MGD S1 Lecture 3 - Amino Acids and Proteins PDF

Amino acids and protein 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. Acid-Base behavior of Amino Acids Classification The 20 Amino acids are most commonly classified by the chemical natur...

Amino acids and protein 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. Acid-Base behavior of Amino Acids Classification The 20 Amino acids are most commonly classified by the chemical nature of their R group. The most common way to do this is to classify them according to their tendency to interact with water at pH 7.0 i.e. their polarity.(polar/nonpolar) • They all have a similar structure : They are composed of a central carbon atom attached to four other chemical groups: an amino group (-NH2), a carboxyl group (COOH), a hydrogen atom and a variable group (R). •Amino acids can also be classified in other ways; for example, amino acids containing a benzene ring are described as aromatic whilst those that lack rings are aliphatic. •The side chains of some amino acids are charged at pH 7.0 and can be classified according to whether they are positively or negatively charged. The acid base properties of amino acids depends on the: • amino and carboxyl groups attached to the α- carbon • The basic, acidic, or other functional groups represented by R. • The pH of the medium. 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 zwitterion. Amino acids can be classified into the following classes according to R groups: Polar uncharged Zwitterionic form of the amino acids that occurs at physiological pH values. Non polar, aliphatic •There are 20 different R groups in the commonly occurring amino acids. PH<Pi •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 Polar charged Nonpolar, Aromatic PH=pi As the pH rises, the carboxyl group loses its proton (deprotonated) while Amino group remains protonated ,and the ampholyte (zwitterion) form appear (Overall charge 0——->no movement) PH>pi With a further increase in pH the amino group (NH3+ ) is deprotonated, resulting in the anionic form of the molecule. ( overall charge - ——-> toward positive) Cysteine is involved in disulfide bond formation. Definition of isomer one of two or more compounds, radicals, or ions that contain the same number of atoms of the same elements but differ in structural arrangement and properties At low pH an amino acid is in its cationic form with both its amino and carboxyl groups are protonated (NH3+ and COOH). (Overall charge + ———>toward negative) Key features of the peptide bond The isoelectric point (pI) 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. (Overall charge is 0) •All the atoms of the bond are in the same plane. pt-PK-tkzpk.PK •The folding of proteins depends on the chemical and physical properties of the amino acids •For negatively charged (acidic) amino acids pI is the average of pK1 and pKR. + •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 three- dimensional structure, determined by the sequence of amino acids •For polar uncharged & nonpolar amino acids pI is the average of pK1 and pK2 A polymer composed of amino acids joined by peptide bonds. • 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 Different amino acids have different pI: Protein Pkr The peptide has a direction 2 The peptide bond has a direction that goes from the amino terminal residue to carboxyl terminal residue (From N terminal—————> C terminal ) •For positively charged (basic) amino acids pI is the average of pK2 and pKR. 101=1%21-1214 •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. , 2 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. At pH = pI, amino acid bears no net charge and therefore does not move in an electric field. Acidic proteins contain many negatively charged amino acids and have a low pI. Peptide bond: A type of covalent bond which joins amino acids in proteins. The bond forms between the carboxyl group of one amino acid and the amino group of the second. Peptide nomenclature By convention, names of peptides are always written from Ieft to right starting with the N-terminal end Basic proteins contain many positively charged amino acids and have a high pI. •One of the most Important Reactions of Amino Acids is the formation of peptide bond by the condensation of two amino acids. Hemi1n