Amino Acids (Foundation Block) 1 Lecture Dr. Usman Ghani What are amino acids? Structure Types Peptide bond Non-standard amino acids Derivatives of amino acids

What are amino acids? Amino acids are composed of Ca, carboxylic group, amino group, a side chain (R) Side chain groups (R) are variable Building blocks of proteins Amino acids are joined together by peptide bond like a chain in a protein Amino acids can act as both acid and base

General structural formula for a-amino acids Page 65 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e General structural formula for a-amino acids

There are 20 “standard” amino acids present in proteins

The amino and carboxylic groups of aa can ionize

Page 65 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e

Isoelectric Point The pH at which the molecule carries no net charge In acidic solution-cationic In alkaline solution- anionic

pK Value It is the ability of an acid to donate a proton (dissociate) Also known as pKa or acid dissociation constant

The pK values of a-carboxylic group is in the range of 2.2 The pK values of a-amino group is in the range of 9.4

Titration curve of glycine pK1- The pH at which 50% of molecules are in cation form and 50% are in zwitterion form pK2- The pH at which 50% of molecules are in anion form and 50% are in zwitterion form Buffering action is maximum around pK values and minimum at pI Page 70 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Titration curve of glycine

Zwitterions An amino acid contains both: Basic amino group and Acidic carboxylic group Creating a negative and a positive charge Amino groups are protonated Carboxylic groups are unprotonated

Page 65 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Zwitterionic form of the a-amino acids that occur at physiological pH values

An amino acid can therefore act as both an acid and a base At physiological pH, amino acids contain both positive and negative charges with a net charge of zero Equal number of positive and negative charges

Types There are 20 “standard” amino acids found in proteins All have Ca, carboxylic and amino groups All have different side chains (R groups)

Three major types of amino acids: Nonpolar Uncharged polar Charged polar

Nonpolar: Glycine Alanine Valine Leucine Isoleucine Methionine Proline Phenylalanine Tryptophan

Proline It is an imino acid It has a secondary amino group

Amino acids with nonpolar side chains Page 66 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e

Uncharged polar: Serine Threonine Asparagine Glutamine Tyrosine Cysteine

Amino acids with uncharged polar side chains Page 67 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e

Charged polar: Lysine, Arginine Aspartic acid, Glutamic acid Histidine

Amino acids with charged polar side chains Page 67 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Amino acids with charged polar side chains

Peptide bond Amino acids can be polymerized to form chains Polymers are composed of two, three, few (3-10) or more amino acids known as dipeptides, tripeptides, oligopeptides or polypeptides

Condensation of two a-amino acids to form a dipeptide Page 68 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Condensation of two a-amino acids to form a dipeptide

Amino acids are joined together in a chain by peptide bond [CO–NH linkage] Known as peptide bond Each amino acid in a chain makes two peptide bonds

Condensation of two a-amino acids to form a dipeptide Page 68 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Condensation of two a-amino acids to form a dipeptide

The amino acids at the two ends of a chain make only one peptide bond The aa with a free amino group is called amino terminus or N-terminus The aa with a free carboxylic group is called carboxyl terminus or C-terminus

The tetrapeptide Ala-Tyr-Asp-Gly Page 71 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e The tetrapeptide Ala-Tyr-Asp-Gly

Optical activity All aa are optically active except glycine They rotate the plane of polarized light in a polarimeter Optically active molecules are asymmetric: They are not superimposable on their mirror image Asymmetric means Ca is bonded to four different groups

Glycine contains two hydrogen atoms on Ca The Ca of glycine is not asymmetric Therefore glycine is optically inactive

Schematic diagram of a polarimeter Page 72 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Schematic diagram of a polarimeter

Both L and D forms are chemically same L-Amino acids rotate polarized light to the left D-Amino acids rotate polarized light to the right Both L and D forms are chemically same

Non-standard amino acids

Page 77 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Some uncommon amino acid residues that are components of certain proteins

Biologically active amino acids Neurotransmitters Hormones

Page 77 © 2004 John Wiley & Sons, Inc. Voet Biochemistry 3e Some biologically produced derivatives of “standard” amino acids and amino acids that are not components of proteins

That’s all folks!