1. Protein chemistry Lecture - 4 1

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3. Amino acids are the basic structural units of proteins consisting of: - Amino group, (-NH2) - Carboxyl group(-COOH) - Hydrogen atom (H) and - Variable and distinctive (R) group Attached to the central, or alpha carbon Amino acids have R group which is different for each amino acid. The structure and properties of the different R groups make the amino acids different from one another. 3

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5. Classification of amino acids Side chain reaction classification Biological classification Metabolic classification 5

6. Side chain classification Glycine Alanine Valine Leucine Isoleucine Methionine Phenylalanine Tryptophan Proline 2- Hydrophilic (polar) R-group Uncharged Asparagine Glutamine Serine Threonine Cysteine Tyrosine Positively charged Lysine Arginine Histidine Negatively charged Aspartic acid Glutamic acid 1- Hydrophobic (non- polar) R-group) 6

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8. Non polar (hydrophobic) amino acids Amino acids with aliphatic R group (Glycine, Alanine, Amino acids with aliphatic branched R group (Valine, Leucine and Isoleucine). Amino acids with aromatic R group (phenylalanine, and tryptophan) Amino acids with sulfur group (Methionine) Imino acid (Proline). 8

9. Polar (hydrophilic) amino acids Side chains of polar (hydrophilic) amino acids can dissolve in water. Polar (hydrophilic) amino acids are classified into: Polar charged & Polar non-charged. - Polar charged amino acids include: Acidic negatively charged: (aspartic acid and glutamic acid) and Basic positively charged group: (arginine, lysine, histidine). 9

10. Polar non charged amino acids include: Amino acids with OH group (serine, threonine, tyrosine). Amino acids with SH group (cysteine). Amino acids with amide group (glutamine, and asparagine). 10

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12. Biological classification 1- Non essential amino acids: These amino acids are synthesized in the body and are NOT required to be provided in the diet. They are Glycine, Alanine, Serine, Tyrosine, Cysteine, Arginine, Asparagine, Aspartic, Glutamic acid, Glutamine and Proline. 2- Essential amino acids: Amino acids which are not synthesized in the body and must be provided in the diet. They are Valine, Leucine, Isoleucine, Threonine, Methionine,, Lysine, Histidine, Phenylalanine and Tryptophan. 12

13. Metabolic classification -Glucogenic amino acids: These amino acids break down in the body to give glucose. -Purely ketogenic amino acids: They include Leucine & Lysine, and give ketone bodies after its degradation in the body, but no glucose. - Mixed amino acids: These are amino acids that can give both ketone bodies and glucose intermediates. These are Phenylalanine, Tyrosine, Tryptophan, Isoleucine and Lysine. 13

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15. Ionic properties of amino acids Amino acids have amphoteric properties. They contain acidic (COOH) and Basic (NH2) groups. The amino acids are usually ionized at physiological pH. 15

16. Isoelectric point or “pI” At certain pH “specific for each amino acid” the amino acid can exist in the dipolar from : fully ionized but with no net electric charge. The characteristic pH at which the net electric charge is zero is called the Isoelectric point or “pI”. The amino acid at the isoelectric point is called “Zwitter Ion” which is electrically neutral and not migrating in an electric field. Zwitter ion 16

17. Formation of peptide bonds A peptide linkage, which is a covalent bond, forms between the carbon atom of the carboxyl group of one amino acid and the nitrogen atom of the amino group on the other amino acid. Polypeptides are polymers of amino acids, linked by a peptide linkage. Peptide linkages result from condensation reactions. 17

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19. When this bond formed, 1 hydrogen from the amino group and one hydroxyl group from the carboxyl group are removed to form a water molecule. Any two amino acids can be linked together in this way, regardless of the structure of the R group. A peptide chain consisting of two amino acid residues is called a dipeptide, three amino acids a tripeptide (e. g Glutathione, a tripeptide formed from Cysteine, Glycine and Alanine). 19

20. All living organisms use the same 20 amino acids to form all the proteins. The 20 amino acids can be thought of as an alphabets. For example, English alphabet has 26 letters, and we can spell a huge number of words from small set of letters. In the same way amino acids can be linked together in an almost infinite number of different sequences to form different proteins. 20