acids Also Have Important Functions proteins may contain residues created by modification of common residues in a polypeptide 4 hydroxyproline is found in plant cell walls and collagen 5 hydroxylysine found in collagen 6 N Methyllysine is a constituent of myosin a contractile protein of muscle carboxyglutamate is found in the blood clotting protein prothrombin and certain other proteins that bind Ca2 Desmosine is found in the fibrous protein elastin Slenocysteine is introduced during protein synthesis and is a constituent of just a few proteins Some amino acids can be modified temporally to alter the protein s function i e phosphorylation Ornithine and citrulline are intermediates in the biosynthesis of arginine and in the urea cycle Amino Acids Can Act as Acids and Bases The amino and carboxyl groups along with the ionizable R groups of some amino acids function as weak acids and bases When an amino acid lacking an ionizable R group is dissolved in water at neutral pH it exists in solution as the dipolar ion or zwitterion which is amphoteric ampholytes Amino Acids Have Characteristic Titration Curves Titration Curves Predict the Electric Charge of Amino Acids The pH at which the net electric charge is zero is the isoelectric point or isoelectric pH pI o pI can be found by taking the average of the 2 pkas Amino Acids Differ in their Acid Base Properties amino acids with ionizable R groups have complex titration curves with three stages and 3 pkas 3 2 Peptides and Proteins Peptides Are Chains of Amino Acids amino acids are joined by peptide bonds to form peptides o Formed by dehydration condensation o Oligopeptide o Polypeptide when a few amino acids are joined together when many amino acids are joined At the end of a polypeptide chain amino terminal the amino acid at the end with a free carboxyl terminal the amino acid at the end with a free Hydrolysis of a peptide bond is exergonic but occurs slowly because o f a o N terminal amino group carboxyl group o C terminal high activation energy Peptides Can Be Distinguished by Their Ionization Behavior The R groups of some amino acids can ionize which contributes to the acid base behavior of a peptide Peptides have characteristic titration curves and pIs Biologically Active Peptides and Polypeptides Occur in a Vast Range of Sizes and Compositions Some proteins consist of multiple polypeptides called multisubunit proteins associated noncovalently o If at least 2 subunits are identical they are oligomeric and the identical units are protomers Some Proteins Contain Chemical Groups Other Than Amino Acids contain other chemical components in addition to amino Conjugated proteins acids o Non amino acid parts are called prosthetic groups o Lypoproteins o Glycoproteins o Metalloproteins contain a specific metal o Some proteins contain more than one prosthetic group contain lipids contain sugar 3 3 Working with Proteins Proteins Can Be Separated and Purified A pure preparation of a protein is necessary before determining its properties and activities binding properties o Methods for separating proteins take advantage of size charge and First step is to split open the cells containing proteins releasing the proteins into a solution called crude extract Commonly the second step is fractionation separating the proteins into different fractions based on size or charge o Proteins can also be salted out of solution separates proteins from small solutes by taking advantage of a Dialysis protein s large size o Ion exchange chromatography is one of the most powerful methods for Column chromatography fractionation which takes advantage of size charge binding affinity and other properties magnitude of the charge of proteins at a given pH according to size o Affinity chromatography o HPLC spreading of protein bands and improves resolution by reducing the transit time of proteins on the column based on binding affinity or high performance liquid chromatography limits diffusional o Size exclusion chromatography aka gel filtration separates proteins exploits differences in the sign and Proteins Can Be Separated and Characterized by Electrophoresis Electrophoresis of charged proteins in an electric field the process of separating proteins based on the migration o Effective as an analytical method but can damage the structure of proteins o Allows determination of the isoelectric point and approximate o Sodium dodecyl sulfate SDS molecular weight weight It separates proteins almost purely on the