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Amino Acid & Proteins Lecture 3 Dr.Ali H.Dosky 23/2/2023 1 Learning Outcomes 6. Recognise and draw the generalised structure of an amino acid. 7. Classify amino acids according to the properties of their side chains. 8. Explain how the charges on amino acids are affected by pH. 9. Show how a pept...

Amino Acid & Proteins Lecture 3 Dr.Ali H.Dosky 23/2/2023 1 Learning Outcomes 6. Recognise and draw the generalised structure of an amino acid. 7. Classify amino acids according to the properties of their side chains. 8. Explain how the charges on amino acids are affected by pH. 9. Show how a peptide bond is formed and list its key features. 10.Explain how amino acid charge can influence the isoelectric point of a protein. 2 Amino Acids • Amino acids are the building blocks of proteins. • There are 20 different amino acids that are commonly found in proteins. All are α-amino acids. • They all have a similar structure: a carboxyl group General structural formula for α-amino acids. There are 20 different R groups in the commonly occurring amino acids. MGD 2017/ DR.AL-BARQAAWI (-COO-) and an amino group (-NH3+) are covalently bound to a central carbon atom. In addition, the side chain or R group, which differs between amino acids, is also bonded to the central carbon. 3 Amino Acids R groups are vary in structure, size, and electric charge. It influences the solubility of the amino acids in water. The α-carbon atom is a chiral center; so, amino acids have two possible stereoisomers, L or D Cells are able to specifically synthesize the L isomers of amino acids because the active sites of enzymes are asymmetric, causing the reactions they catalyze to be stereospecific. The Amino Acid Residues in Proteins are L - Stereoisomers 4 Amino Acids Classification 1) amino acids with nonpolar R group 5 Amino Acids Classification 1) amino acids with nonpolar R group 6 Amino Acids Classification 2) amino acids with uncharged polar R group 7 Amino Acids Classification 3) amino acids with charged polar R group 8 Another Classification of Amino Acids by R Group Amino acids can be classified into the following classes according to R groups 1. Non polar, aliphatic 2. Aromatic 3. Polar, uncharged 4. Positively Charged (Basic) 5. Negatively Charged (Acidic) Put the name of amino acids under each of the above classes. 9 Acid-Base Behavior of Amino acids The acid base properties of amino acids depends on the: • Amino and Carboxyl groups attached to the α-carbon • On the basic, acidic, or other functional groups represented by R, • The pH of themedium. In the physiological pH range of 7.35- 7.45, the carboxyl group of an amino acid is dissociated and the amino group is protonated, it is called Dipolar ion or ampholyte, or zwitter ion. MGD 2017/ DR.AL-BARQAAWI Zwitterionic form of the amino acids that occurs at physiological pH values. 10 Acid-Base Behavior of Amino acids The Zwitterion can donate proton (H+) And can accept proton, too. MGD 2017/ DR.AL-BARQAAWI 11 Acid-Base Behaviorof Amino acids At low pH an amino acid is in its cationic form with both its amino and carboxyl groups are protonated (NH3+ and COOH). As the pH rises, the carboxyl group loses its proton and the ampholyte form appear at about pH 6. With a further increase in pH the amino group (NH3+) is deprotonated, resulting in the anionic form of the molecule. For example: MGD 2017/ DR.AL-BARQAAWI 12 Titration curve of amino acids with not ionizable R groups. The isoelectric point is the pH at which an amino acid is electrically neutral that is, in which the sum of the positive charges equals the sum of the negative charges. For alanine, that has only two dissociable hydrogens (one from the α-carboxyl and one from the α-amino group), the pI is the average of pK1 and pK2 MGD 2017/ DR.AL-BARQAAWI 13 Titration curve of Amino acids with Acidic R groups Amino acids with ionizable R groups have additional ionic species, depending on the pH of the medium and the pKa of the R group. For glutamic acid: pI is the average of pK1 and pKR. MGD 2017/ DR.AL-BARQAAWI 14 Titration Curve of Amino acids with basic R groups For histidine and other basic amino acids: pI is the average of pK2 and pKR. At pH = pI, amino acid bears no net charge and therefore does not move in an electric field. MGD 2017/ DR.AL-BARQAAWI 15 Peptide Bond One of the most Important Reactions of Amino Acids is the formation of peptide bond by the condensation of two amino acids. MGD 2017/ DR.AL-BARQAAWI 16 Key feature of the peptide bond • All the atoms of the bond are in the same plane. • No rotation about the peptide bonds due to double bond characteristics. • Carbonyl oxygen and Amide hydrogen are in the trans orientation, because of steric clashes that occur in the cis form. MGD 2017/ DR.AL-BARQAAWI 17 The peptide has a direction MGD 2017/ DR.AL-BARQAAWI 18 Peptide Nomenclature The Peptides are named beginning with the aminoterminal residue, which by convention is placed at the left. For example, the below pentapeptide named. serylglycyltyrosylalanylleucine MGD 2017/ DR.AL-BARQAAWI 19 Ionization of peptide Alanylglutamylglycyllysine. This tetrapeptide has one free -amino group, one free carboxyl group, and two ionizable R groups. The groups ionized at pH 7.0 are in red MGD 2017/ DR.AL-BARQAAWI 20 Proteins • Proteins are polypeptides of 20 different amino acids, in a sequence encoded by the gene • The polypeptide chain folds into a complex and highly specific threedimensional structure, determined by the sequence of amino acids • The folding of proteins depends on the chemical and physical properties of the amino acids • The amino acids that make up a protein contribute to the folding and function of that protein. The side chains those of the amino acids are more important in a polypeptide as they contribute to the charge seen on the protein. MGD 2017/ DR.AL-BARQAAWI 21 Isoelectric Point (pI) Of Protein • The isoelectric point (pI) is the pH at which a protein has no overall net charge, so can not move in electrical feild. • Acidic proteins contain many negatively charged amino acids and have a low pI. • Basic proteins contain many positively charged amino acids and have a high pI. MGD 2017/ DR.AL-BARQAAWI 22 Summary MGD 2017/ DR.AL-BARQAAWI 23 Thank you for listening